Merge branch 'release/0.2.1'

.github/workflows/release.yml

@@ -3,13 +3,15 @@ name: Release Nextflow Workflow
 on: 
   push:
     tags:
-    - '*'
+      - '*'
 
 jobs:
   build:
     runs-on: ubuntu-latest
+    environment:
+      name: prod
     steps:
-    - uses: actions/checkout@v2
-    - uses: ncipollo/release-action@v1
-      with:
-        token: ${{ secrets.GITHUB_TOKEN }}
+      - uses: actions/checkout@v2
+      - uses: ncipollo/release-action@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/test.yml

@@ -2,30 +2,29 @@ name: tests
 
 on:
   push:
-    branches: [ main ]
+    branches: [ dev, main ]
   pull_request:
-    branches: [ main ]
+    branches: [ dev, main ]
 
 jobs:
   build:
     runs-on: ubuntu-latest
-
+    environment:
+      name: dev
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python 3.10
-      uses: actions/setup-python@v2
-      with:
-        python-version: "3.10"
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install pytest
-        curl -s https://get.nextflow.io | bash
-        chmod u+x nextflow
-        mkdir bin && mv nextflow bin
-        echo "$(pwd)/bin" >> $GITHUB_PATH
-
-    - name: Run tests
-      run: |
-        pytest
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install pytest
+          curl -s https://get.nextflow.io | bash
+          chmod u+x nextflow
+          mkdir bin && mv nextflow bin
+          echo "$(pwd)/bin" >> $GITHUB_PATH
+      - name: Run tests
+        run: |
+          pytest

README.md

@@ -1,6 +1,10 @@
 # Nextflow - Encyclopedia
 This repository contains the nextflow pipeline for Encyclopedia.
 
+# Git Flow
+We use git flow for features, releases, fixes, etc. Here's an introductory article: https://jeffkreeftmeijer.com/git-flow/.
+And a cheatsheet: https://danielkummer.github.io/git-flow-cheatsheet/index.html.
+
 # Release
 ```
 # See existing tags

main.nf

@@ -6,11 +6,10 @@ include { msstats } from "./modules/msstats.nf"
 
 nextflow.enable.dsl = 2
 
-FILTER = "NO_FILE"
-
 process run_encyclopedia_local {
     echo true
     publishDir params.publish_dir, mode: "copy"
+    storeDir params.store_dir
 
     input:
         path mzml_gz_file
@@ -53,6 +52,7 @@ process run_encyclopedia_local {
 process run_encyclopedia_global {
     echo true
     publishDir params.publish_dir, mode: "copy"
+    storeDir params.store_dir
 
     input:
         path local_files
@@ -63,7 +63,7 @@ process run_encyclopedia_global {
 
     output:
         tuple(
-            path("result-${output_postfix}*.elib"), 
+            path("result-${output_postfix}*.elib"),
             path("result-${output_postfix}*.{peptides,proteins}.txt"),
             path("logs/result-${output_postfix}*.global.log")
         )

modules/msconvert.nf

@@ -5,6 +5,7 @@ nextflow.enable.dsl = 2
 process run_msconvert {
     echo true
     publishDir "${params.mzml_dir}/${outputDir}", mode: "copy"
+    storeDir params.store_dir
 
     input:
         tuple path(raw_input), val(outputDir)

nextflow.config

@@ -66,6 +66,7 @@ params {
     experimentName = 'purple-pig'
     email = '[email protected]'
     publish_dir = ''
+    store_dir = ''
     mzml_dir = ''
     narrow_files = ''
     wide_files = ''
@@ -106,4 +107,4 @@ aws {
     }
 }
 
-//includeConfig 'nextflow_run.config'
+includeConfig 'nextflow_run.config'

nextflow_run.config

@@ -2,9 +2,9 @@ params.encyclopedia.fasta = 'metadata-bucket/uniprot_human_25apr2019.fasta'
 params.encyclopedia.dlib = 'metadata-bucket/uniprot_human_25apr2019.fasta.z2_nce33.dlib'
 
 //params.experimentName = '170823_encyclopedia_msstats_local'
-params.experimentName = '170823_test'
+params.experimentName = '170823_test_3'
 
-params.publish_dir = 'experiment-bucket/170823_test'
+params.publish_dir = 'experiment-bucket/170823_test_3'
 params.mzml_dir = 'mzml-bucket'
 params.narrow_files = 'input_folder/narrow_files.csv'
 params.wide_files = 'input_folder/wide_files.csv'

tests/data/test_no_narrow.config

@@ -0,0 +1,4 @@
+params.narrow_files = 'tests/data/narrow_files_empty.csv'
+params.wide_files = 'tests/data/wide_files.csv'
+params.encyclopedia.fasta = 'tests/data/test.fasta'
+params.encyclopedia.dlib = 'tests/data/test.dlib'