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Replace remaining task.ext.suffix with task.ext.prefix (#1117)

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* Replace remaining task.ext.suffix with task.ext.prefix
This commit is contained in:
Mahesh Binzer-Panchal 2021-12-07 15:00:43 +01:00 committed by GitHub
parent 3b366c7c6a
commit d473a247d2
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GPG key ID: 4AEE18F83AFDEB23
31 changed files with 60 additions and 61 deletions
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4
modules/artic/minion/main.nf
View file

@ -32,8 +32,8 @@ process ARTIC_MINION {
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
def version = scheme_version.toString().toLowerCase().replaceAll('v','')
def fast5 = fast5_dir ? "--fast5-directory $fast5_dir" : ""
def summary = sequencing_summary ? "--sequencing-summary $sequencing_summary" : ""

6
modules/bakta/main.nf
View file

@ -26,8 +26,8 @@ process BAKTA {
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
def proteins_opt = proteins ? "--proteins ${proteins[0]}" : ""
def prodigal_opt = prodigal_tf ? "--prodigal-tf ${prodigal_tf[0]}" : ""
"""
@ -47,7 +47,7 @@ process BAKTA {
"""
stub:
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.embl
touch ${prefix}.faa

4
modules/bcftools/concat/main.nf
View file

@ -15,8 +15,8 @@ process BCFTOOLS_CONCAT {
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
"""
bcftools concat \\
--output ${prefix}.vcf.gz \\

4
modules/bcftools/isec/main.nf
View file

@ -15,8 +15,8 @@ process BCFTOOLS_ISEC {
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
"""
bcftools isec \\
$args \\

4
modules/bcftools/merge/main.nf
View file

@ -15,8 +15,8 @@ process BCFTOOLS_MERGE {
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
"""
bcftools merge -Oz \\
--output ${prefix}.vcf.gz \\

4
modules/bedtools/getfasta/main.nf
View file

@ -16,8 +16,8 @@ process BEDTOOLS_GETFASTA {
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${bed.baseName}${task.ext.suffix}" : "${bed.baseName}"
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${bed.baseName}"
"""
bedtools \\
getfasta \\

4
modules/checkm/lineagewf/main.nf
View file

@ -17,8 +17,8 @@ process CHECKM_LINEAGEWF {
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
"""
checkm \\
lineage_wf \\

4
modules/csvtk/concat/main.nf
View file

@ -17,8 +17,8 @@ process CSVTK_CONCAT {
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
def delimiter = in_format == "tsv" ? "\t" : (in_format == "csv" ? "," : in_format)
def out_delimiter = out_format == "tsv" ? "\t" : (out_format == "csv" ? "," : out_format)
out_extension = out_format == "tsv" ? 'tsv' : 'csv'

4
modules/damageprofiler/main.nf
View file

@ -18,8 +18,8 @@ process DAMAGEPROFILER {
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
def reference = fasta ? "-r $fasta" : ""
def species_list = specieslist ? "-sf $specieslist" : ""
"""

4
modules/dedup/main.nf
View file

@ -18,8 +18,8 @@ process DEDUP {
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
"""
dedup \\

4
modules/fargene/main.nf
View file

@ -32,8 +32,8 @@ process FARGENE {
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
"""
fargene \\
$args \\

4
modules/gatk4/genomicsdbimport/main.nf
View file

@ -20,8 +20,8 @@ process GATK4_GENOMICSDBIMPORT {
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
// settings for running default create gendb mode
inputs_command = input_map ? "--sample-name-map ${vcf[0]}" : "${'-V ' + vcf.join(' -V ')}"

4
modules/gffread/main.nf
View file

@ -15,8 +15,8 @@ process GFFREAD {
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${gff.baseName}${task.ext.suffix}" : "${gff.baseName}"
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${gff.baseName}"
"""
gffread \\
$gff \\

4
modules/leehom/main.nf
View file

@ -24,8 +24,8 @@ process LEEHOM {
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
if (reads.toString().endsWith('.bam')) {
"""

4
modules/msisensor/msi/main.nf
View file

@ -18,8 +18,8 @@ process MSISENSOR_MSI {
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
"""
msisensor \\
msi \\

4
modules/nextclade/main.nf
View file

@ -19,8 +19,8 @@ process NEXTCLADE {
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
"""
nextclade \\
$args \\

6
modules/optitype/main.nf
View file

@ -15,9 +15,9 @@ process OPTITYPE {
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
"""
# Create a config for OptiType on a per sample basis with task.ext.args2

4
modules/plasmidid/main.nf
View file

@ -23,8 +23,8 @@ process PLASMIDID {
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
"""
plasmidID \\
-d $fasta \\

4
modules/prodigal/main.nf
View file

@ -19,8 +19,8 @@ process PRODIGAL {
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
"""
prodigal -i "${genome}" \\
$args \\

4
modules/prokka/main.nf
View file

@ -28,8 +28,8 @@ process PROKKA {
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
def proteins_opt = proteins ? "--proteins ${proteins[0]}" : ""
def prodigal_opt = prodigal_tf ? "--prodigaltf ${prodigal_tf[0]}" : ""
"""

4
modules/qualimap/bamqc/main.nf
View file

@ -17,8 +17,8 @@ process QUALIMAP_BAMQC {
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
def collect_pairs = meta.single_end ? '' : '--collect-overlap-pairs'
def memory = task.memory.toGiga() + "G"

4
modules/qualimap/rnaseq/main.nf
View file

@ -16,8 +16,8 @@ process QUALIMAP_RNASEQ {
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
def paired_end = meta.single_end ? '' : '-pe'
def memory = task.memory.toGiga() + "G"

4
modules/quast/main.nf
View file

@ -19,8 +19,8 @@ process QUAST {
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
prefix = task.ext.suffix ?: 'quast'
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: 'quast'
def features = use_gff ? "--features $gff" : ''
def reference = use_fasta ? "-r $fasta" : ''
"""

4
modules/rsem/calculateexpression/main.nf
View file

@ -23,8 +23,8 @@ process RSEM_CALCULATEEXPRESSION {
tuple val(meta), path("${prefix}.transcript.bam"), optional:true, emit: bam_transcript
script:
def args = task.ext.args ?: ''
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
def strandedness = ''
if (meta.strandedness == 'forward') {

4
modules/salmon/quant/main.nf
View file

@ -20,8 +20,8 @@ process SALMON_QUANT {
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
def reference = "--index $index"
def input_reads = meta.single_end ? "-r $reads" : "-1 ${reads[0]} -2 ${reads[1]}"

4
modules/samtools/merge/main.nf
View file

@ -17,8 +17,8 @@ process SAMTOOLS_MERGE {
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
def file_type = input_files[0].getExtension()
def reference = fasta ? "--reference ${fasta}" : ""
"""

1
modules/seqkit/split2/main.nf
View file

@ -17,7 +17,6 @@ process SEQKIT_SPLIT2 {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
if(meta.single_end){
"""
seqkit \\

4
modules/seqtk/subseq/main.nf
View file

@ -16,8 +16,8 @@ process SEQTK_SUBSEQ {
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ?: ''
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: ''
def ext = "fa"
if ("$sequences" ==~ /.+\.fq|.+\.fq.gz|.+\.fastq|.+\.fastq.gz/) {
ext = "fq"

4
modules/tbprofiler/profile/main.nf
View file

@ -19,8 +19,8 @@ process TBPROFILER_PROFILE {
path "versions.yml" , emit: versions
script:
def args = task.ext.args ?: ''
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
def input_reads = meta.single_end ? "--read1 $reads" : "--read1 ${reads[0]} --read2 ${reads[1]}"
"""
tb-profiler \\

2
tests/modules/gffread/nextflow.config
View file

@ -3,7 +3,7 @@ process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: GFFREAD {
ext.prefix = { "${meta.id}.out" }
ext.prefix = { "${gff.baseName}.out" }
}
}

2
tests/modules/seqtk/subseq/nextflow.config
View file

@ -3,7 +3,7 @@ process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: SEQTK_SUBSEQ {
ext.prefix = { "${meta.id}.filtered" }
ext.prefix = { ".filtered" }
}
}