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test(picard): Add failing test for markduplicates
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@ -37,3 +37,12 @@ workflow test_picard_markduplicates {
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PICARD_MARKDUPLICATES ( input )
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PICARD_MARKDUPLICATES ( input )
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}
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}
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workflow test_picard_markduplicates_not_sorted {
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true) ]
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PICARD_MARKDUPLICATES ( input )
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}
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@ -33,3 +33,11 @@
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- path: output/picard/test.MarkDuplicates.metrics.txt
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- path: output/picard/test.MarkDuplicates.metrics.txt
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- path: output/picard/test.bam
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- path: output/picard/test.bam
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md5sum: 50407a1ee722f2bf6a20471c8a7fd6b0
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md5sum: 50407a1ee722f2bf6a20471c8a7fd6b0
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- name: Run picard MarkDuplicates without a sorted bam file so it fails
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command: nextflow run ./tests/software/picard -profile docker -entry test_picard_markduplicates_not_sorted -c tests/config/nextflow.config
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tags:
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- picard
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- picard_markduplicates
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- should fail
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exit_code: 1
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