Minor tweaks

.gitattributes

@@ -1 +1 @@
-*.nf linguist-language=Groovy
+*.config linguist-language=nextflow

.travis.yml

@@ -4,6 +4,8 @@ language: java
 
 jdk: openjdk8
 
+node_js: "node"
+
 services:
   - docker
 
@@ -25,9 +27,10 @@ env:
 install: # Install Nextflow (and Singularity if needed)
   - "./scripts/install.sh --tool $TOOL_INSTALL"
   - "travis_retry ./scripts/containers.sh --profile $PROFILE --test $TEST"
+  - "npm install -g gnomon"
 
 before_script: # Build references when needed
-  - "./scripts/test.sh --profile $PROFILE --test $TEST --build"
+  - "./scripts/test.sh --profile $PROFILE --test $TEST --build | gnomon --medium 120.0 --high 600.0 --real-time=false"
 
 script:
-  - "./scripts/test.sh --profile $PROFILE --test $TEST"
+  - "./scripts/test.sh --profile $PROFILE --test $TEST | gnomon --medium 120.0 --high 600.0 --real-time=false"

annotate.nf

@@ -1,8 +1,6 @@
 #!/usr/bin/env nextflow
 
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
 kate: syntax groovy; space-indent on; indent-width 2;
 ================================================================================
 =                                 S  A  R  E  K                                =
@@ -301,9 +299,9 @@ def minimalInformationMessage() {
   if (tools) log.info "Tools       : " + tools.join(', ')
   if (annotateTools) log.info "Annotate on : " + annotateTools.join(', ')
   if (annotateVCF) log.info "VCF files   : " +annotateVCF.join(',\n    ')
-  log.info "Containers  :"
-  if (params.repository) log.info "  Repository   : ${params.repository}"
-  else log.info "  ContainerPath: " + params.containerPath
+  log.info "Containers"
+  if (params.repository != "") log.info "  Repository   : " + params.repository
+  if (params.containerPath != "") log.info "  ContainerPath: " + params.containerPath
   log.info "  Tag          : " + params.tag
   log.info "Reference files used:"
   log.info "  snpeffDb    :\n\t" + params.genomes[params.genome].snpeffDb

buildContainers.nf

@@ -1,8 +1,6 @@
 #!/usr/bin/env nextflow
 
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
 kate: syntax groovy; space-indent on; indent-width 2;
 ================================================================================
 =                                 S  A  R  E  K                                =
@@ -234,9 +232,9 @@ def minimalInformationMessage() {
   log.info "Project Dir : " + workflow.projectDir
   log.info "Launch Dir  : " + workflow.launchDir
   log.info "Work Dir    : " + workflow.workDir
-  log.info "Containers  :"
-  if (params.repository) log.info "  Repository   : ${params.repository}"
-  else log.info "  ContainerPath: " + params.containerPath
+  log.info "Containers"
+  if (params.repository != "") log.info "  Repository   : " + params.repository
+  if (params.containerPath != "") log.info "  ContainerPath: " + params.containerPath
   log.info "  Tag          : " + params.tag
 }
 

buildReferences.nf

@@ -1,8 +1,6 @@
 #!/usr/bin/env nextflow
 
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
 kate: syntax groovy; space-indent on; indent-width 2;
 ================================================================================
 =                                 S  A  R  E  K                                =
@@ -321,8 +319,8 @@ def minimalInformationMessage() {
   log.info "Out Dir     : " + params.outDir
   log.info "Genome      : " + params.genome
   log.info "Containers"
-  if (params.repository) log.info "  Repository   :" + params.repository
-  else log.info "  ContainerPath: " + params.containerPath
+  if (params.repository != "") log.info "  Repository   : " + params.repository
+  if (params.containerPath != "") log.info "  ContainerPath: " + params.containerPath
   log.info "  Tag          : " + params.tag
 }
 

configuration/aws-batch.config

@@ -1,6 +1,4 @@
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
  * -------------------------------------------------
  *  Nextflow config file for Sarek
  * -------------------------------------------------

configuration/base.config

@@ -1,6 +1,4 @@
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
  * -------------------------------------------------
  * Nextflow config file for Sarek
  * -------------------------------------------------
@@ -15,8 +13,8 @@ params {
   // set up default params
   annotateTools = '' // Tools to annotate by annotate.nf
   annotateVCF = '' // Files to annotate by annotate.nf
-  containerPath = '.' // Path to Singularity images
-  containers = '.' // List of containers to build in buildContainers.nf
+  containerPath = '' // Path to Singularity images
+  containers = '' // List of containers to build in buildContainers.nf
   docker = false // Don't use Docker to build buildContainers.nf
   download = false // Don't download reference files in buildReferences.nf
   explicitBqsrNeeded = true // Enable recalibration in main.nf

configuration/containers.config

@@ -1,6 +1,4 @@
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
  * -------------------------------------------------
  * Nextflow config file for Sarek
  * -------------------------------------------------

configuration/docker.config

@@ -1,6 +1,4 @@
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
  * -------------------------------------------------
  * Nextflow config file for Sarek
  * -------------------------------------------------

configuration/genomes.config

@@ -1,6 +1,4 @@
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
  * -------------------------------------------------
  * Nextflow config file for Sarek
  * -------------------------------------------------

configuration/singularity-path.config

@@ -1,6 +1,4 @@
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
  * -------------------------------------------------
  * Nextflow config file for Sarek
  * -------------------------------------------------

configuration/singularity.config

@@ -1,6 +1,4 @@
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
  * -------------------------------------------------
  * Nextflow config file for Sarek
  * -------------------------------------------------

configuration/travis.config

@@ -1,6 +1,4 @@
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
  * -------------------------------------------------
  * Nextflow config file for Sarek
  * -------------------------------------------------

configuration/uppmax-localhost.config

@@ -1,6 +1,4 @@
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
  * -------------------------------------------------
  * Nextflow config file for Sarek
  * -------------------------------------------------

configuration/uppmax-slurm.config

@@ -1,6 +1,4 @@
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
  * -------------------------------------------------
  * Nextflow config file for Sarek
  * -------------------------------------------------

germlineVC.nf

@@ -1,8 +1,6 @@
 #!/usr/bin/env nextflow
 
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
 kate: syntax groovy; space-indent on; indent-width 2;
 ================================================================================
 =                                 S  A  R  E  K                                =
@@ -155,7 +153,7 @@ process RunBamQC {
     set idPatient, status, idSample, file(bam), file(bai) from bamForBamQC
 
   output:
-    file("${idSample}") into bamQCreport
+    file(idSample) into bamQCreport
 
   when: !params.noReports && !params.noBAMQC
 
@@ -772,14 +770,13 @@ def minimalInformationMessage() {
   log.info "Launch Dir  : " + workflow.launchDir
   log.info "Work Dir    : " + workflow.workDir
   log.info "Out Dir     : " + params.outDir
-  log.info "TSV file    : ${tsvFile}"
+  log.info "TSV file    : " + tsvFile
   log.info "Genome      : " + params.genome
   log.info "Genome_base : " + params.genome_base
   log.info "Tools       : " + tools.join(', ')
-  log.info "Containers  :"
-  if (params.repository) log.info "  Repository   : ${params.repository}"
-  else log.info "  ContainerPath: " + params.containerPath
-  log.info "  Tag          : " + params.tag
+  log.info "Containers"
+  if (params.repository != "") log.info "  Repository   : " + params.repository
+  if (params.containerPath != "") log.info "  ContainerPath: " + params.containerPath
   log.info "Reference files used:"
   log.info "  dbsnp       :\n\t" + referenceMap.dbsnp
   log.info "\t" + referenceMap.dbsnpIndex

main.nf

@@ -1,8 +1,6 @@
 #!/usr/bin/env nextflow
 
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
 kate: syntax groovy; space-indent on; indent-width 2;
 ================================================================================
 =                                 S  A  R  E  K                                =
@@ -277,7 +275,7 @@ markDuplicatesTSV.map { idPatient, status, idSample, bam, bai ->
   gender = patientGenders[idPatient]
   "${idPatient}\t${gender}\t${status}\t${idSample}\t${directoryMap.nonRealigned}/${bam}\t${directoryMap.nonRealigned}/${bai}\n"
 }.collectFile(
-  name: 'nonRealigned.tsv', sort: true, storeDir: "${directoryMap.nonRealigned}"
+  name: 'nonRealigned.tsv', sort: true, storeDir: directoryMap.nonRealigned
 )
 
 // Create intervals for realignement using both tumor+normal as input
@@ -573,7 +571,7 @@ process RunBamQC {
     set idPatient, status, idSample, file(bam), file(bai) from bamForBamQC
 
   output:
-    file("${idSample}") into bamQCreport
+    file(idSample) into bamQCreport
 
   when: !params.noReports && !params.noBAMQC
 
@@ -884,9 +882,9 @@ def minimalInformationMessage() {
   log.info "Genome      : " + params.genome
   log.info "Genome_base : " + params.genome_base
   log.info "Step        : " + step
-  log.info "Containers  :"
-  if (params.repository) log.info "  Repository   : ${params.repository}"
-  else log.info "  ContainerPath: " + params.containerPath
+  log.info "Containers"
+  if (params.repository != "") log.info "  Repository   : " + params.repository
+  if (params.containerPath != "") log.info "  ContainerPath: " + params.containerPath
   log.info "  Tag          : " + params.tag
   log.info "Reference files used:"
   log.info "  dbsnp       :\n\t" + referenceMap.dbsnp

nextflow.config

@@ -1,6 +1,4 @@
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
  * -------------------------------------------------
  * Nextflow config file for Sarek
  * -------------------------------------------------

runMultiQC.nf

@@ -1,8 +1,6 @@
 #!/usr/bin/env nextflow
 
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
 kate: syntax groovy; space-indent on; indent-width 2;
 ================================================================================
 =                                 S  A  R  E  K                                =
@@ -181,9 +179,9 @@ def minimalInformationMessage() {
   log.info "Out Dir     : " + params.outDir
   log.info "Genome      : " + params.genome
   log.info "Genome_base : " + params.genome_base
-  log.info "Containers  :"
-  if (params.repository) log.info "  Repository   : ${params.repository}"
-  else log.info "  ContainerPath: " + params.containerPath
+  log.info "Containers"
+  if (params.repository != "") log.info "  Repository   : " + params.repository
+  if (params.containerPath != "") log.info "  ContainerPath: " + params.containerPath
   log.info "  Tag          : " + params.tag
 }
 

somaticVC.nf

@@ -1,8 +1,6 @@
 #!/usr/bin/env nextflow
 
 /*
-vim: syntax=groovy
--*- mode: groovy;-*-
 kate: syntax groovy; space-indent on; indent-width 2;
 ================================================================================
 =                                 S  A  R  E  K                                =
@@ -160,7 +158,7 @@ process RunBamQC {
     set idPatient, status, idSample, file(bam), file(bai) from bamForBamQC
 
   output:
-    file("${idSample}") into bamQCreport
+    file(idSample) into bamQCreport
 
   when: !params.noReports && !params.noBAMQC
 
@@ -1021,13 +1019,13 @@ def minimalInformationMessage() {
   log.info "Launch Dir  : " + workflow.launchDir
   log.info "Work Dir    : " + workflow.workDir
   log.info "Out Dir     : " + params.outDir
-  log.info "TSV file    : ${tsvFile}"
+  log.info "TSV file    : " + tsvFile
   log.info "Genome      : " + params.genome
   log.info "Genome_base : " + params.genome_base
   log.info "Tools       : " + tools.join(', ')
-  log.info "Containers  :"
-  if (params.repository) log.info "  Repository   : ${params.repository}"
-  else log.info "  ContainerPath: " + params.containerPath
+  log.info "Containers"
+  if (params.repository != "") log.info "  Repository   : " + params.repository
+  if (params.containerPath != "") log.info "  ContainerPath: " + params.containerPath
   log.info "  Tag          : " + params.tag
   log.info "Reference files used:"
   log.info "  acLoci      :\n\t" + referenceMap.acLoci