Update Syntax for Compatibility with Nextflow 23.04.4

conf/illumina.config

@@ -49,7 +49,7 @@ params {
     // iVar frequency threshold to call variant (ivar variants: -t )
     ivarMinFreqThreshold = 0.25
 
-    // iVar minimum mapQ to call variant (ivar variants: -q)
+    // iVar minimum baseQ to call variant (ivar variants: -q)
     ivarMinVariantQuality = 20
 
     // Typing frequency threshold to call aa consequences of variant. Set to ivarFreqThreshold for consistency with consensus

environments/illumina/environment.yml

@@ -4,15 +4,17 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - python=3
+  - python
   - biopython=1.74
   - libxcb
-  - matplotlib=3.3.3
-  - pandas=0.23.0=py36_1
-  - bwa=0.7.17=pl5.22.0_2
-  - samtools=1.10
-  - bcftools=1.10
-  - trim-galore=0.6.5
-  - ivar=1.3
+  - matplotlib=3
+  - pandas=2
+  - bwa=0.7.17
+  - samtools=1.18
+  - bcftools=1.18
+  - trim-galore=0.6.10
+  - ivar=1.4.2
   - pyvcf=0.6.8
-  - pyyaml=5.3.1
+  - pyyaml=6.0.1
+  - freyja=1.4.7
+  - pangolin=4.3

environments/illumina/environment.yml.bak

@@ -0,0 +1,18 @@
+name: artic-ncov2019-illumina
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - python=3
+  - biopython=1.74
+  - libxcb
+  - matplotlib=3.3.3
+  - pandas=0.23.0=py36_1
+  - bwa=0.7.17=pl5.22.0_2
+  - samtools=1.10
+  - bcftools=1.10
+  - trim-galore=0.6.5
+  - ivar=1.3
+  - pyvcf=0.6.8
+  - pyyaml=5.3.1

main.nf

@@ -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'

modules/illumina.nf

@@ -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:
     """
@@ -38,7 +38,7 @@ process indexReference {
         path(ref)
 
     output:
-        tuple path('ref.fa'), path('ref.fa.*')
+        tuple(path('ref.fa'), path('ref.fa.*'))
 
     script:
         """
@@ -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:
       """
@@ -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){
@@ -121,17 +121,36 @@ process trimPrimerSequences {
         """
 }
 
+process getDepths {
+    tag { sampleName }
+
+    publishDir "${params.outdir}/${task.process.replaceAll(":","_")}", pattern: "${sampleName}.depths.tsv", mode: 'copy'
+
+    input:
+    tuple(val(sampleName), path(bam), path(ref))
+
+    output:
+    tuple(val(sampleName), path("${sampleName}.depths.tsv"), emit: depths)
+
+    script:
+        """
+        samtools mpileup -aa -A -d 0 -Q 0 -q ${params.ivarMinVariantQuality} -B -f ${ref} ${bam} | cut -f1-4 > "${sampleName}.depths.tsv"
+        """
+}
 process callVariants {
 
     tag { sampleName }
 
     publishDir "${params.outdir}/${task.process.replaceAll(":","_")}", pattern: "${sampleName}.variants.tsv", mode: 'copy'
 
+    errorStrategy { sleep(Math.pow(2, task.attempt) * 1 as long); return 'retry' }
+    maxRetries 9999999999
+
     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:
         """
@@ -147,10 +166,10 @@ 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"), emit: consensus)
 
     script:
         """
@@ -160,6 +179,46 @@ process makeConsensus {
         """
 }
 
+process callLineage {
+
+    tag { sampleName }
+
+    publishDir "${params.outdir}/${task.process.replaceAll(":","_")}", pattern: "${sampleName}.pangolin.csv", mode: 'copy'
+
+    errorStrategy { sleep(Math.pow(2, task.attempt) * 1 as long); return 'retry' }
+    maxRetries -1
+
+    input:
+        tuple(val(sampleName), path(consensus))
+
+    output:
+        tuple(val(sampleName), path("${sampleName}.pangolin.csv"))
+
+    script:
+        """
+        pangolin ${consensus} -t 1 --outfile ${sampleName}.pangolin.csv --verbose
+        """
+}
+
+process freyjaDemix {
+    tag { sampleName }
+
+    publishDir "${params.outdir}/${task.process.replaceAll(":","_")}", pattern: "${sampleName}.freyja.demix.tsv", mode: 'copy'
+
+    errorStrategy 'ignore'
+
+    input:
+        tuple(val(sampleName), path(variants), path(depths))
+
+    output:
+        tuple(val(sampleName), path("${sampleName}.freyja.demix.tsv"))
+
+    script:
+        """
+        freyja demix ${variants} ${depths} --output ${sampleName}.freyja.demix.tsv
+        """
+}
+
 process cramToFastq {
     /**
     * Converts CRAM to fastq (http://bio-bwa.sourceforge.net/)
@@ -169,10 +228,10 @@ 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:
         """

modules/qc.nf

@@ -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

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}")

workflows/illuminaNcov.nf

@@ -1,16 +1,19 @@
 #!/usr/bin/env nextflow
 
 // enable dsl2
-nextflow.preview.dsl = 2
+nextflow.enable.dsl = 2
 
 // import modules
 include {articDownloadScheme } from '../modules/artic.nf' 
 include {readTrimming} from '../modules/illumina.nf' 
 include {indexReference} from '../modules/illumina.nf'
 include {readMapping} from '../modules/illumina.nf' 
 include {trimPrimerSequences} from '../modules/illumina.nf' 
+include {getDepths} from '../modules/illumina.nf'
 include {callVariants} from '../modules/illumina.nf'
+include {freyjaDemix} from '../modules/illumina.nf'
 include {makeConsensus} from '../modules/illumina.nf' 
+include {callLineage} from '../modules/illumina.nf'
 include {cramToFastq} from '../modules/illumina.nf'
 
 include {makeQCCSV} from '../modules/qc.nf'
@@ -95,8 +98,14 @@ workflow sequenceAnalysis {
 
       callVariants(trimPrimerSequences.out.ptrim.combine(ch_preparedRef.map{ it[0] })) 
 
+      getDepths(trimPrimerSequences.out.ptrim.combine(ch_preparedRef.map{ it[0] }))
+
+      freyjaDemix(callVariants.out.variants.join(getDepths.out.depths))
+
       makeConsensus(trimPrimerSequences.out.ptrim)
 
+      callLineage(makeConsensus.out.consensus)
+
       makeQCCSV(trimPrimerSequences.out.ptrim.join(makeConsensus.out, by: 0)
                                    .combine(ch_preparedRef.map{ it[0] }))