Merge pull request #662 from SciLifeLab/dev

maxulysse · web-flow · commit 35e7f70682ed · 2018-10-04T11:36:11.000+02:00
Prepare Release 2.2.1
diff --git a/.github/RELEASE_CHECKLIST.md b/.github/RELEASE_CHECKLIST.md
@@ -26,9 +26,11 @@
 7.  Push latest updates
 8.  Make a PR against `dev`
 9.  Merge said PR
-10. Make a [release](https://github.com/SciLifeLab/Sarek/releases) on GitHub
-11. Update [bio.tools](https://bio.tools/Sarek) with the new release details
-12. Tweet that a new version is released
-13. Add a new `Unreleased` section in `CHANGELOG.md` for the `dev` version
-14. Commit and push. Continue making more awesome :metal:
-15. Have fika :cake:
+10.  Make a PR from `dev` to `master`
+11.  Merge said PR
+12. Make a [release](https://github.com/SciLifeLab/Sarek/releases) on GitHub
+13. Update [bio.tools](https://bio.tools/Sarek) with the new release details
+14. Tweet that a new version is released
+15. Add a new `Unreleased` section in `CHANGELOG.md` for the `dev` version
+16. Commit and push. Continue making more awesome :metal:
+17. Have fika :cake:
diff --git a/.travis.yml b/.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"
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,7 +5,18 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
-## [Unreleased]
+## [2.2.1] - 2018-10-04
+
+### `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
 
diff --git a/Dockerfile b/Dockerfile
@@ -7,4 +7,4 @@ LABEL \
 
 COPY environment.yml /
 RUN conda env create -f /environment.yml && conda clean -a
-ENV PATH /opt/conda/envs/sarek-2.2.0/bin:$PATH
+ENV PATH /opt/conda/envs/sarek-2.2.1/bin:$PATH
diff --git a/README.md b/README.md
@@ -133,7 +133,7 @@ Helpful contributors:
 [license-badge]: https://img.shields.io/github/license/SciLifeLab/Sarek.svg
 [license-link]: https://github.com/SciLifeLab/Sarek/blob/master/LICENSE
 [nbis-link]: https://www.nbis.se/
-[nextflow-badge]: https://img.shields.io/badge/nextflow-%E2%89%A50.31.0-brightgreen.svg?logo=data:image/svg+xml;base64,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
+[nextflow-badge]: https://img.shields.io/badge/nextflow-%E2%89%A50.32.0-brightgreen.svg?logo=data:image/svg+xml;base64,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
 [nextflow-link]: https://www.nextflow.io/
 [ngi-link]: https://ngisweden.scilifelab.se/
 [scilifelab-link]: https://www.scilifelab.se/
diff --git a/Singularity b/Singularity
@@ -7,7 +7,7 @@ Bootstrap:docker
     VERSION 2.1.0
 
 %environment
-    PATH=/opt/conda/envs/sarek-2.2.0/bin:$PATH
+    PATH=/opt/conda/envs/sarek-2.2.1/bin:$PATH
     export PATH
 
 %files
diff --git a/annotate.nf b/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() {
diff --git a/bin/pathfindr b/bin/pathfindr
@@ -1 +1 @@
-Subproject commit e94a98df05e24ef0ea1e9676e46fc013a2990840
+Subproject commit 311cd21c7ff297aeaced9b0e1acd098a0ea9cba8
diff --git a/buildContainers.nf b/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() {
diff --git a/buildReferences.nf b/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() {
diff --git a/conf/base.config b/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 {
diff --git a/docs/INSTALL_BIANCA.md b/docs/INSTALL_BIANCA.md
@@ -12,21 +12,13 @@ For more information about using Singularity with UPPMAX, follow the [Singularit
 > ssh -AX [USER]@rackham.uppmax.uu.se
 # Or just open a terminal
 
-# create directories
-> mkdir nextflow_install
-> cd nextflow_install
+# Download the all Nextflow bundle
+> wget https://github.com/nextflow-io/nextflow/releases/download/v[xx.yy.zz]/nextflow-[xx.yy.zz]-all
 
-# Install Nextflow
-> curl -s https://get.nextflow.io | bash
-> cd ..
-
-# Archive Nextflow
-> tar czvf nextflow_v[xx.yy.zz].tgz .nextflow nextflow_install/nextflow
-
-# Send the tar to bianca (here using sftp)
+# Send to bianca (here using sftp)
 # For FileZilla follow the bianca user guide
 > sftp [USER]-[PROJECT]@bianca-sftp.uppmax.uu.se:[USER]-[PROJECT]
-> put nextflow_v[xx.yy.zz].tgz
+> put nextflow-[xx.yy.zz]-all
 
 # Exit sftp
 > exit
@@ -37,37 +29,28 @@ For more information about using Singularity with UPPMAX, follow the [Singularit
 # Go to your project
 > cd /castor/project/proj_nobackup
 
-# Make and go into a Nextflow directoy
+# Make directory for Nextflow
 > mkdir tools
 > mkdir tools/nextflow
-> cd tools/nextflow
-
-# Copy the tar from wharf to the project
-> cp /castor/project/proj_nobackup/wharf/[USER]/[USER]-[PROJECT]/nextflow_v[xx.yy.zz].tgz /castor/project/proj_nobackup/tools/nextflow
-
-# extract Nextflow
-> tar xzvf nextflow_v[xx.yy.zz].tgz
 
-# Move files
-> mv .nextflow nextflow_v[xx.yy.zz]
-> mv nextflow_install nextflow_v[xx.yy.zz]/bin
+# Move Nextflow from wharf to its directory
+> mv /castor/project/proj_nobackup/wharf/[USER]/[USER]-[PROJECT]/nextflow-[xx.yy.zz]-all /castor/project/proj_nobackup/tools/nextflow
 
-# Establish permission for some files
-> chmod 755 nextflow_v[xx.yy.zz]/bin/nextflow
-> chmod 660 nextflow_v[xx.yy.zz]/framework/[xx.yy.zz]/nextflow-[xx.yy.zz]-one.jar
+# Establish permission
+> chmod a+x /castor/project/proj_nobackup/tools/nextflow/nextflow-[xx.yy.zz]-all
 
 # If you want other people to use it
 # Be sure that your group has rights to the directory as well
 
-> chown -R .[PROJECT] nextflow_v[xx.yy.zz]
+> chown -R .[PROJECT] /castor/project/proj_nobackup/tools/nextflow/nextflow-[xx.yy.zz]-all
 
-# Clean directory
-> rm nextflow_v[xx.yy.zz].tgz
+# Make a link to it
+> ln -s /castor/project/proj_nobackup/tools/nextflow/nextflow-[xx.yy.zz]-all /castor/project/proj_nobackup/tools/nextflow/nextflow
 
 # And everytime you're launching Nextflow, don't forget to export the following ENV variables
 # Or add them to your .bashrc file
-> export NXF_HOME=/castor/project/proj/nobackup/tools/nextflow/nextflow_v[xx.yy.zz]
-> export PATH=${NXF_HOME}/bin:${PATH}
+> export NXF_HOME=/castor/project/proj/nobackup/tools/nextflow/
+> export PATH=${NXF_HOME}:${PATH}
 > export NXF_TEMP=$SNIC_TMP
 > export NXF_LAUNCHER=$SNIC_TMP
 ```
diff --git a/environment.yml b/environment.yml
@@ -1,6 +1,6 @@
 # You can use this file to create a conda environment for this pipeline:
 # conda env create -f environment.yml
-name: sarek-2.2.0
+name: sarek-2.2.1
 channels:
   - conda-forge
   - bioconda
diff --git a/germlineVC.nf b/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() {
diff --git a/lib/SarekUtils.groovy b/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"
diff --git a/main.nf b/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() {
diff --git a/nextflow.config b/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 = '2.2.1'
 }
 
 env {
diff --git a/runMultiQC.nf b/runMultiQC.nf
diff --git a/scripts/do_release.sh b/scripts/do_release.sh
diff --git a/scripts/install.sh b/scripts/install.sh
diff --git a/somaticVC.nf b/somaticVC.nf

Original file line number	Diff line number	Diff line change
`@@ -372,7 +372,7 @@ def nextflowMessage() {`
`372`	`372`
`373`	`373`	`def sarekMessage() {`
`374`	`374`	`// Display Sarek message`
`375`		`- log.info "Sarek - Workflow For Somatic And Germline Variations ~ ${params.version} - " + this.grabRevision() + (workflow.commitId ? " [${workflow.commitId}]" : "")`
	`375`	`+ log.info "Sarek - Workflow For Somatic And Germline Variations ~ ${workflow.manifest.version} - " + this.grabRevision() + (workflow.commitId ? " [${workflow.commitId}]" : "")`
`376`	`376`	`}`
`377`	`377`
`378`	`378`	`def startMessage() {`
Original file line number	Diff line number	Diff line change
`@@ -200,7 +200,7 @@ def helpMessage() {`
`200`	`200`	`log.info " --containerPath: Select where to download images"`
`201`	`201`	`log.info " Default: \$PWD"`
`202`	`202`	log.info " --tag`: Choose the tag for the containers"
`203`		`- log.info " Default (version number): " + params.version`
	`203`	`+ log.info " Default (version number): " + workflow.manifest.version`
`204`	`204`	`}`
`205`	`205`
`206`	`206`	`def minimalInformationMessage() {`
`@@ -222,7 +222,7 @@ def nextflowMessage() {`
`222`	`222`
`223`	`223`	`def sarekMessage() {`
`224`	`224`	`// Display Sarek message`
`225`		`- log.info "Sarek ~ ${params.version} - " + this.grabRevision() + (workflow.commitId ? " [${workflow.commitId}]" : "")`
	`225`	`+ log.info "Sarek ~ ${workflow.manifest.version} - " + this.grabRevision() + (workflow.commitId ? " [${workflow.commitId}]" : "")`
`226`	`226`	`}`
`227`	`227`
`228`	`228`	`def startMessage() {`
Original file line number	Diff line number	Diff line change
`@@ -274,7 +274,7 @@ def nextflowMessage() {`
`274`	`274`
`275`	`275`	`def sarekMessage() {`
`276`	`276`	`// Display Sarek message`
`277`		`- log.info "Sarek - Workflow For Somatic And Germline Variations ~ ${params.version} - " + this.grabRevision() + (workflow.commitId ? " [${workflow.commitId}]" : "")`
	`277`	`+ log.info "Sarek - Workflow For Somatic And Germline Variations ~ ${workflow.manifest.version} - " + this.grabRevision() + (workflow.commitId ? " [${workflow.commitId}]" : "")`
`278`	`278`	`}`
`279`	`279`
`280`	`280`	`def startMessage() {`