Merge pull request oicr-gsi#5 from jts/1.6-dev

1.6 dev

conf/base.config

@@ -28,6 +28,9 @@ params{
     // Scheme version
     schemeVersion = 'V3'
 
+    // For ivar's amplicon filter
+    primer_pairs_tsv = false
+
     // Run experimental medaka pipeline? Specify in the command using "--medaka"
     medaka = false
 
@@ -36,18 +39,11 @@ params{
 
     // Run nanopolish pipeline
     nanopolish = false
-
-    // Upload data to CLIMB?
-    upload = false
-
-    // CLIMB username
-    CLIMBUser = false
-
-    // CLIMB SSH pubkey
-    CLIMBkey = false
-
-    // CLIMB hostname
-    CLIMBHostname = false
 }
 
+executor {
+    name   = 'local'
+    cpus   = 20
+    memory = '16GB'
+}
 

environments/illumina/environment.yml

@@ -10,5 +10,5 @@ dependencies:
   - bwa=0.7.17=pl5.22.0_2
   - samtools=1.10
   - trim-galore=0.6.5
-  - ivar=1.2.3
+  - ivar=1.3
   - pysam=0.16.0.1

modules/illumina.nf

@@ -126,7 +126,7 @@ process trimPrimerSequences {
         """
         samtools view -F4 -o ${sampleName}.mapped.bam ${bam}
         samtools index ${sampleName}.mapped.bam
-        ${ivarCmd} -i ${sampleName}.mapped.bam -b ${bedfile} -m ${params.illuminaKeepLen} -q ${params.illuminaQualThreshold} -p ivar.out
+        ${ivarCmd} -i ${sampleName}.mapped.bam -b ${bedfile} -m ${params.illuminaKeepLen} -q ${params.illuminaQualThreshold} -f ${params.primer_pairs_tsv} -p ivar.out
         samtools sort -o ${sampleName}.mapped.primertrimmed.sorted.bam ivar.out.bam
         """
 }

modules/upload.nf

@@ -31,18 +31,3 @@ process prepareUploadDirectory {
     """
 }
 
-
-process uploadToCLIMB {
-    tag { params.prefix }
-
-    input:
-    tuple(path(sshkey), path(uploadDir))
-
-    output:
-
-    script:
-    """
-    rsync -Lav -e "ssh -i ${sshkey} -l ${params.CLIMBUser}" ${uploadDir} ${params.CLIMBHostname}:upload/
-    """
-}
-

workflows/articNcovNanopore.nf

@@ -17,11 +17,6 @@ include {bamToCram} from '../modules/out.nf'
 
 include {collateSamples} from '../modules/upload.nf'
 
-
-// import subworkflows
-include {CLIMBrsync} from './upload.nf'
-
-
 // workflow component for artic pipeline
 workflow sequenceAnalysisNanopolish {
     take:
@@ -127,13 +122,4 @@ workflow articNcovNanopore {
       } else if ( params.medaka ) {
           sequenceAnalysisMedaka(ch_fastqDirs)
       }
-
-      if ( params.upload ) {
-
-        Channel.fromPath("${params.CLIMBkey}")
-               .set{ ch_CLIMBkey }
-
-        CLIMBrsync(sequenceAnalysis.out.qc_pass, ch_CLIMBkey )
-      }
 }
-

workflows/illuminaNcov.nf

@@ -22,10 +22,6 @@ include {bamToCram} from '../modules/out.nf'
 
 include {collateSamples} from '../modules/upload.nf'
 
-// import subworkflows
-include {CLIMBrsync} from './upload.nf'
-
-
 workflow prepareReferenceFiles {
     // Get reference fasta
     if (params.ref) {
@@ -142,16 +138,6 @@ workflow ncovIllumina {
 
       // Actually do analysis
       sequenceAnalysis(performHostFilter.out, prepareReferenceFiles.out.bwaindex, prepareReferenceFiles.out.bedfile)
-
-      // Upload files to CLIMB
-      if ( params.upload ) {
-
-        Channel.fromPath("${params.CLIMBkey}")
-               .set{ ch_CLIMBkey }
-
-        CLIMBrsync(sequenceAnalysis.out.qc_pass, ch_CLIMBkey )
-      }
-
 }
 
 workflow ncovIlluminaCram {