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Fix error messages mentioning suffix (#1190)

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Jose Espinosa-Carrasco 2021-12-23 18:22:07 +01:00 committed by GitHub
parent a6e0629e24
commit cde237e7ce
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GPG key ID: 4AEE18F83AFDEB23
5 changed files with 5 additions and 5 deletions
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2
modules/last/postmask/main.nf
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@ -17,7 +17,7 @@ process LAST_POSTMASK {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
if( "$maf" == "${prefix}.maf.gz" ) error "Input and output names are the same, use the suffix option to disambiguate" if( "$maf" == "${prefix}.maf.gz" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
""" """
last-postmask $args $maf | gzip --no-name > ${prefix}.maf.gz last-postmask $args $maf | gzip --no-name > ${prefix}.maf.gz

2
modules/plink/extract/main.nf
View file

@ -19,7 +19,7 @@ process PLINK_EXTRACT {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
if( "$bed" == "${prefix}.bed" ) error "Input and output names are the same, use the suffix option to disambiguate" if( "$bed" == "${prefix}.bed" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
""" """
plink \\ plink \\
--bfile ${meta.id} \\ --bfile ${meta.id} \\

2
modules/pmdtools/filter/main.nf
View file

@ -22,7 +22,7 @@ process PMDTOOLS_FILTER {
def args3 = task.ext.args3 ?: '' def args3 = task.ext.args3 ?: ''
def split_cpus = Math.floor(task.cpus/2) def split_cpus = Math.floor(task.cpus/2)
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
if ("$bam" == "${prefix}.bam") error "[pmdtools/filter] Input and output names are the same, use the suffix option to disambiguate!" if ("$bam" == "${prefix}.bam") error "[pmdtools/filter] Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
//threshold and header flags activate filtering function of pmdtools //threshold and header flags activate filtering function of pmdtools
""" """
samtools \\ samtools \\

2
modules/samblaster/main.nf
View file

@ -19,7 +19,7 @@ process SAMBLASTER {
def args2 = task.ext.args2 ?: '' def args2 = task.ext.args2 ?: ''
def args3 = task.ext.args3 ?: '' def args3 = task.ext.args3 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
if( "$bam" == "${prefix}.bam" ) error "Input and output names are the same, use the suffix option to disambiguate" if( "$bam" == "${prefix}.bam" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
""" """
samtools view -h $args2 $bam | \\ samtools view -h $args2 $bam | \\
samblaster $args | \\ samblaster $args | \\

2
modules/samtools/fixmate/main.nf
View file

@ -17,7 +17,7 @@ process SAMTOOLS_FIXMATE {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use the suffix option to disambiguate!" if ("$bam" == "${prefix}.bam") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
""" """
samtools \\ samtools \\