Merge branch 'preseq_test'

This commit is contained in:
Edmund Miller 2021-01-15 17:41:13 -06:00
commit daa25b9329
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5 changed files with 61 additions and 29 deletions

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@ -1,15 +1,15 @@
name: phantompeakqualtools
name: preseq_lcextrap
on:
push:
paths:
- software/phantompeakqualtools/**
- .github/workflows/phantompeakqualtools.yml
- tests/software/phantompeakqualtools/**
- software/preseq/lcextrap/**
- .github/workflows/preseq_lcextrap.yml
- tests/software/preseq/**
pull_request:
paths:
- software/phantompeakqualtools/**
- .github/workflows/phantompeakqualtools.yml
- tests/software/phantompeakqualtools/**
- software/preseq/lcextrap/**
- .github/workflows/preseq_lcextrap.yml
- tests/software/preseq/**
jobs:
ci_test:
@ -37,4 +37,4 @@ jobs:
run: python -m pip install --upgrade pip pytest-workflow
# Test the module
- run: pytest --tag phantompeakqualtools --symlink --wt 2
- run: pytest --tag preseq_lcextrap --symlink --wt 2

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@ -1,12 +0,0 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { PHANTOMPEAKQUALTOOLS } from '../../../software/phantompeakqualtools/main.nf' addParams( options: [:] )
workflow test_phantompeakqualtools {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/bam/test.single_end.sorted.bam", checkIfExists: true) ] ]
PHANTOMPEAKQUALTOOLS ( input )
}

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@ -1,9 +0,0 @@
- name: Run phantompeakqualtools test workflow
command: nextflow run ./tests/software/phantompeakqualtools/ -profile docker -entry test_phantompeakqualtools -c tests/config/nextflow.config
tags:
- phantompeakqualtools
files:
- path: output/phantompeakqualtools/test.spp.pdf
- path: output/phantompeakqualtools/test.spp.Rdata
- path: output/phantompeakqualtools/test.spp.out
md5sum: c18220e8082e695995edecc99235ec85

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { PRESEQ_LCEXTRAP as PRESEQ_LCEXTRAP_SE } from '../../../software/preseq/lcextrap/main.nf' addParams( options: [ publish_dir:'test_preseq_single_end' ] )
include { PRESEQ_LCEXTRAP as PRESEQ_LCEXTRAP_PE } from '../../../software/preseq/lcextrap/main.nf' addParams( options: [ publish_dir:'test_preseq_paired_end' ] )
/*
* Test with single-end data
*/
workflow test_preseq_single_end {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
[ file('https://github.com/smithlabcode/preseq/raw/master/data/SRR1003759_5M_subset.mr', checkIfExists: true), ] ]
PRESEQ_LCEXTRAP_SE ( input )
}
/*
* Test with paired-end data
*/
workflow test_preseq_paired_end {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
[ file('https://github.com/smithlabcode/preseq/raw/master/data/SRR1003759_5M_subset.mr', checkIfExists: true), ] ]
PRESEQ_LCEXTRAP_PE ( input )
}

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- name: Run preseq single-end lcextrap
command: nextflow run ./tests/software/preseq -profile docker -entry test_preseq_single_end -c tests/config/nextflow.config
tags:
- preseq
- preseq_lcextrap
files:
- path: output/test_preseq_single_end/test.ccurve.txt
md5sum: 76ae04c8eaf19c94e3210bb69da38498
- path: output/test_preseq_single_end/test.command.log
- name: Run preseq paired-end lcextrap
command: nextflow run ./tests/software/preseq -profile docker -entry test_preseq_paired_end -c tests/config/nextflow.config
tags:
- preseq
- preseq_lcextrap
files:
- path: output/test_preseq_paired_end/test.ccurve.txt
md5sum: 2836d2fabd2213f097fd7063db550276
- path: output/test_preseq_paired_end/test.command.log