update Nextflow to 0.32.0 and fix bugs

.travis.yml

@@ -9,22 +9,23 @@ addons:
 
 env:
   global:
-    - NXF_VER=0.31.0 SGT_VER=2.5.1
+    - NXF_VER=0.32.0
   matrix:
-    - CE=docker      TEST=SOMATIC
-    - CE=docker      TEST=ANNOTATEVEP
-    - CE=docker      TEST=ANNOTATESNPEFF
-    - CE=docker      TEST=GERMLINE
-
+    - TEST=SOMATIC
+    - TEST=ANNOTATEVEP
+    - TEST=ANNOTATESNPEFF
+    - TEST=GERMLINE
 
 install:
-  # Install Nextflow (and Singularity if needed)
-  - "./scripts/install.sh --engine $CE"
+  # Install Nextflow
+  - curl -fsSL get.nextflow.io | bash
+  - chmod +x nextflow
+  - sudo mv nextflow /usr/local/bin/
   # Donwload big containers for ANNOTATEVEP and ANNOTATESNPEF tests)
-  - "travis_retry ./scripts/containers.sh --profile $CE --test $TEST"
+  - "travis_retry ./scripts/containers.sh --profile docker --test $TEST"
 
 # Build references when needed
-before_script: "./scripts/test.sh --profile $CE --test $TEST --build"
+before_script: "./scripts/test.sh --profile docker --test $TEST --build"
 
 # Actual tests
-script: "./scripts/test.sh --profile $CE --test $TEST"
+script: "./scripts/test.sh --profile docker --test $TEST"

CHANGELOG.md

@@ -10,11 +10,13 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ### `Changed`
 
 -   [#646](https://github.com/SciLifeLab/Sarek/pull/646) - Update [`pathfindr`](https://github.com/NBISweden/pathfindr) submodule
+-   [#659](https://github.com/SciLifeLab/Sarek/pull/659) - Update Nextflow to `0.32.0`
 -   [#660](https://github.com/SciLifeLab/Sarek/pull/660) - Update docs
 
 ### `Fixed`
 
 -   [#657](https://github.com/SciLifeLab/Sarek/pull/657) - Fix `RunMultiQC.nf` bug
+-   [#659](https://github.com/SciLifeLab/Sarek/pull/659) - Fix bugs due to updating Nextflow
 
 ## [2.2.0] - Skårki - 2018-09-21
 

annotate.nf

@@ -372,7 +372,7 @@ def nextflowMessage() {
 
 def sarekMessage() {
   // Display Sarek message
-  log.info "Sarek - Workflow For Somatic And Germline Variations ~ ${params.version} - " + this.grabRevision() + (workflow.commitId ? " [${workflow.commitId}]" : "")
+  log.info "Sarek - Workflow For Somatic And Germline Variations ~ ${workflow.manifest.version} - " + this.grabRevision() + (workflow.commitId ? " [${workflow.commitId}]" : "")
 }
 
 def startMessage() {

buildContainers.nf

@@ -200,7 +200,7 @@ def helpMessage() {
   log.info "    --containerPath: Select where to download images"
   log.info "       Default: \$PWD"
   log.info "    --tag`: Choose the tag for the containers"
-  log.info "       Default (version number): " + params.version
+  log.info "       Default (version number): " + workflow.manifest.version
 }
 
 def minimalInformationMessage() {
@@ -222,7 +222,7 @@ def nextflowMessage() {
 
 def sarekMessage() {
   // Display Sarek message
-  log.info "Sarek ~ ${params.version} - " + this.grabRevision() + (workflow.commitId ? " [${workflow.commitId}]" : "")
+  log.info "Sarek ~ ${workflow.manifest.version} - " + this.grabRevision() + (workflow.commitId ? " [${workflow.commitId}]" : "")
 }
 
 def startMessage() {

buildReferences.nf

@@ -274,7 +274,7 @@ def nextflowMessage() {
 
 def sarekMessage() {
   // Display Sarek message
-  log.info "Sarek - Workflow For Somatic And Germline Variations ~ ${params.version} - " + this.grabRevision() + (workflow.commitId ? " [${workflow.commitId}]" : "")
+  log.info "Sarek - Workflow For Somatic And Germline Variations ~ ${workflow.manifest.version} - " + this.grabRevision() + (workflow.commitId ? " [${workflow.commitId}]" : "")
 }
 
 def startMessage() {

conf/base.config

@@ -36,7 +36,6 @@ params {
   targetBED = false // no targets by default
   test = false // Not testing by default
   verbose = false // Enable for more verbose information
-  version = '2.2.0' // Workflow version
 }
 
 process {

germlineVC.nf

@@ -223,7 +223,7 @@ process CreateIntervalBeds {
 
 bedIntervals = bedIntervals
   .map { intervalFile ->
-    final duration = 0.0
+    def duration = 0.0
     for (line in intervalFile.readLines()) {
       final fields = line.split('\t')
       if (fields.size() >= 5) duration += fields[4].toFloat()
@@ -673,7 +673,7 @@ def nextflowMessage() {
 
 def sarekMessage() {
   // Display Sarek message
-  log.info "Sarek - Workflow For Somatic And Germline Variations ~ ${params.version} - " + this.grabRevision() + (workflow.commitId ? " [${workflow.commitId}]" : "")
+  log.info "Sarek - Workflow For Somatic And Germline Variations ~ ${workflow.manifest.version} - " + this.grabRevision() + (workflow.commitId ? " [${workflow.commitId}]" : "")
 }
 
 def startMessage() {

lib/SarekUtils.groovy

@@ -114,7 +114,7 @@ class SarekUtils {
     def f = file(fileToCheck)
     // this is an expanded wildcard: we can assume all files exist
     if (f instanceof List && f.size() > 0) return true
-    else if (!f.exists()) { 
+    else if (!f.exists()) {
 			println  "Missing references: ${referenceFile} ${fileToCheck}"
       return false
     }
@@ -184,7 +184,7 @@ class SarekUtils {
 
   // Compare params to list of verified params
   static def isAllowedParams(params) {
-    final test = true
+    def test = true
     params.each{
       if (!checkParams(it.toString().split('=')[0])) {
         println "params ${it.toString().split('=')[0]} is unknown"

main.nf

@@ -454,7 +454,7 @@ def checkUppmaxProject() {
 }
 
 def checkExactlyOne(list) {
-  final n = 0
+  def n = 0
   list.each{n += it ? 1 : 0}
   return n == 1
 }
@@ -668,7 +668,7 @@ def nextflowMessage() {
 
 def sarekMessage() {
   // Display Sarek message
-  log.info "Sarek - Workflow For Somatic And Germline Variations ~ ${params.version} - " + this.grabRevision() + (workflow.commitId ? " [${workflow.commitId}]" : "")
+  log.info "Sarek - Workflow For Somatic And Germline Variations ~ ${workflow.manifest.version} - " + this.grabRevision() + (workflow.commitId ? " [${workflow.commitId}]" : "")
 }
 
 def startMessage() {

nextflow.config

@@ -9,11 +9,13 @@
  */
 
 manifest {
+  author = 'Szilvester Juhos, Maxime Garcia'
   description = 'Sarek - Workflow For Somatic And Germline Variations'
   homePage = 'http://sarek.scilifelab.se'
   mainScript = 'main.nf'
   name = 'Sarek'
-  nextflowVersion = '>=0.31.0'
+  nextflowVersion = '>=0.32.0'
+  version = '2.2.0'
 }
 
 env {

runMultiQC.nf

@@ -63,7 +63,7 @@ process GetVersionAll {
   bwa &> v_bwa.txt 2>&1 || true
   configManta.py --version > v_manta.txt 2>&1 || true
   configureStrelkaGermlineWorkflow.py --version > v_strelka.txt 2>&1 || true
-  echo "${params.version}" &> v_sarek.txt 2>&1 || true
+  echo "${workflow.manifest.version}" &> v_sarek.txt 2>&1 || true
   echo "${workflow.nextflow.version}" &> v_nextflow.txt 2>&1 || true
   fastqc -v > v_fastqc.txt 2>&1 || true
   freebayes --version > v_freebayes.txt 2>&1 || true
@@ -132,7 +132,7 @@ def checkUppmaxProject() {
 def createMultiQCconfig() {
   def file = workDir.resolve('multiqc_config.yaml')
   file.text  = """
-  custom_logo: ${baseDir}/doc/images/Sarek_no_Border.png
+  custom_logo: ${baseDir}/docs/images/Sarek_no_Border.png
   custom_logo_url: http://opensource.scilifelab.se/projects/sarek
   custom_logo_title: 'Sarek'
   report_header_info:
@@ -191,7 +191,7 @@ def nextflowMessage() {
 
 def sarekMessage() {
   // Display Sarek message
-  log.info "Sarek - Workflow For Somatic And Germline Variations ~ ${params.version} - " + this.grabRevision() + (workflow.commitId ? " [${workflow.commitId}]" : "")
+  log.info "Sarek - Workflow For Somatic And Germline Variations ~ ${workflow.manifest.version} - " + this.grabRevision() + (workflow.commitId ? " [${workflow.commitId}]" : "")
 }
 
 def startMessage() {

scripts/do_release.sh

@@ -39,6 +39,6 @@ sed -i "s/\[Unreleased\]/[$RELEASE] - $CODENAME - $(date +'%Y-%m-%d')/g" CHANGEL
 sed -i "s/sarek-[0-9\.]\+/sarek-$RELEASE/g" Dockerfile
 sed -i "s/sarek-[0-9\.]\+/sarek-$RELEASE/g" environment.yml
 sed -i "s/sarek-[0-9\.]\+/sarek-$RELEASE/g" Singularity
-sed -i "s/version = '[0-9\.]\+'/version = '$RELEASE'/g" conf/base.config
+sed -i "s/version = '[0-9\.]\+'/version = '$RELEASE'/g" nextflow.config
 
-git commit CHANGELOG.md Dockerfile environment.yml Singularity conf/base.config -m "preparing release $RELEASE [skip ci]"
+git commit CHANGELOG.md Dockerfile environment.yml Singularity nextflow.config -m "preparing release $RELEASE [skip ci]"

somaticVC.nf

@@ -233,7 +233,7 @@ process CreateIntervalBeds {
 
 bedIntervals = bedIntervals
   .map { intervalFile ->
-    final duration = 0.0
+    def duration = 0.0
     for (line in intervalFile.readLines()) {
       final fields = line.split('\t')
       if (fields.size() >= 5) duration += fields[4].toFloat()
@@ -955,7 +955,7 @@ def returnStatus(it) {
 
 def sarekMessage() {
   // Display Sarek message
-  log.info "Sarek - Workflow For Somatic And Germline Variations ~ ${params.version} - " + this.grabRevision() + (workflow.commitId ? " [${workflow.commitId}]" : "")
+  log.info "Sarek - Workflow For Somatic And Germline Variations ~ ${workflow.manifest.version} - " + this.grabRevision() + (workflow.commitId ? " [${workflow.commitId}]" : "")
 }
 
 def startMessage() {