Analyses forks, contributors, etc.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "import numpy as np\n",
    "import pandas as pd\n",
    "import matplotlib.pyplot as plt\n",
    "import glob, os, shutil\n",
    "import statistics\n",
    "import json \n",
    "import requests\n",
    "from difflib import SequenceMatcher\n",
    "import sys\n",
    "#sys.path.insert(1, '/home/marinedjaffardjy/Documents/wf_features/src/parsing')\n",
    "#import parsing_snkmk as ps\n",
    "#import get_characteristics as t\n",
    "import json"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "def importing_json_files(file_wf):\n",
    "    f_wf = open(file_wf) #informations for nf\n",
    "    # returns JSON object as\n",
    "    # a dictionary\n",
    "    wf = json.load(f_wf)\n",
    "    f_wf.close\n",
    "    return wf"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "#importing the process info\n",
    "proc_nf = importing_json_files('json/nf_all_proc.json')\n",
    "proc_nf_tool = importing_json_files('json/nf_proc_tool.json')\n",
    "proc_snk = importing_json_files('json/snk_rule_info.json')\n",
    "proc_snk_tool = importing_json_files('json/snk_rule_info_tool.json')\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "#importing the wf and auth dict (github info)\n",
    "dict_nf = importing_json_files('json/wf_new_crawl_nextflow.json')\n",
    "auth_nf = importing_json_files('json/author_clem_nf.json')\n",
    "dict_snk = importing_json_files('json/wf_crawl_snakemake.json')\n",
    "auth_snk = importing_json_files('json/author_clem_snk.json')\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Most used tools"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [],
   "source": [
    "def find_unique_tools(proc_list):\n",
    "    tools = []\n",
    "    for proc in proc_list:\n",
    "        for tool in proc[\"tools\"]:\n",
    "            tools.append(tool)\n",
    "    return list(set(tools))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "641"
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tools_nf = find_unique_tools(proc_nf_tool)\n",
    "len(tools_nf)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "338"
      ]
     },
     "execution_count": 20,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tools_snk = find_unique_tools(proc_snk_tool)\n",
    "len(tools_snk)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [],
   "source": [
    "def infos_usage_tools(proc_list):\n",
    "    tools = find_unique_tools(proc_list)\n",
    "    df_tools = pd.DataFrame(columns=['toolname', 'nb_proc', 'list_proc', 'nb_wf', 'list_wf', 'nb_own', 'list_own'])\n",
    "    for tool in tools:\n",
    "        proc_t = []\n",
    "        proc_nb = 0\n",
    "        wf_t = []\n",
    "        own_t = []\n",
    "        for proc in proc_list:\n",
    "            if(tool in proc[\"tools\"]):\n",
    "                proc_t.append(proc)\n",
    "                proc_nb+=1\n",
    "                wf_t.append(proc[\"wf_orig\"])\n",
    "                own_t.append(proc[\"owner\"])\n",
    "        df_tools = df_tools.append({'toolname': tool, \n",
    "                                    'nb_proc': proc_nb, \n",
    "                                    'list_proc': proc_t, \n",
    "                                    'nb_wf' :len(set(wf_t)), \n",
    "                                    'list_wf': set(wf_t), \n",
    "                                    'nb_own': len(set(own_t)), \n",
    "                                    'list_own': set(own_t)}, ignore_index = True)\n",
    "    return df_tools.sort_values(by=['nb_wf'], ascending = False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>toolname</th>\n",
       "      <th>nb_proc</th>\n",
       "      <th>list_proc</th>\n",
       "      <th>nb_wf</th>\n",
       "      <th>list_wf</th>\n",
       "      <th>nb_own</th>\n",
       "      <th>list_own</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>500</th>\n",
       "      <td>SAMtools</td>\n",
       "      <td>2128</td>\n",
       "      <td>[{'owner': 'ABMicroBioinf', 'wf_orig': 'magph'...</td>\n",
       "      <td>562</td>\n",
       "      <td>{isoseq, LG-PACT, covbench, rna_nf, benchmarki...</td>\n",
       "      <td>375</td>\n",
       "      <td>{SJLeeY10, h3abionet, khigashi1987, elyadlezmi...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>48</th>\n",
       "      <td>FastQC</td>\n",
       "      <td>842</td>\n",
       "      <td>[{'owner': 'ABMicroBioinf', 'wf_orig': 'magph'...</td>\n",
       "      <td>542</td>\n",
       "      <td>{nf-core-radseq, 2018_coral_16S, new-rnaseq, n...</td>\n",
       "      <td>361</td>\n",
       "      <td>{h3abionet, khigashi1987, sickle-in-africa, mo...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>384</th>\n",
       "      <td>MultiQC</td>\n",
       "      <td>779</td>\n",
       "      <td>[{'owner': 'ABMicroBioinf', 'wf_orig': 'magph'...</td>\n",
       "      <td>517</td>\n",
       "      <td>{nf-core-radseq, 2018_coral_16S, new-rnaseq, n...</td>\n",
       "      <td>307</td>\n",
       "      <td>{h3abionet, khigashi1987, sickle-in-africa, mo...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>598</th>\n",
       "      <td>BWA</td>\n",
       "      <td>393</td>\n",
       "      <td>[{'owner': 'ABMicroBioinf', 'wf_orig': 'nf-tb'...</td>\n",
       "      <td>206</td>\n",
       "      <td>{mnaseseq, mgp1000, useful-nextflow-patterns, ...</td>\n",
       "      <td>157</td>\n",
       "      <td>{SJLeeY10, h3abionet, sickle-in-africa, jianho...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>60</th>\n",
       "      <td>BCFtools</td>\n",
       "      <td>600</td>\n",
       "      <td>[{'owner': 'ABMicroBioinf', 'wf_orig': 'nf-tb'...</td>\n",
       "      <td>169</td>\n",
       "      <td>{nfvacal, strelka2-nf, mgp1000, table_annovar-...</td>\n",
       "      <td>116</td>\n",
       "      <td>{h3abionet, sickle-in-africa, elyadlezmi, mahe...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>498</th>\n",
       "      <td>BEDTools</td>\n",
       "      <td>320</td>\n",
       "      <td>[{'owner': 'ATpoint', 'wf_orig': 'atac_chip_pr...</td>\n",
       "      <td>156</td>\n",
       "      <td>{csrna, mnaseseq, mgp1000, LG-PACT, nextflow-p...</td>\n",
       "      <td>129</td>\n",
       "      <td>{salzmanlab, heuermh, lwratten, khigashi1987, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>473</th>\n",
       "      <td>Bowtie</td>\n",
       "      <td>291</td>\n",
       "      <td>[{'owner': 'ABMicroBioinf', 'wf_orig': 'magph'...</td>\n",
       "      <td>127</td>\n",
       "      <td>{csrna, pe_stacks_pipeline, as-mapping, rna_nf...</td>\n",
       "      <td>103</td>\n",
       "      <td>{exsquire, erikrikarddaniel, khigashi1987, jia...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>531</th>\n",
       "      <td>GATK</td>\n",
       "      <td>993</td>\n",
       "      <td>[{'owner': 'Akazhiel', 'wf_orig': 'NeoPred-NF'...</td>\n",
       "      <td>125</td>\n",
       "      <td>{gatk, mgp1000, covbench, nf-core-gatkcohortca...</td>\n",
       "      <td>83</td>\n",
       "      <td>{h3abionet, sickle-in-africa, elyadlezmi, DLBP...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>366</th>\n",
       "      <td>Picard</td>\n",
       "      <td>290</td>\n",
       "      <td>[{'owner': 'ATpoint', 'wf_orig': 'atac_chip_pr...</td>\n",
       "      <td>121</td>\n",
       "      <td>{csrna, mnaseseq, as-mapping, rna_nf, nf-dnase...</td>\n",
       "      <td>89</td>\n",
       "      <td>{salzmanlab, csf-ngs, uct-cbio, mahesh-panchal...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>348</th>\n",
       "      <td>STAR</td>\n",
       "      <td>256</td>\n",
       "      <td>[{'owner': 'Akazhiel', 'wf_orig': 'NeoPred-NF'...</td>\n",
       "      <td>120</td>\n",
       "      <td>{as-mapping, icpipe-nextflow, rna_nf, clipseq....</td>\n",
       "      <td>99</td>\n",
       "      <td>{guigolab, bhagesh-codebeast, elyadlezmi, mahe...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>411</th>\n",
       "      <td>fastPHASE</td>\n",
       "      <td>146</td>\n",
       "      <td>[{'owner': 'AlexsLemonade', 'wf_orig': 'scpca-...</td>\n",
       "      <td>113</td>\n",
       "      <td>{nf-cleanplex-preprocess, nextNEOpi, nextflow-...</td>\n",
       "      <td>90</td>\n",
       "      <td>{mahesh-panchal, vpeddu, thanhleviet, kingzhuk...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>175</th>\n",
       "      <td>Minimap2</td>\n",
       "      <td>161</td>\n",
       "      <td>[{'owner': 'ABMicroBioinf', 'wf_orig': 'magph'...</td>\n",
       "      <td>80</td>\n",
       "      <td>{isoseq, tCANS, hybrid-assembly, artic, sarseq...</td>\n",
       "      <td>67</td>\n",
       "      <td>{ABMicroBioinf, replikation, alemenze, jiangwe...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>507</th>\n",
       "      <td>QualiMap</td>\n",
       "      <td>110</td>\n",
       "      <td>[{'owner': 'Akazhiel', 'wf_orig': 'NeoPred-NF'...</td>\n",
       "      <td>74</td>\n",
       "      <td>{Nextflow, lRNA-Seq, mycosnp-nf, mgp1000, nf-u...</td>\n",
       "      <td>48</td>\n",
       "      <td>{sickle-in-africa, cirrina, Akazhiel, gongyh, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>107</th>\n",
       "      <td>Salmon</td>\n",
       "      <td>156</td>\n",
       "      <td>[{'owner': 'ATpoint', 'wf_orig': 'rnaseq_prepr...</td>\n",
       "      <td>72</td>\n",
       "      <td>{NextflowModules, new-rnaseq, Nextflow, lRNA-S...</td>\n",
       "      <td>62</td>\n",
       "      <td>{t-neumann, PiscatorX, bhagesh-codebeast, cirr...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>629</th>\n",
       "      <td>Cutadapt</td>\n",
       "      <td>95</td>\n",
       "      <td>[{'owner': 'AGROSAVIABIOUNIT', 'wf_orig': 'nex...</td>\n",
       "      <td>70</td>\n",
       "      <td>{rnaSeq_byBABS, demultiplexing, clipseq1, RNAS...</td>\n",
       "      <td>54</td>\n",
       "      <td>{alemenze, exsquire, mbradyneeley, bhagesh-cod...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>458</th>\n",
       "      <td>FeatureCounts</td>\n",
       "      <td>87</td>\n",
       "      <td>[{'owner': 'ATpoint', 'wf_orig': 'atac_chip_pr...</td>\n",
       "      <td>68</td>\n",
       "      <td>{Groupe10_Hackaton, NextflowModules, RNASeq_Pi...</td>\n",
       "      <td>62</td>\n",
       "      <td>{SarahMaman, erikrikarddaniel, lwratten, mbrad...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>236</th>\n",
       "      <td>seqtk</td>\n",
       "      <td>98</td>\n",
       "      <td>[{'owner': 'ABMicroBioinf', 'wf_orig': 'magph'...</td>\n",
       "      <td>66</td>\n",
       "      <td>{mycosnp-nf, nf-repeatexplorer, raven-nf, dock...</td>\n",
       "      <td>53</td>\n",
       "      <td>{ABMicroBioinf, replikation, h3abionet, jiangw...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>529</th>\n",
       "      <td>kraken2</td>\n",
       "      <td>97</td>\n",
       "      <td>[{'owner': 'ABMicroBioinf', 'wf_orig': 'magph'...</td>\n",
       "      <td>63</td>\n",
       "      <td>{nf-nanopore-assembly, raven-nf, Discovery2, R...</td>\n",
       "      <td>55</td>\n",
       "      <td>{ABMicroBioinf, alemenze, jiangweiyao, ksumngs...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>133</th>\n",
       "      <td>MarkDuplicates (IP)</td>\n",
       "      <td>61</td>\n",
       "      <td>[{'owner': 'Akazhiel', 'wf_orig': 'NeoPred-NF'...</td>\n",
       "      <td>60</td>\n",
       "      <td>{Nextflow, lRNA-Seq, mycosnp-nf, batch_somatic...</td>\n",
       "      <td>40</td>\n",
       "      <td>{h3abionet, brucemoran, sickle-in-africa, rayg...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>235</th>\n",
       "      <td>HISAT2</td>\n",
       "      <td>83</td>\n",
       "      <td>[{'owner': 'BenNolann', 'wf_orig': 'rsi_analys...</td>\n",
       "      <td>54</td>\n",
       "      <td>{WF-NF-rnassembly, Nextflow, ANAPURNA-seq_old,...</td>\n",
       "      <td>51</td>\n",
       "      <td>{agalitsyna, raygozag, lifebit-ai, csiro-crop-...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "                toolname nb_proc  \\\n",
       "500             SAMtools    2128   \n",
       "48                FastQC     842   \n",
       "384              MultiQC     779   \n",
       "598                  BWA     393   \n",
       "60              BCFtools     600   \n",
       "498             BEDTools     320   \n",
       "473               Bowtie     291   \n",
       "531                 GATK     993   \n",
       "366               Picard     290   \n",
       "348                 STAR     256   \n",
       "411            fastPHASE     146   \n",
       "175             Minimap2     161   \n",
       "507             QualiMap     110   \n",
       "107               Salmon     156   \n",
       "629             Cutadapt      95   \n",
       "458        FeatureCounts      87   \n",
       "236                seqtk      98   \n",
       "529              kraken2      97   \n",
       "133  MarkDuplicates (IP)      61   \n",
       "235               HISAT2      83   \n",
       "\n",
       "                                             list_proc nb_wf  \\\n",
       "500  [{'owner': 'ABMicroBioinf', 'wf_orig': 'magph'...   562   \n",
       "48   [{'owner': 'ABMicroBioinf', 'wf_orig': 'magph'...   542   \n",
       "384  [{'owner': 'ABMicroBioinf', 'wf_orig': 'magph'...   517   \n",
       "598  [{'owner': 'ABMicroBioinf', 'wf_orig': 'nf-tb'...   206   \n",
       "60   [{'owner': 'ABMicroBioinf', 'wf_orig': 'nf-tb'...   169   \n",
       "498  [{'owner': 'ATpoint', 'wf_orig': 'atac_chip_pr...   156   \n",
       "473  [{'owner': 'ABMicroBioinf', 'wf_orig': 'magph'...   127   \n",
       "531  [{'owner': 'Akazhiel', 'wf_orig': 'NeoPred-NF'...   125   \n",
       "366  [{'owner': 'ATpoint', 'wf_orig': 'atac_chip_pr...   121   \n",
       "348  [{'owner': 'Akazhiel', 'wf_orig': 'NeoPred-NF'...   120   \n",
       "411  [{'owner': 'AlexsLemonade', 'wf_orig': 'scpca-...   113   \n",
       "175  [{'owner': 'ABMicroBioinf', 'wf_orig': 'magph'...    80   \n",
       "507  [{'owner': 'Akazhiel', 'wf_orig': 'NeoPred-NF'...    74   \n",
       "107  [{'owner': 'ATpoint', 'wf_orig': 'rnaseq_prepr...    72   \n",
       "629  [{'owner': 'AGROSAVIABIOUNIT', 'wf_orig': 'nex...    70   \n",
       "458  [{'owner': 'ATpoint', 'wf_orig': 'atac_chip_pr...    68   \n",
       "236  [{'owner': 'ABMicroBioinf', 'wf_orig': 'magph'...    66   \n",
       "529  [{'owner': 'ABMicroBioinf', 'wf_orig': 'magph'...    63   \n",
       "133  [{'owner': 'Akazhiel', 'wf_orig': 'NeoPred-NF'...    60   \n",
       "235  [{'owner': 'BenNolann', 'wf_orig': 'rsi_analys...    54   \n",
       "\n",
       "                                               list_wf nb_own  \\\n",
       "500  {isoseq, LG-PACT, covbench, rna_nf, benchmarki...    375   \n",
       "48   {nf-core-radseq, 2018_coral_16S, new-rnaseq, n...    361   \n",
       "384  {nf-core-radseq, 2018_coral_16S, new-rnaseq, n...    307   \n",
       "598  {mnaseseq, mgp1000, useful-nextflow-patterns, ...    157   \n",
       "60   {nfvacal, strelka2-nf, mgp1000, table_annovar-...    116   \n",
       "498  {csrna, mnaseseq, mgp1000, LG-PACT, nextflow-p...    129   \n",
       "473  {csrna, pe_stacks_pipeline, as-mapping, rna_nf...    103   \n",
       "531  {gatk, mgp1000, covbench, nf-core-gatkcohortca...     83   \n",
       "366  {csrna, mnaseseq, as-mapping, rna_nf, nf-dnase...     89   \n",
       "348  {as-mapping, icpipe-nextflow, rna_nf, clipseq....     99   \n",
       "411  {nf-cleanplex-preprocess, nextNEOpi, nextflow-...     90   \n",
       "175  {isoseq, tCANS, hybrid-assembly, artic, sarseq...     67   \n",
       "507  {Nextflow, lRNA-Seq, mycosnp-nf, mgp1000, nf-u...     48   \n",
       "107  {NextflowModules, new-rnaseq, Nextflow, lRNA-S...     62   \n",
       "629  {rnaSeq_byBABS, demultiplexing, clipseq1, RNAS...     54   \n",
       "458  {Groupe10_Hackaton, NextflowModules, RNASeq_Pi...     62   \n",
       "236  {mycosnp-nf, nf-repeatexplorer, raven-nf, dock...     53   \n",
       "529  {nf-nanopore-assembly, raven-nf, Discovery2, R...     55   \n",
       "133  {Nextflow, lRNA-Seq, mycosnp-nf, batch_somatic...     40   \n",
       "235  {WF-NF-rnassembly, Nextflow, ANAPURNA-seq_old,...     51   \n",
       "\n",
       "                                              list_own  \n",
       "500  {SJLeeY10, h3abionet, khigashi1987, elyadlezmi...  \n",
       "48   {h3abionet, khigashi1987, sickle-in-africa, mo...  \n",
       "384  {h3abionet, khigashi1987, sickle-in-africa, mo...  \n",
       "598  {SJLeeY10, h3abionet, sickle-in-africa, jianho...  \n",
       "60   {h3abionet, sickle-in-africa, elyadlezmi, mahe...  \n",
       "498  {salzmanlab, heuermh, lwratten, khigashi1987, ...  \n",
       "473  {exsquire, erikrikarddaniel, khigashi1987, jia...  \n",
       "531  {h3abionet, sickle-in-africa, elyadlezmi, DLBP...  \n",
       "366  {salzmanlab, csf-ngs, uct-cbio, mahesh-panchal...  \n",
       "348  {guigolab, bhagesh-codebeast, elyadlezmi, mahe...  \n",
       "411  {mahesh-panchal, vpeddu, thanhleviet, kingzhuk...  \n",
       "175  {ABMicroBioinf, replikation, alemenze, jiangwe...  \n",
       "507  {sickle-in-africa, cirrina, Akazhiel, gongyh, ...  \n",
       "107  {t-neumann, PiscatorX, bhagesh-codebeast, cirr...  \n",
       "629  {alemenze, exsquire, mbradyneeley, bhagesh-cod...  \n",
       "458  {SarahMaman, erikrikarddaniel, lwratten, mbrad...  \n",
       "236  {ABMicroBioinf, replikation, h3abionet, jiangw...  \n",
       "529  {ABMicroBioinf, alemenze, jiangweiyao, ksumngs...  \n",
       "133  {h3abionet, brucemoran, sickle-in-africa, rayg...  \n",
       "235  {agalitsyna, raygozag, lifebit-ai, csiro-crop-...  "
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_tools_nf = infos_usage_tools(proc_nf_tool)\n",
    "df_tools_nf.head(20)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>toolname</th>\n",
       "      <th>nb_proc</th>\n",
       "      <th>list_proc</th>\n",
       "      <th>nb_wf</th>\n",
       "      <th>list_wf</th>\n",
       "      <th>nb_own</th>\n",
       "      <th>list_own</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>272</th>\n",
       "      <td>SAMtools</td>\n",
       "      <td>1532</td>\n",
       "      <td>[{'name': 'sort_alignments', 'code': '(name='s...</td>\n",
       "      <td>572</td>\n",
       "      <td>{fcarelli/glre/47, filcfig/PCP/3, WatsonLab/Go...</td>\n",
       "      <td>290</td>\n",
       "      <td>{Exenter, mdjaffardjy, philippmuench, ecalfee,...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>271</th>\n",
       "      <td>BEDTools</td>\n",
       "      <td>501</td>\n",
       "      <td>[{'name': 'intersect_crosslink_sites_with_peak...</td>\n",
       "      <td>194</td>\n",
       "      <td>{bioxfu/iCLIP/1, alexzaccaron/2021_enec_mt/5, ...</td>\n",
       "      <td>108</td>\n",
       "      <td>{vodkatad, mmontemurro, ecalfee, bioxfu, filcf...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>319</th>\n",
       "      <td>BWA</td>\n",
       "      <td>327</td>\n",
       "      <td>[{'name': 'rRNAContamination', 'code': '(name=...</td>\n",
       "      <td>187</td>\n",
       "      <td>{fcarelli/glre/5, alexzaccaron/2021_enec_mt/5,...</td>\n",
       "      <td>100</td>\n",
       "      <td>{vodkatad, philippmuench, ecalfee, dfguan, rat...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>19</th>\n",
       "      <td>FastQC</td>\n",
       "      <td>236</td>\n",
       "      <td>[{'name': 'fastqc', 'code': '(name='fastqc', l...</td>\n",
       "      <td>170</td>\n",
       "      <td>{alneberg/2015-04-BARM-Concoct/1, bioxfu/iCLIP...</td>\n",
       "      <td>117</td>\n",
       "      <td>{aya49, mdjaffardjy, vodkatad, ecalfee, UofABi...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>28</th>\n",
       "      <td>BCFtools</td>\n",
       "      <td>274</td>\n",
       "      <td>[{'name': 'merge_vcf', 'code': '(name='merge_v...</td>\n",
       "      <td>124</td>\n",
       "      <td>{leahkemp/testing_seattleflu_assembly/3, iqbal...</td>\n",
       "      <td>78</td>\n",
       "      <td>{vodkatad, dfguan, Shmuppel, hevmarriott, AlBi...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>260</th>\n",
       "      <td>Bowtie</td>\n",
       "      <td>177</td>\n",
       "      <td>[{'name': 'PhiXContamination', 'code': '(name=...</td>\n",
       "      <td>108</td>\n",
       "      <td>{AlexanderMoerseburg/ATAC-Seq/1, leahkemp/test...</td>\n",
       "      <td>77</td>\n",
       "      <td>{philippmuench, bioxfu, seb-mueller, iqbal-lab...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>215</th>\n",
       "      <td>MultiQC</td>\n",
       "      <td>137</td>\n",
       "      <td>[{'name': 'multiqc', 'code': '(name='multiqc',...</td>\n",
       "      <td>100</td>\n",
       "      <td>{pawel125/RNAseq_hpc_workflow/1, bioinformatic...</td>\n",
       "      <td>66</td>\n",
       "      <td>{vodkatad, ecalfee, AAFC-BICoE, LUDC-bioinform...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>185</th>\n",
       "      <td>STAR</td>\n",
       "      <td>152</td>\n",
       "      <td>[{'name': 'starAlignment', 'code': '(name='sta...</td>\n",
       "      <td>72</td>\n",
       "      <td>{ahryho/snakemake-tutorial/8, mgildea87/RNAseq...</td>\n",
       "      <td>53</td>\n",
       "      <td>{Exenter, mdjaffardjy, sztankatt, LUDC-bioinfo...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>91</th>\n",
       "      <td>Minimap2</td>\n",
       "      <td>118</td>\n",
       "      <td>[{'name': 'create_bam', 'code': '(name='create...</td>\n",
       "      <td>71</td>\n",
       "      <td>{bhattlab/bhattlab_workflows/8, jmeppley/np_re...</td>\n",
       "      <td>41</td>\n",
       "      <td>{callumparr, jmeppley, AlBi-HHU, dfloresDIL, C...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>334</th>\n",
       "      <td>Cutadapt</td>\n",
       "      <td>81</td>\n",
       "      <td>[{'name': 'Remove_sequencing_adapters', 'code'...</td>\n",
       "      <td>63</td>\n",
       "      <td>{bioxfu/iCLIP/1, Hajibabaei-Lab/SCVUC_COI_meta...</td>\n",
       "      <td>44</td>\n",
       "      <td>{jcmcnch, bioxfu, slebedeva, sterrettJD, dflor...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>254</th>\n",
       "      <td>FeatureCounts</td>\n",
       "      <td>63</td>\n",
       "      <td>[{'name': 'create_counts_table', 'code': '(nam...</td>\n",
       "      <td>55</td>\n",
       "      <td>{mgildea87/RNAseq_PE/1, Tina04021997/How-to-RN...</td>\n",
       "      <td>40</td>\n",
       "      <td>{mdjaffardjy, LUDC-bioinformatics, UofABioinfo...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>288</th>\n",
       "      <td>GATK</td>\n",
       "      <td>251</td>\n",
       "      <td>[{'name': 'mergewt', 'code': '(name='mergewt',...</td>\n",
       "      <td>49</td>\n",
       "      <td>{fingerfen/WES_Short_Variant_and_CNV_Pipeline/...</td>\n",
       "      <td>24</td>\n",
       "      <td>{vodkatad, hevmarriott, oskarvid, dfloresDIL, ...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>204</th>\n",
       "      <td>Picard</td>\n",
       "      <td>99</td>\n",
       "      <td>[{'name': 'Extract_Unmapped_host_Reads', 'code...</td>\n",
       "      <td>46</td>\n",
       "      <td>{Miachol/hamlet/9, Miachol/hamlet/3, mydennisl...</td>\n",
       "      <td>28</td>\n",
       "      <td>{vodkatad, kmgibson, philippmuench, Bella2347,...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>95</th>\n",
       "      <td>Trimmomatic</td>\n",
       "      <td>50</td>\n",
       "      <td>[{'name': 'trimmomatic', 'code': '(name='trimm...</td>\n",
       "      <td>45</td>\n",
       "      <td>{naturalis/brassicaceae-hybseq-pipeline/1, sue...</td>\n",
       "      <td>25</td>\n",
       "      <td>{naturalis, kmgibson, bioxfu, suecharo, leahke...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>118</th>\n",
       "      <td>seqtk</td>\n",
       "      <td>93</td>\n",
       "      <td>[{'name': 'sub_sample0', 'code': '(name='sub_s...</td>\n",
       "      <td>45</td>\n",
       "      <td>{dbrg77/plate_scATAC-seq/4, mscharmann/sexdeli...</td>\n",
       "      <td>32</td>\n",
       "      <td>{jcmcnch, andnischneider, LoGT-KULeuven, nate-...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>134</th>\n",
       "      <td>Snakemake</td>\n",
       "      <td>49</td>\n",
       "      <td>[{'name': 'rulegraph', 'code': '(name='rulegra...</td>\n",
       "      <td>44</td>\n",
       "      <td>{jbloomlab/SARSr-CoV_RBD_MAP/1, jbloomlab/SARS...</td>\n",
       "      <td>24</td>\n",
       "      <td>{populationgenomics, mumichae, theislab, jbloo...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>289</th>\n",
       "      <td>kallisto</td>\n",
       "      <td>58</td>\n",
       "      <td>[{'name': 'create_kallisto_index', 'code': '(n...</td>\n",
       "      <td>37</td>\n",
       "      <td>{Terkild/CITE-seq_optimization/2, sanjaprisela...</td>\n",
       "      <td>26</td>\n",
       "      <td>{Exenter, pimentel, sztankatt, UofABioinformat...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>292</th>\n",
       "      <td>Prokka</td>\n",
       "      <td>41</td>\n",
       "      <td>[{'name': 'prokka', 'code': '(name='prokka', l...</td>\n",
       "      <td>36</td>\n",
       "      <td>{bhattlab/bhattlab_workflows/8, dst-umms/MAMBA...</td>\n",
       "      <td>19</td>\n",
       "      <td>{gradlab, tyhsu389, shigdon, franciscozorrilla...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>46</th>\n",
       "      <td>Salmon</td>\n",
       "      <td>52</td>\n",
       "      <td>[{'name': 'salmon_build_index', 'code': '(name...</td>\n",
       "      <td>33</td>\n",
       "      <td>{kauralasoo/macrophage-tuQTLs/2, leboralli/pip...</td>\n",
       "      <td>23</td>\n",
       "      <td>{kevinrue, LIniguez, UofABioinformaticsHub, ca...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>252</th>\n",
       "      <td>bedGraphToBigWig</td>\n",
       "      <td>93</td>\n",
       "      <td>[{'name': 'bigwig', 'code': '(name='bigwig', l...</td>\n",
       "      <td>33</td>\n",
       "      <td>{fcarelli/glre/5, fcarelli/glre/6, mydennislab...</td>\n",
       "      <td>20</td>\n",
       "      <td>{seb-mueller, mgalland, kauralasoo, Frankjacob...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "             toolname nb_proc  \\\n",
       "272          SAMtools    1532   \n",
       "271          BEDTools     501   \n",
       "319               BWA     327   \n",
       "19             FastQC     236   \n",
       "28           BCFtools     274   \n",
       "260            Bowtie     177   \n",
       "215           MultiQC     137   \n",
       "185              STAR     152   \n",
       "91           Minimap2     118   \n",
       "334          Cutadapt      81   \n",
       "254     FeatureCounts      63   \n",
       "288              GATK     251   \n",
       "204            Picard      99   \n",
       "95        Trimmomatic      50   \n",
       "118             seqtk      93   \n",
       "134         Snakemake      49   \n",
       "289          kallisto      58   \n",
       "292            Prokka      41   \n",
       "46             Salmon      52   \n",
       "252  bedGraphToBigWig      93   \n",
       "\n",
       "                                             list_proc nb_wf  \\\n",
       "272  [{'name': 'sort_alignments', 'code': '(name='s...   572   \n",
       "271  [{'name': 'intersect_crosslink_sites_with_peak...   194   \n",
       "319  [{'name': 'rRNAContamination', 'code': '(name=...   187   \n",
       "19   [{'name': 'fastqc', 'code': '(name='fastqc', l...   170   \n",
       "28   [{'name': 'merge_vcf', 'code': '(name='merge_v...   124   \n",
       "260  [{'name': 'PhiXContamination', 'code': '(name=...   108   \n",
       "215  [{'name': 'multiqc', 'code': '(name='multiqc',...   100   \n",
       "185  [{'name': 'starAlignment', 'code': '(name='sta...    72   \n",
       "91   [{'name': 'create_bam', 'code': '(name='create...    71   \n",
       "334  [{'name': 'Remove_sequencing_adapters', 'code'...    63   \n",
       "254  [{'name': 'create_counts_table', 'code': '(nam...    55   \n",
       "288  [{'name': 'mergewt', 'code': '(name='mergewt',...    49   \n",
       "204  [{'name': 'Extract_Unmapped_host_Reads', 'code...    46   \n",
       "95   [{'name': 'trimmomatic', 'code': '(name='trimm...    45   \n",
       "118  [{'name': 'sub_sample0', 'code': '(name='sub_s...    45   \n",
       "134  [{'name': 'rulegraph', 'code': '(name='rulegra...    44   \n",
       "289  [{'name': 'create_kallisto_index', 'code': '(n...    37   \n",
       "292  [{'name': 'prokka', 'code': '(name='prokka', l...    36   \n",
       "46   [{'name': 'salmon_build_index', 'code': '(name...    33   \n",
       "252  [{'name': 'bigwig', 'code': '(name='bigwig', l...    33   \n",
       "\n",
       "                                               list_wf nb_own  \\\n",
       "272  {fcarelli/glre/47, filcfig/PCP/3, WatsonLab/Go...    290   \n",
       "271  {bioxfu/iCLIP/1, alexzaccaron/2021_enec_mt/5, ...    108   \n",
       "319  {fcarelli/glre/5, alexzaccaron/2021_enec_mt/5,...    100   \n",
       "19   {alneberg/2015-04-BARM-Concoct/1, bioxfu/iCLIP...    117   \n",
       "28   {leahkemp/testing_seattleflu_assembly/3, iqbal...     78   \n",
       "260  {AlexanderMoerseburg/ATAC-Seq/1, leahkemp/test...     77   \n",
       "215  {pawel125/RNAseq_hpc_workflow/1, bioinformatic...     66   \n",
       "185  {ahryho/snakemake-tutorial/8, mgildea87/RNAseq...     53   \n",
       "91   {bhattlab/bhattlab_workflows/8, jmeppley/np_re...     41   \n",
       "334  {bioxfu/iCLIP/1, Hajibabaei-Lab/SCVUC_COI_meta...     44   \n",
       "254  {mgildea87/RNAseq_PE/1, Tina04021997/How-to-RN...     40   \n",
       "288  {fingerfen/WES_Short_Variant_and_CNV_Pipeline/...     24   \n",
       "204  {Miachol/hamlet/9, Miachol/hamlet/3, mydennisl...     28   \n",
       "95   {naturalis/brassicaceae-hybseq-pipeline/1, sue...     25   \n",
       "118  {dbrg77/plate_scATAC-seq/4, mscharmann/sexdeli...     32   \n",
       "134  {jbloomlab/SARSr-CoV_RBD_MAP/1, jbloomlab/SARS...     24   \n",
       "289  {Terkild/CITE-seq_optimization/2, sanjaprisela...     26   \n",
       "292  {bhattlab/bhattlab_workflows/8, dst-umms/MAMBA...     19   \n",
       "46   {kauralasoo/macrophage-tuQTLs/2, leboralli/pip...     23   \n",
       "252  {fcarelli/glre/5, fcarelli/glre/6, mydennislab...     20   \n",
       "\n",
       "                                              list_own  \n",
       "272  {Exenter, mdjaffardjy, philippmuench, ecalfee,...  \n",
       "271  {vodkatad, mmontemurro, ecalfee, bioxfu, filcf...  \n",
       "319  {vodkatad, philippmuench, ecalfee, dfguan, rat...  \n",
       "19   {aya49, mdjaffardjy, vodkatad, ecalfee, UofABi...  \n",
       "28   {vodkatad, dfguan, Shmuppel, hevmarriott, AlBi...  \n",
       "260  {philippmuench, bioxfu, seb-mueller, iqbal-lab...  \n",
       "215  {vodkatad, ecalfee, AAFC-BICoE, LUDC-bioinform...  \n",
       "185  {Exenter, mdjaffardjy, sztankatt, LUDC-bioinfo...  \n",
       "91   {callumparr, jmeppley, AlBi-HHU, dfloresDIL, C...  \n",
       "334  {jcmcnch, bioxfu, slebedeva, sterrettJD, dflor...  \n",
       "254  {mdjaffardjy, LUDC-bioinformatics, UofABioinfo...  \n",
       "288  {vodkatad, hevmarriott, oskarvid, dfloresDIL, ...  \n",
       "204  {vodkatad, kmgibson, philippmuench, Bella2347,...  \n",
       "95   {naturalis, kmgibson, bioxfu, suecharo, leahke...  \n",
       "118  {jcmcnch, andnischneider, LoGT-KULeuven, nate-...  \n",
       "134  {populationgenomics, mumichae, theislab, jbloo...  \n",
       "289  {Exenter, pimentel, sztankatt, UofABioinformat...  \n",
       "292  {gradlab, tyhsu389, shigdon, franciscozorrilla...  \n",
       "46   {kevinrue, LIniguez, UofABioinformaticsHub, ca...  \n",
       "252  {seb-mueller, mgalland, kauralasoo, Frankjacob...  "
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_tools_snk = infos_usage_tools(proc_snk_tool)\n",
    "df_tools_snk.head(20)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Role of the contributors\n",
    "\n",
    "How many wf have been developped by the top 10/20 contributors ?\n",
    "How many contributors have created only 1 wf ? How many wf have they created ?"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'AAFC-BICoE/snakemake-barcoding-assembly-pipeline/1'"
      ]
     },
     "execution_count": 34,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "proc_snk_tool[0][\"wf_orig\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 57,
   "metadata": {},
   "outputs": [],
   "source": [
    "def get_list_wf(proc_list):\n",
    "    list_wf = []\n",
    "    for proc in proc_list:\n",
    "        list_wf.append(proc[\"wf_orig\"])\n",
    "    return list(set(list_wf))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 59,
   "metadata": {},
   "outputs": [],
   "source": [
    "def get_list_wf_nf(proc_list):\n",
    "    list_wf = []\n",
    "    for proc in proc_list:\n",
    "        list_wf.append(proc[\"owner\"]+\"/\"+proc[\"wf_orig\"])\n",
    "    return list(set(list_wf))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 51,
   "metadata": {},
   "outputs": [],
   "source": [
    "def get_list_contrib_snk(wf_list, dict_wf):\n",
    "    list_contrib = []\n",
    "    for wf in wf_list:\n",
    "        wf_name = wf.split(\"/\")[0]+\"/\"+wf.split(\"/\")[1]\n",
    "        for el in dict_wf[wf_name][\"contributors\"]:\n",
    "            list_contrib.append(el)\n",
    "    return list(set(list_contrib))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 70,
   "metadata": {},
   "outputs": [],
   "source": [
    "def get_list_contrib_nf(wf_list, dict_wf):\n",
    "    list_contrib = []\n",
    "    for wf_name in wf_list:\n",
    "        if(wf_name in dict_wf.keys()):\n",
    "            for el in dict_wf[wf_name][\"contributors\"]:\n",
    "                list_contrib.append(el)\n",
    "    return list(set(list_contrib))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "dict_keys(['files', 'name', 'id', 'git_url', 'update_date', 'creation_date', 'actual_date', 'last_push', 'owner', 'description', 'forks', 'stars', 'watchers', 'subscribers', 'languages', 'topics', 'archived', 'link', 'contributors', 'license'])"
      ]
     },
     "execution_count": 36,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dict_nf['joshua-d-campbell/nf-GATK_Exome_Preprocess'].keys()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 56,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'magph'"
      ]
     },
     "execution_count": 56,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "proc_nf_tool[0][\"wf_orig\"]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 84,
   "metadata": {},
   "outputs": [],
   "source": [
    "def create_df_contrib_snk(proc_list, dict_wf):\n",
    "    wf_list = get_list_wf(proc_list)\n",
    "    contribs = get_list_contrib_snk(wf_list, dict_wf)\n",
    "    df_contrib = pd.DataFrame(columns=['contributor', 'nb_wf', 'list_wf'])\n",
    "    for contr in contribs:\n",
    "        print(contr)\n",
    "        list_wf = []\n",
    "        for wf in wf_list:\n",
    "            wf_name = wf.split(\"/\")[0]+\"/\"+wf.split(\"/\")[1]\n",
    "            if(contr in dict_wf[wf_name][\"contributors\"]):\n",
    "                list_wf.append(wf)\n",
    "        df_contrib = df_contrib.append({'contributor':contr,\n",
    "                                'nb_wf':len(set(list_wf)),\n",
    "                                'list_wf':set(list_wf)}, ignore_index=True)\n",
    "    return df_contrib.sort_values(by=['nb_wf'], ascending = False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 85,
   "metadata": {},
   "outputs": [],
   "source": [
    "def create_df_contrib_nf(proc_list, dict_wf):\n",
    "    wf_list = get_list_wf_nf(proc_list)\n",
    "    contribs = get_list_contrib_nf(wf_list, dict_wf)\n",
    "    df_contrib = pd.DataFrame(columns=['contributor', 'nb_wf', 'list_wf'])\n",
    "    for contr in contribs:\n",
    "        print(contr)\n",
    "        list_wf = []\n",
    "        for wf_name in wf_list:\n",
    "            if(wf_name in dict_wf.keys()):\n",
    "                if(contr in dict_wf[wf_name][\"contributors\"]):\n",
    "                    list_wf.append(wf_name)\n",
    "        print(list_wf)    \n",
    "        df_contrib = df_contrib.append({'contributor':contr,\n",
    "                                    'nb_wf':len(set(list_wf)),\n",
    "                                    'list_wf':set(list_wf)}, ignore_index=True)\n",
    "    return df_contrib.sort_values(by=['nb_wf'], ascending = False)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 86,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "vodkatad\n",
      "ecalfee\n",
      "hevmarriott\n",
      "filcfig\n",
      "calchoo\n",
      "BrandonJRomano\n",
      "DCGenomics\n",
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      "MarineP-IODAA\n",
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      "c-mertes\n",
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      "amberr098\n",
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      "engreitz\n",
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      "Kanomble\n",
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      "sbamin\n",
      "GitStudentKanomble\n",
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      "paulimer\n",
      "mathbionerd\n",
      "Tjitskedv\n",
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      "fcarelli\n",
      "lyijin\n",
      "hellosoni\n",
      "shiandy\n",
      "razielar\n",
      "kpatel427\n",
      "yuxuth\n",
      "mirand863\n",
      "gummystick\n",
      "Faitero\n",
      "mmchaouchi\n",
      "dadahan\n",
      "cmuyehara\n",
      "CFarcy\n",
      "sfrenk\n",
      "fieldima\n",
      "jaboehm\n",
      "drdariarago\n",
      "SarahEJensen\n",
      "gaofan83\n",
      "arcadianlyric\n",
      "rbonneville\n",
      "ashwin-s-ranade\n",
      "wuv21\n",
      "jmeppley\n",
      "anaghadesh\n",
      "mrbarbitoff\n",
      "mumichae\n",
      "bergeycm\n",
      "tjense25\n",
      "mgalland\n",
      "dbespiatykh\n",
      "tkanholm\n",
      "haansi\n",
      "mikheyev\n",
      "tyh-19\n",
      "agata-sm\n",
      "caipine\n",
      "evodify\n",
      "scbaca\n",
      "Kirovez\n",
      "FleurGaBru\n",
      "xiamaz\n",
      "EulleSA\n",
      "jrhawley\n",
      "ChDied\n",
      "vindarbot\n",
      "tatumdmortimer\n",
      "RachelRodgers\n",
      "wdeleeuw\n",
      "thw17\n",
      "niekh-13\n",
      "pkozyulina\n",
      "CharlotteAnne\n",
      "shannonmargaret\n",
      "xindong95\n",
      "jeskowagner\n",
      "ngocemy\n",
      "mauerjh\n",
      "jmonlong\n",
      "linsalrob\n",
      "jakob-he\n",
      "leboralli\n",
      "cck42\n",
      "mcornwell1957\n",
      "tianwen0003\n",
      "mberacochea\n",
      "ddurai\n",
      "JyotiDalal93\n",
      "cvoinot\n"
     ]
    }
   ],
   "source": [
    "df_contrib_snk = create_df_contrib_snk(proc_snk_tool, dict_snk)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 87,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
       "<style scoped>\n",
       "    .dataframe tbody tr th:only-of-type {\n",
       "        vertical-align: middle;\n",
       "    }\n",
       "\n",
       "    .dataframe tbody tr th {\n",
       "        vertical-align: top;\n",
       "    }\n",
       "\n",
       "    .dataframe thead th {\n",
       "        text-align: right;\n",
       "    }\n",
       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>contributor</th>\n",
       "      <th>nb_wf</th>\n",
       "      <th>list_wf</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>46</th>\n",
       "      <td>elimoss</td>\n",
       "      <td>47</td>\n",
       "      <td>{bhattlab/bhattlab_workflows/8, bhattlab/bhatt...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>283</th>\n",
       "      <td>bsiranosian</td>\n",
       "      <td>42</td>\n",
       "      <td>{bhattlab/bhattlab_workflows/8, bhattlab/bhatt...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>309</th>\n",
       "      <td>jribado</td>\n",
       "      <td>40</td>\n",
       "      <td>{bhattlab/bhattlab_workflows/8, bhattlab/bhatt...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>415</th>\n",
       "      <td>tamburinif</td>\n",
       "      <td>40</td>\n",
       "      <td>{bhattlab/bhattlab_workflows/8, bhattlab/bhatt...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>374</th>\n",
       "      <td>navajain</td>\n",
       "      <td>40</td>\n",
       "      <td>{bhattlab/bhattlab_workflows/8, bhattlab/bhatt...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "     contributor nb_wf                                            list_wf\n",
       "46       elimoss    47  {bhattlab/bhattlab_workflows/8, bhattlab/bhatt...\n",
       "283  bsiranosian    42  {bhattlab/bhattlab_workflows/8, bhattlab/bhatt...\n",
       "309      jribado    40  {bhattlab/bhattlab_workflows/8, bhattlab/bhatt...\n",
       "415   tamburinif    40  {bhattlab/bhattlab_workflows/8, bhattlab/bhatt...\n",
       "374     navajain    40  {bhattlab/bhattlab_workflows/8, bhattlab/bhatt..."
      ]
     },
     "execution_count": 87,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "df_contrib_snk.head(5)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 88,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_contrib_snk.to_csv(\"csv/df_contrib_snk.csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 89,
   "metadata": {},
   "outputs": [],
   "source": [
    "tot_wf_snk = len(get_list_wf(proc_snk_tool))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 90,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "223\n",
      "0.17740652346857597\n"
     ]
    }
   ],
   "source": [
    "tot_20_snk = []\n",
    "for wf_list in list(df_contrib_snk.head(20)[\"list_wf\"]):\n",
    "    for wf in wf_list:\n",
    "        tot_20_snk.append(wf)\n",
    "print(len(set(tot_20_snk)))\n",
    "print(len(set(tot_20_snk))/tot_wf_snk)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 92,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "133\n",
      "0.10580747812251393\n"
     ]
    }
   ],
   "source": [
    "tot_10_snk = []\n",
    "for wf_list in list(df_contrib_snk.head(10)[\"list_wf\"]):\n",
    "    for wf in wf_list:\n",
    "        tot_10_snk.append(wf)\n",
    "print(len(set(tot_10_snk)))\n",
    "print(len(set(tot_10_snk))/tot_wf_snk)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 100,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "299\n",
      "0.23786793953858393\n"
     ]
    }
   ],
   "source": [
    "tot_1_snk = []\n",
    "for wf_list in list(df_contrib_snk.loc[df_contrib_snk[\"nb_wf\"]==1][\"list_wf\"]):\n",
    "    for wf in wf_list:\n",
    "        tot_1_snk.append(wf)\n",
    "print(len(set(tot_1_snk)))\n",
    "print(len(set(tot_1_snk))/tot_wf_snk)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 96,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "395"
      ]
     },
     "execution_count": 96,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(df_contrib_snk.loc[df_contrib_snk[\"nb_wf\"]==1][\"list_wf\"])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 97,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "714"
      ]
     },
     "execution_count": 97,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(df_contrib_snk)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 98,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "0.5532212885154062"
      ]
     },
     "execution_count": 98,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "len(df_contrib_snk.loc[df_contrib_snk[\"nb_wf\"]==1][\"list_wf\"])/len(df_contrib_snk)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 101,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "bj8th\n",
      "['sheynkman-lab/IsoSeq-Nextflow']\n",
      "femiliani\n",
      "['mckennalab/NextLineage']\n",
      "KochTobi\n",
      "['nf-core/hlatyping']\n",
      "khigashi1987\n",
      "['khigashi1987/CUTRUN_Nextflow']\n",
      "DarianHole\n",
      "['phac-nml/ncov-dehoster']\n",
      "elyadlezmi\n",
      "['elyadlezmi/RNA2CM']\n",
      "winni2k\n",
      "['markgene/cutnrun', 'jiangfuqing/Chip-seq', 'nf-core/chipseq']\n",
      "lukfor\n",
      "['genepi/nf-gwas', 'askimed/nf-test-examples']\n",
      "monikaBrandt\n",
      "['monikaBrandt/nf-core-mynewpipeline']\n",
      "jbrestel\n",
      "['VEuPathDB/proteinToGenomeAlignment']\n",
      "rolivella\n",
      "['elixir-cloud-proteomics-workflows/elixir_proteomics_QC', 'proteomicsunitcrg/qcloud2-pipeline']\n",
      "DCGenomics\n",
      "['NCBI-Hackathons/Nasty_Metagenomes']\n",
      "idot\n",
      "['csf-ngs/controldna']\n",
      "vsoch\n",
      "['marcodelapierre/demo-shpc-nf', 'GMS6804-master/rnatoy']\n",
      "chrstphdm\n",
      "['chrstphdm/nxf_course']\n",
      "george-hall-ucl\n",
      "['harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "gsteinhardt\n",
      "['GoalConsortium/goal_misc']\n",
      "alvinwt\n",
      "['icgc-argo-workflows/icgc-argo-sv-copy-number']\n",
      "lukasjelonek\n",
      "['lukasjelonek/sequencing-technology-usage-diagram']\n",
      "angelovangel\n",
      "['nf-core/bacass', 'angelovangel/nxf-kraken2', 'replikation/poreCov', 'angelovangel/nxf-fastqc']\n",
      "amchakra\n",
      "['luslab/nf-core-modules', 'luslab/luslab-nf-modules', 'nf-core/clipseq', 'luslab/nf-clip']\n",
      "ChristopherBrunner\n",
      "['ChristopherBrunner/sRNAFinder']\n",
      "ning-y\n",
      "['GTK-lab/nextflow-awsbatch']\n",
      "ssun1116\n",
      "['ssun1116/meripseqpipe']\n",
      "sharma-shruti\n",
      "['nf-modules/fastqc', 'nf-modules/trimmomatic']\n",
      "adrlar\n",
      "['sickle-in-africa/saw.sarek', 'nf-core/sarek', 'sripaladugu/germline_somatic', 'Genomic-Medicine-Linkoping/nf-core-sarek', 'UMCUGenetics/sarek_ubec']\n",
      "BioWilko\n",
      "['BioWilko/Papaya', 'BioWilko/genotyping-pipeline']\n",
      "sirselim\n",
      "['nf-core/smrnaseq']\n",
      "Ninomoriaty\n",
      "['likelet/MesKit']\n",
      "cjw85\n",
      "['epi2me-labs/wf-transcript-target']\n",
      "mzager\n",
      "['FredHutch/dvc-pipelines']\n",
      "marchoeppner\n",
      "['marchoeppner/kinseq', 'marchoeppner/esga2', 'marchoeppner/outbreak-monitoring', 'ikmb/pacbio-preprocess', 'ikmb/vep', 'marchoeppner/trinoflow', 'ikmb/flye-assembly', 'eQTL-Catalogue/rnaseq', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'ikmb/ngs-qc', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "alex-aug\n",
      "['zenomeplatform/nf-germline-mapping']\n",
      "tiwarialok\n",
      "['tiwarialok/new-rnaseq']\n",
      "cguyomar\n",
      "['cguyomar/nf-ase', 'FAANG/analysis-TAGADA']\n",
      "Juke34\n",
      "['NBISweden/pipelines-nextflow']\n",
      "adrienlemeur\n",
      "['Thomas-LeCoent/reprohackathon-bioinfo']\n",
      "aanil\n",
      "['eQTL-Catalogue/rnaseq', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "chuan-wang\n",
      "['markgene/cutnrun', 'jiangfuqing/Chip-seq', 'nf-core/smrnaseq', 'nf-core/chipseq', 'eQTL-Catalogue/rnaseq', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "mcamarad\n",
      "['lifebit-ai/phewas']\n",
      "jemten\n",
      "['nf-core/smrnaseq', 'nf-core/raredisease', 'eQTL-Catalogue/rnaseq', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'nf-core/modules', 'genomic-medicine-sweden/RareDisease_RNA_workflow', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "kmurat1\n",
      "['nf-core/modules']\n",
      "peterk87\n",
      "['peterk87/nf-iav-illumina', 'peterk87/nf-cleanplex-preprocess', 'peterk87/nf-virontus', 'peterk87/nf-illmap', 'peterk87/nf-biohansel-sra-benchmark', 'nhhaidee/scovtree', 'peterk87/nf-biohansel-snippy-comparison', 'peterk87/nf-ionampliseq', 'peterk87/nf-villumina']\n",
      "nicni16\n",
      "['nicni16/nfcore-maxquant']\n",
      "naveen584\n",
      "['naveen584/nextflow-variantcalling']\n",
      "aleksandrabliznina\n",
      "['nf-core/modules']\n",
      "wheelern\n",
      "['zamanianlab/RNAseq-VC-nf']\n",
      "viktorlj\n",
      "['viktorlj/SarekCLLPostProcess', 'viktorlj/SarGet']\n",
      "ZIWEI-WONG\n",
      "['likelet/MesKit']\n",
      "c-mertes\n",
      "['nf-core/modules', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "Huisquare\n",
      "['Huisquare/nfdv']\n",
      "pblaney\n",
      "['pblaney/mgp1000']\n",
      "darcyabjones\n",
      "['darcyabjones/panann']\n",
      "alexharston\n",
      "['goodwright/imaps-nf']\n",
      "Gustius\n",
      "['Gustius/MOFA', 'Gustius/omics-analyser']\n",
      "SusiJo\n",
      "['nf-core/modules']\n",
      "KlausVG\n",
      "['KlausVG/reproHack']\n",
      "cyrildw\n",
      "['cyrildw/nf-MappingOrMerging']\n",
      "alexthiery\n",
      "['Streit-lab/streitlab-nf-modules', 'luslab/nf-core-modules', 'luslab/luslab-nf-modules', 'luslab/nf-clip']\n",
      "oisinmccaffrey\n",
      "['oisinmccaffrey/clipseq.nextflow']\n",
      "chrisjackson-pellicle\n",
      "['chrisjackson-pellicle/HybPiper-RBGV']\n",
      "DaneVass\n",
      "['DaneVass/BARtab']\n",
      "ggabernet\n",
      "['ggabernet/dsltwotest', 'sickle-in-africa/saw.sarek', 'nf-core/eager', 'FriederikeHanssen/bamtofastq', 'nf-core/sarek', 'nf-core/bactmap', 'qbic-pipelines/vcreport', 'nf-core/airrflow', 'sripaladugu/germline_somatic', 'Genomic-Medicine-Linkoping/nf-core-sarek', 'nf-core/viralrecon', 'nf-core/proteomicslfq', 'nf-core/mag', 'qbic-pipelines/cellranger', 'UMCUGenetics/sarek_ubec', 'lengfei5/atacseq_nf', 'ggabernet/elixir', 'nf-core/scrnaseq', 'rastiks/viralrecon', 'nf-core/hlatyping', 'nf-core/ampliseq', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'nf-core/modules', 'nf-core/testpipeline', 'harleenduggal/nfcore-rnaseq', 'nf-core/epitopeprediction', 'nf-core/atacseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ', 'Leon-Bichmann/Phosphoproteomics']\n",
      "gtuckerkellogg\n",
      "['GTK-lab/nextflow-awsbatch']\n",
      "zmaas\n",
      "['Dowell-Lab/Nascent-Flow', 'Dowell-Lab/RNAseq-Flow']\n",
      "anvlasova\n",
      "['CRG-CNAG/CalliNGS-NF']\n",
      "lucacozzuto\n",
      "['biocorecrg/SIB_course_nextflow_Nov_2021', 'lucacozzuto/elixir_NF', 'biocorecrg/allele_specific_RNAseq', 'elixir-cloud-proteomics-workflows/elixir_proteomics_QC', 'biocorecrg/C4LWG-2018', 'biocorecrg/BioNextflow', 'biocorecrg/ELIXIR_containers_nextflow', 'proteomicsunitcrg/qcloud2-pipeline', 'biocorecrg/indrop', 'biocorecrg/CoursesCRG_Containers_Nextflow_May_2021', 'nextflow-io/elixir-workshop-21', 'biocorecrg/PHIND_course_nextflow_Feb_2022', 'biocorecrg/transcriptome_assembly', 'biocorecrg/vectorQC']\n",
      "antunderwood\n",
      "['nf-core/bactmap', 'antunderwood/amr_prediction', 'nf-core/viralrecon', 'antunderwood/nextflow-aws-batch-issue-1024', 'nf-core/modules']\n",
      "jgallowa07\n",
      "['jgallowa07/Nextflow-Example']\n",
      "glormph\n",
      "['glormph/nf-core-lfquandenser', 'sickle-in-africa/saw.structural-variants', 'glormph/nf-core-dda-quant-proteomics', 'glormph/nf-core-labelcheck']\n",
      "mak2508\n",
      "['YounisLab/rnaseq-pipeline']\n",
      "saioruganti\n",
      "['SystemsGenetics/GEMmaker', 'mmcogle/GEMmakerCam']\n",
      "Chiamh\n",
      "['Chiamh/meta-omics-nf']\n",
      "BioinformaticsLabAtMUN\n",
      "['BioinformaticsLabAtMUN/sRNA-Detect', 'BioinformaticsLabAtMUN/sRNACharP-sRNARanking', 'BioinformaticsLabAtMUN/sRNACharP']\n",
      "orionzhou\n",
      "['alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "paulklemm\n",
      "['alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "AlexVCaron\n",
      "['AlexVCaron/mrHARDIflow']\n",
      "elimoss\n",
      "['bhattlab/wits_workshop']\n",
      "daviesdrew\n",
      "['daviesdrew/variantcalling']\n",
      "loipf\n",
      "['loipf/SOMvc-pipeline', 'loipf/DNAsmash-pipeline', 'loipf/DNAseq-pipeline']\n",
      "azure-pipelines[bot]\n",
      "['gis-rpd/rpd-sg10k-grch38-gatk4-gvcf-freebayes-vcf']\n",
      "brucemoran\n",
      "['brucemoran/DNAseq_references', 'brucemoran/tumour_only', 'brucemoran/batch_somatic', 'brucemoran/RNAseq_kallisto', 'brucemoran/somatic_n-of-1', 'brucemoran/nanopore_gDNA_CNA', 'cgpu/somatic_exome_n-of-1']\n",
      "Emilyaoc\n",
      "['Emilyaoc/Nextflow-selection-workflow']\n",
      "SannaAb\n",
      "['SannaAb/Mutation_Calling', 'SannaAb/RNA_Seq_Pipe']\n",
      "aurelieGabriel\n",
      "['IARCbioinfo/Imputation-nf', 'Monia234/IARC-imputation']\n",
      "remiolsen\n",
      "['nf-core/cookiecutter', 'remiolsen/hicscaff', 'nf-core/neutronstar', 'remiolsen/nf-core-radseq', 'remiolsen/outlaw']\n",
      "Takadonet\n",
      "['phac-nml/ncov-dehoster']\n",
      "kojix2\n",
      "['nf-core/modules', 'CRG-CNAG/CalliNGS-NF', 'kojix2/simple_mixcr_nextflow']\n",
      "evagradovich\n",
      "['lifebit-ai/phewas', 'lifebit-ai/metagwas', 'lifebit-ai/prs']\n",
      "clemensma\n",
      "['clemensma/symbiontDivider']\n",
      "t-f-freeman\n",
      "['trev-f/SRAlign', 'trev-f/SRAtac']\n",
      "federicacitarrella\n",
      "['federicacitarrella/FusionFlow']\n",
      "PaulusBoskabouter\n",
      "['PaulusBoskabouter/BasicPhylo']\n",
      "JasperO98\n",
      "['ErasmusMC-Bioinformatics/NextFlow-VC-pipeline']\n",
      "JWDebler\n",
      "['JWDebler/nf-assembly']\n",
      "juneb4869\n",
      "['ssun1116/meripseqpipe', 'juneb4869/new_meripseqpipe', 'kingzhuky/meripseqpipe', 'canceromics/MeRIPseqPipe']\n",
      "redst4r\n",
      "['redst4r/nf-10x-kallisto']\n",
      "yuukiiwa\n",
      "['nf-core/modules', 'nf-core/nanoseq']\n",
      "gavinf97\n",
      "['gavinf97/groupnextflow', 'gavinf97/Nextflow_AntiSMASH']\n",
      "trambau\n",
      "['Thomas-LeCoent/reprohackathon-bioinfo']\n",
      "abhi18av\n",
      "['abhi18av/nextflow_grid_search', 'bioinformatics-lab/trigenome-analysis-nf', 'nf-modules/samtools', 'bioinformatics-lab/nf-core-singlegenometese', 'seqeralabs/gatk4-germline-snps-indels', 'abhi18av/cookiecutter-nextflow', 'nf-modules/gatk', 'nf-core/gwas', 'nf-modules/fastqc', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'nf-core/modules', 'nf-modules/picard', 'nf-modules/trimmomatic', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "jaserud\n",
      "['icgc-argo-workflows/nextflow-data-processing-utility-tools']\n",
      "ChadFibke\n",
      "['ChadFibke/germ']\n",
      "darlenewagner\n",
      "['darlenewagner/nextflowViral']\n",
      "mclaugsf\n",
      "['mclaugsf/seqtk-nextflow']\n",
      "LiuJie1117\n",
      "['likelet/MesKit']\n",
      "SergFern\n",
      "['SergFern/Variant_Calling']\n",
      "lkuchenb\n",
      "['Leon-Bichmann/diaproteomics', 'nf-core/epitopeprediction']\n",
      "jasteen\n",
      "['SoutheyLab/nextflow-workflows']\n",
      "rastiks\n",
      "['rastiks/viralrecon']\n",
      "rannick\n",
      "['nf-core/raredisease', 'nf-core/modules']\n",
      "Erkison\n",
      "['nf-core/modules']\n",
      "MiguelJulia\n",
      "['nf-core/viralrecon', 'rastiks/viralrecon']\n",
      "paulu-aws\n",
      "['goldfinchbio/sentieon-nextflow']\n",
      "dengshuang0116\n",
      "['likelet/circPipe']\n",
      "asl\n",
      "['ablab/graphamr']\n",
      "ehatch9\n",
      "['FredHutch/cellprofiler-batch-nf']\n",
      "chbk\n",
      "['FAANG/analysis-TAGADA']\n",
      "Mark-S-Hill\n",
      "['nf-core/modules']\n",
      "suzannejin\n",
      "['suzannejin/nf-proportionality', 'nf-core/modules']\n",
      "Jani-94\n",
      "['FAANG/GSM-pipeline']\n",
      "valleem\n",
      "['IARCbioinfo/NGSCheckMate-nf', 'IARCbioinfo/gatk4-DataPreProcessing-nf', 'IARCbioinfo/gatk4-GenotypeGVCFs-nf', 'Monia234/gatk4-GenotypeGVCFs-IARC', 'IARCbioinfo/gatk4-HaplotypeCaller-nf', 'IARCbioinfo/qualimap-nf']\n",
      "TrisKast\n",
      "['nf-core/cageseq']\n",
      "hynesgra\n",
      "['msmallegan/rmghc-workshop-19']\n",
      "christophstach\n",
      "['christophstach/live-pipeline-nextflow']\n",
      "nimbusFarzaneh\n",
      "['BCCDC-PHL/troika-nf']\n",
      "dgg32\n",
      "['dgg32/metagenome-binning-nextflow']\n",
      "jvierstra\n",
      "['jvierstra/nf-index', 'jvierstra/nf-genotyping']\n",
      "jambler24\n",
      "['h3abionet/h3arefgraph', 'jambler24/bac_pangenome', 'uct-cbio/bacterial_variant_calling', 'jambler24/bacterial_transcriptomics']\n",
      "ashdederich\n",
      "['ashdederich/Symbiont_genomeAssembly']\n",
      "bhbhjs\n",
      "['b600a/tuber', 'CENMIG/snpplet']\n",
      "mzamanian\n",
      "['zamanianlab/Core_RNAseq-nf']\n",
      "Thadouard\n",
      "['AnneCharlotteMichel/Reprohackathon']\n",
      "Rahul1711arora\n",
      "['luslab/nf-clip']\n",
      "photocyte\n",
      "['photocyte/repeatModeler2_nf', 'photocyte/genomeScope_nf', 'photocyte/luciferase-PPX-predictor-nf', 'photocyte/doSameSpeciesLiftOver_nextflow']\n",
      "praveenraj2018\n",
      "['nf-core/rnavar', 'nf-core/modules']\n",
      "Bontempogianpaolo1\n",
      "['federicacitarrella/FusionFlow']\n",
      "mariach\n",
      "['lifebit-ai/DeepVariantTrain', 'lifebit-ai/DeepVariantWGS', 'Biocentric/DeepVariantNF', 'lifebit-ai/DeepVariant']\n",
      "mpozuelo\n",
      "['mpozuelo/QC_demux', 'mpozuelo/illumina_demux', 'mpozuelo/MGI_demux', 'mpozuelo/demultiplexing', 'mpozuelo/exome_mosdepth']\n",
      "jaesvi\n",
      "['icgc-argo-workflows/icgc-argo-sv-copy-number']\n",
      "silastittes\n",
      "['silastittes/panand_structure']\n",
      "RitzelC\n",
      "['TRON-Bioinformatics/tronflow-mutect2']\n",
      "NajlaBioinfo\n",
      "['NajlaBioinfo/hisq_paired_rnasq']\n",
      "hseabolt\n",
      "['CDCgov/mycosnp-nf', 'nf-core/modules']\n",
      "rpetit3\n",
      "['CDCgov/mycosnp-nf', 'nf-core/modules', 'bactopia/bactopia']\n",
      "DSchreyer\n",
      "['Jojanneke-S/PRECODE']\n",
      "jhayer\n",
      "['HadrienG/nanoflow']\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "jherrero\n",
      "['UCL-BLIC/nf-ginkgo', 'UCL-BLIC/wgsalign']\n",
      "bschiffthaler\n",
      "['bschiffthaler/nf-radseq', 'bschiffthaler/nf-modules', 'bschiffthaler/nf-pseudopipe']\n",
      "michaelbale\n",
      "['michaelbale/JLab-IPSeqFlow', 'michaelbale/JLab-ATACFlow']\n",
      "noirot\n",
      "['nf-core/methylseq', 'FAANG/GSM-pipeline']\n",
      "jimmyliu1326\n",
      "['jimmyliu1326/SamnSero_Nextflow', 'jimmyliu1326/tCANS']\n",
      "michieitel\n",
      "['PalMuc/TransPi']\n",
      "danrlu\n",
      "['czbiohub/sc2-illumina-pipeline']\n",
      "jermth\n",
      "['jermth/hls-workshop']\n",
      "jordeu\n",
      "['nf-core/cutandrun']\n",
      "jiangweiyao\n",
      "['jiangweiyao/RefNAAP_nf', 'jiangweiyao/kraken2_biom_nf', 'jiangweiyao/quaisar_nf', 'jiangweiyao/paramsReadernf2', 'jiangweiyao/sra_mash_nf', 'jiangweiyao/metaphlan_nf', 'jiangweiyao/coregenome_align_nf']\n",
      "ckandoth\n",
      "['GoalConsortium/goal_misc']\n",
      "gn5\n",
      "['wtsi-hgi/nf_irods_to_lustre', 'wtsi-hgi/nf_scrna_deconvolution', 'wtsi-hgi/nextflow-pipelines', 'wtsi-hgi/nextflow_ci']\n",
      "anwarMZ\n",
      "['anwarMZ/nf-upcoast-v', 'cidgoh/cidgoh_qc']\n",
      "FalkoHof\n",
      "['Gregor-Mendel-Institute/isoseq3']\n",
      "cagescudero\n",
      "['PalMuc/TransPi']\n",
      "bfssi-forest-dussault\n",
      "['BFSSI-Bioinformatics-Lab/bfssi-assembly-pipeline']\n",
      "cying111\n",
      "['nf-core/nanoseq']\n",
      "gaotian52\n",
      "['AndersenLab/PEmRNA-seq-nf']\n",
      "xiaoli-dong\n",
      "['ABMicroBioinf/pathogen', 'ABMicroBioinf/magph', 'ABMicroBioinf/nf-tb', 'xiaoli-dong/pathogen', 'ABMicroBioinf/nf-qc', 'xiaoli-dong/magph']\n",
      "nilesh-tawari-elanco\n",
      "['nilesh-tawari/blast-pipeline']\n",
      "savytskanatalia\n",
      "['savytskanatalia/STARmap']\n",
      "jtk622\n",
      "['GMS6804-master/Sarek']\n",
      "Landris18\n",
      "['aduvermy/quantitative_nucleosome_analysis']\n",
      "KevinSayers\n",
      "['nextflow-io/nf-hack18', 'tobsecret/BADAS_Nextflow_Tutorial', 'nextflow-io/nf-hack17-tutorial']\n",
      "alexhbnr\n",
      "['nf-core/eager', 'maxibor/madman']\n",
      "clemgoub\n",
      "['clemgoub/dnaPipeTE2']\n",
      "FirasSadiyah\n",
      "['FirasSadiyah/NF-Workflow']\n",
      "IdoBar\n",
      "['nf-core/eager']\n",
      "AnneCharlotteMichel\n",
      "['AnneCharlotteMichel/Reprohackathon']\n",
      "tdelhomme\n",
      "['IARCbioinfo/fastqc-nf', 'IARCbioinfo/qualimap-nf', 'IARCbioinfo/TCGA_platypus-nf', 'IARCbioinfo/table_annovar-nf', 'Monia234/IARC-fastqc', 'tdelhomme/vcf_ancestry-nf']\n",
      "chenjy327\n",
      "['likelet/MesKit']\n",
      "jamez-eh\n",
      "['jamez-eh/nf-fh-pcp-wes-align', 'jamez-eh/nf-fh-pcp-wes-mutect2']\n",
      "dzerbino\n",
      "['eQTL-Catalogue/qtlmap']\n",
      "fredericlemoine\n",
      "['evolbioinfo/booster-workflows', 'evolbioinfo/gotree_usecase']\n",
      "gnetsanet\n",
      "['SJLeeY10/crispedit']\n",
      "mwalzer\n",
      "['bigbio/nf-workflows']\n",
      "fbdtemme\n",
      "['nf-core/modules']\n",
      "projectoriented\n",
      "['nf-core/raredisease', 'nf-core/modules', 'genomic-medicine-sweden/RareDisease_RNA_workflow']\n",
      "Thatguy027\n",
      "['Thatguy027/CePopulationGenetics-nf']\n",
      "mistyskye\n",
      "['EBIvariation/variant-remapping']\n",
      "svarona\n",
      "['nf-core/viralrecon', 'BU-ISCIII/SARS_Cov2_consensus-nf', 'rastiks/viralrecon', 'BU-ISCIII/panelLowFreq-nf']\n",
      "MozesBlom\n",
      "['MozesBlom/nf-polish']\n",
      "mohammedkhalfan\n",
      "['gencorefacility/nf-workflows', 'gencorefacility/variant-calling-pipeline-gatk4']\n",
      "iferres\n",
      "['iferres/CSI-nf', 'microgenlab/porefile']\n",
      "fanninpm\n",
      "['UPHL-BioNGS/Cecret', 'usafsam/mad_river_wf']\n",
      "lucky-nj\n",
      "['pandora414/dna']\n",
      "FriederikeHanssen\n",
      "['sickle-in-africa/saw.sarek', 'FriederikeHanssen/bamtofastq', 'nf-core/sarek', 'FriederikeHanssen/babysarek', 'sripaladugu/germline_somatic', 'Genomic-Medicine-Linkoping/nf-core-sarek', 'UMCUGenetics/sarek_ubec', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'nf-core/modules', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "klamkiew\n",
      "['klamkiew/viralclust']\n",
      "kateeasoncrukci\n",
      "['icgc-argo-workflows/icgc-argo-sv-copy-number']\n",
      "nriddiford\n",
      "['nriddiford/nf-core-lohcator']\n",
      "LucileSol\n",
      "['NBISweden/pipelines-nextflow']\n",
      "mjmansfi\n",
      "['luslab/nf-core-denovohybrid', 'luslab/luslab-nf-modules']\n",
      "MatteoSchiavinato\n",
      "['MatteoSchiavinato/MAG_recovery']\n",
      "DataSpott\n",
      "['replikation/poreCov']\n",
      "ericaenjoy3\n",
      "['ericaenjoy3/rna_nf']\n",
      "chenyuetian\n",
      "['chenyuetian/nextflow']\n",
      "seppinho\n",
      "['genepi/nf-gwas', 'askimed/nf-test-examples']\n",
      "QuentinLetourneur\n",
      "['QuentinLetourneur/Let-it-bin']\n",
      "yqshao\n",
      "['yqshao/tips']\n",
      "wathom\n",
      "['matthiasheinig/scworkflows']\n",
      "idfarbanecha\n",
      "['metagenlab/nanopore']\n",
      "rfara\n",
      "['goodwright/imaps-nf']\n",
      "thibaultdestanque\n",
      "['thibaultdestanque/RNA_seq_Nextflow']\n",
      "bokelund\n",
      "['Clinical-Genomics-Linkoping/gms-JASEN', 'genomic-medicine-sweden/JASEN']\n",
      "BABS-STP1\n",
      "['alam1988/Nextflow', 'crickbabs/BABS-RNASeq', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "sguizard\n",
      "['sguizard/nf-feelnc', 'sguizard/nf-core-tamanmd', 'sguizard/isoseq', 'nf-core/modules']\n",
      "fullama\n",
      "['nf-core/modules']\n",
      "lstevens17\n",
      "['tolkit/nemADSQ', 'lstevens17/busco-nf', 'lstevens17/nemAsm']\n",
      "aersoares81\n",
      "['NBISweden/pipelines-nextflow', 'NBISweden/Earth-Biogenome-Project-pilot']\n",
      "pericsson\n",
      "['nf-core/smrnaseq', 'nf-core/modules']\n",
      "vmurigneu\n",
      "['Vikash84/micropipe']\n",
      "tiagochst\n",
      "['markgene/cutnrun', 'jiangfuqing/Chip-seq', 'nf-core/chipseq']\n",
      "cmdoret\n",
      "['cmdoret/vapormap']\n",
      "alexpiper\n",
      "['alexpiper/piperline']\n",
      "espirado\n",
      "['espirado/lncrna_annotation_nextflow']\n",
      "drejom\n",
      "['alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'drejom/bam2fastq-nf', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "luomei308\n",
      "['luomei308/RNA_Seq']\n",
      "adigenova\n",
      "['IARCbioinfo/NGSCheckMate-nf', 'Monia234/IARC-RNA-seq', 'IARCbioinfo/nf-gene-fusions', 'IARCbioinfo/purple-nf', 'IARCbioinfo/bam2cram']\n",
      "brgew\n",
      "['bbi-lab/bbi-sci']\n",
      "yuifu\n",
      "['rikenbit/ramdaq', 'rikenbit/RamDAQ-prototype', 'bioinfo-tsukuba/nf-fastqc', 'yuifu/nextflow_cwl_example']\n",
      "shaunchuah\n",
      "['shaunchuah/cfdna_nextflow']\n",
      "aneichyk\n",
      "['independentdatalab/nf-riboseq']\n",
      "rutendos\n",
      "['Dowell-Lab/Bidirectional-Flow']\n",
      "stekaz\n",
      "['ampatchlab/nf-dnaseq', 'ampatchlab/nf-rnasnv', 'ampatchlab/nf-rnaseq', 'ampatchlab/nf-typeHLA', 'ampatchlab/nf-isoseq', 'ampatchlab/nf-bam2fastq', 'ampatchlab/nf-pdx']\n",
      "peterwharrison\n",
      "['sguizard/isoseq', 'FAANG/analysis-TAGADA']\n",
      "embatty\n",
      "['connor-lab/ncov2019-artic-nf']\n",
      "DossenaCarolina\n",
      "['DossenaCarolina/TF_footprint']\n",
      "MarieGurke\n",
      "['MarieGurke/nfvacal', 'MarieGurke/nfmap', 'MarieGurke/nfconsensus']\n",
      "Akazhiel\n",
      "['Akazhiel/NeoPred-NF']\n",
      "vntasis\n",
      "['vntasis/stan-nf']\n",
      "GhadaNOUAIRIA\n",
      "['erikrikarddaniel/pfitmap-nextflow']\n",
      "glmanhtu\n",
      "['glmanhtu/nf-workflows']\n",
      "BHNtools\n",
      "['NajlaBioinfo/hisq_paired_rnasq']\n",
      "BrianLohman\n",
      "['BrianLohman/star-rsem-scrnaseq-nf', 'BrianLohman/pdx-nf', 'BrianLohman/RNAseq-variant-calling-nf']\n",
      "pranathivemuri\n",
      "['czbiohub/nf-predictorthologs', 'nf-core/kmermaid', 'czbiohub/nf-unsplicedcds', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "sarahdrury\n",
      "['gavinf97/groupnextflow']\n",
      "Ed-G655\n",
      "['Ed-G655/nf-miRNA-SNPs-classify.nf']\n",
      "mal2017\n",
      "['mal2017/sfr']\n",
      "jbelyeu\n",
      "['jbelyeu/sv_calling_nf']\n",
      "cometsong\n",
      "['cometsong/ATAC_Seq_nxf']\n",
      "coraliegimonnet\n",
      "['coraliegimonnet/BS-Seq_pipeline', 'coraliegimonnet/ChIP-seq_pipeline']\n",
      "james-dtg\n",
      "['jdurbin/nf']\n",
      "bingzhang16\n",
      "['bzhanglab/neoflow']\n",
      "jonbra\n",
      "['jonbra/nf-desensitize']\n",
      "MicrobialGenomics\n",
      "['MicrobialGenomics/TTrichiura_Tubulin']\n",
      "Danilo2771\n",
      "['nf-core/modules']\n",
      "MSBradshaw\n",
      "['ryanlayerlab/layer_lab_chco', 'javaidm/layer_lab_vc']\n",
      "ffmmulder\n",
      "['UMCUGenetics/NextflowModules', 'UMCUGenetics/sarek_ubec']\n",
      "santiagorevale\n",
      "['nf-core/modules']\n",
      "vladsaveliev\n",
      "['vladsaveliev/umcaw', 'vladsaveliev/cawdor']\n",
      "phue\n",
      "['nf-core/methylseq', 'Gregor-Mendel-Institute/aradeepopsis', 'nf-core/eager', 'FAANG/GSM-pipeline', 'phue/GWAS-nf', 'Gregor-Mendel-Institute/kWIP-nf', 'nf-core/modules', 'phue/aradeepopsis']\n",
      "LordRust\n",
      "['Clinical-Genomics-Linkoping/gms-JASEN', 'genomic-medicine-sweden/JASEN']\n",
      "jimmybgammyknee\n",
      "['sagc-bioinformatics/modules']\n",
      "GFrosi\n",
      "['GFrosi/Nextflow-BEDtoBAM-IndexBAM']\n",
      "episkadlo\n",
      "['episkadlo/anglerFISH']\n",
      "waffle-iron\n",
      "['GMS6804-master/Sarek', 'sickle-in-africa/saw.structural-variants', 'melnel000/Sarek_CBIO']\n",
      "kkuret\n",
      "['luslab/nf-clip']\n",
      "fredjaya\n",
      "['fredjaya/mutscape', 'fredjaya/msmc-nf']\n",
      "ljmesi\n",
      "['nf-core/taxprofiler', 'nf-core/raredisease', 'nf-core/modules', 'genomic-medicine-sweden/JASEN']\n",
      "hpliner\n",
      "['bbi-lab/bbi-sci']\n",
      "drice-codeathons\n",
      "['NCBI-Codeathons/lung-rna-seq']\n",
      "adamd3\n",
      "['adamd3/StrainSeq']\n",
      "JIAYING2021\n",
      "['JIAYING2021/Hackathon021']\n",
      "sunitj\n",
      "['FischbachLab/nf-readqc', 'FischbachLab/nf-reads-profiler', 'FischbachLab/nf-midas']\n",
      "madhyastha\n",
      "['madhyastha/gatk-nextflow-sample']\n",
      "xmeng\n",
      "['FischbachLab/nf-reads-profiler']\n",
      "jinmingda\n",
      "['lengfei5/atacseq_nf', 'nf-core/modules', 'nf-core/atacseq']\n",
      "nhhaidee\n",
      "['peterk87/phylogenetictree', 'nhhaidee/scovtree']\n",
      "ChristinaVasil\n",
      "['nebfield/snpQT']\n",
      "phelelani\n",
      "['phelelani/nf-rnaSeqMetagen', 'phelelani/nf-rnaSeqCount']\n",
      "robsyme\n",
      "['nf-core/methylseq', 'FAANG/GSM-pipeline', 'robsyme/nf-nucmercoverage', 'c3g/genflow-dnaseq', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'c3g/runvalidation', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "tamuanand\n",
      "['nf-core/modules']\n",
      "dweemx\n",
      "['vib-singlecell-nf/vsn-pipelines']\n",
      "mmeier93\n",
      "['lifebit-ai/phewas', 'lifebit-ai/metagwas', 'lifebit-ai/simulate', 'lifebit-ai/prs']\n",
      "salzmanlab\n",
      "['salzmanlab/ReadZS']\n",
      "Foxcapades\n",
      "['VEuPathDB/proteinToGenomeAlignment']\n",
      "exsquire\n",
      "['exsquire/diminion']\n",
      "heuermh\n",
      "['heuermh/sars-cov-2', 'tobsecret/covid19', 'nf-core/viralrecon', 'nf-core/mag', 'heuermh/nf-core-hlatyping2', 'rastiks/viralrecon', 'nf-core/modules', 'mahesh-panchal/nextflow-docker-actions-test', 'subwaystation/pangenome', 'heuermh/artic']\n",
      "lwratten\n",
      "['lwratten/nanorna-bam', 'lwratten/nanorna', 'lwratten/nf_example', 'nf-core/nanoseq']\n",
      "jianhong\n",
      "['jianhong/ATACseqQCnextflow', 'jianhong/nextflowTutorial', 'jianhong/nf-core-hicar', 'nf-core/modules', 'jianhong/universalModule', 'jianhong/16S_pipeline', 'jianhong/shotgun']\n",
      "ChristopherBarrington\n",
      "['crickbabs/BABS-RNASeq']\n",
      "mderan-da\n",
      "['aws-samples/aws-gatk-recipe-nextflow-pipeline']\n",
      "AGROSAVIABIOUNIT\n",
      "['AGROSAVIABIOUNIT/MT', 'AGROSAVIABIOUNIT/nextflow_conda_cutadapt']\n",
      "vezzi\n",
      "['eQTL-Catalogue/rnaseq', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "mahesh-panchal\n",
      "['mahesh-panchal/test_nfcore_workflow_chain', 'NBISweden/pipelines-nextflow', 'mahesh-panchal/NBIS_project_template', 'mahesh-panchal/nf-core-alttemplate', 'Emilyaoc/Nextflow-selection-workflow', 'NBISweden/Earth-Biogenome-Project-pilot', 'nf-core/modules', 'mahesh-panchal/nextflow-docker-actions-test', 'GroundB/RepeatDefeaters', 'harleenduggal/nfcore-rnaseq', 'mahesh-panchal/nf-core_modules_demo', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "tcezard\n",
      "['EBIvariation/variant-remapping']\n",
      "jun-wan\n",
      "['eQTL-Catalogue/rnaseq', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "rynge\n",
      "['rynge/searchsra-nextflow']\n",
      "jfnavarro\n",
      "['sickle-in-africa/saw.sarek', 'nf-core/sarek', 'sripaladugu/germline_somatic', 'Genomic-Medicine-Linkoping/nf-core-sarek', 'UMCUGenetics/sarek_ubec', 'nf-core/modules']\n",
      "aidaanva\n",
      "['nf-core/eager']\n",
      "vpeddu\n",
      "['vpeddu/ev-meta', 'vpeddu/Slowqc', 'michellejlin/covid_swift_pipeline']\n",
      "aaronmck\n",
      "['mckennalab/NextLineage']\n",
      "bioShaun\n",
      "['bioShaun/xms-rnaseq-nf']\n",
      "perllb\n",
      "['perllb/ctg-exome']\n",
      "DLBPointon\n",
      "['DLBPointon/annotation-pipeline-nextflow']\n",
      "mamanambiya\n",
      "['mamanambiya/phasing_vcf_eagle', 'mamanambiya/popfreqs', 'h3abionet/recalling', 'h3abionet/popfreqs', 'h3abionet/chipimputation_evaluate_chips']\n",
      "fabubaker\n",
      "['YounisLab/rnaseq-pipeline']\n",
      "manabuishii\n",
      "['rikenbit/RamDAQ-prototype']\n",
      "aalinebini\n",
      "['aalinebini/ampliconseq']\n",
      "mjcipriano\n",
      "['nf-core/modules']\n",
      "mjakobs\n",
      "['nf-core/modules']\n",
      "angarb\n",
      "['TheJacksonLaboratory/Star_indices', 'TheJacksonLaboratory/splicing-pipelines-nf']\n",
      "spficklin\n",
      "['SystemsGenetics/GEMmaker', 'mmcogle/GEMmakerCam', 'SystemsGenetics/transcript_corral', 'nf-core/modules']\n",
      "samlhao\n",
      "['samlhao/nextflow-spid', 'samlhao/hgtsimulation', 'czbiohub/sc2-ngs-analysis', 'czbiohub/sc2-illumina-pipeline']\n",
      "ArnaudM22\n",
      "['KlausVG/reproHack']\n",
      "sruthipsuresh\n",
      "['nf-core/modules']\n",
      "sofiahaglund\n",
      "['markgene/cutnrun', 'jiangfuqing/Chip-seq', 'nf-core/chipseq', 'eQTL-Catalogue/rnaseq', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "Aveglia\n",
      "['Aveglia/vAMPirus']\n",
      "katiesevans\n",
      "['AndersenLab/post-gatk-nf', 'AndersenLab/genomes-nf', 'AndersenLab/nil-ril-nf', 'AndersenLab/wi-gatk', 'AndersenLab/annotation-nf', 'AndersenLab/scan2-nf', 'AndersenLab/alignment-nf']\n",
      "CJREID\n",
      "['CJREID/snplord-nf']\n",
      "nodrogluap\n",
      "['connor-lab/ncov2019-artic-nf']\n",
      "Darcy220606\n",
      "['nf-core/modules', 'nf-core/funcscan']\n",
      "keoughkath\n",
      "['keoughkath/AcceleratedRegionsNF']\n",
      "MorganePhilipp\n",
      "['hugovaysset/ReproHackaton']\n",
      "kevinpryan\n",
      "['kevinpryan/rtp_workshop']\n",
      "pontus\n",
      "['NBISweden/pipelines-nextflow']\n",
      "BrunoGrandePhD\n",
      "['nf-core/sarek', 'UMCUGenetics/sarek_ubec']\n",
      "esteinig\n",
      "['np-core/modules']\n",
      "bede\n",
      "['oxfordmmm/SARS-CoV2_workflows']\n",
      "Vlad-Dembrovskyi\n",
      "['TheJacksonLaboratory/Star_indices', 'lifebit-ai/relate', 'lifebit-ai/pcgr-nf', 'TheJacksonLaboratory/splicing-pipelines-nf', 'lifebit-ai/DeepVariant']\n",
      "markgene\n",
      "['markgene/cutnrun']\n",
      "chaeyoung-lee\n",
      "['chaeyoung-lee/gcp_genomics_api']\n",
      "cjfields\n",
      "['h3abionet/h3arefgraph', 'nf-core/cutandrun', 'h3abionet/node-accreditation', 'HPCBio/16S-rDNA-dada2-pipeline', 'h3abionet/HPCBio-Refgraph_pipeline']\n",
      "shyaman\n",
      "['AgBC-UoP/seq-contamination-QC-nf', 'AgBC-UoP/mapNclean-nf']\n",
      "Jeremy1805\n",
      "['Jeremy1805/nf-core-influenzangs', 'nf-core/modules']\n",
      "kcleal\n",
      "['brentp/rare-disease-wf']\n",
      "jrdemasi\n",
      "['msmallegan/rmghc-workshop-19']\n",
      "sima-r\n",
      "['nf-core/modules']\n",
      "BeibeiDu\n",
      "['luslab/nf-clip']\n",
      "austinreidmanny\n",
      "['austinreidmanny/raven-nf']\n",
      "lbarquist\n",
      "['bhagesh-codebeast/nextflowdualrnaseq', 'nf-core/dualrnaseq']\n",
      "emi80\n",
      "['nextflow-io/nf-hack18', 'CRG-CNAG/CalliNGS-NF', 'guigolab/rnaseq-nf']\n",
      "JoseEspinosa\n",
      "['cbcrg/nf-phdcourse20', 'nf-core/viralrecon', 'cbcrg/nf-phdcourse21', 'rastiks/viralrecon', 'biocorecrg/ELIXIR_containers_nextflow', 'nf-core/modules', 'harleenduggal/nfcore-rnaseq', 'JoseEspinosa/nf-core-benchmark', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "Zethson\n",
      "['jiangfuqing/CRISPR-Cas-off-target-identification', 'nf-core/proteomicslfq', 'subwaystation/pangenome', 'Leon-Bichmann/Phosphoproteomics']\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "fmaguire\n",
      "['fmaguire/filter_flow', 'fmaguire/mag_binning_workflow', 'fmaguire/mag_sweep', 'fmaguire/diamond_workflow', 'bactopia/bactopia']\n",
      "Thyra\n",
      "['NAMlab/rnaseq-mapper']\n",
      "mikek498\n",
      "['mikek498/artic-gls', 'connor-lab/ncov2019-artic-nf']\n",
      "mchimenti\n",
      "['mchimenti/ATAC_seq_nextflow']\n",
      "slimnsour\n",
      "['jerdra/TIGR_PURR']\n",
      "craigwindell\n",
      "['eresearchqut/VirReport']\n",
      "jguhlin\n",
      "['jguhlin/useful-nextflow-patterns']\n",
      "cirrina\n",
      "['cirrina/ctg-rnaseq']\n",
      "raygozag\n",
      "['raygozag/rnaseq']\n",
      "saramonzon\n",
      "['nf-core/viralrecon', 'BU-ISCIII/SARS_Cov2_consensus-nf', 'rastiks/viralrecon', 'BU-ISCIII/panelLowFreq-nf']\n",
      "leebrian\n",
      "['CDCgov/mycosnp-nf']\n",
      "martinghunt\n",
      "['oxfordmmm/preprocessing']\n",
      "kenyon-alexander\n",
      "['ChadFibke/germ']\n",
      "jhlegarreta\n",
      "['scilus/tractoflow']\n",
      "dvolk\n",
      "['tiwarialok/new-rnaseq', 'davideyre/bug-flow']\n",
      "joshua-d-campbell\n",
      "['joshua-d-campbell/nf-GATK_Exome_Preprocess']\n",
      "lars20070\n",
      "['OpenMSConsulting/NextflowLFQ']\n",
      "Niinleslie\n",
      "['likelet/MesKit']\n",
      "alakob\n",
      "['alakob/ena-bracken-annotation']\n",
      "marcodelapierre\n",
      "['marcodelapierre/demo-shpc-nf', 'marcodelapierre/trinity-nf', 'marcodelapierre/illumina-nf', 'marcodelapierre/nanopore-nf']\n",
      "kalanir\n",
      "['czbiohub/nf-bowtie']\n",
      "MillironX\n",
      "['nf-core/modules', 'ksumngs/v-met', 'ksumngs/nf-modules']\n",
      "BatoolMM\n",
      "['nf-core/modules']\n",
      "sjsabin\n",
      "['supark87/minion_hrp2']\n",
      "cnoel-sebimer\n",
      "['ifremer-bioinformatics/FLORA', 'ifremer-bioinformatics/samba']\n",
      "l-modolo\n",
      "['clemgoub/dnaPipeTE2', 'LBMC/readthroughpombe']\n",
      "myourshaw\n",
      "['GoalConsortium/goal_misc']\n",
      "MattHuff\n",
      "['MattHuff/Nextflow_Pipelines']\n",
      "YussAb\n",
      "['YussAb/mergeVCF_MutectStrelka']\n",
      "jgolob\n",
      "['jgolob/maliampi', 'Golob-Minot/geneshot']\n",
      "wenbostar\n",
      "['bzhanglab/neoflow', 'bzhanglab/DeepRescore']\n",
      "lmtani\n",
      "['lmtani/wf-human-mito']\n",
      "shbrief\n",
      "['seandavi/curatedMetagenomicsNextflow']\n",
      "XinHuang87\n",
      "['NCBI-Hackathons/Nasty_Metagenomes']\n",
      "sdjebali\n",
      "['nf-core/smrnaseq', 'FAANG/analysis-TAGADA']\n",
      "BrianSanderson\n",
      "['TheJacksonLaboratory/mmrSVD']\n",
      "Nine-s\n",
      "['Nine-s/workflow_comparison_analysis']\n",
      "JohnHadish\n",
      "['SystemsGenetics/GEMmaker', 'mmcogle/GEMmakerCam']\n",
      "drpowell\n",
      "['harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "Hammarn\n",
      "['nf-core/methylseq', 'Hammarn/Popolipo', 'FAANG/GSM-pipeline', 'nf-core/smrnaseq', 'eQTL-Catalogue/rnaseq', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'Gregor-Mendel-Institute/nf-methylpy', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnafusion', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "willemdek11\n",
      "['ErasmusMC-Bioinformatics/NextFlow-VC-pipeline']\n",
      "lisemangiante\n",
      "['lisemangiante/test_nextflow']\n",
      "Subhodeep13\n",
      "['Subhodeep13/Nextflow-Fastqc']\n",
      "baptisteruiz\n",
      "['AnneCharlotteMichel/Reprohackathon']\n",
      "na399\n",
      "['eQTL-Catalogue/rnaseq', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "gdevailly\n",
      "['nf-core/methylseq', 'FAANG/GSM-pipeline']\n",
      "Thomieh73\n",
      "['NorwegianVeterinaryInstitute/Talos', 'NorwegianVeterinaryInstitute/Nepal']\n",
      "xingaulaglag\n",
      "['laclac102/ampliseq']\n",
      "zhiaos\n",
      "['bzhanglab/nf-rnaseq']\n",
      "oschwengers\n",
      "['nf-core/modules']\n",
      "patricksorn\n",
      "['TRON-Bioinformatics/covigator-ngs-pipeline']\n",
      "mingxinliu\n",
      "['mingxinliu/nfp4MBC']\n",
      "ameintjes\n",
      "['h3abionet/popfreqs', 'h3abionet/chipimputation_evaluate_chips']\n",
      "mbosio85\n",
      "['mbosio85/nf-core-gatkcohortcall', 'mbosio85/ngs_variant_calling', 'mbosio85/CNVcall', 'inab/RDConnect_RNASeq']\n",
      "hknahal\n",
      "['icgc-argo-workflows/sanger-wxs-variant-calling', 'icgc-argo-workflows/dna-seq-processing-wfs', 'icgc-argo-workflows/sanger-wgs-variant-calling']\n",
      "allissadillman\n",
      "['NCBI-Hackathons/Nasty_Metagenomes']\n",
      "palatinate\n",
      "['philDTU/plasmidPublication']\n",
      "mbradyneeley\n",
      "['mbradyneeley/RNASeq_Pipeline']\n",
      "reganhayward\n",
      "['bhagesh-codebeast/nextflowdualrnaseq', 'nf-core/dualrnaseq']\n",
      "jasmezz\n",
      "['nf-core/funcscan']\n",
      "bigmonty12\n",
      "['bigmonty12/peakCallingBenchmark']\n",
      "ferygood\n",
      "['ferygood/nf-STAR-TEtranscript']\n",
      "bjlang\n",
      "['cbcrg/nf-phdcourse21']\n",
      "kusalananda\n",
      "['sickle-in-africa/saw.structural-variants']\n",
      "ywilke\n",
      "['UMCUGenetics/NextflowModules']\n",
      "adrodrzywolski\n",
      "['adrodrzywolski/rnaseq_analysis_pipeline']\n",
      "sven1103\n",
      "['nf-core/methylseq', 'nf-core/cookiecutter', 'FAANG/GSM-pipeline', 'nf-core/hlatyping', 'eQTL-Catalogue/rnaseq', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'Gregor-Mendel-Institute/nf-methylpy', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "milescsmith\n",
      "['milescsmith/gcls-rnaseq-nf']\n",
      "evaham1\n",
      "['Streit-lab/streitlab-nf-modules']\n",
      "d4straub\n",
      "['nf-core/bacass', 'nf-core/mag', 'nf-core/ampliseq', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'nf-core/modules', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "robinfchan\n",
      "['robinfchan/citeseq-nf', 'robinfchan/bisulfite_align_nf']\n",
      "JackCurragh\n",
      "['JackCurragh/riboseq_data_processing']\n",
      "trev-f\n",
      "['trev-f/SRAlign', 'trev-f/SRAtac']\n",
      "ErikaKvalem\n",
      "['nf-core/viralrecon']\n",
      "IARC-genetics\n",
      "['IARC-genetics/random_nf_scripts']\n",
      "klkeys\n",
      "['nf-core/modules']\n",
      "ellendejong\n",
      "['UMCUGenetics/NextflowModules', 'UMCUGenetics/DxNextflowWES']\n",
      "oxfordfun\n",
      "['oxfordfun/FunSnippy', 'oxfordmmm/preprocessing']\n",
      "mnagari\n",
      "['BioinformaticsLabAtMUN/sRNACharP']\n",
      "brwnj\n",
      "['brwnj/freebayes-nf', 'quinlan-lab/preon', 'BigelowLab/gorg-classifier', 'brwnj/upward', 'brwnj/seqcover-nf']\n",
      "canceromics\n",
      "['canceromics/MeRIPseqPipe']\n",
      "leipzig\n",
      "['leipzig/m6a']\n",
      "jordwil\n",
      "['alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'jordwil/nextflow-bowtie2', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "letovesnoi\n",
      "['letovesnoi/clusterassembly']\n",
      "daichengxin\n",
      "['bigbio/proteomicstmt', 'bigbio/quantms']\n",
      "isugif\n",
      "['isugifNF/freebayes', 'isugifNF/blast']\n",
      "yassineS\n",
      "['yassineS/nf-demux']\n",
      "Gwennid\n",
      "['nf-core/raredisease', 'nf-core/modules']\n",
      "RaverJay\n",
      "['replikation/poreCov']\n",
      "nalcala\n",
      "['IARCbioinfo/NGSCheckMate-nf', 'IARCbioinfo/fastqc-nf', 'IARCbioinfo/qualimap-nf', 'Monia234/IARC-alignement', 'IARCbioinfo/BQSR-nf', 'IARCbioinfo/table_annovar-nf', 'IARCbioinfo/strelka2-nf', 'Monia234/IARC-fastqc']\n",
      "didillysquat\n",
      "['didillysquat/yamada', 'didillysquat/kopp_2021_fowl']\n",
      "jrkirk61\n",
      "['HPCBio/16S-rDNA-dada2-pipeline']\n",
      "olgabot\n",
      "['czbiohub/nf-extractcoding', 'sickle-in-africa/saw.sarek', 'nf-core/eager', 'czbiohub/nf-predictorthologs', 'nf-core/sarek', 'czbiohub/nextflow-tutorial-2019', 'nf-core/kmermaid', 'czbiohub/nf-ortholog', 'sripaladugu/germline_somatic', 'Genomic-Medicine-Linkoping/nf-core-sarek', 'czbiohub/nf-large-assembly', 'UMCUGenetics/sarek_ubec', 'nf-core/scrnaseq', 'czbiohub/splicemotifs', 'nf-core/crisprvar', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'czbiohub/nf-core-test', 'czbiohub/nf-simulaternaseq', 'harleenduggal/nfcore-rnaseq', 'czbiohub/nf-tracer', 'czbiohub/demux', 'czbiohub/sc2-illumina-pipeline', 'czbiohub/nf-bowtie', 'czbiohub/nf-sicilian', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "Etjean\n",
      "['Etjean/Long_project']\n",
      "palfalvi\n",
      "['palfalvi/nanoporeseq', 'palfalvi/rnaseq']\n",
      "alam1988\n",
      "['alam1988/Nextflow']\n",
      "Clinical-Genomics-Linkoping\n",
      "['Clinical-Genomics-Linkoping/artic-pangolin-nf']\n",
      "davideyre\n",
      "['davideyre/bug-flow']\n",
      "cahaisv\n",
      "['IARCbioinfo/strelka2-nf']\n",
      "AntoniaSchuster\n",
      "['nf-core/mag', 'nf-core/modules']\n",
      "herczegrobert\n",
      "['herczegrobert/ownpipeline']\n",
      "nebfield\n",
      "['PGScatalog/pgsc_calc', 'nf-core/modules', 'nebfield/snpQT']\n",
      "tbugfinder\n",
      "['nf-core/airrflow']\n",
      "ralsallaq\n",
      "['ralsallaq/metaGx_nf']\n",
      "stevekm\n",
      "['stevekm/MuTect2_target_chunking', 'stevekm/vep-annotation-nf', 'NYU-Molecular-Pathology/NGS580-nf', 'tobsecret/BADAS_Nextflow_Tutorial', 'nf-core/viralrecon', 'stevekm/nextflow-demos', 'stevekm/nextflow-samplesheet-demo', 'rastiks/viralrecon', 'stevekm/fastq-bed-subset', 'nf-core/modules', 'stevekm/nextflow-pipeline-demo', 'NYU-Molecular-Pathology/LG-PACT', 'stevekm/vcf-filter-annotate']\n",
      "porchard\n",
      "['porchard/ATACseq-NextFlow', 'porchard/RNAseq-NextFlow']\n",
      "FitzsimmonsCM\n",
      "['FitzsimmonsCM/RNAseq_Nextflow']\n",
      "njspix\n",
      "['njspix/ref_genomes', 'nf-core/modules']\n",
      "ac55-sanger\n",
      "['connor-lab/ncov2019-artic-nf']\n",
      "snewhouse\n",
      "['baiyuanxiang/ngs_nextflow']\n",
      "alesssia\n",
      "['nf-core/methylseq', 'alesssia/YAMP', 'FAANG/GSM-pipeline', 'GMS6804-master/YAMP', 'kviljoen/fastq_QC', 'HadrienG/nanoflow']\n",
      "MeghanaKB-Rheos\n",
      "['MeghanaKB-Rheos/rnaseqpca']\n",
      "mpozuelo-flomics\n",
      "['mpozuelo/demultiplexing']\n",
      "jtangrot\n",
      "['nf-core/ampliseq']\n",
      "Simontuk\n",
      "['Simontuk/sprint_covseq']\n",
      "matthiasheinig\n",
      "['matthiasheinig/scworkflows']\n",
      "radhika-kataria\n",
      "['cancerbioinformatics/PATCH-pipeline']\n",
      "J35P312\n",
      "['GMS6804-master/Sarek', 'melnel000/Sarek_CBIO', 'genomic-medicine-sweden/RareDisease_RNA_workflow']\n",
      "cvaske\n",
      "['IARCbioinfo/gatk4-HaplotypeCaller-nf']\n",
      "wbazant\n",
      "['wbazant/CORALE']\n",
      "drpatelh\n",
      "['nf-core/bacass', 'nf-core/methylseq', 't-neumann/slamseq', 'nf-core/eager', 'markgene/cutnrun', 'jiangfuqing/Chip-seq', 'nf-core/bactmap', 'FAANG/GSM-pipeline', 'nf-core/mnaseseq', 'tobsecret/covid19', 'gwright99/nf-core-dragen', 'nf-core/smrnaseq', 'nf-core/viralrecon', 'nf-core/cageseq', 'nf-core/chipseq', 'lengfei5/atacseq_nf', 'paulstretenowich/nf-core-viralrecon', 'nf-core/clipseq', 'rastiks/viralrecon', 'nf-core/gwas', 'nf-core/ampliseq', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'nf-core/modules', 'drpatelh/nf-core-sgrnaquant', 'csawye01/nf-core-demultiplex', 'harleenduggal/nfcore-rnaseq', 'jiangfuqing/atac-seq', 'drpatelh/nf-core-fetchdata', 'nf-core/atacseq', 'nf-core/nanoseq', 'heuermh/artic', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "lleroi\n",
      "['ifremer-bioinformatics/samba']\n",
      "yonghah\n",
      "['yonghah/geodata-pipeline']\n",
      "sb43\n",
      "['connor-lab/ncov2019-artic-nf']\n",
      "smlmbrt\n",
      "['PGScatalog/pgsc_calc']\n",
      "luiskuhn\n",
      "['luiskuhn/liverctanalysis']\n",
      "BenNolann\n",
      "['BenNolann/rsi_analysis']\n",
      "mzahm\n",
      "['cbirbes/NextFlowPipeline']\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Mxrcon\n",
      "['Mxrcon/Savio_alignments_nf', 'nf-core/modules', 'Mxrcon/Gustavo_protein_anotation_nf', 'bactopia/bactopia', 'Mxrcon/Nextflow-study']\n",
      "dianamarek\n",
      "['biocorecrg/SIB_course_nextflow_Nov_2021']\n",
      "LeahRoberts\n",
      "['Vikash84/micropipe']\n",
      "sminot\n",
      "['FredHutch/ccs-nf', 'FredHutch/PGAP-nf', 'FredHutch/circulator-nf', 'FredHutch/index-genomes-nf', 'FredHutch/VMAA', 'FredHutch/prokka-nf', 'FredHutch/AMGMA', 'jgolob/maliampi', 'FredHutch/nf-sra', 'Golob-Minot/geneshot', 'FredHutch/nf-pacbio-bacterial', 'FredHutch/cellprofiler-batch-nf', 'FredHutch/flye-nf', 'FredHutch/diamond-build-tax-db', 'FredHutch/unicycler-nf', 'FredHutch/microbial-rnaseq']\n",
      "esrice\n",
      "['WarrenLab/longread-svs-nf', 'WarrenLab/shortread-polish-nf', 'esrice/workflows', 'WarrenLab/longread-polish-nf', 'WarrenLab/purge-haplotigs-nf']\n",
      "vincenthhu\n",
      "['vincenthhu/nf-core-westest']\n",
      "imendes93\n",
      "['lifebit-ai/pcgr-nf', 'lifebit-ai/bam2cram', 'imendes93/ReleaseTheKraken', 'lifebit-ai/ReleaseTheKraken', 'imendes93/sv-nf']\n",
      "cdiener\n",
      "['Gibbons-Lab/pipelines']\n",
      "myoshimura080822\n",
      "['rikenbit/ramdaq', 'rikenbit/RamDAQ-prototype']\n",
      "noahaus\n",
      "['salvadorlab/mbovpan']\n",
      "prenderj\n",
      "['evotools/nf-LO']\n",
      "Eletham\n",
      "['nf-core/crisprvar']\n",
      "zhangtong516\n",
      "['zhangtong516/icpipe-nextflow']\n",
      "marc-jones\n",
      "['luslab/nf-core-modules', 'luslab/luslab-nf-modules', 'marc-jones/nextflow-example', 'goodwright/imaps-nf']\n",
      "naryamanesh\n",
      "['naryamanesh/nf-bismarkAlignment']\n",
      "WhalleyT\n",
      "['WhalleyT/RECIPIENT', 'WhalleyT/neoantigen_prediction']\n",
      "adamrtalbot\n",
      "['adamrtalbot/kallisto_nf']\n",
      "apriltuesday\n",
      "['EBIvariation/variant-remapping']\n",
      "pufetin\n",
      "['genomicsITER/NanoCLUST']\n",
      "kevbrick\n",
      "['kevbrick/pipeIt', 'kevbrick/ssds_nfcore', 'nf-core/ssds', 'nf-core/modules']\n",
      "nimarafati\n",
      "['NBISweden/pipelines-nextflow']\n",
      "matq007\n",
      "['nf-core/rnafusion']\n",
      "lobleya\n",
      "['lobleya/GATK4_WGS']\n",
      "noelnamai\n",
      "['noelnamai/differential-expression-analysis', 'bzhanglab/neoflow']\n",
      "anna-saukkonen\n",
      "['anna-saukkonen/PAC']\n",
      "jcohenadad\n",
      "['courtois-neuromod/anat-processing']\n",
      "chewbeckie\n",
      "['chewbeckie/Outbreak_EnrichmentCulture', 'chewbeckie/BacAss', 'chewbeckie/flye_ntedit_polish_graph_workflow']\n",
      "chelauk\n",
      "['sickle-in-africa/saw.sarek', 'nf-core/sarek', 'chelauk/nf-core-hlatyping', 'sripaladugu/germline_somatic', 'chelauk/test_nextflow_sarek', 'Genomic-Medicine-Linkoping/nf-core-sarek', 'chelauk/nf-core-blasr', 'chelauk/nf-core-partial-umi', 'UMCUGenetics/sarek_ubec', 'chelauk/nf-core-umipreprocessing', 'chelauk/nf-core-umi_preprocessing', 'chelauk/nf-core-mutectplatypus', 'chelauk/nf-core-egatransfer', 'chelauk/nf-core-trimmomatic', 'chelauk/nf-core-platypus', 'chelauk/nf-core-deepsnv']\n",
      "amayer21\n",
      "['alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "luisas\n",
      "['lifebit-ai/freebayes', 'lifebit-ai/kallisto-sra', 'lifebit-ai/DeepVariantTrain', 'lifebit-ai/strelka2', 'lifebit-ai/DeepVariantWGS', 'Biocentric/DeepVariantNF', 'lifebit-ai/DeepVariant']\n",
      "maxulysse\n",
      "['nf-core/bacass', 'nf-core/methylseq', 'cgpu/PGP-UK-sarek', 't-neumann/slamseq', 'sickle-in-africa/saw.sarek', 'nf-core/eager', 'nf-core/sarek', 'nf-core/cookiecutter', 'FAANG/GSM-pipeline', 'nf-core/kmermaid', 'nf-core/mnaseseq', 'nf-core/airrflow', 'nf-core/rnavar', 'nf-core/smrnaseq', 'sripaladugu/germline_somatic', 'maxibor/coproID', 'nf-core/vipr', 'GMS6804-master/Sarek', 'Genomic-Medicine-Linkoping/nf-core-sarek', 'nf-core/viralrecon', 'nf-core/proteomicslfq', 'nf-core/mag', 'nf-core/cageseq', 'nf-core/chipseq', 'nf-core/exoseq', 'UMCUGenetics/sarek_ubec', 'lengfei5/atacseq_nf', 'nf-core/scrnaseq', 'rastiks/viralrecon', 'nf-core/hlatyping', 'melnel000/Sarek_CBIO', 'eQTL-Catalogue/rnaseq', 'nf-core/ampliseq', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'nf-core/modules', 'Gregor-Mendel-Institute/nf-methylpy', 'harleenduggal/nfcore-rnaseq', 'Leon-Bichmann/diaproteomics', 'nf-core/rnafusion', 'nf-core/epitopeprediction', 'nf-core/atacseq', 'nf-core/nanoseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ', 'Leon-Bichmann/Phosphoproteomics']\n",
      "annacprice\n",
      "['annacprice/autodatabase', 'oxfordmmm/preprocessing', 'nf-core/modules']\n",
      "m3hdad\n",
      "['nf-core/rnavar']\n",
      "dalmiaa\n",
      "['dalmiaa/Sample_NF']\n",
      "olavurmortensen\n",
      "['fargenfo/linkseq-demux', 'fargenfo/linkseq', 'fargenfo/gatk-joint-genotyping', 'olavurmortensen/demuxlink']\n",
      "mciprianoCDC\n",
      "['CDCgov/mycosnp-nf']\n",
      "Wangxin555\n",
      "['likelet/MesKit']\n",
      "jyguo\n",
      "['jyguo/optitype']\n",
      "ThamLe2601\n",
      "['PI-Bioinfo/thamlee-nxf-rnaseq', 'ThamLe2601/nextflow-rnaseq-modules']\n",
      "kmayerb\n",
      "['kmayerb/knead-docker', 'kmayerb/nf-mixcr', 'kmayerb/nf-corncob']\n",
      "sureshhewabi\n",
      "['bigbio/nf-workflows']\n",
      "ggrimes\n",
      "['ggrimes/nf_fastqc', 'ggrimes/nextflow_rnaseq_training_dataset', 'ggrimes/clair_nf', 'ggrimes/crispy-chainsaw', 'ggrimes/ttseq', 'ggrimes/nf-fastp']\n",
      "pditommaso\n",
      "['pditommaso/nf-foo', 'nf-core/methylseq', 'CAMI-challenge/CAMITAX', 'lifebit-ai/kallisto-sra', 'alesssia/YAMP', 'tiwarialok/new-rnaseq', 'nextflow-io/gccbosc18-training', 'nf-core/cookiecutter', 'nextflow-io/nf-hack18', 'FAANG/GSM-pipeline', 'nextflow-io/rnaseq-nf', 'nf-core/smrnaseq', 'cbcrg/nf-phdcourse19', 'cbcrg/nf-phdcourse20', 'GMS6804-master/Sarek', 'mageshwarm/rnaseq-nf-magesh', 'tobsecret/BADAS_Nextflow_Tutorial', 'IARCbioinfo/gatk4-HaplotypeCaller-nf', 'nextflow-io/blast-example', 'stevekm/nextflow-demos', 'nextflow-io/nf-hack17-tutorial', 'cbcrg/nf-phdcourse21', 'evanfloden/nf-module-demo', 'lauramble/rnaseq-vizfada', 'biocorecrg/C4LWG-2018', 'nf-core/hlatyping', 'melnel000/Sarek_CBIO', 'pilm-bioinformatics/pipelines-nf-fastrnaseq', 'HPCBio/16S-rDNA-dada2-pipeline', 'biocorecrg/BioNextflow', 'mageshwarm/blast-example-magesh', 'eQTL-Catalogue/rnaseq', 'alam1988/Nextflow', 'GMS6804-master/rnatoy', 'GMS6804-master/YAMP', 'junyu-boston/dicerna-rnaseq', 'nf-core/modules', 'biocorecrg/indrop', 'CRG-CNAG/CalliNGS-NF', 'harleenduggal/nfcore-rnaseq', 'nextflow-io/elixir-workshop-21', 'pditommaso/nf-course-unimi-2021', 'gis-rpd/rpd-sg10k-grch38-gatk4-gvcf-freebayes-vcf', 'Biocentric/rnaseq_debug', 'milescsmith/gcls-rnaseq-nf', 'biocorecrg/vectorQC', 'nextflow-io/nfcamp-tutorial', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "tmc-hematopath\n",
      "['tmc-hematopath/NextSeq_MIPS_NextflowMutationDetector', 'tmc-hematopath/smMIPS-Detection-Pipeline']\n",
      "transmute-ngs\n",
      "['finnor/sample-renamer']\n",
      "abremges\n",
      "['CAMI-challenge/CAMITAX']\n",
      "maxibor\n",
      "['maxibor/test-nf-core-pipeline', 'nf-core/eager', 'maxibor/metaphlan-nf', 'maxibor/coproID', 'nf-core/mag', 'maxibor/enaprep', 'nf-core/taxprofiler', 'maxibor/dada2-nf', 'maxibor/anonymap', 'ParisDiderot-Bioinfo/nextflow-intro', 'nf-core/modules', 'maxibor/madman', 'maxibor/kraken-nf', 'maxibor/admapipe', 'maxibor/humann-nf', 'maxibor/bowtie2-lca']\n",
      "dependabot[bot]\n",
      "['lifebit-ai/bam2cram', 'vib-singlecell-nf/vsn-pipelines']\n",
      "propan2one\n",
      "['propan2one/variantcallerbench']\n",
      "andreas-wilm\n",
      "['gis-rpd/rpd-sg10k-grch38-gatk4-gvcf-freebayes-vcf']\n",
      "gaow\n",
      "['gaow/fastqc-nf']\n",
      "csawye01\n",
      "['csawye01/nf-core-demultiplex', 'nf-core/nanoseq']\n",
      "senthil10\n",
      "['nf-core/exoseq', 'eQTL-Catalogue/rnaseq', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "ameynert\n",
      "['ameynert/base-space-download-fastq-with-checksums', 'ameynert/bam2fastq']\n",
      "erinyoung\n",
      "['UPHL-BioNGS/Cecret', 'UPHL-BioNGS/Grandeur', 'UPHL-BioNGS/Donut_Falls']\n",
      "markxiao\n",
      "['markxiao/PRS-dev']\n",
      "erikrikarddaniel\n",
      "['LNUc-EEMiS/magmap', 'bioatlas/ampliflow', 'LNUc-EEMiS/metatdenovo-dsl1', 'nf-core/ampliseq', 'nf-core/modules', 'erikrikarddaniel/pfitmap-nextflow', 'erikrikarddaniel/magmap']\n",
      "lmurba\n",
      "['TheJacksonLaboratory/splicing-pipelines-nf']\n",
      "royfrancis\n",
      "['NBISweden/pipelines-nextflow']\n",
      "philDTU\n",
      "['philDTU/plasmidPublication']\n",
      "pallolason\n",
      "['GMS6804-master/Sarek', 'sickle-in-africa/saw.structural-variants', 'melnel000/Sarek_CBIO']\n",
      "kkerns85\n",
      "['kkerns85/midas_nextflow', 'kkerns85/midas_nf_tower']\n",
      "MarieLataretu\n",
      "['replikation/poreCov', 'hoelzer/clean']\n",
      "evdomene\n",
      "['evdomene/brbseqnf']\n",
      "abumadsen\n",
      "['Emilyaoc/Nextflow-selection-workflow']\n",
      "Oliver-Tautz\n",
      "['Oliver-Tautz/helloNextflow']\n",
      "asthara10\n",
      "['asthara10/insertseq']\n",
      "christopher-mohr\n",
      "['nf-core/hlatyping', 'nf-core/epitopeprediction']\n",
      "arnaudbore\n",
      "['scilus/tractoflow']\n",
      "alexwhan\n",
      "['csiro-crop-informatics/reproducible_poc', 'csiro-crop-informatics/repset']\n",
      "druvus\n",
      "['genomicsITER/NanoCLUST']\n",
      "ashleethomson\n",
      "['sagc-bioinformatics/modules']\n",
      "multimeric\n",
      "['multimeric/AwsNextflowBug']\n",
      "snafees\n",
      "['nf-core/kmermaid', 'czbiohub/nf-unsplicedcds']\n",
      "ewels\n",
      "['nf-core/bacass', 'nf-core/methylseq', 'nf-core/eager', 'markgene/cutnrun', 'jiangfuqing/Chip-seq', 'nf-core/sarek', 'nf-core/bactmap', 'nf-core/cookiecutter', 'FAANG/GSM-pipeline', 'nf-core/kmermaid', 'nf-core/airrflow', 'nf-core/smrnaseq', 'nf-core/vipr', 'GMS6804-master/Sarek', 'ewels/nf-core-dsl2pipelinetest', 'nf-core/viralrecon', 'nf-core/mag', 'nf-core/cageseq', 'nf-core/chipseq', 'nf-core/cutandrun', 'nf-core/exoseq', 'UMCUGenetics/sarek_ubec', 'lengfei5/atacseq_nf', 'nf-core/clipseq', 'rastiks/viralrecon', 'nf-core/hlatyping', 'melnel000/Sarek_CBIO', 'nf-core/gwas', 'eQTL-Catalogue/rnaseq', 'jianhong/nf-core-hicar', 'nf-core/ampliseq', 'alam1988/Nextflow', 'nf-core/neutronstar', 'junyu-boston/dicerna-rnaseq', 'nf-core/modules', 'nf-core/testpipeline', 'Gregor-Mendel-Institute/nf-methylpy', 'harleenduggal/nfcore-rnaseq', 'Leon-Bichmann/diaproteomics', 'jiangfuqing/atac-seq', 'nf-core/rnafusion', 'nf-core/atacseq', 'nf-core/nanoseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "a-lud\n",
      "['danielyao12/Sanders-workflows', 'sagc-bioinformatics/modules']\n",
      "charlotte-west\n",
      "['nf-core/cutandrun', 'luslab/nf-core-modules', 'luslab/luslab-nf-modules', 'nf-core/clipseq']\n",
      "asafpr\n",
      "['nf-core/ampliseq']\n",
      "jackkamm\n",
      "['czbiohub/sc2-illumina-pipeline']\n",
      "clairecoleman1\n",
      "['clairecoleman1/clipseq1']\n",
      "bibo3\n",
      "['bibo3/popbom']\n",
      "MoritzBauer\n",
      "['biocorecrg/allele_specific_RNAseq']\n",
      "sofsta\n",
      "['Clinical-Genomics-Linkoping/gms-JASEN', 'genomic-medicine-sweden/JASEN']\n",
      "abotzki\n",
      "['vibbits/rnaseq-editing']\n",
      "lindaxiang\n",
      "['icgc-argo-workflows/open-access-variant-filtering', 'icgc-argo-workflows/sanger-wxs-variant-calling', 'icgc-argo-workflows/dna-seq-processing-wfs', 'icgc-argo-workflows/nextflow-data-processing-utility-tools', 'icgc-argo-workflows/sanger-wgs-variant-calling']\n",
      "BarryDigby\n",
      "['BarryDigby/circ', 'BarryDigby/nextflow_bits']\n",
      "viklund\n",
      "['sickle-in-africa/saw.structural-variants']\n",
      "clairealix\n",
      "['lifebit-ai/ukbb-tutorial']\n",
      "gf-atebbe\n",
      "['goldfinchbio/gatk-nextflow', 'goldfinchbio/sentieon-nextflow']\n",
      "andricDu\n",
      "['icgc-argo-workflows/dna-seq-processing-wfs', 'icgc-argo-workflows/nextflow-data-processing-utility-tools']\n",
      "laure182\n",
      "['ifremer-bioinformatics/samba']\n",
      "ojziff\n",
      "['luslab/nf-clip']\n",
      "lauramble\n",
      "['lauramble/rnaseq-vizfada']\n",
      "drbecavin\n",
      "['becavin-lab/nf-blast', 'becavin-lab/nf-rnaseq']\n",
      "ghuls\n",
      "['vib-singlecell-nf/vsn-pipelines']\n",
      "Reda94\n",
      "['Reda94/GDC-RNAseq-pipeline']\n",
      "trickytank\n",
      "['trickytank/rna_circular-nf']\n",
      "zsteve\n",
      "['zsteve/nf-ATAC']\n",
      "eameyer\n",
      "['salzmanlab/ReadZS']\n",
      "nickhsmith\n",
      "['nf-core/modules']\n",
      "FredDodd6\n",
      "['connor-lab/ncov2019-artic-nf']\n",
      "weiqijin\n",
      "['likelet/circPipe']\n",
      "jfy133\n",
      "['nf-core/eager', 'maxibor/coproID', 'nf-core/mag', 'nf-core/taxprofiler', 'jfy133/archaeodiet', 'nf-core/modules', 'maxibor/madman', 'nf-core/funcscan']\n",
      "cavei\n",
      "['icbi-lab/nextNEOpi']\n",
      "jchoude\n",
      "['scilus/tractoflow', 'scilus/tractoflow-pve']\n",
      "beise93\n",
      "['beise93/afs505_u3']\n",
      "colindaven\n",
      "['nf-core/methylseq', 'FAANG/GSM-pipeline', 'eQTL-Catalogue/rnaseq', 'nf-core/ampliseq', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "pcantalupo\n",
      "['sickle-in-africa/saw.sarek', 'nf-core/sarek', 'sripaladugu/germline_somatic', 'Genomic-Medicine-Linkoping/nf-core-sarek', 'UMCUGenetics/sarek_ubec', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "ppoulin91\n",
      "['scilus/tractoflow']\n",
      "burkej1\n",
      "['SoutheyLab/nextflow-workflows']\n",
      "sofstam\n",
      "['nf-core/modules']\n",
      "dangeles\n",
      "['egenesis/WF-NF-rnassembly']\n",
      "kenyonalexander-alloy\n",
      "['ChadFibke/germ']\n",
      "znestor\n",
      "['znestor/chainsaw-test']\n",
      "huhehaotecrystal\n",
      "['xmuyulab/scRNAseq_pipelines']\n",
      "lorentzben\n",
      "['lorentzben/automate_16_nf']\n",
      "katharily\n",
      "['katharily/pe_stacks_pipeline']\n",
      "brentp\n",
      "['Monia234/IARC-alignement', 'brentp/rare-disease-wf']\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "k-florek\n",
      "['wslh-bio/dryad', 'UPHL-BioNGS/Cecret', 'k-florek/mirkwater', 'wslh-bio/spriggan']\n",
      "fethalen\n",
      "['ThiloSchulze/eukaryotic-genome-assembly']\n",
      "chenthorn\n",
      "['zamanianlab/Core_RNAseq-nf']\n",
      "priyanka-surana\n",
      "['sanger-tol/readmapping']\n",
      "malinlarsson\n",
      "['sickle-in-africa/saw.sarek', 'nf-core/sarek', 'sripaladugu/germline_somatic', 'GMS6804-master/Sarek', 'Genomic-Medicine-Linkoping/nf-core-sarek', 'UMCUGenetics/sarek_ubec', 'melnel000/Sarek_CBIO']\n",
      "turrisita\n",
      "['AGROSAVIABIOUNIT/MT']\n",
      "replikation\n",
      "['RVanDamme/MUFFIN', 'nanozoo/wf_prepare_submission_dammit', 'replikation/blastn_so_hot', 'replikation/poreCov', 'replikation/docker_pipelines']\n",
      "lmyiing\n",
      "['xmuyulab/scRNAseq_pipelines']\n",
      "helrick\n",
      "['icgc-argo-workflows/icgc-argo-sv-copy-number']\n",
      "finnor\n",
      "['finnor/sample-renamer']\n",
      "verku\n",
      "['NBISweden/pipelines-nextflow']\n",
      "fruce-ki\n",
      "['ZuberLab/crispr-process-nf']\n",
      "v-clarissa\n",
      "['czbiohub/nf-tracer']\n",
      "lekhakaranam\n",
      "['czbiohub/nf-predictorthologs', 'czbiohub/nextflow-tutorial-2019']\n",
      "agalitsyna\n",
      "['agalitsyna/RedClib']\n",
      "alemenze\n",
      "['alemenze/bact-builder', 'alemenze/ONT-multi-assembly', 'alemenze/ONT-polish', 'alemenze/magicuniqueamplicons', 'alemenze/Illumina-ShotgunQuant', 'alemenze/ONT-basecalling']\n",
      "PiscatorX\n",
      "['PiscatorX/ezRAD-Pool-seq', 'PiscatorX/pool-ezRAD', 'PiscatorX/videre-pipeline']\n",
      "mattsoup\n",
      "['nebiolabs/EM-seq']\n",
      "zxl124\n",
      "['alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "archgen\n",
      "['archgen/ACAD_Nextflow_Pipeline']\n",
      "davidealbanese\n",
      "['metashot/prok-pan', 'metashot/mag-illumina', 'metashot/prok-quality', 'metashot/busco', 'metashot/kraken2', 'metashot/prok-snp', 'metashot/prok-annotate']\n",
      "rcappa1\n",
      "['nebfield/snpQT']\n",
      "ryanlayer\n",
      "['javaidm/obsolete_layer_lab_caw', 'javaidm/layer_lab_dna_seq_vc']\n",
      "louisedem\n",
      "['hugovaysset/ReproHackaton']\n",
      "fayetteklaassen\n",
      "['covidestim/dailyFlow']\n",
      "Guillermo-Gorines\n",
      "['GuilleGorines/nfcore-pikavirus-legacy']\n",
      "lengfei5\n",
      "['lengfei5/nf_visium_kallisto', 'lengfei5/atacseq_nf', 'lengfei5/smallRNA_nf']\n",
      "grendon\n",
      "['h3abionet/HPCBio-Refgraph_pipeline']\n",
      "merszym\n",
      "['mpieva/quicksand', 'mpieva/quicksand-build']\n",
      "szabogtamas\n",
      "['szabogtamas/repertoireseq_container']\n",
      "tbukur\n",
      "['TRON-Bioinformatics/covigator-ngs-pipeline']\n",
      "MaddalenaCella\n",
      "['MaddalenaCella/nf-lcWGS-mapping-and-imputation']\n",
      "chloea31\n",
      "['Ilchaffurin/Pipeline-RBMS']\n",
      "zhumiao1989\n",
      "['pandora414/dna']\n",
      "JPWerling\n",
      "['Clinical-Genomics-Linkoping/gms-JASEN', 'genomic-medicine-sweden/JASEN']\n",
      "mikson60\n",
      "['aleks96n/BioInfoKallisto']\n",
      "TCLamnidis\n",
      "['nf-core/eager']\n",
      "tamara-hodgetts\n",
      "['nf-core/modules', 'tamara-hodgetts/nf-atac-seq']\n",
      "erikwaskiewicz\n",
      "['erikwaskiewicz/ctdna-project', 'erikwaskiewicz/bamsurgeon-nextflow']\n",
      "Channing-Zeng\n",
      "['Channing-Zeng/metagenomics-nf']\n",
      "jdurbin\n",
      "['jdurbin/nf']\n",
      "HeshamElAbd\n",
      "['HeshamElAbd/nf-core-deviptcore']\n",
      "happykhan\n",
      "['happykhan/nf-scripts', 'happykhan/nf-klebtest']\n",
      "skiniry\n",
      "['JackCurragh/riboseq_data_processing']\n",
      "harryscholes\n",
      "['harryscholes/giga']\n",
      "giusmar\n",
      "['RosaDeSa/RNAseq_dsl2']\n",
      "jwokaty\n",
      "['seandavi/curatedMetagenomicsNextflow']\n",
      "matt-sd-watson\n",
      "['matt-sd-watson/nextflow_for_nextstrain', 'matt-sd-watson/nextflow_misc']\n",
      "jcurado-flomics\n",
      "['Flomics/joao-test', 'nf-core/viralrecon', 'rastiks/viralrecon']\n",
      "sdomanskyi\n",
      "['nf-core/spatialtranscriptomics']\n",
      "yocra3\n",
      "['nf-core/modules']\n",
      "jeslipp\n",
      "['ZuberLab/crispr-nf', 'ZuberLab/crispr-process-nf']\n",
      "benpastore\n",
      "['benpastore/nf-smrna-seq']\n",
      "jlboat\n",
      "['jlboat/NextflowScripts']\n",
      "fmalmeida\n",
      "['fmalmeida/bacannot', 'fmalmeida/MpGAP', 'fmalmeida/ngs-preprocess', 'nf-core/modules']\n",
      "tamburinif\n",
      "['bhattlab/wits_workshop']\n",
      "nservant\n",
      "['bioinfo-pf-curie/annotationMaker', 'bioinfo-pf-curie/as-mapping', 'bioinfo-pf-curie/nf-VIF']\n",
      "lcabus-flomics\n",
      "['nf-core/smrnaseq']\n",
      "mjsteinbaugh\n",
      "['nf-core/smrnaseq']\n",
      "bcantarel\n",
      "['GoalConsortium/goal_misc']\n",
      "lskatz\n",
      "['lskatz/Kessel-run', 'nf-core/modules', 'lskatz/nf-core-mlst']\n",
      "lDesiree\n",
      "['icgc-argo-workflows/icgc-argo-sv-copy-number']\n",
      "dfornika\n",
      "['BCCDC-PHL/troika-nf', 'BCCDC-PHL/routine-assembly', 'BCCDC-PHL/ncov-tools-nf', 'dfornika/nextflow-artic-ncov2019', 'dfornika/nf-core-cpo', 'dfornika/simulate-outbreak-dataset', 'dfornika/callVariants-with-codons', 'BCCDC-PHL/mlst-nf', 'dfornika/snippy-phylogenomics-nf', 'dfornika/stringmlst-nf', 'BCCDC-PHL/mykrobe-nf', 'BCCDC-PHL/consensus-align-utr-trim', 'dfornika/simulate-reads', 'connor-lab/ncov2019-artic-nf']\n",
      "Laura-Gomez\n",
      "['INMEGEN/conservationLandscape']\n",
      "jtmccr1\n",
      "['jtmccr1/bft-nf']\n",
      "andresfsilva\n",
      "['EBIvariation/variant-remapping']\n",
      "telatin\n",
      "['telatin/nextflow-example', 'NailouZhang/nf-core-virome']\n",
      "bozmik\n",
      "['bhagesh-codebeast/nextflowdualrnaseq', 'nf-core/dualrnaseq']\n",
      "jkirangw\n",
      "['jkirangw/WORMpipe']\n",
      "cimendes\n",
      "['NCBI-Hackathons/Nasty_Metagenomes', 'cimendes/metaFlow', 'imendes93/sv-nf']\n",
      "YanFangBio\n",
      "['NCBI-Codeathons/lung-rna-seq']\n",
      "grbot\n",
      "['grbot/nf-core-example', 'h3abionet/recalling', 'grbot/nf-core-test', 'HPCBio/16S-rDNA-dada2-pipeline', 'grbot/run-fastqc']\n",
      "Accio\n",
      "['bactopia/bactopia']\n",
      "liameabbott\n",
      "['gates-mri-bioinformatics/reference-database', 'liameabbott/reference-database', 'liameabbott/drop-seq-tools-pipeline', 'liameabbott/bulk-rna-seq-pipeline']\n",
      "MDegener\n",
      "['MDegener/RNAseq-pipeline']\n",
      "ElisabetThomsen\n",
      "['fargenfo/linkseq']\n",
      "chadisaad\n",
      "['nf-core/rnafusion']\n",
      "Haelmorn\n",
      "['DEMBresearch/rnaseq_qc']\n",
      "phupe\n",
      "['bioinfo-pf-curie/geniac-template', 'bioinfo-pf-curie/geniac-demo-dsl2']\n",
      "Solyris83\n",
      "['Solyris83/xPORE_nextflow']\n",
      "cgroza\n",
      "['cgroza/nextflow_scripts']\n",
      "TeresaRubio\n",
      "['ConesaLab/TCR_nextflow']\n",
      "ypriverol\n",
      "['bigbio/proteomicstmt', 'BlackburnLab/pgdb', 'bigbio/quantms', 'nf-core/proteomicslfq', 'BlackburnLab/nfcorepgdb', 'bigbio/nf-workflows', 'bigbio/pgdb']\n",
      "rsuchecki\n",
      "['csiro-crop-informatics/reproducible_poc', 'csiro-crop-informatics/nextflow-embl-abr-webinar', 'eQTL-Catalogue/rnaseq', 'csiro-crop-informatics/repset', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "andrewprzh\n",
      "['ablab/metaGT']\n",
      "sarahjeeeze\n",
      "['epi2me-labs/wf-transcript-target']\n",
      "shashidhar22\n",
      "['WarrenLabFH/viral_genomics']\n",
      "sylvinite\n",
      "['Clinical-Genomics-Linkoping/gms-JASEN', 'genomic-medicine-sweden/JASEN']\n",
      "TatsuyaDaniel\n",
      "['Thomas-LeCoent/reprohackathon-bioinfo']\n",
      "pwanj\n",
      "['GoalConsortium/goal_misc']\n",
      "jennomics\n",
      "['jennomics/parallel-blast']\n",
      "ATpoint\n",
      "['ATpoint/rnaseq_preprocess', 'ATpoint/atac_chip_preprocess', 'ATpoint/sc_preprocess', 'ATpoint/nf_blank']\n",
      "idelim09\n",
      "['Irvibena/Groupe10_Hackaton']\n",
      "ramprasadn\n",
      "['nf-core/raredisease', 'nf-core/modules']\n",
      "Emiller88\n",
      "['nf-core/modules', 'harleenduggal/nfcore-rnaseq', 'NCBI-Codeathons/lung-rna-seq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "junjun-zhang\n",
      "['icgc-argo-workflows/sanger-wxs-variant-calling', 'icgc-argo-workflows/dna-seq-processing-wfs', 'icgc-argo-workflows/icgc-argo-sv-copy-number', 'icgc-argo-workflows/nextflow-data-processing-utility-tools', 'icgc-argo-workflows/sanger-wgs-variant-calling']\n",
      "ramadatta\n",
      "['ramadatta/nextflow']\n",
      "mageshwarm\n",
      "['mageshwarm/rnaseq-nf-magesh', 'mageshwarm/blast-example-magesh']\n",
      "dlemas\n",
      "['GMS6804-master/rnatoy', 'GMS6804-master/YAMP']\n",
      "sateeshperi\n",
      "['CDCgov/mycosnp-nf', 'nf-core/modules']\n",
      "toniher\n",
      "['biocorecrg/SIB_course_nextflow_Nov_2021', 'biocorecrg/C4LWG-2018', 'biocorecrg/BioNextflow', 'biocorecrg/ELIXIR_containers_nextflow', 'proteomicsunitcrg/qcloud2-pipeline', 'biocorecrg/CoursesCRG_Containers_Nextflow_May_2021', 'biocorecrg/PHIND_course_nextflow_Feb_2022', 'biocorecrg/vectorQC']\n",
      "rbpisupati\n",
      "['rbpisupati/nf-haplocaller', 'rbpisupati/nf-repeatexplorer', 'Gregor-Mendel-Institute/nf-methylpy']\n",
      "agahkarakuzu\n",
      "['agahkarakuzu/mtsatflow', 'courtois-neuromod/anat-processing']\n",
      "silviamorins\n",
      "['alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "nf-core-bot\n",
      "['nf-core/bacass', 'nf-core/methylseq', 'sickle-in-africa/saw.sarek', 'nf-core/eager', 'nf-core/sarek', 'FAANG/GSM-pipeline', 'nf-core/kmermaid', 'nf-core/airrflow', 'nf-core/rnavar', 'nf-core/smrnaseq', 'sripaladugu/germline_somatic', 'bigbio/quantms', 'Genomic-Medicine-Linkoping/nf-core-sarek', 'nf-core/viralrecon', 'nf-core/proteomicslfq', 'nf-core/mag', 'nf-core/cageseq', 'nf-core/cutandrun', 'UMCUGenetics/sarek_ubec', 'nf-core/taxprofiler', 'nf-core/scrnaseq', 'bhagesh-codebeast/nextflowdualrnaseq', 'nf-core/clipseq', 'nf-core/raredisease', 'nf-core/hlatyping', 'nf-core/gwas', 'jianhong/nf-core-hicar', 'nf-core/ampliseq', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'nf-core/testpipeline', 'harleenduggal/nfcore-rnaseq', 'Leon-Bichmann/diaproteomics', 'subwaystation/pangenome', 'nf-core/epitopeprediction', 'nf-core/nanoseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ', 'nf-core/dualrnaseq', 'nf-core/funcscan']\n",
      "sarahbonnin\n",
      "['biocorecrg/ELIXIR_containers_nextflow', 'biocorecrg/CoursesCRG_Containers_Nextflow_May_2021']\n",
      "muffato\n",
      "['nf-core/modules']\n",
      "PhilPalmer\n",
      "['lifebit-ai/ExpansionHunter', 'lifebit-ai/HipSTR', 'lifebit-ai/somatic-variant-caller', 'lifebit-ai/strelka2', 'pprieto/dragen', 'TheJacksonLaboratory/splicing-pipelines-nf', 'raonyguimaraes/fast-ngs-admix', 'lifebit-ai/GangSTR', 'PhilPalmer/lbf-hack-tutorial', 'PhilPalmer/get-sra-nf', 'lifebit-ai/sanger-demo-rnaseq', 'lifebit-ai/consensus-variant-caller', 'nf-core/ampliseq', 'lifebit-ai/DeepVariant', 'lifebit-ai/phewas', 'lifebit-ai/hisat2', 'lifebit-ai/roary', 'lifebit-ai/Tardis', 'lifebit-ai/fam-gwas', 'lifebit-ai/qc-nf', 'lifebit-ai/vcf-annotator', 'lifebit-ai/prs', 'lifebit-ai/qc-dsl2', 'lifebit-ai/long-reads']\n",
      "phiweger\n",
      "['phiweger/isolate_pe']\n",
      "Mondale-tw\n",
      "['CommonMindConsortium/RAPiD-nf']\n",
      "mdziurzynski\n",
      "['DEMBresearch/rnaseq_qc']\n",
      "ntanh1999\n",
      "['ntanh1999/nextflow']\n",
      "steepale\n",
      "['steepale/nf-core-mutenrich', 'steepale/wgsfastqtobam']\n",
      "jackmo375\n",
      "['sickle-in-africa/saw.sarek', 'sickle-in-africa/saw.snv-indel', 'sickle-in-africa/saw.structural-variants']\n",
      "edg1983\n",
      "['edg1983/WGS_pipeline', 'edg1983/NF_variant_annotation']\n",
      "asadprodhan\n",
      "['asadprodhan/How-to-run-Kraken2-on-HPC-using-Singularity-container-and-Nextflow']\n",
      "bioinformatist\n",
      "['likelet/circPipe', 'bioinformatist/nf-core-metaamplicon']\n",
      "Sanger-ad7\n",
      "['wtsi-hgi/associations', 'wtsi-hgi/eqtl']\n",
      "fminneci\n",
      "['genomicsengland/minimal_subset_genomic_dataset']\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "alexandregilardet\n",
      "['nf-core/eager', 'nf-core/bactmap', 'nf-core/modules']\n",
      "lpantano\n",
      "['egenesis/WF-NF-rnassembly', 'nf-core/smrnaseq', 'pilm-bioinformatics/pipelines-nf-genomes', 'pilm-bioinformatics/pipelines-nf-fastrnaseq', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'pilm-bioinformatics/pipelines-nf-circtools', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "evanfloden\n",
      "['lifebit-ai/kallisto-sra', 'nf-core/eager', 'tiwarialok/new-rnaseq', 'nextflow-io/nf-hack18', 'nextflow-io/rnaseq-nf', 'cbcrg/nf-phdcourse19', 'cbcrg/nf-phdcourse20', 'mageshwarm/rnaseq-nf-magesh', 'tobsecret/BADAS_Nextflow_Tutorial', 'seqeralabs/gatk4-germline-snps-indels', 'nextflow-io/nf-hack17-tutorial', 'cbcrg/nf-phdcourse21', 'evanfloden/nf-module-demo', 'lauramble/rnaseq-vizfada', 'pilm-bioinformatics/pipelines-nf-fastrnaseq', 'evanfloden/transXpress-nf', 'CRG-CNAG/CalliNGS-NF', 'Biocentric/rnaseq_debug', 'milescsmith/gcls-rnaseq-nf', 'nextflow-io/nfcamp-tutorial']\n",
      "Lcornet\n",
      "['Lcornet/ORPER']\n",
      "calkan\n",
      "['calkan/TARDIS-CRAM-NextFlow']\n",
      "alneberg\n",
      "['nf-core/methylseq', 'cgpu/PGP-UK-sarek', 'sickle-in-africa/saw.sarek', 'nf-core/sarek', 'nf-core/cookiecutter', 'FAANG/GSM-pipeline', 'sripaladugu/germline_somatic', 'nf-core/vipr', 'GMS6804-master/Sarek', 'Genomic-Medicine-Linkoping/nf-core-sarek', 'nf-core/mag', 'nf-core/exoseq', 'UMCUGenetics/sarek_ubec', 'melnel000/Sarek_CBIO', 'eQTL-Catalogue/rnaseq', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'nf-core/nanoseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "Jokendo-collab\n",
      "['Jokendo-collab/MS_database_search']\n",
      "aleks96n\n",
      "['aleks96n/BioInfoKallisto']\n",
      "LaurenceKuhl\n",
      "['qbic-pipelines/vcreport', 'FriederikeHanssen/shrnacount', 'LaurenceKuhl/shrnacount']\n",
      "rubenchazarra\n",
      "['ebi-gene-expression-group/cell-types-eval-control-workflow-cross-validation']\n",
      "michael-ta\n",
      "['michael-ta/longitudinal-GWAS-pipeline']\n",
      "mvanins\n",
      "['mvanins/stress_granule_RNA_manuscript', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "seandavi\n",
      "['seandavi/cmgd_coordinator', 'seandavi/curatedMetagenomicsNextflow', 'seandavi/nf-core-cmgd']\n",
      "GuilleGorines\n",
      "['GuilleGorines/nfcore-pikavirus-legacy']\n",
      "FloWuenne\n",
      "['nf-core/modules']\n",
      "vmikk\n",
      "['telatin/nextflow-example']\n",
      "andrewmlynn\n",
      "['naveen584/nextflow-variantcalling']\n",
      "aduvermy\n",
      "['aduvermy/quantitative_nucleosome_analysis']\n",
      "aferriz\n",
      "['icgc-argo-workflows/icgc-argo-sv-copy-number']\n",
      "jgriss\n",
      "['bigbio/nf-workflows']\n",
      "sripaladugu\n",
      "['sripaladugu/nextflow_align']\n",
      "cflerin\n",
      "['vib-singlecell-nf/vsn-pipelines']\n",
      "husensofteng\n",
      "['bigbio/nf-workflows']\n",
      "Alexey-ebi\n",
      "['sguizard/isoseq']\n",
      "ecerami\n",
      "['ecerami/nextflow_sandbox']\n",
      "matrulda\n",
      "['FriederikeHanssen/bamtofastq', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "BonaBeavis\n",
      "['BonaBeavis/nf-core-prototype']\n",
      "Puumanamana\n",
      "['hawaiidatascience/metaflowmics', 'Puumanamana/nf-modules']\n",
      "Shuaishuail-mun\n",
      "['BioinformaticsLabAtMUN/sRNA-Detect', 'BioinformaticsLabAtMUN/sRNACharP-sRNARanking']\n",
      "CENMIG\n",
      "['CENMIG/snpplet']\n",
      "ZandraFagernas\n",
      "['nf-core/eager']\n",
      "hirenbioinfo\n",
      "['hirenbioinfo/nextflow_pipeline', 'hirenbioinfo/Nanopipe']\n",
      "b16joski\n",
      "['jkirangw/WORMpipe']\n",
      "MaxGreil\n",
      "['MaxGreil/sradcqc']\n",
      "jonasscheid\n",
      "['nf-core/epitopeprediction']\n",
      "SimonDMurray\n",
      "['SimonDMurray/DNA-pipeline']\n",
      "octavia-c\n",
      "['biomedbigdata/nf-core-circRNA-sponging']\n",
      "friesac\n",
      "['usafsam/mad_river_wf']\n",
      "wtsi-mercury\n",
      "['wtsi-hgi/nf_irods_to_lustre', 'wtsi-hgi/nf_scrna_deconvolution', 'wtsi-hgi/nextflow-pipelines', 'wtsi-hgi/nextflow_ci']\n",
      "c-guzman\n",
      "['heinzlab/chip-seq-pipeline', 'heinzlab/csrna', 'heinzlab/smrna-seq-pipeline']\n",
      "rernst\n",
      "['UMCUGenetics/NextflowModules', 'UMCUGenetics/DxNextflowWES']\n",
      "schorlton\n",
      "['awilson0/bugseq-pipeline']\n",
      "gabiherman\n",
      "['jerdra/TIGR_PURR']\n",
      "pgonzale60\n",
      "['tolkit/nemADSQ', 'pgonzale60/genokmer_hifi']\n",
      "sc13-bioinf\n",
      "['nf-core/eager']\n",
      "Biocentric\n",
      "['Biocentric/DeepVariantNF', 'Biocentric/rnaseq_debug']\n",
      "shaze\n",
      "['HadrienG/nanoflow']\n",
      "priesgo\n",
      "['TRON-Bioinformatics/covigator-ngs-pipeline', 'TRON-Bioinformatics/tronflow-bam-preprocessing', 'TRON-Bioinformatics/tronflow-haplotype-caller', 'TRON-Bioinformatics/tronflow-mutect2', 'TRON-Bioinformatics/tronflow-template']\n",
      "hoelzer\n",
      "['hoelzer/treat', 'hoelzer-lab/treat', 'hoelzer/mgnify-lr', 'hoelzer/nf_example', 'hoelzer/nf_blast', 'nanozoo/wf_prepare_submission_dammit', 'hoelzer/nanovirus', 'hoelzer/NEMO', 'replikation/poreCov', 'hoelzer/dammit-nf', 'hoelzer/virify', 'phiweger/isolate_pe', 'hoelzer/wuhan', 'hoelzer/clean']\n",
      "veeravalli\n",
      "['gis-rpd/rpd-rnaseq', 'eQTL-Catalogue/rnaseq', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'gis-rpd/rpd-sg10k-grch38-gatk4-gvcf-freebayes-vcf', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "grst\n",
      "['icbi-lab/smartseq2_pipeline', 'grst/bd_rhapsody_velocyto', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'nf-core/modules', 'harleenduggal/nfcore-rnaseq', 'grst/nf-core-test', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "nick297\n",
      "['oxfordmmm/SARS-CoV2_workflows']\n",
      "avantonder\n",
      "['nf-core/bactmap', 'avantonder/assembleBAC', 'nf-core/modules']\n",
      "rene-janssen\n",
      "['RJ333/calculate-functional-trees']\n",
      "cgpu\n",
      "['cgpu/PGP-UK-sarek', 'cgpu/sarek-mirror', 'cgpu/pgp-chronek', 'lifebit-ai/relate', 'cgpu/valibam', 'Shicheng-Guo/gwasgsa', 'cgpu/haplosarek', 'lifebit-ai/pcgr-nf', 'lifebit-ai/bam2cram', 'cgpu/samtools-index-nf', 'lifebit-ai/tinynf', 'cgpu/sarek-genomechronicler', 'cgpu/multiVCF-chopper', 'cgpu/covbench', 'cgpu/sparkling-gatk', 'cgpu/ion-somatic-variant-calling', 'cgpu/sparkling-preprocessing', 'cgpu/SelectVariants', 'lifebit-ai/sanger-demo-rnaseq', 'lifebit-ai/phewas', 'cgpu/bamerge', 'lifebit-ai/simulate', 'cgpu/sarek-mirror-cache', 'lifebit-ai/panelR', 'lifebit-ai/GenomeChronicler-Sarek-nf', 'cgpu/panelR', 'cgpu/Mutect2TumorOnlyMode-nf', 'cgpu/PON', 'lifebit-ai/long-reads']\n",
      "thomcuddihy\n",
      "['Vikash84/micropipe']\n",
      "batson\n",
      "['czbiohub/sc2-illumina-pipeline']\n",
      "Thomas-LeCoent\n",
      "['Thomas-LeCoent/reprohackathon-bioinfo']\n",
      "josephhalstead\n",
      "['josephhalstead/nextflow_small_germline_panel']\n",
      "kstawiski\n",
      "['nf-core/smrnaseq']\n",
      "scarlhoff\n",
      "['nf-core/eager']\n",
      "rnharmening\n",
      "['rnharmening/nf-multipleReferenceMapper']\n",
      "fuxialexander\n",
      "['fuxialexander/nf-cojo']\n",
      "ssnn-airr\n",
      "['ConesaLab/TCR_nextflow']\n",
      "dthorburn\n",
      "['dthorburn/Genomic_Read_Processing', 'dthorburn/Agam_Methylation']\n",
      "phoenixAja\n",
      "['czbiohub/nf-predictorthologs', 'nf-core/kmermaid']\n",
      "zlye\n",
      "['zlye/RVE']\n",
      "RJ333\n",
      "['RJ333/calculate-functional-trees']\n",
      "sinonkt\n",
      "['sinonkt/gemini-load-nf']\n",
      "BBJamge\n",
      "['BBJamge/bedtools_Danpos_NF']\n",
      "dembra96\n",
      "['zenomeplatform/nf-germline-mapping']\n",
      "KevinMenden\n",
      "['nf-core/bacass', 'nf-core/airrflow', 'nf-core/rnavar', 'KevinMenden/tf-activity', 'nf-core/smrnaseq', 'nf-core/viralrecon', 'nf-core/mag', 'nf-core/cageseq', 'nf-core/cutandrun', 'nf-core/raredisease', 'KevinMenden/hybrid-assembly', 'nf-core/gwas', 'nf-core/ampliseq', 'KevinMenden/testpipe', 'nf-core/modules', 'harleenduggal/nfcore-rnaseq', 'KevinMenden/nf-core-testpipeline', 'nf-core/epitopeprediction', 'nf-core/nanoseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "anfederico\n",
      "['montilab/pipeliner-2', 'montilab/pipeliner']\n",
      "GroundB\n",
      "['GroundB/RepeatDefeaters']\n",
      "kaitlinchaung\n",
      "['salzmanlab/ReadZS', 'czbiohub/nf-sicilian']\n",
      "athbaltzis\n",
      "['athbaltzis/diff-AS-nf']\n",
      "aldembert\n",
      "['lifebit-ai/relate']\n",
      "genomicsITER\n",
      "['genomicsITER/NanoCLUST']\n",
      "neevor\n",
      "['czbiohub/nextflow-tutorial-2019', 'czbiohub/sc2-illumina-pipeline']\n",
      "leomrtns\n",
      "['food-safety-bioinformatics-hackathon/benchmarking-refseq']\n",
      "sarseq\n",
      "['sarseq/sarseq2']\n",
      "Eugloh\n",
      "['Eugloh/AmpliconPCR-nf']\n",
      "BaronKoy\n",
      "['EBIvariation/variant-remapping']\n",
      "szilvajuhos\n",
      "['sickle-in-africa/saw.sarek', 'nf-core/sarek', 'sripaladugu/germline_somatic', 'GMS6804-master/Sarek', 'Genomic-Medicine-Linkoping/nf-core-sarek', 'UMCUGenetics/sarek_ubec', 'melnel000/Sarek_CBIO', 'nf-core/rnafusion']\n",
      "V-Catherine\n",
      "['Monia234/IARC-alignement', 'IARCbioinfo/BQSR-nf']\n",
      "GCJMackenzie\n",
      "['nf-core/modules']\n",
      "likelet\n",
      "['likelet/circPipe', 'likelet/MesKit', 'canceromics/MeRIPseqPipe']\n",
      "lescai\n",
      "['sickle-in-africa/saw.sarek', 'nf-core/sarek', 'nibscbioinformatics/scranger', 'nibscbioinformatics/humgen', 'sripaladugu/germline_somatic', 'nibscbioinformatics/modules', 'Genomic-Medicine-Linkoping/nf-core-sarek', 'nibscbioinformatics/scoop', 'UMCUGenetics/sarek_ubec', 'nf-core/modules', 'nibscbioinformatics/viralevo']\n",
      "manoj039\n",
      "['tiwarialok/new-rnaseq']\n",
      "bwlang\n",
      "['nebiolabs/EM-seq', 'replikation/poreCov', 'AGROSAVIABIOUNIT/nextflow_conda_cutadapt']\n",
      "phileastbioinf\n",
      "['crickbabs/BABS-aDNASeq', 'crickbabs/nextflow_toolbox']\n",
      "michellejlin\n",
      "['greninger-lab/demux', 'michellejlin/covid_swift_pipeline']\n",
      "ignaciot\n",
      "['Dowell-Lab/Nascent-Flow', 'nf-core/nascent']\n",
      "sheenamt\n",
      "['sheenamt/hrd_pipeline']\n",
      "arzwa\n",
      "['arzwa/whaleprep']\n",
      "ajodeh-juma\n",
      "['ajodeh-juma/viclara', 'ajodeh-juma/rvfvtyping', 'nf-core/modules', 'Vikash84/viclara']\n",
      "davidmasp\n",
      "['sickle-in-africa/saw.sarek', 'nf-core/sarek', 'sripaladugu/germline_somatic', 'Genomic-Medicine-Linkoping/nf-core-sarek', 'UMCUGenetics/sarek_ubec']\n",
      "samuell\n",
      "['sickle-in-africa/saw.structural-variants']\n",
      "xmzhuo\n",
      "['xmzhuo/fastp-nf']\n",
      "LeuThrAsp\n",
      "['StaPH-B/mycosnp']\n",
      "Bhagyshree\n",
      "['Bhagyshree/bedtools_NF']\n",
      "tronbfxdev\n",
      "['TRON-Bioinformatics/covigator-ngs-pipeline', 'TRON-Bioinformatics/tronflow-bam-preprocessing', 'TRON-Bioinformatics/tronflow-mutect2']\n",
      "tmuylder\n",
      "['vibbits/nextflow-jnj', 'vibbits/chipseq-nextflow', 'biocorecrg/ELIXIR_containers_nextflow']\n",
      "kazumaxneo\n",
      "['kazumaxneo/Nextflow_test_code']\n",
      "Rotholandus\n",
      "['markgene/cutnrun', 'jiangfuqing/Chip-seq', 'nf-core/chipseq']\n",
      "pprieto\n",
      "['lifebit-ai/freebayes', 'lifebit-ai/ExpansionHunter', 'lifebit-ai/HipSTR', 'lifebit-ai/kallisto-sra', 'lifebit-ai/DeepVariantTrain', 'pprieto/dragen', 'TheJacksonLaboratory/splicing-pipelines-nf', 'lifebit-ai/ukbb-tutorial', 'lifebit-ai/GangSTR', 'lifebit-ai/consensus-variant-caller', 'lifebit-ai/DeepVariantWGS', 'Biocentric/DeepVariantNF', 'lifebit-ai/DeepVariant', 'lifebit-ai/long-reads']\n",
      "Galithil\n",
      "['eQTL-Catalogue/rnaseq', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "abeaude\n",
      "['hugovaysset/ReproHackaton']\n",
      "t-neumann\n",
      "['t-neumann/slamseq', 'PavriLab/repliseq-nf', 'ZuberLab/crispr-process-nf', 't-neumann/salmon-nf']\n",
      "frheault\n",
      "['scilus/tractoflow']\n",
      "bhagesh-codebeast\n",
      "['bhagesh-codebeast/nextflowdualrnaseq']\n",
      "TGotwig\n",
      "['bactopia/bactopia']\n",
      "bunop\n",
      "['bunop/nextflow-training', 'nf-core/modules']\n",
      "duanjunhyq\n",
      "['cidgoh/cidgoh_qc']\n",
      "emmakwiener\n",
      "['emmakwiener/PhD-CNV-Analysis']\n",
      "simozhou\n",
      "['simozhou/epi-awesome']\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "msmallegan\n",
      "['msmallegan/rmghc-workshop-19']\n",
      "lconde-ucl\n",
      "['sickle-in-africa/saw.sarek', 'nf-core/sarek', 'sripaladugu/germline_somatic', 'Genomic-Medicine-Linkoping/nf-core-sarek', 'UMCUGenetics/sarek_ubec', 'UCL-BLIC/rnaseq_variant_calling', 'UCL-BLIC/wgsalign']\n",
      "Lipinski-B\n",
      "['IARCbioinfo/Imputation-nf', 'Monia234/IARC-imputation']\n",
      "kaurravneet4123\n",
      "['nibscbioinformatics/nf-core-conva', 'nibscbioinformatics/nf-core-viralevo', 'nf-core/modules']\n",
      "thanhleviet\n",
      "['food-safety-bioinformatics-hackathon/benchmarking-refseq', 'thanhleviet/nf-nanopore-assembly', 'nf-core/bactmap', 'nf-core/modules', 'connor-lab/ncov2019-artic-nf']\n",
      "lassefolkersen\n",
      "['nf-core/modules']\n",
      "i-pletenev\n",
      "['nf-core/modules']\n",
      "dshafranskaya\n",
      "['ablab/metaGT', 'ablab/graphamr']\n",
      "veitveit\n",
      "['veitveit/nf-core-wombatp']\n",
      "Ichaffurin\n",
      "['Ilchaffurin/Pipeline-RBMS']\n",
      "mikecormier\n",
      "['mikecormier/neoseq-seqcover-nf']\n",
      "riederd\n",
      "['icbi-lab/nextNEOpi', 'nf-core/modules']\n",
      "peikovakate\n",
      "['peikovakate/fastq']\n",
      "kingzhuky\n",
      "['ssun1116/meripseqpipe', 'kingzhuky/meripseqpipe']\n",
      "JingQiChong\n",
      "['JingQiChong/nf_CRACpipeline']\n",
      "bartcharbon\n",
      "['bartcharbon/nextflowVipPoc']\n",
      "Ramanandan\n",
      "['Ramanandan/rnaseq_nextflow']\n",
      "WhoisDonlee\n",
      "['ErasmusMC-Bioinformatics/NextFlow-VC-pipeline']\n",
      "kkowalden\n",
      "['h3abionet/HPCBio-Refgraph_pipeline']\n",
      "mtmcgowan\n",
      "['SystemsGenetics/transcript_corral']\n",
      "piotr-faba-ardigen\n",
      "['nf-core/modules']\n",
      "tlawrence3\n",
      "['tlawrence3/covid_nextflow']\n",
      "bjohnnyd\n",
      "['nf-core/modules']\n",
      "davismcc\n",
      "['davismcc/nf-hipsci-fibro']\n",
      "abenjak\n",
      "['icgc-argo-workflows/icgc-argo-sv-copy-number']\n",
      "brunoand\n",
      "['brunoand/NMP']\n",
      "Linxian0816\n",
      "['AnneCharlotteMichel/Reprohackathon']\n",
      "fbeghini\n",
      "['seandavi/curatedMetagenomicsNextflow']\n",
      "ray1919\n",
      "['ray1919/lRNA-Seq']\n",
      "BBQuercus\n",
      "['episkadlo/anglerFISH']\n",
      "SpikyClip\n",
      "['SpikyClip/llrnaseq', 'Lewsey-Lab/lims-rnaseq', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "npacc\n",
      "['npacc/HIV-Drug-Resistance']\n",
      "torchij\n",
      "['torchij/nextflow']\n",
      "supark87\n",
      "['supark87/minion_hrp2', 'supark87/prac_nextflow']\n",
      "mgcam\n",
      "['connor-lab/ncov2019-artic-nf']\n",
      "rfenouil\n",
      "['eQTL-Catalogue/rnaseq', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "j23414\n",
      "['isugifNF/freebayes', 'j23414/desc_workflows', 'j23414/wgcna_nf', 'isugifNF/RNAseq', 'isugifNF/blast', 'j23414/compare_workflows']\n",
      "biggstd\n",
      "['SystemsGenetics/GEMmaker', 'biggstd/nf-core-gsfworkflow', 'mmcogle/GEMmakerCam']\n",
      "marcelm\n",
      "['GMS6804-master/Sarek', 'sickle-in-africa/saw.structural-variants', 'melnel000/Sarek_CBIO']\n",
      "anu9109\n",
      "['anu9109/nf']\n",
      "MohammadSorkhian\n",
      "['BioinformaticsLabAtMUN/sRNACharP']\n",
      "FilipThorn\n",
      "['FilipThorn/nf-GL_popstructure', 'FilipThorn/nf-variantcaller', 'FilipThorn/nf_mito-mania']\n",
      "bleazard\n",
      "['nibscbioinformatics/humgen', 'nibscbioinformatics/viralevo']\n",
      "raonyguimaraes\n",
      "['raonyguimaraes/nextflow-hello']\n",
      "hugovaysset\n",
      "['hugovaysset/ReproHackaton']\n",
      "tristanpwdennis\n",
      "['tristanpwdennis/basicwgs']\n",
      "mashehu\n",
      "['nf-core/methylseq', 'FAANG/GSM-pipeline', 'nf-core/cageseq', 'nf-core/chipseq', 'lengfei5/atacseq_nf', 'alam1988/Nextflow', 'mashehu/nf-core_test', 'junyu-boston/dicerna-rnaseq', 'nf-core/modules', 'harleenduggal/nfcore-rnaseq', 'nf-core/atacseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "melferink\n",
      "['UMCUGenetics/NextflowModules', 'UMCUGenetics/DxNextflowWES']\n",
      "KaiLiCn\n",
      "['bzhanglab/neoflow', 'bzhanglab/DeepRescore']\n",
      "pettestor\n",
      "['Clinical-Genomics-Lund/nextflow_oxfordnanopore_sv']\n",
      "sandrocarollo\n",
      "['icbi-lab/smartseq2_pipeline']\n",
      "Paul-rk-cruz\n",
      "['Paul-rk-cruz/HRV_Pipeline']\n",
      "lilu-martin\n",
      "['bbi-lab/bbi-sci']\n",
      "xec-cm\n",
      "['MicrobialGenomics/TTrichiura_Tubulin']\n",
      "SarahMaman\n",
      "['SarahMaman/NextflowRNAseq']\n",
      "nschan\n",
      "['Gregor-Mendel-Institute/aradeepopsis', 'phue/aradeepopsis']\n",
      "slsevilla\n",
      "['NCBI-Hackathons/Nasty_Metagenomes']\n",
      "oskarvid\n",
      "['oskarvid/nextflow-GermlineVarCall']\n",
      "hustal\n",
      "['hustal/rnasequmi']\n",
      "dstrib\n",
      "['RenneLab/CnR-flow']\n",
      "morpholino\n",
      "['rastiks/viralrecon']\n",
      "bluegenes\n",
      "['czbiohub/nf-predictorthologs']\n",
      "ErikDanielsson\n",
      "['nf-core/smrnaseq']\n",
      "ImaneLboukili\n",
      "['IARCbioinfo/fastqc-nf', 'IARCbioinfo/qualimap-nf', 'Monia234/IARC-fastqc']\n",
      "KrisDavie\n",
      "['vib-singlecell-nf/vsn-pipelines']\n",
      "bentsherman\n",
      "['SystemsGenetics/GEMmaker', 'mmcogle/GEMmakerCam', 'SystemsGenetics/KINC-nf']\n",
      "RemyNicolle\n",
      "['RemyNicolle/DummyNF']\n",
      "plarosa\n",
      "['bioinfo-pf-curie/geniac-demo-dsl2']\n",
      "danielecook\n",
      "['AndersenLab/genomes-nf', 'AndersenLab/variant-simulations-nf', 'AndersenLab/nil-ril-nf', 'AndersenLab/wi-gatk', 'AndersenLab/alignment-nf']\n",
      "Tingvall\n",
      "['Tingvall/macs2_idr', 'Tingvall/cutntag']\n",
      "ksaunders73\n",
      "['NCBI-Codeathons/lung-rna-seq']\n",
      "emnilsson\n",
      "['LNUc-EEMiS/metatdenovo', 'nf-core/ampliseq', 'nf-core/modules']\n",
      "jvpon\n",
      "['biocorecrg/SIB_course_nextflow_Nov_2021', 'biocorecrg/ELIXIR_containers_nextflow', 'biocorecrg/CoursesCRG_Containers_Nextflow_May_2021', 'biocorecrg/vectorQC']\n",
      "lsuhpchelp\n",
      "['chenyuetian/nextflow']\n",
      "ppericard\n",
      "['alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "skrakau\n",
      "['sickle-in-africa/saw.sarek', 'nf-core/sarek', 'sripaladugu/germline_somatic', 'Genomic-Medicine-Linkoping/nf-core-sarek', 'nf-core/mag', 'UMCUGenetics/sarek_ubec', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'nf-core/epitopeprediction', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "edgano\n",
      "['edgano/C3G_longRead2020', 'edgano/TCoffee-NatureProtocol-nf', 'edgano/nf_phylo3D']\n",
      "ralf-tambets\n",
      "['eQTL-Catalogue/genimpute', 'eQTL-Catalogue/qtlmap']\n",
      "twesigomwedavid\n",
      "['twesigomwedavid/open-science']\n",
      "RHReynolds\n",
      "['nf-core/modules']\n",
      "Sebastian-D\n",
      "['GMS6804-master/Sarek', 'melnel000/Sarek_CBIO']\n",
      "DevNambi\n",
      "['FredHutch/cellprofiler-batch-nf']\n",
      "Paulrkcruz\n",
      "['Paul-rk-cruz/HRV_Pipeline']\n",
      "aishwaryagogate\n",
      "['bbi-lab/bbi-sci']\n",
      "Remi-Montagne\n",
      "['bioinfo-pf-curie/annotationMaker']\n",
      "maallen3\n",
      "['Dowell-Lab/Nascent-Flow', 'Dowell-Lab/RNAseq-Flow']\n",
      "SPPearce\n",
      "['nf-core/modules']\n",
      "jerdra\n",
      "['jerdra/TIGR_PURR', 'jerdra/BOONStim']\n",
      "dkj\n",
      "['connor-lab/ncov2019-artic-nf']\n",
      "rmoran7\n",
      "['rmoran7/dx_sarek', 'rmoran7/custom_sarek']\n",
      "rmcolq\n",
      "['virus-evolution/phylopipe', 'COG-UK/datapipe']\n",
      "doudoufeishangtian\n",
      "['doudoufeishangtian/WGSpipe-nf', 'doudoufeishangtian/RNApipe-nf', 'doudoufeishangtian/smRNApipe-nf', 'doudoufeishangtian/bacDENOVO-nf']\n",
      "jpfeuffer\n",
      "['bigbio/proteomicstmt', 'bigbio/quantms', 'nf-core/proteomicslfq', 'Leon-Bichmann/Phosphoproteomics']\n",
      "tobsecret\n",
      "['tobsecret/covid19', 'tobsecret/BADAS_Nextflow_Tutorial']\n",
      "andersgs\n",
      "['MDU-PHL/kovid-trees-nf', 'nf-core/modules']\n",
      "m-bull\n",
      "['connor-lab/PenGU-testdata-build', 'mikek498/artic-gls', 'connor-lab/qc_nextflow', 'connor-lab/ncov2019-artic-nf']\n",
      "sb10\n",
      "['connor-lab/ncov2019-artic-nf']\n",
      "nvk747\n",
      "['nf-core/methylseq', 'FAANG/GSM-pipeline', 'nf-core/hlatyping']\n",
      "s-andrews\n",
      "['s-andrews/nextflow_pipelines']\n",
      "ashildv\n",
      "['nf-core/eager']\n",
      "naliebe\n",
      "['vpeddu/Slowqc']\n",
      "aghozlane\n",
      "['QuentinLetourneur/Let-it-bin']\n",
      "RichardCorbett\n",
      "['bcgsc/TMBur']\n",
      "Diren52\n",
      "['Diren52/ExpansionHunter-nf']\n",
      "faithman\n",
      "['faithman/variant-nf', 'AndersenLab/wi-gatk', 'AndersenLab/alignment-nf', 'AndersenLab/SEmRNA-seq-nf']\n",
      "dmalzl\n",
      "['PavriLab/repliseq-nf']\n",
      "ssnnm\n",
      "['ConesaLab/TCR_nextflow']\n",
      "Amanj1\n",
      "['Amanj1/Discovery2', 'Amanj1/TTVnucleoTranslations', 'Amanj1/variantSeeker', 'Amanj1/PhyloProtTTV', 'Amanj1/TTV-primer-analysis']\n",
      "plateau-gao\n",
      "['plateau-gao/CUTnTag']\n",
      "StongeEtienne\n",
      "['scilus/tractoflow-pve']\n",
      "TDMedina\n",
      "['TDMedina/Nextflow_test']\n",
      "gongyh\n",
      "['gongyh/nf-core-scp', 'gongyh/nf-core-scgs']\n",
      "lynn-sanford\n",
      "['Dowell-Lab/Nascent-Flow', 'Dowell-Lab/Bidirectional-Flow', 'Dowell-Lab/RNAseq-Flow']\n",
      "xlinxlin\n",
      "['nf-core/bacass']\n",
      "jburos\n",
      "['alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "jmarvil\n",
      "['ASKAP-EMUCat/emucat_workflows']\n",
      "CGUTA\n",
      "['CGUTA/hugeheat']\n",
      "alexa-salsbury\n",
      "['NCBI-Codeathons/lung-rna-seq']\n",
      "heathervant\n",
      "['awilson0/bugseq-pipeline']\n",
      "stjacqrm\n",
      "['stjacqrm/berrywood']\n",
      "kauralasoo\n",
      "['eQTL-Catalogue/genimpute', 'eQTL-Catalogue/colocalisation', 'eQTL-Catalogue/qtlmap', 'eQTL-Catalogue/rnaseq', 'eQTL-Catalogue/genotype_qc', 'letaylor/qtlmap', 'eQTL-Catalogue/qcnorm']\n",
      "leiendeckerlu\n",
      "['ObenaufLab/sv-calling-nf']\n",
      "hysteron\n",
      "['Monia234/IARC-alignement', 'IARCbioinfo/table_annovar-nf']\n",
      "cbirbes\n",
      "['cbirbes/NextFlowPipeline']\n",
      "bioinformaticscloudhk\n",
      "['bioinformaticsclouds/nextflow']\n",
      "ppedrioli\n",
      "['digitalproteomes/NF-CometTPP', 'digitalproteomes/NF-DIAUmpire', 'digitalproteomes/NF-SpectraST']\n",
      "bewt85\n",
      "['nf-core/bacass']\n",
      "ortzf\n",
      "['vibbits/NextFlow_pipelines']\n",
      "ythaworn\n",
      "['b600a/tuber', 'CENMIG/snpplet']\n",
      "jeantristanb\n",
      "['jeantristanb/h3abionetimp_spezone']\n",
      "kviljoen\n",
      "['kviljoen/16S_quick_QC', 'HPCBio/16S-rDNA-dada2-pipeline', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'harleenduggal/nfcore-rnaseq', 'kviljoen/fastq_QC', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "davepallot\n",
      "['ASKAP-EMUCat/emucat_workflows']\n",
      "nanjalaruth\n",
      "['nanjalaruth/HLA-typing']\n",
      "DiegoBrambilla\n",
      "['bioatlas/ampliflow', 'nf-core/ampliseq']\n",
      "varshini712\n",
      "['NYU-Molecular-Pathology/NGS580-nf', 'varshini712/mutect2-nf', 'NYU-Molecular-Pathology/LG-PACT']\n",
      "mdesco\n",
      "['scilus/tractoflow']\n",
      "rivera10\n",
      "['nf-core/bacass', 'PalMuc/TransPi', 'Aveglia/vAMPirus']\n",
      "yuantianhpc\n",
      "['h3abionet/HPCBio-Refgraph_pipeline']\n",
      "abner24\n",
      "['abner24/AbinitioTraining']\n",
      "noamteyssier\n",
      "['noamteyssier/nextflow_pipelines']\n",
      "keng404\n",
      "['keng404/nextflow_test']\n",
      "IngoMue\n",
      "['IngoMue/nf-umap']\n",
      "tranwin\n",
      "['tranwin/nextflow-rnaseq']\n",
      "candiceh08\n",
      "['luslab/luslab-nf-modules', 'nf-core/modules', 'luslab/nf-clip']\n",
      "kjsanger\n",
      "['connor-lab/ncov2019-artic-nf']\n",
      "cschu\n",
      "['zellerlab/gaga2', 'cschu/vortex_knight', 'zellerlab/vortex_light']\n",
      "DimmestP\n",
      "['DimmestP/nextflow_paired_reads_pipeline']\n",
      "samirelanduk\n",
      "['goodwright/imaps-nf']\n",
      "misssoft\n",
      "['tiwarialok/new-rnaseq']\n",
      "lepsalex\n",
      "['icgc-argo-workflows/dna-seq-processing-wfs', 'lepsalex/nextflow-pcawg-bwa-mem-workflow', 'icgc-argo-workflows/nextflow-data-processing-utility-tools']\n",
      "HadrienG\n",
      "['nf-core/mag', 'HadrienG/gwas_benchmarks', 'HadrienG/2018_coral_16S', 'HadrienG/nanoflow', 'HadrienG/arbetsprov']\n",
      "Crone0610\n",
      "['Crone0610/nf-core-refcaller']\n",
      "AndreaGuarracino\n",
      "['subwaystation/pangenome']\n",
      "alperyilmaz\n",
      "['alperyilmaz/nextflow-rnaseq']\n",
      "haqle314\n",
      "['PlantGGHLab/qiime2-nf']\n",
      "jashapiro\n",
      "['AlexsLemonade/scpca-nf']\n",
      "lbresadola\n",
      "['TRON-Bioinformatics/tronflow-bam-preprocessing']\n",
      "nathanhaigh\n",
      "['sagc-bioinformatics/modules']\n",
      "SimiliSerpent\n",
      "['Irvibena/Groupe10_Hackaton']\n",
      "mfoll\n",
      "['IARCbioinfo/NGSCheckMate-nf', 'IARCbioinfo/fastqc-nf', 'IARCbioinfo/Imputation-nf', 'IARCbioinfo/qualimap-nf', 'Monia234/IARC-alignement', 'lisemangiante/test_nextflow', 'IARCbioinfo/BQSR-nf', 'IARCbioinfo/table_annovar-nf', 'Monia234/IARC-imputation', 'IARCbioinfo/strelka2-nf', 'IARCbioinfo/nf_coverage_demo', 'Monia234/IARC-fastqc']\n",
      "JezSw\n",
      "['oxfordmmm/SARS-CoV2_workflows']\n",
      "cmatKhan\n",
      "['cmatKhan/bartNPNF', 'cmatKhan/rnaseq_pipeline_rewrite', 'cmatKhan/nf-core-rw', 'cmatKhan/brentlab_rnaseq_nf']\n",
      "damjanaram\n",
      "['nextflow-io/nf-hack18']\n",
      "sawibo\n",
      "['UMCUGenetics/NextflowModules']\n",
      "GuillaumeTh\n",
      "['scilus/tractoflow']\n",
      "razielar\n",
      "['razielar/lncRNA_annotation_cufflinks_nf']\n",
      "yuxuth\n",
      "['jianhong/nf-core-hicar']\n",
      "mdeloger\n",
      "['bioinfo-pf-curie/annotationMaker']\n",
      "RenzoTale88\n",
      "['RenzoTale88/nf-LO', 'evotools/nf-LO']\n",
      "harleenduggal\n",
      "['harleenduggal/NEXTFLOW-fastqc']\n",
      "luissian\n",
      "['luissian/nf-core-assemblybacterias']\n",
      "marissaDubbelaar\n",
      "['nf-core/epitopeprediction']\n",
      "AlfredUg\n",
      "['galaxyuvri-ea/UvriMetaSeq', 'galaxyuvri-ea/qiime2-pipeline', 'AlfredUg/QuasiFlow']\n",
      "Navrique\n",
      "['Navrique/ANAPURNA-seq_old']\n",
      "MJDelas\n",
      "['luslab/briscoe-nf-tobias']\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Leon-Bichmann\n",
      "['Leon-Bichmann/diaproteomics']\n",
      "maxemil\n",
      "['maxemil/PhyloMagnet']\n",
      "alexandrebouchard\n",
      "['UBC-Stat-ML/humi2']\n",
      "garf0012\n",
      "['garfinjm/legsta-nf']\n",
      "apeltzer\n",
      "['nf-core/bacass', 'nf-core/methylseq', 'cgpu/PGP-UK-sarek', 'sickle-in-africa/saw.sarek', 'nf-core/eager', 'markgene/cutnrun', 'jiangfuqing/Chip-seq', 'nf-core/sarek', 'nf-core/bactmap', 'nf-core/cookiecutter', 'FAANG/GSM-pipeline', 'nf-core/airrflow', 'tobsecret/covid19', 'nf-core/smrnaseq', 'sripaladugu/germline_somatic', 'maxibor/coproID', 'nf-core/vipr', 'Genomic-Medicine-Linkoping/nf-core-sarek', 'nf-core/mag', 'nf-core/cageseq', 'nf-core/chipseq', 'nf-core/exoseq', 'UMCUGenetics/sarek_ubec', 'lengfei5/atacseq_nf', 'nf-core/nascent', 'nf-core/scrnaseq', 'bhagesh-codebeast/nextflowdualrnaseq', 'nf-core/hlatyping', 'glormph/nf-core-dda-quant-proteomics', 'eQTL-Catalogue/rnaseq', 'nf-core/ampliseq', 'alam1988/Nextflow', 'nf-core/nanostring', 'junyu-boston/dicerna-rnaseq', 'nf-core/modules', 'harleenduggal/nfcore-rnaseq', 'jiangfuqing/atac-seq', 'nf-core/epitopeprediction', 'nf-core/atacseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ', 'nf-core/dualrnaseq']\n",
      "jongtaek-kim\n",
      "['GMS6804-master/Sarek']\n",
      "Midnighter\n",
      "['UnseenBio/bracken-nf', 'UnseenBio/build-sourmash-index', 'nf-core/modules', 'UnseenBio/shotgun-qc-nf', 'nf-core/funcscan']\n",
      "genericdata\n",
      "['gencorefacility/variant-calling-pipeline-gatk4']\n",
      "fullerharrison\n",
      "['fullerharrison/afs505_u3_project']\n",
      "garfinjm\n",
      "['garfinjm/legsta-nf']\n",
      "vadimzalunin\n",
      "['NCBI-Hackathons/Nasty_Metagenomes']\n",
      "wjv\n",
      "['mpieva/quicksand']\n",
      "adomingues\n",
      "['harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "dladd\n",
      "['nf-core/cutandrun']\n",
      "AbigailShockey\n",
      "['wslh-bio/dryad', 'AbigailShockey/augur-nf', 'wslh-bio/spriggan']\n",
      "marcocrotti\n",
      "['marcocrotti/radseq-processing-nf']\n",
      "sysbiocoder\n",
      "['nf-core/modules']\n",
      "cwytko\n",
      "['SystemsGenetics/GEMmaker', 'mmcogle/GEMmakerCam']\n",
      "louperelo\n",
      "['louperelo/longmetarg', 'nf-core/modules']\n",
      "vivianepasteau\n",
      "['Irvibena/Groupe10_Hackaton']\n",
      "lakinsm\n",
      "['lakinsm/bear-wgs']\n",
      "nidhi12k\n",
      "['tmc-hematopath/smMIPS-Detection-Pipeline']\n",
      "alex-botzki\n",
      "['vibbits/rnaseq-editing']\n",
      "ntoda03\n",
      "['ntoda03/cycleassembler', 'nf-core/modules']\n",
      "b600a\n",
      "['b600a/tuber', 'CENMIG/snpplet']\n",
      "arontommi\n",
      "['sickle-in-africa/saw.sarek', 'nf-core/sarek', 'arontommi/nf-mixcr', 'sripaladugu/germline_somatic', 'GMS6804-master/Sarek', 'Genomic-Medicine-Linkoping/nf-core-sarek', 'UMCUGenetics/sarek_ubec', 'melnel000/Sarek_CBIO', 'alam1988/Nextflow', 'junyu-boston/dicerna-rnaseq', 'nf-core/modules', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "ielis\n",
      "['ielis/nextflow-example']\n",
      "RVanDamme\n",
      "['RVanDamme/MUFFIN']\n",
      "FelixKrueger\n",
      "['nf-core/methylseq', 'FAANG/GSM-pipeline', 's-andrews/nextflow_pipelines', 'nf-core/modules']\n",
      "cjjossart\n",
      "['CDCgov/mycosnp-nf']\n",
      "allyhawkins\n",
      "['AlexsLemonade/scpca-nf']\n",
      "tiagofilipe12\n",
      "['tiagofilipe12/pATLAS-db-creation', 'ielis/nextflow-example']\n",
      "LehmannN\n",
      "['LehmannN/scAnnotatiONT']\n",
      "MrMarkW\n",
      "['MrMarkW/nf-core-readtwoalign']\n",
      "jhagberg\n",
      "['sickle-in-africa/saw.structural-variants']\n",
      "thomasyu888\n",
      "['Sage-Bionetworks-Challenges/nf-model2data']\n",
      "aarandad\n",
      "['aarandad/demuxer']\n",
      "drewjbeh\n",
      "['nf-core/chipseq', 'lengfei5/atacseq_nf', 'nf-core/atacseq']\n",
      "caspargross\n",
      "['imgag/plasmIDent', 'caspargross/HybridAssembly', 'caspargross/plasmIDent', 'caspargross/nf-core-denovohybrid']\n",
      "rwtaylor\n",
      "['rwtaylor/mpcr-analyses-pipelines', 'rwtaylor/nextflow-pipelines']\n",
      "laurabiggins\n",
      "['s-andrews/nextflow_pipelines']\n",
      "oalmelid\n",
      "['oalmelid/lift-over-nf']\n",
      "sk-sahu\n",
      "['lifebit-ai/drs-nf', 'Shicheng-Guo/gwasgsa', 'TheJacksonLaboratory/splicing-pipelines-nf', 'codingene/nextflow-base', 'nf-core/scrnaseq', 'lifebit-ai/htslib-s3-nf', 'lifebit-ai/prs']\n",
      "kerimoff\n",
      "['eQTL-Catalogue/genimpute', 'eQTL-Catalogue/colocalisation', 'eQTL-Catalogue/qtlmap', 'eQTL-Catalogue/rnaseq', 'letaylor/qtlmap', 'kerimoff/qtlquant', 'eQTL-Catalogue/qcnorm']\n",
      "charles-plessy\n",
      "['nf-core/eager', 'oist/plessy_draft_nf-busco', 'luslab/luslab-nf-modules', 'nf-core/modules', 'oist/plessy_Nextflow_SpliceLeaderCAGE', 'oist/plessy_CAGEscan_Nextflow']\n",
      "R-Cardenas\n",
      "['R-Cardenas/nextflow_pipelines']\n",
      "subwaystation\n",
      "['nf-core/airrflow', 'nf-core/modules', 'subwaystation/pangenome']\n",
      "aivo0\n",
      "['taltechnlp/est-asr-pipeline']\n",
      "amazon-auto\n",
      "['aws-samples/aws-gatk-recipe-nextflow-pipeline']\n",
      "CharlotteAnne\n",
      "['luslab/nf-core-modules', 'nf-core/clipseq', 'luslab/nf-clip', 'goodwright/imaps-nf']\n",
      "lmfaber\n",
      "['hoelzer-lab/treat']\n",
      "BrianReevz\n",
      "['BrianReevz/GoogleCloudLifeSciSeq']\n",
      "sghurst\n",
      "['fmalmeida/bacannot']\n",
      "abyssum\n",
      "['icbi-lab/nextNEOpi']\n",
      "pinin4fjords\n",
      "['ebi-gene-expression-group/scanpy-workflow', 'ebi-gene-expression-group/scxa-droplet-quantification-workflow', 'ebi-gene-expression-group/isl_refs_to_refgenie', 'ebi-gene-expression-group/scxa-bundle-workflow']\n",
      "maelyg\n",
      "['eresearchqut/VirReport']\n",
      "higsch\n",
      "['higsch/togetherforever', 'nf-core/rnafusion']\n",
      "javaidm\n",
      "['ryanlayerlab/layer_lab_chco', 'javaidm/layer_lab_somatic_sv', 'javaidm/obsolete_layer_lab_caw', 'javaidm/layer_lab_dna_seq_vc', 'ryanlayerlab/layer_lab_caw', 'javaidm/layer_lab_vc']\n",
      "alexcorm\n",
      "['ifremer-bioinformatics/samba', 'alexcorm/quick_phylo_BUSCO', 'ifremer-bioinformatics/pallor']\n",
      "MGordon09\n",
      "['MGordon09/nf-core-bagobugs', 'nibscbioinformatics/nf-core-bagobugs', 'MGordon09/nf-core-buggybarcodes', 'nf-core/modules', 'nibscbioinformatics/nf-core-buggybarcodes']\n",
      "carlo-berg\n",
      "['Clinical-Genomics-Linkoping/gms-JASEN', 'genomic-medicine-sweden/JASEN']\n",
      "tskir\n",
      "['EBIvariation/variant-remapping']\n",
      "espelpz\n",
      "['espelpz/genebygenebact']\n",
      "ThiloSchulze\n",
      "['ThiloSchulze/orthology-inference', 'ThiloSchulze/eukaryotic-genome-assembly']\n",
      "agower\n",
      "['compbiomed/RNA_Seq']\n",
      "stevin-wilson\n",
      "['nf-core/viralrecon']\n",
      "lizheng141026\n",
      "['likelet/MesKit']\n",
      "Rhine-cats\n",
      "['KlausVG/reproHack']\n",
      "chris-cheshire\n",
      "['luslab/briscoe-nf-tobias', 'nf-core/cutandrun', 'luslab/nf-core-modules', 'luslab/luslab-nf-modules', 'nf-core/modules', 'luslab/nf-clip', 'harleenduggal/nfcore-rnaseq', 'nf-core/rnaseq', 'harleenduggal/RNASEQ']\n",
      "sivakhno\n",
      "['lifebit-ai/DeepVariantTrain', 'lifebit-ai/DeepVariantWGS']\n",
      "molecules\n",
      "['nextflow-io/rnaseq-nf']\n",
      "kaizhang\n",
      "['kaizhang/scATAC-benchmark']\n",
      "sidorov-si\n",
      "['luslab/luslab-nf-modules', 'nf-core/modules']\n",
      "AJHodgkinson\n",
      "['anna-saukkonen/PAC']\n",
      "PeterBailey\n",
      "['nf-core/scrnaseq', 'jiangfuqing/scrna-seq']\n",
      "mult1fractal\n",
      "['replikation/docker_pipelines']\n",
      "marcusrussi\n",
      "['covidestim/dailyFlow']\n",
      "JamesChoi94\n",
      "['JamesChoi94/LipidModule']\n",
      "ktrns\n",
      "['nf-core/viralrecon', 'rastiks/viralrecon']\n",
      "hclimente\n",
      "['hclimente/gwas-tools']\n",
      "elowy01\n",
      "['elowy01/nf-core-testworkflow']\n"
     ]
    }
   ],
   "source": [
    "df_contrib_nf = create_df_contrib_nf(proc_nf_tool, dict_nf)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 102,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_contrib_nf.to_csv(\"csv/df_contrib_nf.csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 103,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "223\n",
      "0.17740652346857597\n",
      "133\n",
      "0.10580747812251393\n",
      "299\n",
      "0.23786793953858393\n"
     ]
    }
   ],
   "source": [
    "tot_wf_snk = len(get_list_wf(proc_snk_tool))\n",
    "tot_20_snk = []\n",
    "for wf_list in list(df_contrib_snk.head(20)[\"list_wf\"]):\n",
    "    for wf in wf_list:\n",
    "        tot_20_snk.append(wf)\n",
    "print(len(set(tot_20_snk)))\n",
    "print(len(set(tot_20_snk))/tot_wf_snk)\n",
    "tot_10_snk = []\n",
    "for wf_list in list(df_contrib_snk.head(10)[\"list_wf\"]):\n",
    "    for wf in wf_list:\n",
    "        tot_10_snk.append(wf)\n",
    "print(len(set(tot_10_snk)))\n",
    "print(len(set(tot_10_snk))/tot_wf_snk)\n",
    "tot_1_snk = []\n",
    "for wf_list in list(df_contrib_snk.loc[df_contrib_snk[\"nb_wf\"]==1][\"list_wf\"]):\n",
    "    for wf in wf_list:\n",
    "        tot_1_snk.append(wf)\n",
    "print(len(set(tot_1_snk)))\n",
    "print(len(set(tot_1_snk))/tot_wf_snk)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 104,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "395\n",
      "714\n",
      "0.5532212885154062\n"
     ]
    }
   ],
   "source": [
    "print(len(df_contrib_snk.loc[df_contrib_snk[\"nb_wf\"]==1][\"list_wf\"]))\n",
    "print(len(df_contrib_snk))\n",
    "print(len(df_contrib_snk.loc[df_contrib_snk[\"nb_wf\"]==1][\"list_wf\"])/len(df_contrib_snk))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Statistiques star, forks,..."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 109,
   "metadata": {},
   "outputs": [],
   "source": [
    "list_wf_snk = [ el.split(\"/\")[0]+\"/\"+el.split(\"/\")[1] for el in get_list_wf(proc_snk_tool)]\n",
    "list_wf_nf = get_list_wf_nf(proc_nf_tool)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 107,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "dict_keys(['files', 'name', 'id', 'git_url', 'update_date', 'creation_date', 'actual_date', 'last_push', 'owner', 'description', 'forks', 'stars', 'watchers', 'subscribers', 'languages', 'topics', 'archived', 'link', 'contributors', 'license'])"
      ]
     },
     "execution_count": 107,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "dict_nf['joshua-d-campbell/nf-GATK_Exome_Preprocess'].keys()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 112,
   "metadata": {},
   "outputs": [],
   "source": [
    "def create_df_star_fork(list_wf, dict_wf):\n",
    "    df_star = pd.DataFrame(columns=[\"name\", \"forks\", \"stars\", \"watchers\", 'subscribers'])\n",
    "    for wf in list_wf:\n",
    "        if(wf in dict_wf.keys()):\n",
    "            df_star = df_star.append({\"name\":wf, \n",
    "                                      \"forks\":dict_wf[wf][\"forks\"], \n",
    "                                      \"stars\":dict_wf[wf][\"stars\"], \n",
    "                                      \"watchers\":dict_wf[wf][\"watchers\"], \n",
    "                                      'subscribers':dict_wf[wf][\"subscribers\"]}, ignore_index=True)\n",
    "    return df_star"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 113,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_star_snk = create_df_star_fork(list_wf_snk, dict_snk)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 114,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_star_nf = create_df_star_fork(list_wf_nf, dict_nf)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 117,
   "metadata": {},
   "outputs": [],
   "source": [
    "def print_stats_forks(df_stars):\n",
    "    print(\"Forks : moy \"+str(df_stars[\"forks\"].mean())+ \" max \"+str(df_stars[\"forks\"].max()))\n",
    "    print(\"Stars : moy \"+str(df_stars[\"stars\"].mean())+ \" max \"+str(df_stars[\"stars\"].max()))\n",
    "    print(\"Watchers : moy \"+str(df_stars[\"watchers\"].mean())+ \" max \"+str(df_stars[\"watchers\"].max()))\n",
    "    print(\"Subscribers : moy \"+str(df_stars[\"subscribers\"].mean())+ \" max \"+str(df_stars[\"subscribers\"].max()))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 118,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Snk :\n",
      "Forks : moy 1.4351630867143994 max 59\n",
      "Stars : moy 3.443914081145585 max 208\n",
      "Watchers : moy 3.443914081145585 max 208\n",
      "Subscribers : moy 2.4184566428003182 max 32\n",
      "Nf :\n",
      "Forks : moy 2.4984177215189876 max 419\n",
      "Stars : moy 3.1455696202531644 max 436\n",
      "Watchers : moy 3.1455696202531644 max 436\n",
      "Subscribers : moy 4.69620253164557 max 157\n"
     ]
    }
   ],
   "source": [
    "print(\"Snk :\")\n",
    "print_stats_forks(df_star_snk)\n",
    "print(\"Nf :\")\n",
    "print_stats_forks(df_star_nf)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "df_star_snk.to_csv(\"csv/\")"
   ]
  }
 ],
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