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Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110)

Browse source 
* Add comment line for consistency

* Remove all functions.nf

* Remove include functions.nf and publishDir options

* Replace options.args3 with task.ext.args3 - 3 modules

* Replace options.args3 with task.ext.args3 - 17 modules

* Replace {task.cpus} with task.cpus

* Replace off on off off off off off off off on off on off on off off off on off off off on on off off off on on off off off off off off off on off off off off on off on on off off off on on on on off off off on off on on off on on off off on on on off on on off on off off off off on off off off on off off on off on off off off on on off on off on off off on off off off on off off off on off off off off on off off off on on on off on on off off on off on on on off on on off on on on off off off off off on on off off on off off off off off on off off on on off on on off on off off off on off off off off on on off on off off on off off on off on off off off off off off off off on on off on off off off.args with

* Add def args = task.ext.args line to all modules in script section

* Replace options.args with args and args_list

* Initialise args2 and args3 properly

* Replace container syntax

* Revert container changes for cellranger/mkref

* Replace getProcessName in all modules

* Replace getSoftwareName in all modules

* Unify modules using VERSION variable

* Replae options.suffix with task.ext.suffix

* Remove NF version restriction for CI

* Bump NF version in README

* Replace task.process.tokenize logic with task.process

* Minor tweaks to unify syntax in tests main.nf

* Add a separate nextflow.config for each module

* Transfer remaining module options to nextflow.config

* Remove addParams from tests main.nf

* Remove TODO statements

* Use -c to import module specific config

* Bump NF version to 21.10.3

* Fix tests for artic/minion

* Fix broken publishDir syntax

* Standardise and fix obvious failing module tests

* Remove kronatools to krona

* Comment out tags in subworkflow test.yml

* Fix failing module tests

* Add consistent indentation to nextflow.config

* Comment out subworklow definitions

* Fix kallistobustools/ref

* Fix rmarkdownnotebook

* Fix jupyternotebook

* Quote task.process

* Add plink2/vcf to pytest_modules.yml

* Remove NF_CORE_MODULES_TEST from pytest CI

* Fix more tests

* Move bacteroides_fragilis to prokaryotes folder

* Fix cooler merge tests

* Fix kallistobustools/count tests

* Fix kallistobustools/ref tests

* Update test_10x_1_fastq_gz file for kallistobustools/count tests

* Fix bcftools/query tests

* Fix delly/call tests

* Fix cooler/zoomify tests

* Fix csvtk/split tests

* Fix gatk4/intervallisttools tests

* Fix gatk4/variantfiltration

* Fix pydamage/filter tests

* Fix test data for unicycler

* Fix gstama/collapse module

* Fix leehom tests

* Fix metaphlan3 tests

* Fix pairtools/select tests

* Update nextflow.config

* Update nextflow.config

* feat: update syntax

* Fix arriba tests

* Fix more failing tests

* Update test syntax

* Remove comments from tests nextflow.config

* Apply suggestions from code review

* Fix kallistobustools/count module

* Update dumpsoftwareversions module

* Update custom/dumpsoftwareversions

* Add args2 to untar module

* Update leftover modules

* Remove last remaining addParams

* Change syntax from task.ext.suffix to tast.ext.prefix

* Change nextflow.config in all tests to use ext.prefix instead of ext.suffix

Co-authored-by: JoseEspinosa <kadomu@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
This commit is contained in:
Harshil Patel 2021-12-02 12:39:55 +00:00 committed by GitHub
parent 1f8f86b793
commit 9d0cad583b
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
309 changed files with 312 additions and 312 deletions
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2
modules/abacas/main.nf
View file

@ -17,7 +17,7 @@ process ABACAS {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
abacas.pl \\
-r $fasta \\

2
modules/adapterremoval/main.nf
View file

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

2
modules/agrvate/main.nf
View file

@ -17,7 +17,7 @@ process AGRVATE {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
agrvate \\
$args \\

2
modules/allelecounter/main.nf
View file

@ -18,7 +18,7 @@ process ALLELECOUNTER {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def reference_options = fasta ? "-r $fasta": ""
"""

2
modules/arriba/main.nf
View file

@ -19,7 +19,7 @@ process ARRIBA {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def blacklist = (args.contains('-b')) ? '' : '-f blacklist'
"""
arriba \\

2
modules/artic/guppyplex/main.nf
View file

@ -16,7 +16,7 @@ process ARTIC_GUPPYPLEX {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
artic \\
guppyplex \\

2
modules/assemblyscan/main.nf
View file

@ -16,7 +16,7 @@ process ASSEMBLYSCAN {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
assembly-scan $assembly > ${prefix}.json

2
modules/ataqv/ataqv/main.nf
View file

@ -21,7 +21,7 @@ process ATAQV_ATAQV {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def peak = peak_file ? "--peak-file $peak_file" : ''
def tss = tss_file ? "--tss-file $tss_file" : ''
def excl_regs = excl_regs_file ? "--excluded-region-file $excl_regs_file" : ''

2
modules/bamaligncleaner/main.nf
View file

@ -16,7 +16,7 @@ process BAMALIGNCLEANER {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
bamAlignCleaner \\

2
modules/bamtools/split/main.nf
View file

@ -16,7 +16,7 @@ process BAMTOOLS_SPLIT {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
bamtools \\
split \\

2
modules/bamutil/trimbam/main.nf
View file

@ -16,7 +16,7 @@ process BAMUTIL_TRIMBAM {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
bam \\
trimBam \\

2
modules/bandage/image/main.nf
View file

@ -17,7 +17,7 @@ process BANDAGE_IMAGE {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
Bandage image $gfa ${prefix}.png $args
Bandage image $gfa ${prefix}.svg $args

2
modules/bbmap/align/main.nf
View file

@ -18,7 +18,7 @@ process BBMAP_ALIGN {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
input = meta.single_end ? "in=${fastq}" : "in=${fastq[0]} in2=${fastq[1]}"

2
modules/bbmap/bbduk/main.nf
View file

@ -18,7 +18,7 @@ process BBMAP_BBDUK {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def raw = meta.single_end ? "in=${reads[0]}" : "in1=${reads[0]} in2=${reads[1]}"
def trimmed = meta.single_end ? "out=${prefix}.fastq.gz" : "out1=${prefix}_1.fastq.gz out2=${prefix}_2.fastq.gz"
def contaminants_fa = contaminants ? "ref=$contaminants" : ''

2
modules/bbmap/bbsplit/main.nf
View file

@ -22,7 +22,7 @@ process BBMAP_BBSPLIT {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def avail_mem = 3
if (!task.memory) {

2
modules/bcftools/consensus/main.nf
View file

@ -16,7 +16,7 @@ process BCFTOOLS_CONSENSUS {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
cat $fasta | bcftools consensus $vcf $args > ${prefix}.fa
header=\$(head -n 1 ${prefix}.fa | sed 's/>//g')

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

@ -16,7 +16,7 @@ process BCFTOOLS_FILTER {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
bcftools filter \\
--output ${prefix}.vcf.gz \\

2
modules/bcftools/index/main.nf
View file

@ -17,7 +17,7 @@ process BCFTOOLS_INDEX {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
bcftools \\

2
modules/bcftools/mpileup/main.nf
View file

@ -21,7 +21,7 @@ process BCFTOOLS_MPILEUP {
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def args3 = task.ext.args3 ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
echo "${meta.id}" > sample_name.list

2
modules/bcftools/norm/main.nf
View file

@ -17,7 +17,7 @@ process BCFTOOLS_NORM {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
bcftools norm \\
--fasta-ref ${fasta} \\

2
modules/bcftools/query/main.nf
View file

@ -19,7 +19,7 @@ process BCFTOOLS_QUERY {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def regions_file = regions ? "--regions-file ${regions}" : ""
def targets_file = targets ? "--targets-file ${targets}" : ""
def samples_file = samples ? "--samples-file ${samples}" : ""

2
modules/bcftools/reheader/main.nf
View file

@ -18,7 +18,7 @@ process BCFTOOLS_REHEADER {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def update_sequences = fai ? "-f $fai" : ""
def new_header = header ? "-h $header" : ""
"""

2
modules/bcftools/stats/main.nf
View file

@ -16,7 +16,7 @@ process BCFTOOLS_STATS {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
bcftools stats $args $vcf > ${prefix}.bcftools_stats.txt
cat <<-END_VERSIONS > versions.yml

2
modules/bcftools/view/main.nf
View file

@ -19,7 +19,7 @@ process BCFTOOLS_VIEW {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def regions_file = regions ? "--regions-file ${regions}" : ""
def targets_file = targets ? "--targets-file ${targets}" : ""
def samples_file = samples ? "--samples-file ${samples}" : ""

2
modules/bedtools/bamtobed/main.nf
View file

@ -16,7 +16,7 @@ process BEDTOOLS_BAMTOBED {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
bedtools \\
bamtobed \\

2
modules/bedtools/complement/main.nf
View file

@ -17,7 +17,7 @@ process BEDTOOLS_COMPLEMENT {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
bedtools \\
complement \\

2
modules/bedtools/genomecov/main.nf
View file

@ -24,7 +24,7 @@ process BEDTOOLS_GENOMECOV {
args += " -bg"
}
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
if (intervals.name =~ /\.bam/) {
"""
bedtools \\

2
modules/bedtools/intersect/main.nf
View file

@ -17,7 +17,7 @@ process BEDTOOLS_INTERSECT {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
bedtools \\
intersect \\

2
modules/bedtools/makewindows/main.nf
View file

@ -17,7 +17,7 @@ process BEDTOOLS_MAKEWINDOWS {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def arg_input = use_bed ? "-b $regions" : "-g $regions"
"""
bedtools \\

2
modules/bedtools/maskfasta/main.nf
View file

@ -17,7 +17,7 @@ process BEDTOOLS_MASKFASTA {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
bedtools \\
maskfasta \\

2
modules/bedtools/merge/main.nf
View file

@ -16,7 +16,7 @@ process BEDTOOLS_MERGE {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
bedtools \\
merge \\

2
modules/bedtools/slop/main.nf
View file

@ -17,7 +17,7 @@ process BEDTOOLS_SLOP {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
bedtools \\
slop \\

2
modules/bedtools/sort/main.nf
View file

@ -17,7 +17,7 @@ process BEDTOOLS_SORT {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
bedtools \\
sort \\

2
modules/bedtools/subtract/main.nf
View file

@ -16,7 +16,7 @@ process BEDTOOLS_SUBTRACT {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
bedtools \\
subtract \\

2
modules/bismark/align/main.nf
View file

@ -19,7 +19,7 @@ process BISMARK_ALIGN {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def fastq = meta.single_end ? reads : "-1 ${reads[0]} -2 ${reads[1]}"
"""
bismark \\

2
modules/bismark/deduplicate/main.nf
View file

@ -17,7 +17,7 @@ process BISMARK_DEDUPLICATE {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def seqtype = meta.single_end ? '-s' : '-p'
"""
deduplicate_bismark \\

2
modules/blast/blastn/main.nf
View file

@ -17,7 +17,7 @@ process BLAST_BLASTN {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
DB=`find -L ./ -name "*.ndb" | sed 's/.ndb//'`
blastn \\

2
modules/bowtie/align/main.nf
View file

@ -20,7 +20,7 @@ process BOWTIE_ALIGN {
script:
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def unaligned = params.save_unaligned ? "--un ${prefix}.unmapped.fastq" : ''
def endedness = meta.single_end ? "$reads" : "-1 ${reads[0]} -2 ${reads[1]}"
"""

2
modules/bowtie2/align/main.nf
View file

@ -20,7 +20,7 @@ process BOWTIE2_ALIGN {
script:
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
if (meta.single_end) {
def unaligned = params.save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
"""

2
modules/bwa/aln/main.nf
View file

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

2
modules/bwa/mem/main.nf
View file

@ -18,7 +18,7 @@ process BWA_MEM {
script:
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
"""
INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`

2
modules/bwa/sampe/main.nf
View file

@ -17,7 +17,7 @@ process BWA_SAMPE {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def read_group = meta.read_group ? "-r ${meta.read_group}" : ""
"""

2
modules/bwa/samse/main.nf
View file

@ -17,7 +17,7 @@ process BWA_SAMSE {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def read_group = meta.read_group ? "-r ${meta.read_group}" : ""
"""

2
modules/bwamem2/mem/main.nf
View file

@ -18,7 +18,7 @@ process BWAMEM2_MEM {
script:
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
"""
INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`

2
modules/bwameth/align/main.nf
View file

@ -18,7 +18,7 @@ process BWAMETH_ALIGN {
script:
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
"""
INDEX=`find -L ${index} -name "*.bwameth.c2t" | sed 's/.bwameth.c2t//'`

2
modules/cat/fastq/main.nf
View file

@ -16,7 +16,7 @@ process CAT_FASTQ {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def readList = reads.collect{ it.toString() }
if (meta.single_end) {
if (readList.size > 1) {

2
modules/chromap/chromap/main.nf
View file

@ -28,7 +28,7 @@ process CHROMAP_CHROMAP {
script:
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def args_list = args.tokenize()
def file_extension = args.contains("--SAM") ? 'sam' : args.contains("--TagAlign")? 'tagAlign' : args.contains("--pairs")? 'pairs' : 'bed'

2
modules/clonalframeml/main.nf
View file

@ -21,7 +21,7 @@ process CLONALFRAMEML {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
ClonalFrameML \\
$newick \\

2
modules/cmseq/polymut/main.nf
View file

@ -18,7 +18,7 @@ process CMSEQ_POLYMUT {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def fasta_refid = fasta ? "-c $fasta" : ""
def sortindex = bai ? "" : "--sortindex"
"""

2
modules/cooler/cload/main.nf
View file

@ -18,7 +18,7 @@ process COOLER_CLOAD {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def nproc = args.contains('pairix') || args.contains('tabix')? "--nproc $task.cpus" : ''
"""

2
modules/cooler/dump/main.nf
View file

@ -17,7 +17,7 @@ process COOLER_DUMP {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def suffix = resolution ? "::$resolution" : ""
"""
cooler dump \\

2
modules/cooler/merge/main.nf
View file

@ -16,7 +16,7 @@ process COOLER_MERGE {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
cooler merge \\
$args \\

2
modules/cooler/zoomify/main.nf
View file

@ -16,7 +16,7 @@ process COOLER_ZOOMIFY {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
cooler zoomify \\
$args \\

2
modules/csvtk/split/main.nf
View file

@ -18,7 +18,7 @@ process CSVTK_SPLIT {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def delimiter = in_format == "tsv" ? "--tabs" : (in_format == "csv" ? "--delimiter ',' " : in_format)
def out_delimiter = out_format == "tsv" ? "--out-tabs" : (out_format == "csv" ? "--out-delimiter ',' " : out_format)
out_extension = out_format == "tsv" ? 'tsv' : 'csv'

2
modules/cutadapt/main.nf
View file

@ -17,7 +17,7 @@ process CUTADAPT {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def trimmed = meta.single_end ? "-o ${prefix}.trim.fastq.gz" : "-o ${prefix}_1.trim.fastq.gz -p ${prefix}_2.trim.fastq.gz"
"""
cutadapt \\

2
modules/dastool/dastool/main.nf
View file

@ -28,7 +28,7 @@ process DASTOOL_DASTOOL {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def bin_list = bins instanceof List ? bins.join(",") : "$bins"
def engine = search_engine ? "--search_engine $search_engine" : "--search_engine diamond"
def db_dir = db_directory ? "--db_directory $db_directory" : ""

2
modules/dastool/scaffolds2bin/main.nf
View file

@ -17,7 +17,7 @@ process DASTOOL_SCAFFOLDS2BIN {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def file_extension = extension ? extension : "fasta"
"""

2
modules/deeptools/computematrix/main.nf
View file

@ -18,7 +18,7 @@ process DEEPTOOLS_COMPUTEMATRIX {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
computeMatrix \\
$args \\

2
modules/deeptools/plotfingerprint/main.nf
View file

@ -18,7 +18,7 @@ process DEEPTOOLS_PLOTFINGERPRINT {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def extend = (meta.single_end && params.fragment_size > 0) ? "--extendReads ${params.fragment_size}" : ''
"""
plotFingerprint \\

2
modules/deeptools/plotheatmap/main.nf
View file

@ -17,7 +17,7 @@ process DEEPTOOLS_PLOTHEATMAP {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
plotHeatmap \\
$args \\

2
modules/deeptools/plotprofile/main.nf
View file

@ -17,7 +17,7 @@ process DEEPTOOLS_PLOTPROFILE {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
plotProfile \\
$args \\

2
modules/delly/call/main.nf
View file

@ -19,7 +19,7 @@ process DELLY_CALL {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
delly \\
call \\

2
modules/diamond/blastp/main.nf
View file

@ -19,7 +19,7 @@ process DIAMOND_BLASTP {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'`

2
modules/diamond/blastx/main.nf
View file

@ -19,7 +19,7 @@ process DIAMOND_BLASTX {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
DB=`find -L ./ -name "*.dmnd" | sed 's/.dmnd//'`

2
modules/dshbio/exportsegments/main.nf
View file

@ -16,7 +16,7 @@ process DSHBIO_EXPORTSEGMENTS {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
dsh-bio \\
export-segments \\

2
modules/dshbio/filterbed/main.nf
View file

@ -16,7 +16,7 @@ process DSHBIO_FILTERBED {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
dsh-bio \\
filter-bed \\

2
modules/dshbio/filtergff3/main.nf
View file

@ -16,7 +16,7 @@ process DSHBIO_FILTERGFF3 {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
dsh-bio \\
filter-gff3 \\

2
modules/dshbio/splitbed/main.nf
View file

@ -16,7 +16,7 @@ process DSHBIO_SPLITBED {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
dsh-bio \\
split-bed \\

2
modules/dshbio/splitgff3/main.nf
View file

@ -16,7 +16,7 @@ process DSHBIO_SPLITGFF3 {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
dsh-bio \\
split-gff3 \\

2
modules/ectyper/main.nf
View file

@ -18,7 +18,7 @@ process ECTYPER {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def is_compressed = fasta.getName().endsWith(".gz") ? true : false
def fasta_name = fasta.getName().replace(".gz", "")
"""

2
modules/emmtyper/main.nf
View file

@ -16,7 +16,7 @@ process EMMTYPER {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
emmtyper \\
$args \\

2
modules/ensemblvep/main.nf
View file

@ -24,7 +24,7 @@ process ENSEMBLVEP {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def dir_cache = task.ext.use_cache ? "\${PWD}/${cache}" : "/.vep"
"""
mkdir $prefix

2
modules/expansionhunter/main.nf
View file

@ -18,7 +18,7 @@ process EXPANSIONHUNTER {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def gender = (meta.gender == 'male' || meta.gender == 1 || meta.gender == 'XY') ? "male" : "female"
"""
ExpansionHunter \\

2
modules/fastani/main.nf
View file

@ -17,7 +17,7 @@ process FASTANI {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
if (meta.batch_input) {
"""

2
modules/fastp/main.nf
View file

@ -24,7 +24,7 @@ process FASTP {
script:
def args = task.ext.args ?: ''
// Added soft-links to original fastqs for consistent naming in MultiQC
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
if (meta.single_end) {
def fail_fastq = save_trimmed_fail ? "--failed_out ${prefix}.fail.fastq.gz" : ''
"""

2
modules/fastqc/main.nf
View file

@ -18,7 +18,7 @@ process FASTQC {
script:
def args = task.ext.args ?: ''
// Add soft-links to original FastQs for consistent naming in pipeline
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
if (meta.single_end) {
"""
[ ! -f ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz

2
modules/fastqscan/main.nf
View file

@ -16,7 +16,7 @@ process FASTQSCAN {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
zcat $reads | \\
fastq-scan \\

2
modules/fgbio/callmolecularconsensusreads/main.nf
View file

@ -16,7 +16,7 @@ process FGBIO_CALLMOLECULARCONSENSUSREADS {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
fgbio \\
CallMolecularConsensusReads \\

2
modules/fgbio/fastqtobam/main.nf
View file

@ -17,7 +17,7 @@ process FGBIO_FASTQTOBAM {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
mkdir tmp

2
modules/fgbio/groupreadsbyumi/main.nf
View file

@ -18,7 +18,7 @@ process FGBIO_GROUPREADSBYUMI {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
mkdir tmp

2
modules/fgbio/sortbam/main.nf
View file

@ -16,7 +16,7 @@ process FGBIO_SORTBAM {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
fgbio \\
SortBam \\

2
modules/filtlong/main.nf
View file

@ -16,7 +16,7 @@ process FILTLONG {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def short_reads = meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}"
"""
filtlong \\

2
modules/flash/main.nf
View file

@ -15,7 +15,7 @@ process FLASH {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
flash \\
$args \\

2
modules/freebayes/main.nf
View file

@ -22,7 +22,7 @@ process FREEBAYES {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def input = input_2 ? "${input_1} ${input_2}" : "${input_1}"
def targets_file = targets ? "--target ${targets}" : ""
def samples_file = samples ? "--samples ${samples}" : ""

2
modules/gatk4/applybqsr/main.nf
View file

@ -20,7 +20,7 @@ process GATK4_APPLYBQSR {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def interval = intervals ? "-L ${intervals}" : ""
if (!task.memory) {
log.info '[GATK ApplyBQSR] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'

2
modules/gatk4/baserecalibrator/main.nf
View file

@ -22,7 +22,7 @@ process GATK4_BASERECALIBRATOR {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def intervalsCommand = intervalsBed ? "-L ${intervalsBed}" : ""
def sitesCommand = knownSites.collect{"--known-sites ${it}"}.join(' ')

2
modules/gatk4/bedtointervallist/main.nf
View file

@ -17,7 +17,7 @@ process GATK4_BEDTOINTERVALLIST {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
gatk BedToIntervalList \\
-I $bed \\

2
modules/gatk4/calculatecontamination/main.nf
View file

@ -18,7 +18,7 @@ process GATK4_CALCULATECONTAMINATION {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def matched_command = matched ? " -matched ${matched} " : ''
def segment_command = segmentout ? " -segments ${prefix}.segmentation.table" : ''
"""

2
modules/gatk4/createsomaticpanelofnormals/main.nf
View file

@ -20,7 +20,7 @@ process GATK4_CREATESOMATICPANELOFNORMALS {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
gatk \\
CreateSomaticPanelOfNormals \\

2
modules/gatk4/estimatelibrarycomplexity/main.nf
View file

@ -19,7 +19,7 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def crams = cram.collect(){ x -> "-I ".concat(x.toString()) }.join(" ")
def avail_mem = 3

2
modules/gatk4/fastqtosam/main.nf
View file

@ -16,7 +16,7 @@ process GATK4_FASTQTOSAM {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def read_files = meta.single_end ? "-F1 $reads" : "-F1 ${reads[0]} -F2 ${reads[1]}"
"""
gatk FastqToSam \\

2
modules/gatk4/filtermutectcalls/main.nf
View file

@ -21,7 +21,7 @@ process GATK4_FILTERMUTECTCALLS {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def orientationbias_options = ''
if (orientationbias) {

2
modules/gatk4/genotypegvcfs/main.nf
View file

@ -22,7 +22,7 @@ process GATK4_GENOTYPEGVCFS {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def dbsnp_options = dbsnp ? "-D ${dbsnp}" : ""
def interval_options = intervals_bed ? "-L ${intervals_bed}" : ""
def gvcf_options = gvcf.name.endsWith(".vcf") || gvcf.name.endsWith(".vcf.gz") ? "$gvcf" : "gendb://$gvcf"

2
modules/gatk4/getpileupsummaries/main.nf
View file

@ -19,7 +19,7 @@ process GATK4_GETPILEUPSUMMARIES {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def sitesCommand = ''
sitesCommand = sites ? " -L ${sites} " : " -L ${variants} "

2
modules/gatk4/haplotypecaller/main.nf
View file

@ -23,7 +23,7 @@ process GATK4_HAPLOTYPECALLER {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def interval_option = interval ? "-L ${interval}" : ""
def dbsnp_option = dbsnp ? "-D ${dbsnp}" : ""
def avail_mem = 3

2
modules/gatk4/intervallisttools/main.nf
View file

@ -16,7 +16,7 @@ process GATK4_INTERVALLISTTOOLS {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
mkdir ${prefix}_split

2
modules/gatk4/learnreadorientationmodel/main.nf
View file

@ -16,7 +16,7 @@ process GATK4_LEARNREADORIENTATIONMODEL {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def inputs_list = []
f1r2.each() { a -> inputs_list.add(" -I " + a) }
"""

2
modules/gatk4/markduplicates/main.nf
View file

@ -18,7 +18,7 @@ process GATK4_MARKDUPLICATES {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
def bam_list = bams.collect(){ bam -> "--INPUT ".concat(bam.toString()) }.join(" ")
def avail_mem = 3
if (!task.memory) {

2
modules/gatk4/mergebamalignment/main.nf
View file

@ -19,7 +19,7 @@ process GATK4_MERGEBAMALIGNMENT {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
"""
gatk MergeBamAlignment \\
ALIGNED=$aligned \\

2
modules/gatk4/mergevcfs/main.nf
View file

@ -18,7 +18,7 @@ process GATK4_MERGEVCFS {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
def prefix = task.ext.prefix ?: "${meta.id}"
// Make list of VCFs to merge
def input = ""

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