Merge pull request #115 from Functional-Genomics-Lab/stringtie_test

Added testing for Stringtie

.github/workflows/stringtie.yml

@@ -0,0 +1,40 @@
+name: stringtie
+on:
+  push:
+    paths:
+      - software/stringtie/**
+      - .github/workflows/stringtie.yml
+      - tests/software/stringtie/**
+  pull_request:
+    paths:
+      - software/stringtie/**
+      - .github/workflows/stringtie.yml
+      - tests/software/stringtie/**
+
+jobs:
+  ci_test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        nxf_version: [20.11.0-edge]
+    env:
+      NXF_ANSI_LOG: false
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Install Nextflow
+        env:
+          NXF_VER: ${{ matrix.nxf_version }}
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: "3.x"
+      - name: Install dependencies
+        run: python -m pip install --upgrade pip pytest-workflow
+
+      # Test the module
+      - run: pytest --tag stringtie --symlink --wt 2

tests/software/stringtie/main.nf

@@ -0,0 +1,34 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { STRINGTIE as STRINGTIE_FORWARD } from '../../../software/stringtie/main.nf'  addParams( options: [ publish_dir:'test_stringtie_forward' ] )
+include { STRINGTIE as STRINGTIE_REVERSE } from '../../../software/stringtie/main.nf'  addParams( options: [ publish_dir:'test_stringtie_reverse' ] )
+
+/*
+ * Test with forward strandedness
+ */
+workflow test_stringtie_forward {
+    def input = []
+    input = [ [ id:'test', strandedness:'forward' ], // meta map
+              [ file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ] ]
+
+    STRINGTIE_FORWARD (
+        input,
+        file("${launchDir}/tests/data/gff/a.gtf", checkIfExists: true)
+    )
+}
+
+/*
+ * Test with reverse strandedness
+ */
+workflow test_stringtie_reverse {
+    def input = []
+    input = [ [ id:'test', strandedness:'reverse' ], // meta map
+              [ file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ] ]
+
+    STRINGTIE_REVERSE (
+        input,
+        file("${launchDir}/tests/data/gff/a.gtf", checkIfExists: true)
+    )
+}

tests/software/stringtie/test.yml

@@ -0,0 +1,43 @@
+- name: Run stringtie forward strand test workflow
+  command: nextflow run ./tests/software/stringtie/ -profile docker -entry test_stringtie_forward -c tests/config/nextflow.config
+  tags:
+    - stringtie
+  files:
+    - path: output/test_stringtie_forward/test.gene_abundance.txt
+      md5sum: cea2e346f4e8137da13265b9b0a4c573
+    - path: output/test_stringtie_forward/test.transcripts.gtf
+      md5sum: f1b5baa8d94f86e499556a4ec419a75a
+    - path: output/test_stringtie_forward/test.coverage.gtf
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/test_stringtie_forward/test.ballgown/e_data.ctab
+      md5sum: 48d5ddf52a3d203d9f85aded9600edb9
+    - path: output/test_stringtie_forward/test.ballgown/e2t.ctab
+      md5sum: f828838a28ae74dbc21cd5fc75b6d068
+    - path: output/test_stringtie_forward/test.ballgown/i_data.ctab
+      md5sum: 4651c095a12836aa3f7bc4d97ae7b877
+    - path: output/test_stringtie_forward/test.ballgown/i2t.ctab
+      md5sum: 6d598e0e28ef911d50783cd382e80ae6
+    - path: output/test_stringtie_forward/test.ballgown/t_data.ctab
+      md5sum: 0106f70121a8b520d98b8739aed92915
+
+- name: Run stringtie reverse strand test workflow
+  command: nextflow run ./tests/software/stringtie/ -profile docker -entry test_stringtie_reverse -c tests/config/nextflow.config
+  tags:
+    - stringtie
+  files:
+    - path: output/test_stringtie_reverse/test.gene_abundance.txt
+      md5sum: cea2e346f4e8137da13265b9b0a4c573
+    - path: output/test_stringtie_reverse/test.transcripts.gtf
+      md5sum: cb0367e5f98f19fcc2043d248deb513c
+    - path: output/test_stringtie_reverse/test.coverage.gtf
+      md5sum: d41d8cd98f00b204e9800998ecf8427e
+    - path: output/test_stringtie_reverse/test.ballgown/e_data.ctab
+      md5sum: 48d5ddf52a3d203d9f85aded9600edb9
+    - path: output/test_stringtie_reverse/test.ballgown/e2t.ctab
+      md5sum: f828838a28ae74dbc21cd5fc75b6d068
+    - path: output/test_stringtie_reverse/test.ballgown/i_data.ctab
+      md5sum: 4651c095a12836aa3f7bc4d97ae7b877
+    - path: output/test_stringtie_reverse/test.ballgown/i2t.ctab
+      md5sum: 6d598e0e28ef911d50783cd382e80ae6
+    - path: output/test_stringtie_reverse/test.ballgown/t_data.ctab
+      md5sum: 0106f70121a8b520d98b8739aed92915