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

* 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>

modules/abacas/main.nf

@@ -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 \\

modules/adapterremoval/main.nf

@@ -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) {
         """

modules/agrvate/main.nf

@@ -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 \\

modules/allelecounter/main.nf

@@ -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": ""
 
     """

modules/arriba/main.nf

@@ -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 \\

modules/artic/guppyplex/main.nf

@@ -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 \\

modules/assemblyscan/main.nf

@@ -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
 

modules/ataqv/ataqv/main.nf

@@ -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"       : ''

modules/bamaligncleaner/main.nf

@@ -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 \\

modules/bamtools/split/main.nf

@@ -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 \\

modules/bamutil/trimbam/main.nf

@@ -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 \\

modules/bandage/image/main.nf

@@ -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

modules/bbmap/align/main.nf

@@ -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]}"
 

modules/bbmap/bbduk/main.nf

@@ -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" : ''

modules/bbmap/bbsplit/main.nf

@@ -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) {

modules/bcftools/consensus/main.nf

@@ -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')

modules/bcftools/filter/main.nf

@@ -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 \\

modules/bcftools/index/main.nf

@@ -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 \\

modules/bcftools/mpileup/main.nf

@@ -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
 

modules/bcftools/norm/main.nf

@@ -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} \\

modules/bcftools/query/main.nf

@@ -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}" : ""

modules/bcftools/reheader/main.nf

@@ -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" : ""
     """

modules/bcftools/stats/main.nf

@@ -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

modules/bcftools/view/main.nf

@@ -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}" : ""

modules/bedtools/bamtobed/main.nf

@@ -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 \\

modules/bedtools/complement/main.nf

@@ -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 \\

modules/bedtools/genomecov/main.nf

@@ -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 \\

modules/bedtools/intersect/main.nf

@@ -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 \\

modules/bedtools/makewindows/main.nf

@@ -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 \\

modules/bedtools/maskfasta/main.nf

@@ -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 \\

modules/bedtools/merge/main.nf

@@ -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 \\

modules/bedtools/slop/main.nf

@@ -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 \\

modules/bedtools/sort/main.nf

@@ -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 \\

modules/bedtools/subtract/main.nf

@@ -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 \\

modules/bismark/align/main.nf

@@ -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 \\

modules/bismark/deduplicate/main.nf

@@ -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 \\

modules/blast/blastn/main.nf

@@ -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 \\

modules/bowtie/align/main.nf

@@ -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]}"
     """

modules/bowtie2/align/main.nf

@@ -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" : ''
         """

modules/bwa/aln/main.nf

@@ -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) {
         """

modules/bwa/mem/main.nf

@@ -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//'`

modules/bwa/sampe/main.nf

@@ -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}" : ""
 
     """

modules/bwa/samse/main.nf

@@ -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}" : ""
 
     """

modules/bwamem2/mem/main.nf

@@ -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//'`

modules/bwameth/align/main.nf

@@ -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//'`

modules/cat/fastq/main.nf

@@ -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) {

modules/chromap/chromap/main.nf

@@ -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'

modules/clonalframeml/main.nf

@@ -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 \\

modules/cmseq/polymut/main.nf

@@ -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"
     """

modules/cooler/cload/main.nf

@@ -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" : ''
 
     """

modules/cooler/dump/main.nf

@@ -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 \\

modules/cooler/merge/main.nf

@@ -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 \\

modules/cooler/zoomify/main.nf

@@ -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 \\

modules/csvtk/split/main.nf

@@ -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'

modules/cutadapt/main.nf

@@ -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 \\

modules/dastool/dastool/main.nf

@@ -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" : ""

modules/dastool/scaffolds2bin/main.nf

@@ -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"
 
     """

modules/deeptools/computematrix/main.nf

@@ -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 \\

modules/deeptools/plotfingerprint/main.nf

@@ -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 \\

modules/deeptools/plotheatmap/main.nf

@@ -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 \\

modules/deeptools/plotprofile/main.nf

@@ -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 \\

modules/delly/call/main.nf

@@ -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 \\

modules/diamond/blastp/main.nf

@@ -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//'`
 

modules/diamond/blastx/main.nf

@@ -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//'`
 

modules/dshbio/exportsegments/main.nf

@@ -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 \\

modules/dshbio/filterbed/main.nf

@@ -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 \\

modules/dshbio/filtergff3/main.nf

@@ -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 \\

modules/dshbio/splitbed/main.nf

@@ -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 \\

modules/dshbio/splitgff3/main.nf

@@ -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 \\

modules/ectyper/main.nf

@@ -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", "")
     """

modules/emmtyper/main.nf

@@ -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 \\

modules/ensemblvep/main.nf

@@ -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

modules/expansionhunter/main.nf

@@ -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 \\

modules/fastani/main.nf

@@ -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) {
         """

modules/fastp/main.nf

@@ -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" : ''
         """

modules/fastqc/main.nf

@@ -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

modules/fastqscan/main.nf

@@ -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 \\

modules/fgbio/callmolecularconsensusreads/main.nf

@@ -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 \\

modules/fgbio/fastqtobam/main.nf

@@ -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
 

modules/fgbio/groupreadsbyumi/main.nf

@@ -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

modules/fgbio/sortbam/main.nf

@@ -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 \\

modules/filtlong/main.nf

@@ -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 \\

modules/flash/main.nf

@@ -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 \\

modules/freebayes/main.nf

@@ -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}"         : ""

modules/gatk4/applybqsr/main.nf

@@ -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.'

modules/gatk4/baserecalibrator/main.nf

@@ -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(' ')
 

modules/gatk4/bedtointervallist/main.nf

@@ -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 \\

modules/gatk4/calculatecontamination/main.nf

@@ -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" : ''
     """

modules/gatk4/createsomaticpanelofnormals/main.nf

@@ -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 \\

modules/gatk4/estimatelibrarycomplexity/main.nf

@@ -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

modules/gatk4/fastqtosam/main.nf

@@ -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 \\

modules/gatk4/filtermutectcalls/main.nf

@@ -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) {

modules/gatk4/genotypegvcfs/main.nf

@@ -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"

modules/gatk4/getpileupsummaries/main.nf

@@ -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} "

modules/gatk4/haplotypecaller/main.nf

@@ -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

modules/gatk4/intervallisttools/main.nf

@@ -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

modules/gatk4/learnreadorientationmodel/main.nf

@@ -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) }
     """

modules/gatk4/markduplicates/main.nf

@@ -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) {

modules/gatk4/mergebamalignment/main.nf

@@ -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 \\

modules/gatk4/mergevcfs/main.nf

@@ -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 = ""