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Fix dsl2 syntax errors #128

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Fix dsl2 syntax errors #128

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c501e8b
Merge pull request #1 from connor-lab/master
rdeborja Jun 1, 2020
05bfe78
Merge pull request #2 from connor-lab/master
rdeborja Jun 22, 2020
2f8f3ce
Merge pull request #3 from connor-lab/master
rdeborja Jun 29, 2020
ca18263
Merge pull request #4 from connor-lab/master
rdeborja Jul 14, 2020
fb97ff5
Merge pull request #5 from connor-lab/master
rdeborja Sep 14, 2020
dca34bd
Merge pull request #6 from connor-lab/master
rdeborja Sep 17, 2020
275955c
Merge branch 'connor-lab:master' into master
rdeborja Oct 14, 2022
525a52d
added dsl2 fixes including syntax updates
Oct 17, 2022
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2 changes: 1 addition & 1 deletion main.nf
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
#!/usr/bin/env nextflow

// enable dsl2
nextflow.preview.dsl = 2
nextflow.enable.dsl=2

// include modules
include {printHelp} from './modules/help.nf'
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20 changes: 10 additions & 10 deletions modules/artic.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -54,10 +54,10 @@ 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("${sampleName}.consensus.fasta"), emit: consensus_fasta
tuple sampleName, file("${sampleName}.pass.vcf.gz"), emit: vcf
tuple val(sampleName), file("${sampleName}.primertrimmed.rg.sorted.bam"), emit: ptrim
tuple val(sampleName), file("${sampleName}.sorted.bam"), emit: mapped
tuple val(sampleName), file("${sampleName}.consensus.fasta"), emit: consensus_fasta
tuple val(sampleName), file("${sampleName}.pass.vcf.gz"), emit: vcf

script:
// Make an identifier from the fastq filename
Expand Down Expand Up @@ -102,10 +102,10 @@ 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("${sampleName}.consensus.fasta"), emit: consensus_fasta
tuple sampleName, file("${sampleName}.pass.vcf.gz"), emit: vcf
tuple val(sampleName), file("${sampleName}.primertrimmed.rg.sorted.bam"), emit: ptrim
tuple val(sampleName), file("${sampleName}.sorted.bam"), emit: mapped
tuple val(sampleName), file("${sampleName}.consensus.fasta"), emit: consensus_fasta
tuple val(sampleName), file("${sampleName}.pass.vcf.gz"), emit: vcf

script:
// Make an identifier from the fastq filename
Expand Down Expand Up @@ -144,10 +144,10 @@ 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:
"""
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30 changes: 15 additions & 15 deletions modules/illumina.nf
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Original file line number Diff line number Diff line change
@@ -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 }
Expand All @@ -12,10 +12,10 @@ process readTrimming {
cpus 2

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:
"""
Expand Down Expand Up @@ -62,10 +62,10 @@ 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:
"""
Expand All @@ -82,11 +82,11 @@ 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){
Expand Down Expand Up @@ -128,10 +128,10 @@ 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("${sampleName}.variants.tsv"), emit: variants
tuple val(sampleName), path("${sampleName}.variants.tsv"), emit: variants

script:
"""
Expand All @@ -147,10 +147,10 @@ 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:
"""
Expand All @@ -169,10 +169,10 @@ 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:
"""
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6 changes: 3 additions & 3 deletions modules/out.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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:
"""
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2 changes: 1 addition & 1 deletion modules/qc.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ 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
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2 changes: 1 addition & 1 deletion modules/upload.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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}")
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2 changes: 1 addition & 1 deletion workflows/articNcovNanopore.nf
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Original file line number Diff line number Diff line change
@@ -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'
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2 changes: 1 addition & 1 deletion workflows/illuminaNcov.nf
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Original file line number Diff line number Diff line change
@@ -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'
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