Merge pull request #63 from genepi/add_credits

Add credits

CITATION.cff

@@ -0,0 +1,12 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: Amstler
+  given-names: Stephan
+  orcid: https://orcid.org/0009-0007-7214-7481
+title: "Umi-pipeline-nf - A nextflow pipeline to analyse UMI-tagged amplicons from nanopore sequencing."
+version: 0.2.0
+identifiers:
+  - type: doi
+    value: 10.1101/2024.03.01.582741
+url: https://github.com/genepi/umi-pipeline-nf

README.md

@@ -6,7 +6,7 @@ Umi-pipeline-nf
 
 **Umi-pipeline-nf** creates highly accurate single-molecule consensus sequences for unique molecular identifier (UMI)-tagged amplicons from nanopore sequencing data.  
 The pipeline can be run for the whole fastq_pass folder of your nanopore run and, per default, outputs the aligned consensus sequences of each UMI cluster in bam file. The optional variant calling creates a vcf file for all variants that are found in the consensus sequences.
-umi-pipeline-nf is inspired by a snakemake-based analysis pipeline ([ONT UMI analysis pipeline](https://github.com/nanoporetech/pipeline-umi-amplicon); originally developed by [Karst et al, Nat Biotechnol 18:165–169, 2021](https://www.nature.com/articles/s41592-020-01041-y)). We migrated the pipeline in [Nextflow](https://www.nextflow.io), included several optimizations and [additional functionalities](#main-adaptations).  
+Umi-pipeline-nf orignates from a snakemake-based analysis pipeline ([pipeline-umi-amplicon](https://github.com/nanoporetech/pipeline-umi-amplicon); originally developed by [Karst et al, Nat Biotechnol 18:165–169, 2021](https://www.nature.com/articles/s41592-020-01041-y)). We migrated the pipeline to [Nextflow](https://www.nextflow.io) and included several optimizations and [additional functionalities](#main-adaptations).  
 
 ![Workflow](docs/images/umi-pipeline-nf_metro-map.svg)
 
@@ -58,5 +58,5 @@ nextflow run genepi/umi-pipeline-nf -r v0.1.0 -c <custom.config> -profile docker
 
 The pipeline was written by ([@StephanAmstler](https://github.com/AmstlerStephan)).  
 Nextflow template pipeline: [EcSeq](https://github.com/ecSeq).  
-Snakemake-based ONT pipeline: [nanoporetech/pipeline-umi-amplicon](https://github.com/nanoporetech/pipeline-umi-amplicon).  
+Snakemake-based ONT pipeline for UMI nanopore sequencing analysis: [nanoporetech/pipeline-umi-amplicon](https://github.com/nanoporetech/pipeline-umi-amplicon).  
 UMI-corrected nanopore sequencing analysis first shown by: [SorenKarst/longread_umi](https://github.com/SorenKarst/longread_umi).

bin/extract_umis.py

@@ -1,3 +1,8 @@
+"""
+This is a modified version of the code present in:
+https://github.com/nanoporetech/pipeline-umi-amplicon/blob/master/lib/umi_amplicon_tools/extract_umis.py
+"""
+
 import argparse
 import logging
 import os

bin/filter_reads.py

@@ -1,3 +1,7 @@
+"""
+This is a modified version of the code present in:
+https://github.com/nanoporetech/pipeline-umi-amplicon/blob/master/lib/umi_amplicon_tools/filter_reads.py
+"""
 import argparse
 import logging
 import os

bin/parse_clusters.py

@@ -1,3 +1,8 @@
+"""
+This is a modified version of the code present in:
+https://github.com/nanoporetech/pipeline-umi-amplicon/blob/master/lib/umi_amplicon_tools/parse_clusters.py
+"""
+
 import argparse
 import logging
 import os

bin/reformat_consensus.py

@@ -1,3 +1,8 @@
+"""
+This is a modified version of the code present in:
+https://github.com/nanoporetech/pipeline-umi-amplicon/blob/master/lib/umi_amplicon_tools/reformat_consensus.py
+"""
+
 import argparse
 import logging
 import sys