Merge pull request #1 from jts/fix_dsl2_syntax

updated code to support nextflow 22.04.5, fixed dls2 syntax
jts · Oct 25, 2022 · 6ecf07b · 6ecf07b
2 parents b6d4d46 + eb2fa7c
commit 6ecf07b
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Showing 9 changed files with 40 additions and 40 deletions.
diff --git a/main.nf b/main.nf
@@ -1,10 +1,10 @@
 #!/usr/bin/env nextflow
 
 // enable dsl2
-nextflow.preview.dsl = 2
+nextflow.enable.dsl=2
 
 // include modules
-include printHelp from './modules/help.nf'
+include { printHelp } from './modules/help.nf'
 
 // import subworkflows
 include {articNcovNanopore} from './workflows/articNcovNanopore.nf' 

diff --git a/modules/artic.nf b/modules/artic.nf
@@ -54,9 +54,9 @@ process articMinIONMedaka {
     output:
     file("${sampleName}.*")
 
-    tuple sampleName, file("${sampleName}.primertrimmed.rg.sorted.bam"), emit: ptrim
-    tuple sampleName, file("${sampleName}.sorted.bam"), emit: mapped
-    tuple sampleName, file("${sampleName}.consensus.fasta"), emit: consensus_fasta
+    tuple val(sampleName), file("${sampleName}.primertrimmed.rg.sorted.bam"), emit: ptrim
+    tuple val(sampleName), file("${sampleName}.sorted.bam"), emit: mapped
+    tuple val(sampleName), file("${sampleName}.consensus.fasta"), emit: consensus_fasta
 
     script:
     // Make an identifier from the fastq filename
@@ -101,9 +101,9 @@ process articMinIONNanopolish {
     output:
     file("${sampleName}.*")
 
-    tuple sampleName, file("${sampleName}.primertrimmed.rg.sorted.bam"), emit: ptrim
-    tuple sampleName, file("${sampleName}.sorted.bam"), emit: mapped
-    tuple sampleName, file("${sampleName}.consensus.fasta"), emit: consensus_fasta
+    tuple val(sampleName), file("${sampleName}.primertrimmed.rg.sorted.bam"), emit: ptrim
+    tuple val(sampleName), file("${sampleName}.sorted.bam"), emit: mapped
+    tuple val(sampleName), file("${sampleName}.consensus.fasta"), emit: consensus_fasta
 
     script:
     // Make an identifier from the fastq filename
@@ -142,10 +142,10 @@ process articRemoveUnmappedReads {
     cpus 1
 
     input:
-    tuple(sampleName, path(bamfile))
+    tuple(val(sampleName), path(bamfile))
 
     output:
-    tuple( sampleName, file("${sampleName}.mapped.sorted.bam"))
+    tuple( val(sampleName), file("${sampleName}.mapped.sorted.bam"))
 
     script:
     """

diff --git a/modules/illumina.nf b/modules/illumina.nf
@@ -1,8 +1,8 @@
 process readTrimming {
     /**
     * Trims paired fastq using trim_galore (https://github.com/FelixKrueger/TrimGalore)
-    * @input tuple(sampleName, path(forward), path(reverse))
-    * @output trimgalore_out tuple(sampleName, path("*_val_1.fq.gz"), path("*_val_2.fq.gz"))
+    * @input tuple(val(sampleName), path(forward), path(reverse))
+    * @output trimgalore_out tuple(val(sampleName), path("*_val_1.fq.gz"), path("*_val_2.fq.gz"))
     */
 
     tag { sampleName }
@@ -12,10 +12,10 @@ process readTrimming {
     cpus 1
 
     input:
-    tuple(sampleName, path(forward), path(reverse))
+    tuple(val(sampleName), path(forward), path(reverse))
 
     output:
-    tuple(sampleName, path("*_val_1.fq.gz"), path("*_val_2.fq.gz")) optional true
+    tuple(val(sampleName), path("*_val_1.fq.gz"), path("*_val_2.fq.gz")) optional true
 
     script:
     """
@@ -30,8 +30,8 @@ process readTrimming {
 process filterResidualAdapters {
     /**
     * Discard reads that contain residual adapter sequences that indicate trimming may have failed
-    * @input tuple(sampleName, path(forward), path(reverse))
-    * @output untrim_filter_out tuple(sampleName, path("*_val_1.fq.gz"), path("*_val_2.fq.gz"))
+    * @input tuple(val(sampleName), path(forward), path(reverse))
+    * @output untrim_filter_out tuple(val(sampleName), path("*_val_1.fq.gz"), path("*_val_2.fq.gz"))
     */
 
     tag { sampleName }
@@ -41,10 +41,10 @@ process filterResidualAdapters {
     cpus 1
 
     input:
-    tuple(sampleName, path(forward), path(reverse))
+    tuple(val(sampleName), path(forward), path(reverse))
 
     output:
-    tuple(sampleName, path("*1_posttrim_filter.fq.gz"), path("*2_posttrim_filter.fq.gz")) optional true
+    tuple(val(sampleName), path("*1_posttrim_filter.fq.gz"), path("*2_posttrim_filter.fq.gz")) optional true
 
     script:
     """
@@ -91,10 +91,10 @@ process readMapping {
     publishDir "${params.outdir}/${task.process.replaceAll(":","_")}", pattern: "${sampleName}.sorted.bam", mode: 'copy'
 
     input:
-        tuple sampleName, path(forward), path(reverse), path(ref), path("*")
+        tuple val(sampleName), path(forward), path(reverse), path(ref), path("*")
 
     output:
-        tuple(sampleName, path("${sampleName}.sorted.bam"))
+        tuple(val(sampleName), path("${sampleName}.sorted.bam"))
 
     script:
         """
@@ -111,11 +111,11 @@ process trimPrimerSequences {
     publishDir "${params.outdir}/${task.process.replaceAll(":","_")}", pattern: "${sampleName}.mapped.primertrimmed.sorted.bam", mode: 'copy'
 
     input:
-    tuple sampleName, path(bam), path(bedfile)
+    tuple val(sampleName), path(bam), path(bedfile)
 
     output:
-    tuple sampleName, path("${sampleName}.mapped.bam"), emit: mapped
-    tuple sampleName, path("${sampleName}.mapped.primertrimmed.sorted.bam" ), emit: ptrim
+    tuple val(sampleName), path("${sampleName}.mapped.bam"), emit: mapped
+    tuple val(sampleName), path("${sampleName}.mapped.primertrimmed.sorted.bam" ), emit: ptrim
 
     script:
     if (params.allowNoprimer){
@@ -138,10 +138,10 @@ process callVariants {
     publishDir "${params.outdir}/${task.process.replaceAll(":","_")}", pattern: "${sampleName}.variants.tsv", mode: 'copy'
 
     input:
-    tuple(sampleName, path(bam), path(ref))
+    tuple(val(sampleName), path(bam), path(ref))
 
     output:
-    tuple sampleName, path("${sampleName}.variants.tsv")
+    tuple val(sampleName), path("${sampleName}.variants.tsv")
 
     script:
         """
@@ -158,10 +158,10 @@ process makeConsensus {
     publishDir "${params.outdir}/${task.process.replaceAll(":","_")}", pattern: "${sampleName}.primertrimmed.consensus.fa", mode: 'copy'
 
     input:
-        tuple(sampleName, path(bam))
+        tuple(val(sampleName), path(bam))
 
     output:
-        tuple(sampleName, path("${sampleName}.primertrimmed.consensus.fa"))
+        tuple(val(sampleName), path("${sampleName}.primertrimmed.consensus.fa"))
 
     script:
         """
@@ -179,11 +179,11 @@ process callConsensusFreebayes {
     publishDir "${params.outdir}/${task.process.replaceAll(":","_")}", pattern: "${sampleName}.variants.norm.vcf", mode: 'copy'
 
     input:
-    tuple(sampleName, path(bam), path(ref))
+    tuple(val(sampleName), path(bam), path(ref))
 
     output:
-    tuple sampleName, path("${sampleName}.consensus.fasta")
-    tuple sampleName, path("${sampleName}.variants.norm.vcf")
+    tuple val(sampleName), path("${sampleName}.consensus.fasta")
+    tuple val(sampleName), path("${sampleName}.variants.norm.vcf")
 
     script:
         """
@@ -235,10 +235,10 @@ process cramToFastq {
     */
 
     input:
-        tuple sampleName, file(cram)
+        tuple val(sampleName), file(cram)
 
     output:
-        tuple sampleName, path("${sampleName}_1.fastq.gz"), path("${sampleName}_2.fastq.gz")
+        tuple val(sampleName), path("${sampleName}_1.fastq.gz"), path("${sampleName}_2.fastq.gz")
 
     script:
         """

diff --git a/modules/out.nf b/modules/out.nf
@@ -11,11 +11,11 @@ process bamToCram {
     publishDir "${params.outdir}/${task.process.replaceAll(":","_")}", pattern: "${bam.baseName}.cram.crai", mode: 'copy'
 
     input:
-        tuple(sampleName, path(bam), path(ref))
+        tuple(val(sampleName), path(bam), path(ref))
 
     output:
-        tuple sampleName, path("${bam.baseName}.cram"), emit: cramed
-        tuple sampleName, path("${bam.baseName}.cram.crai"), emit: cramedidx
+        tuple val(sampleName), path("${bam.baseName}.cram"), emit: cramed
+        tuple val(sampleName), path("${bam.baseName}.cram.crai"), emit: cramedidx
 
     script:
         """

diff --git a/modules/qc.nf b/modules/qc.nf
@@ -6,7 +6,7 @@ process makeQCCSV {
     publishDir "${params.outdir}/qc_plots", pattern: "${sampleName}.depth.png", mode: 'copy'
 
     input:
-    tuple sampleName, path(bam), path(fasta), path(ref)
+    tuple val(sampleName), path(bam), path(fasta), path(ref)
 
     output:
     path "${params.prefix}.${sampleName}.qc.csv", emit: csv

diff --git a/modules/upload.nf b/modules/upload.nf
@@ -4,7 +4,7 @@ process collateSamples {
     publishDir "${params.outdir}/qc_pass_climb_upload/${params.prefix}", pattern: "${sampleName}", mode: 'copy'
 
     input:
-    tuple(sampleName, path(bam), path(fasta))
+    tuple(val(sampleName), path(bam), path(fasta))
 
     output:
     path("${sampleName}")

diff --git a/modules/utils.nf b/modules/utils.nf
@@ -5,7 +5,7 @@ process performHostFilter {
     input:
         tuple(val(sampleId), path(forward), path(reverse))
     output:
-        tuple sampleId, path("${sampleId}_hostfiltered_R1.fastq.gz"), path("${sampleId}_hostfiltered_R2.fastq.gz"), emit: fastqPairs
+        tuple val(sampleId), path("${sampleId}_hostfiltered_R1.fastq.gz"), path("${sampleId}_hostfiltered_R2.fastq.gz"), emit: fastqPairs
 
     script:
         """

diff --git a/workflows/articNcovNanopore.nf b/workflows/articNcovNanopore.nf
@@ -1,7 +1,7 @@
 // ARTIC ncov workflow
 
 // enable dsl2
-nextflow.preview.dsl = 2
+nextflow.enable.dsl = 2
 
 // import modules
 include {articDownloadScheme} from '../modules/artic.nf' 

diff --git a/workflows/illuminaNcov.nf b/workflows/illuminaNcov.nf
@@ -1,7 +1,7 @@
 #!/usr/bin/env nextflow
 
 // enable dsl2
-nextflow.preview.dsl = 2
+nextflow.enable.dsl = 2
 
 // import modules
 include {articDownloadScheme } from '../modules/artic.nf'