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fix output glob (#1552)
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2 changed files with 3 additions and 3 deletions
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@ -23,7 +23,7 @@ process ELPREP_FILTER {
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output:
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tuple val(meta), path("**.{bam,sam}") ,emit: bam
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tuple val(meta), path("output/**.{bam,sam}") ,emit: bam
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tuple val(meta), path("*.metrics.txt") ,optional: true, emit: metrics
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tuple val(meta), path("*.recall") ,optional: true, emit: recall
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tuple val(meta), path("*.vcf.gz") ,optional: true, emit: gvcf
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@ -65,7 +65,7 @@ process ELPREP_FILTER {
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def assembly_regions_cmd = get_assembly_regions ? " --assembly-regions ${prefix}.assembly_regions.igv": ""
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"""
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elprep filter ${bam} ${prefix}.${suffix} \\
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elprep filter ${bam} output/${prefix}.${suffix} \\
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${reference_sequences_cmd} \\
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${filter_regions_cmd} \\
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${markdup_cmd} \\
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@ -6,7 +6,7 @@
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files:
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- path: output/elprep/test.activity_profile.igv
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- path: output/elprep/test.assembly_regions.igv
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- path: output/elprep/test.bam
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- path: output/elprep/output/test.bam
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- path: output/elprep/test.g.vcf.gz
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- path: output/elprep/test.metrics.txt
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- path: output/elprep/test.recall
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