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test(samtools): Refactor idxstats to use pytest-workflow

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Edmund Miller 2020-11-24 20:01:05 -06:00
parent 34d86427a6
commit 16cb794892
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GPG key ID: BD387FF7BC10AA9D
7 changed files with 20 additions and 43 deletions
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1
software/samtools/idxstats/test/input/test.paired_end.sorted.bam
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@ -1 +0,0 @@
../../../../../tests/data/bam/test.paired_end.sorted.bam

1
software/samtools/idxstats/test/input/test.paired_end.sorted.bam.bai
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../../../../../tests/data/bam/test.paired_end.sorted.bam.bai

19
software/samtools/idxstats/test/main.nf
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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SAMTOOLS_IDXSTATS } from '../main.nf' addParams( options: [:] )
workflow test {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${baseDir}/input/test.paired_end.sorted.bam", checkIfExists: true),
file("${baseDir}/input/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
SAMTOOLS_IDXSTATS ( input )
}
workflow {
test()
}

20
software/samtools/idxstats/test/nextflow.config
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@ -1,20 +0,0 @@
params {
outdir = "output/"
publish_dir_mode = "copy"
enable_conda = false
}
profiles {
conda {
params.enable_conda = true
}
docker {
docker.enabled = true
docker.runOptions = '-u \$(id -u):\$(id -g)'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
}
}

2
software/samtools/idxstats/test/output/samtools/test.paired_end.sorted.bam.idxstats
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gi|170079663|ref|NC_010473.1| 4686137 20000 0
* 0 0 0

11
tests/software/samtools/main.nf
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@ -3,6 +3,7 @@
nextflow.enable.dsl = 2
include { SAMTOOLS_FLAGSTAT } from '../../../software/samtools/flagstat/main.nf' addParams( options: [:] )
include { SAMTOOLS_IDXSTATS } from '../../../software/samtools/idxstats/main.nf' addParams( options: [:] )
workflow test_samtools_flagstat {
@ -13,3 +14,13 @@ workflow test_samtools_flagstat {
SAMTOOLS_FLAGSTAT ( input )
}
workflow test_samtools_idxstats {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ]
SAMTOOLS_IDXSTATS ( input )
}

9
tests/software/samtools/test.yml
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@ -6,3 +6,12 @@
files:
- path: output/samtools/test.paired_end.sorted.bam.flagstat
md5sum: 80590621c74f5ee43ada20d010a3837f
- name: Run samtools idxstats test workflow
command: nextflow run ./tests/software/samtools/ -profile docker -entry test_samtools_idxstats -c tests/config/nextflow.config
tags:
- samtools
- samtools_idxstats
files:
- path: output/samtools/test.paired_end.sorted.bam.idxstats
md5sum: 3bee8b7d55e412da2b3816c5a18d60d5