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Merge pull request #115 from Functional-Genomics-Lab/stringtie_test
Added testing for Stringtie
This commit is contained in:
Harshil Patel
GitHub
commit
27dbe8b52a
4 changed files with 3167 additions and 0 deletions
40
.github/workflows/stringtie.yml
vendored
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40
.github/workflows/stringtie.yml
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name: stringtie
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on:
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push:
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paths:
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- software/stringtie/**
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- .github/workflows/stringtie.yml
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- tests/software/stringtie/**
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pull_request:
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paths:
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- software/stringtie/**
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- .github/workflows/stringtie.yml
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- tests/software/stringtie/**
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jobs:
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ci_test:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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nxf_version: [20.11.0-edge]
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env:
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NXF_ANSI_LOG: false
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steps:
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- uses: actions/checkout@v2
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- name: Install Nextflow
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env:
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NXF_VER: ${{ matrix.nxf_version }}
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: "3.x"
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- name: Install dependencies
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run: python -m pip install --upgrade pip pytest-workflow
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# Test the module
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- run: pytest --tag stringtie --symlink --wt 2
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3050
tests/data/gff/a.gtf
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3050
tests/data/gff/a.gtf
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34
tests/software/stringtie/main.nf
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34
tests/software/stringtie/main.nf
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { STRINGTIE as STRINGTIE_FORWARD } from '../../../software/stringtie/main.nf' addParams( options: [ publish_dir:'test_stringtie_forward' ] )
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include { STRINGTIE as STRINGTIE_REVERSE } from '../../../software/stringtie/main.nf' addParams( options: [ publish_dir:'test_stringtie_reverse' ] )
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/*
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* Test with forward strandedness
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*/
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workflow test_stringtie_forward {
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def input = []
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input = [ [ id:'test', strandedness:'forward' ], // meta map
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[ file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ] ]
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STRINGTIE_FORWARD (
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input,
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file("${launchDir}/tests/data/gff/a.gtf", checkIfExists: true)
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)
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}
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/*
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* Test with reverse strandedness
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*/
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workflow test_stringtie_reverse {
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def input = []
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input = [ [ id:'test', strandedness:'reverse' ], // meta map
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[ file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ] ]
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STRINGTIE_REVERSE (
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input,
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file("${launchDir}/tests/data/gff/a.gtf", checkIfExists: true)
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)
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}
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43
tests/software/stringtie/test.yml
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43
tests/software/stringtie/test.yml
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- name: Run stringtie forward strand test workflow
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command: nextflow run ./tests/software/stringtie/ -profile docker -entry test_stringtie_forward -c tests/config/nextflow.config
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tags:
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- stringtie
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files:
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- path: output/test_stringtie_forward/test.gene_abundance.txt
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md5sum: cea2e346f4e8137da13265b9b0a4c573
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- path: output/test_stringtie_forward/test.transcripts.gtf
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md5sum: f1b5baa8d94f86e499556a4ec419a75a
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- path: output/test_stringtie_forward/test.coverage.gtf
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md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/test_stringtie_forward/test.ballgown/e_data.ctab
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md5sum: 48d5ddf52a3d203d9f85aded9600edb9
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- path: output/test_stringtie_forward/test.ballgown/e2t.ctab
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md5sum: f828838a28ae74dbc21cd5fc75b6d068
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- path: output/test_stringtie_forward/test.ballgown/i_data.ctab
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md5sum: 4651c095a12836aa3f7bc4d97ae7b877
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- path: output/test_stringtie_forward/test.ballgown/i2t.ctab
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md5sum: 6d598e0e28ef911d50783cd382e80ae6
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- path: output/test_stringtie_forward/test.ballgown/t_data.ctab
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md5sum: 0106f70121a8b520d98b8739aed92915
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- name: Run stringtie reverse strand test workflow
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command: nextflow run ./tests/software/stringtie/ -profile docker -entry test_stringtie_reverse -c tests/config/nextflow.config
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tags:
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- stringtie
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files:
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- path: output/test_stringtie_reverse/test.gene_abundance.txt
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md5sum: cea2e346f4e8137da13265b9b0a4c573
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- path: output/test_stringtie_reverse/test.transcripts.gtf
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md5sum: cb0367e5f98f19fcc2043d248deb513c
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- path: output/test_stringtie_reverse/test.coverage.gtf
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md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/test_stringtie_reverse/test.ballgown/e_data.ctab
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md5sum: 48d5ddf52a3d203d9f85aded9600edb9
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- path: output/test_stringtie_reverse/test.ballgown/e2t.ctab
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md5sum: f828838a28ae74dbc21cd5fc75b6d068
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- path: output/test_stringtie_reverse/test.ballgown/i_data.ctab
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md5sum: 4651c095a12836aa3f7bc4d97ae7b877
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- path: output/test_stringtie_reverse/test.ballgown/i2t.ctab
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md5sum: 6d598e0e28ef911d50783cd382e80ae6
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- path: output/test_stringtie_reverse/test.ballgown/t_data.ctab
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md5sum: 0106f70121a8b520d98b8739aed92915
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