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maxulyssemaxulysse
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Merge remote-tracking branch 'upstream/master' into MinorTweaks
2 parents d38420e + a57b5d4 commit 9f59f08

20 files changed

Lines changed: 34 additions & 68 deletions

‎.gitattributes‎

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

‎.travis.yml‎

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

‎annotate.nf‎

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

‎buildContainers.nf‎

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

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

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/*
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vim: syntax=groovy
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-*- mode: groovy;-*-
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* -------------------------------------------------
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* Nextflow config file for Sarek
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* -------------------------------------------------

‎configuration/base.config‎

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

‎configuration/containers.config‎

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/*
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vim: syntax=groovy
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-*- mode: groovy;-*-
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* -------------------------------------------------
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* Nextflow config file for Sarek
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* -------------------------------------------------

‎configuration/docker.config‎

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/*
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vim: syntax=groovy
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-*- mode: groovy;-*-
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* -------------------------------------------------
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* Nextflow config file for Sarek
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* -------------------------------------------------

‎configuration/genomes.config‎

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/*
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vim: syntax=groovy
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-*- mode: groovy;-*-
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* -------------------------------------------------
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* Nextflow config file for Sarek
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* -------------------------------------------------

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