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fix optional output detection
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parent
d0db186e84
commit
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2 changed files with 13 additions and 5 deletions
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@ -23,8 +23,8 @@ process BIOBAMBAM_BAMMERGE {
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script:
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script:
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def args = task.ext.args ?: ''
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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prefix = task.ext.prefix ?: "${meta.id}"
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indexfilename = args.contains("indexfilename=") ? args =~ /indexfilename=([^\s]+)/ : ""
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indexfilename = args.contains("indexfilename=") ? (args =~ /indexfilename=([^\s]+)/)[0][1] : ""
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md5filename = args.contains("md5filename=") ? args =~ /md5filename=([^\s]+)/ : ""
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md5filename = args.contains("md5filename=") ? (args =~ /md5filename=([^\s]+)/)[0][1] : ""
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def input_string = bam.join(" I=")
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def input_string = bam.join(" I=")
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"""
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"""
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@ -6,6 +6,10 @@
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files:
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files:
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- path: output/biobambam/test.bam
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- path: output/biobambam/test.bam
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md5sum: bc3d32ab6a54d1894ca7cc79387dec57
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md5sum: bc3d32ab6a54d1894ca7cc79387dec57
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- path: output/biobambam/test.bam.bai
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md5sum: b8ae542a37a73d79de1c15c765207c53
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- path: output/biobambam/test.md5
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md5sum: 31c59857990ceb392242136429e30243
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- name: biobambam bammerge test_biobambam_bammerge_single
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- name: biobambam bammerge test_biobambam_bammerge_single
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command: nextflow run ./tests/modules/biobambam/bammerge -entry test_biobambam_bammerge_single -c ./tests/config/nextflow.config -c ./tests/modules/biobambam/bammerge/nextflow.config
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command: nextflow run ./tests/modules/biobambam/bammerge -entry test_biobambam_bammerge_single -c ./tests/config/nextflow.config -c ./tests/modules/biobambam/bammerge/nextflow.config
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@ -15,3 +19,7 @@
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files:
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files:
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- path: output/biobambam/test.bam
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- path: output/biobambam/test.bam
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md5sum: 86185d3d6895a7722d3b3a09c6f91bfc
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md5sum: 86185d3d6895a7722d3b3a09c6f91bfc
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- path: output/biobambam/test.bam.bai
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md5sum: 973680feb6bc73cd1051ea83c7219418
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- path: output/biobambam/test.md5
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md5sum: 244a9d1cbc6d74724285c80220e5e427
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