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Explicitly name the output files to avoid the gzi index being flown through the output channel (#2136)

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Matthieu Muffato 2022-09-30 13:31:48 +01:00 committed by GitHub
parent ebc466caac
commit 31c0b49f65
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1 changed files with 7 additions and 6 deletions
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11
modules/tabix/bgzip/main.nf
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@ -11,8 +11,8 @@ process TABIX_BGZIP {
tuple val(meta), path(input) tuple val(meta), path(input)
output: output:
tuple val(meta), path("${prefix}*"), emit: output tuple val(meta), path("${output}") , emit: output
tuple val(meta), path("*gzi") , emit: gzi, optional: true tuple val(meta), path("${output}.gzi"), emit: gzi, optional: true
path "versions.yml" , emit: versions path "versions.yml" , emit: versions
when: when:
@ -21,12 +21,13 @@ process TABIX_BGZIP {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}" prefix = task.ext.prefix ?: "${meta.id}"
in_bgzip = input.toString().endsWith(".gz") in_bgzip = ["gz", "bgz", "bgzf"].contains(input.getExtension())
output = in_bgzip ? input.getBaseName() : "${prefix}.${input.getExtension()}.gz"
command1 = in_bgzip ? '-d' : '-c' command1 = in_bgzip ? '-d' : '-c'
command2 = in_bgzip ? '' : " > ${prefix}.${input.getExtension()}.gz" command2 = in_bgzip ? '' : " > ${output}"
// Name the index according to $prefix, unless a name has been requested // Name the index according to $prefix, unless a name has been requested
if ((args.matches("(^| )-i\\b") || args.matches("(^| )--index(\$| )")) && !args.matches("(^| )-I\\b") && !args.matches("(^| )--index-name\\b")) { if ((args.matches("(^| )-i\\b") || args.matches("(^| )--index(\$| )")) && !args.matches("(^| )-I\\b") && !args.matches("(^| )--index-name\\b")) {
args = args + " -I ${prefix}.${input.getExtension()}.gz.gzi" args = args + " -I ${output}.gzi"
} }
""" """
bgzip $command1 $args -@${task.cpus} $input $command2 bgzip $command1 $args -@${task.cpus} $input $command2