Fixed test and removed phantompeak tests

This commit is contained in:
sruthipsuresh 2021-01-12 18:04:12 -06:00
parent 3b581d1912
commit b297f7aea1
4 changed files with 3 additions and 62 deletions

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@ -1,40 +0,0 @@
name: phantompeakqualtools
on:
push:
paths:
- software/phantompeakqualtools/**
- .github/workflows/phantompeakqualtools.yml
- tests/software/phantompeakqualtools/**
pull_request:
paths:
- software/phantompeakqualtools/**
- .github/workflows/phantompeakqualtools.yml
- tests/software/phantompeakqualtools/**
jobs:
ci_test:
runs-on: ubuntu-latest
strategy:
matrix:
nxf_version: [20.07.1, ""]
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 phantompeakqualtools --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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@ -8,6 +8,7 @@
- path: output/test_preseq_single_end/test.ccurve.txt
md5sum: 5253ffcfd4b6162851631efdbfe16f92
- path: output/test_preseq_single_end/test.command.log
md5sum: ad83871098825d36d267e375c2b46f01
- name: Run preseq paired-end lcextrap
command: nextflow run ./tests/software/preseq -profile docker -entry test_preseq_paired_end -c tests/config/nextflow.config
@ -18,4 +19,5 @@
files:
- path: output/test_preseq_paired_end/test.ccurve.txt
md5sum: 66b339780630fc1aa72dcfbd0a4490fd
- path: output/test_preseq_paired_end/test.command.log
- path: output/test_preseq_paired_end/test.log
md5sum: d41d8cd98f00b204e9800998ecf8427e