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test(picard): Add failing test for markduplicates

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Edmund Miller 2020-11-24 19:38:49 -06:00
parent 7848019cdb
commit d1a77b2fb2
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2 changed files with 17 additions and 0 deletions
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9
tests/software/picard/main.nf
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@ -37,3 +37,12 @@ workflow test_picard_markduplicates {
PICARD_MARKDUPLICATES ( input ) PICARD_MARKDUPLICATES ( input )
} }
workflow test_picard_markduplicates_not_sorted {
def input = []
input = [ [ id:'test', single_end:false ], // meta map
file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true) ]
PICARD_MARKDUPLICATES ( input )
}

8
tests/software/picard/test.yml
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@ -33,3 +33,11 @@
- path: output/picard/test.MarkDuplicates.metrics.txt - path: output/picard/test.MarkDuplicates.metrics.txt
- path: output/picard/test.bam - path: output/picard/test.bam
md5sum: 50407a1ee722f2bf6a20471c8a7fd6b0 md5sum: 50407a1ee722f2bf6a20471c8a7fd6b0
- name: Run picard MarkDuplicates without a sorted bam file so it fails
command: nextflow run ./tests/software/picard -profile docker -entry test_picard_markduplicates_not_sorted -c tests/config/nextflow.config
tags:
- picard
- picard_markduplicates
- should fail
exit_code: 1