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Address Jose's comments in #780 (#781)

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* Remove def software line

* Replace version with versions in emit statement

* Fix default software names

* Address Jose's comments in #780
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Harshil Patel 2021-10-01 14:54:50 +01:00 committed by GitHub
parent 7b3315591a
commit cf15ece503
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2 changed files with 69 additions and 71 deletions
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1
modules/unzip/main.nf
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@ -29,7 +29,6 @@ process UNZIP {
script: script:
if ( archive instanceof List && archive.name.size > 1 ) { exit 1, "[UNZIP] error: 7za only accepts a single archive as input. Please check module input." } if ( archive instanceof List && archive.name.size > 1 ) { exit 1, "[UNZIP] error: 7za only accepts a single archive as input. Please check module input." }
""" """
7za \\ 7za \\
e \\ e \\

7
modules/vcftools/main.nf
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@ -24,12 +24,10 @@ process VCFTOOLS {
// Other optional input files can be utilised in a similar way to below but we do not exhaustively itterate through all // Other optional input files can be utilised in a similar way to below but we do not exhaustively itterate through all
// possible options. Instead we leave that to the user. // possible options. Instead we leave that to the user.
tuple val(meta), path(variant_file) tuple val(meta), path(variant_file)
path bed) path bed
path diff_variant_file path diff_variant_file
output: output:
path "versions.yml", emit: versions
tuple val(meta), path("*.vcf") , optional:true, emit: vcf tuple val(meta), path("*.vcf") , optional:true, emit: vcf
tuple val(meta), path("*.bcf") , optional:true, emit: bcf tuple val(meta), path("*.bcf") , optional:true, emit: bcf
tuple val(meta), path("*.frq") , optional:true, emit: frq tuple val(meta), path("*.frq") , optional:true, emit: frq
@ -92,6 +90,7 @@ process VCFTOOLS {
tuple val(meta), path("*.diff.indv") , optional:true, emit: diff_indv tuple val(meta), path("*.diff.indv") , optional:true, emit: diff_indv
tuple val(meta), path("*.diff.discordance.matrix"), optional:true, emit: diff_discd_matrix tuple val(meta), path("*.diff.discordance.matrix"), optional:true, emit: diff_discd_matrix
tuple val(meta), path("*.diff.switch") , optional:true, emit: diff_switch_error tuple val(meta), path("*.diff.switch") , optional:true, emit: diff_switch_error
path "versions.yml" , emit: versions
script: script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
@ -121,7 +120,7 @@ process VCFTOOLS {
--out $prefix \\ --out $prefix \\
${args.join(' ')} \\ ${args.join(' ')} \\
$bed_arg \\ $bed_arg \\
$diff_variant_arg \\ $diff_variant_arg
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}: ${getProcessName(task.process)}: