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Merge pull request #25 from IARCbioinfo/dev
deployment added and bugs fixed
2 parents 05bb59c + db4903f commit 972c280

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‎README.md

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@@ -50,5 +50,5 @@ profiles {
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}
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}
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```
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#### pipeline DAG
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<img align="center" src="https://cloud.githubusercontent.com/assets/13535602/22242881/5acb8852-e225-11e6-8954-dc0443729ccc.png" width="600">
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## Directed Acyclic Graph
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[![DAG](dag.png)](http://htmlpreview.github.io/?https://github.com/IARCbioinfo/mutect-nf/blob/dev/dag.html)

‎bin/cut_into_small_beds.r

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@@ -20,6 +20,7 @@ options("scipen"=100)
2020

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nb_pieces=as.numeric(commandArgs(TRUE)[1])
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bed=read.table(pipe('cat /dev/stdin'),stringsAsFactors = F)
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bed[,3]=bed[,3]-1 #do not consider end positions to count number of total bases
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bed_cum_size=cumsum(bed[,3]-bed[,2]+1)
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if(nb_pieces>bed_cum_size[length(bed_cum_size)]) nb_pieces=bed_cum_size[length(bed_cum_size)]
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if(nb_pieces==1) { cat(paste(bed[,1],"\t",bed[,2],"\t",bed[,3], sep=""), sep="\n", file=paste(bed[1,1],"_",bed[1,2],"-",bed[dim(bed)[1],1],"_",bed[dim(bed)[1],3],"_regions.bed",sep="")) } else {
@@ -37,12 +38,14 @@ if(nb_pieces==1) { cat(paste(bed[,1],"\t",bed[,2],"\t",bed[,3], sep=""), sep="\n
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ends=bed[1:cut_data[1,i],3]
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ends[length(ends)]=cut_data[2,i]-1
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if(cut_data[2,i]-1<starts[length(starts)]) { chrs=chrs[1:(length(chrs)-1)];starts=starts[1:(length(starts)-1)];ends=ends[1:(length(ends)-1)] }
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ends=ends+1 #see bed specification
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cat(paste(chrs,"\t",starts,"\t",ends, sep=""), sep="\n", file=paste(chrs[1],"_",starts[1],"-",chrs[length(chrs)],"_",ends[length(ends)],"_regions.bed",sep=""))
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} else if (i==nb_pieces) {
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chrs=bed[cut_data[1,i-1]:dim(bed)[1],1]
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starts=bed[cut_data[1,i-1]:dim(bed)[1],2]
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starts[1]=cut_data[2,i-1]
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ends=bed[cut_data[1,i-1]:dim(bed)[1],3]
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ends=ends+1 #see bed specification
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cat(paste(chrs,"\t",starts,"\t",ends, sep=""), sep="\n", file=paste(chrs[1],"_",starts[1],"-",chrs[length(chrs)],"_",ends[length(ends)],"_regions.bed",sep=""))
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} else {
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chrs=bed[cut_data[1,i-1]:cut_data[1,i],1]
@@ -51,6 +54,7 @@ if(nb_pieces==1) { cat(paste(bed[,1],"\t",bed[,2],"\t",bed[,3], sep=""), sep="\n
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starts[1]=cut_data[2,i-1]
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ends[length(ends)]=cut_data[2,i]-1
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if(cut_data[2,i]-1<starts[length(starts)]){ chrs=chrs[1:(length(chrs)-1)];starts=starts[1:(length(starts)-1)];ends=ends[1:(length(ends)-1)] }
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ends=ends+1 #see bed specification
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cat(paste(chrs,"\t",starts,"\t",ends, sep=""), sep="\n", file=paste(chrs[1],"_",starts[1],"-",chrs[length(chrs)],"_",ends[length(ends)],"_regions.bed",sep=""))
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}
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}

‎circle.yml

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machine:
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services:
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- docker
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post:
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- wget -qO- get.nextflow.io | bash ; chmod 755 nextflow ; sudo ln -s ~/nextflow /usr/local/bin/; sudo apt-get install graphviz
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- wget https://github.com/MaxUlysse/CAW-containers/blob/master/containers/gatk/GenomeAnalysisTK-3.7.tar.bz2?raw=true
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- git clone https://github.com/IARCbioinfo/data_test.git
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- wget https://github.com/broadinstitute/mutect/releases/download/1.1.5/muTect-1.1.5-bin.zip
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- sudo apt-get install bedtools
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- sudo add-apt-repository "deb http://cran.rstudio.com//bin/linux/debian jessie-cran3/"; sudo apt-get install --no-install-recommends -y r-base
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test:
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override:
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- | #Unzip muTect-1 and test it with good java version (1.7)
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cd ~ && unzip muTect-1.1.5-bin.zip && /usr/lib/jvm/jdk1.7.0/bin/java -jar muTect-1.1.5.jar --help
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- | #Rename and untar GATK3.7
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cd ~ && mv GenomeAnalysisTK-3.7.tar.bz2?raw=true GenomeAnalysisTK.jar.tar.bz2 && tar -jxf GenomeAnalysisTK.jar.tar.bz2
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- | #Test GATK3.7
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cd ~ && chmod +x GenomeAnalysisTK.jar && java -jar GenomeAnalysisTK.jar --help
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- | #Launch muTect-1
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nextflow run ~/mutect-nf/mutect.nf --tumor_bam_folder ~/data_test/BAM/test/ --normal_bam_folder ~/data_test/BAM/test/ --bed ~/data_test/BED/TP53_exon2_11.bed --ref ~/data_test/REF/17.fasta --mutect_jar ~/muTect-1.1.5.jar --nsplit 2 --java /usr/lib/jvm/jdk1.7.0/bin/java -with-dag dag.png
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- | #Launch muTect-1(v2)
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nextflow run ~/mutect-nf/mutect.nf --tumor_bam_folder ~/data_test/BAM/test/ --normal_bam_folder ~/data_test/BAM/test/ --bed ~/data_test/BED/TP53_exon2_11.bed --ref ~/data_test/REF/17.fasta --mutect_jar ~/muTect-1.1.5.jar --nsplit 2 --java /usr/lib/jvm/jdk1.7.0/bin/java -with-dag dag.html
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- | #Launch muTect-2
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nextflow run ~/mutect-nf/mutect.nf --tumor_bam_folder ~/data_test/BAM/test/ --normal_bam_folder ~/data_test/BAM/test/ --bed ~/data_test/BED/TP53_exon2_11.bed --ref ~/data_test/REF/17.fasta --mutect2_jar ~/GenomeAnalysisTK.jar --nsplit 2 --out_folder mutect2_results
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- | #Check for results muTect-1
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ls ~/mutect-nf/mutect_results
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- | #Check for results muTect-2
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ls ~/mutect-nf/mutect2_results
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deployment:
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git:
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branch: [master, dev]
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commands:
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- chmod +x deploy.sh && ./deploy.sh

‎dag.html

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<!--
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~ Copyright (c) 2013-2017, Centre for Genomic Regulation (CRG).
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~ Copyright (c) 2013-2017, Paolo Di Tommaso and the respective authors.
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~
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~ This file is part of 'Nextflow'.
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~
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~ Nextflow is free software: you can redistribute it and/or modify
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~ it under the terms of the GNU General Public License as published by
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~ the Free Software Foundation, either version 3 of the License, or
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~ (at your option) any later version.
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~
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~ Nextflow is distributed in the hope that it will be useful,
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~ but WITHOUT ANY WARRANTY; without even the implied warranty of
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~ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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~ GNU General Public License for more details.
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~
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~ You should have received a copy of the GNU General Public License
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~ along with Nextflow. If not, see <http://www.gnu.org/licenses/>.
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-->
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<html>
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<head>
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<title>Nextflow Cytoscape.js with Dagre</title>
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<meta name="viewport" content="width=device-width, user-scalable=no, initial-scale=1, maximum-scale=1">
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<script type="text/javascript">
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var prot = (("https:" == document.location.protocol) ? "https://" : "http://");
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document.write(unescape("%3Cscript src='" + prot + "code.jquery.com/jquery-2.0.3.min.js' type='text/javascript' %3E%3C/script%3E"));
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document.write(unescape("%3Cscript src='" + prot + "cdnjs.cloudflare.com/ajax/libs/cytoscape/2.6.12/cytoscape.min.js' type='text/javascript' %3E%3C/script%3E"));
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document.write(unescape("%3Cscript src='" + prot + "cdn.rawgit.com/cpettitt/dagre/v0.7.4/dist/dagre.min.js' type='text/javascript' %3E%3C/script%3E"));
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document.write(unescape("%3Cscript src='" + prot + "cdn.rawgit.com/cytoscape/cytoscape.js-dagre/1.1.2/cytoscape-dagre.js' type='text/javascript' %3E%3C/script%3E"));
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</script>
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<style>
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body {
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font-family: helvetica;
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font-size: 14px;
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}
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#cy {
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width: 100%;
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height: 100%;
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position: absolute;
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left: 0;
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top: 0;
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z-index: 999;
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}
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h1 {
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opacity: 0.5;
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font-size: 1em;
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}
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</style>
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<script>
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$(function(){
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var cy = window.cy = cytoscape({
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container: document.getElementById('cy'),
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boxSelectionEnabled: false,
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autounselectify: true,
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layout: {
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name: 'dagre'
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},
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style: cytoscape.stylesheet()
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.selector( 'node')
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.css({
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'width': 10,
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'height': 10,
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'content': 'data(label)',
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'text-valign': 'center',
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'text-halign': 'center',
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'text-opacity': 0.5,
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})
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.selector('node.PROCESS')
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.css({
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'width': 100,
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'height': 50,
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'text-opacity': 0.9,
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'background-color': '#009911'
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})
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.selector('node.OPERATOR')
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.css({
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'background-color': '#11479e',
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'text-halign': 'right',
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})
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.selector('node.ORIGIN')
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.css({
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'background-color': '#999999',
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'text-halign': 'right',
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})
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.selector('node.TERMINATION')
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.css({
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'background-color': '#999999',
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'text-halign': 'right',
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})
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.selector('edge')
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.css({
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'content': 'data(label)',
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'text-opacity': 0.5,
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'width': 4,
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'target-arrow-shape': 'triangle',
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'line-color': '#9dbaea',
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'target-arrow-color': '#9dbaea'
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}),
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elements: {
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nodes: [
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{ data: { id: 'p0', label: 'Channel.fromPath'}, classes: 'ORIGIN' },
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{ data: { id: 'p1', label: 'ifEmpty'}, classes: 'OPERATOR' },
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{ data: { id: 'p2', label: 'map'}, classes: 'OPERATOR' },
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{ data: { id: 'p3', label: 'Channel.fromPath'}, classes: 'ORIGIN' },
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{ data: { id: 'p4', label: 'ifEmpty'}, classes: 'OPERATOR' },
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{ data: { id: 'p5', label: 'map'}, classes: 'OPERATOR' },
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{ data: { id: 'p6', label: 'phase'}, classes: 'OPERATOR' },
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{ data: { id: 'p7', label: 'map'}, classes: 'OPERATOR' },
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{ data: { id: 'p8', label: 'Channel.fromPath'}, classes: 'ORIGIN' },
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{ data: { id: 'p9', label: 'ifEmpty'}, classes: 'OPERATOR' },
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{ data: { id: 'p10', label: 'map'}, classes: 'OPERATOR' },
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{ data: { id: 'p11', label: 'Channel.fromPath'}, classes: 'ORIGIN' },
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{ data: { id: 'p12', label: 'ifEmpty'}, classes: 'OPERATOR' },
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{ data: { id: 'p13', label: 'map'}, classes: 'OPERATOR' },
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{ data: { id: 'p14', label: 'phase'}, classes: 'OPERATOR' },
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{ data: { id: 'p15', label: 'map'}, classes: 'OPERATOR' },
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{ data: { id: 'p16', label: 'phase'}, classes: 'OPERATOR' },
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{ data: { id: 'p17', label: 'map'}, classes: 'OPERATOR' },
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{ data: { id: 'p18', label: 'bed'}, classes: 'PROCESS' },
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{ data: { id: 'p19', label: 'split_bed'}, classes: 'PROCESS' },
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{ data: { id: 'p20', label: 'spread'}, classes: 'OPERATOR' },
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{ data: { id: 'p21'}, classes: 'ORIGIN' },
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{ data: { id: 'p22'}, classes: 'ORIGIN' },
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{ data: { id: 'p23'}, classes: 'ORIGIN' },
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{ data: { id: 'p24'}, classes: 'ORIGIN' },
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{ data: { id: 'p25'}, classes: 'ORIGIN' },
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{ data: { id: 'p26'}, classes: 'ORIGIN' },
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{ data: { id: 'p27'}, classes: 'ORIGIN' },
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{ data: { id: 'p28', label: 'mutect'}, classes: 'PROCESS' },
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{ data: { id: 'p29', label: 'count'}, classes: 'OPERATOR' },
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{ data: { id: 'p30'}, classes: 'NODE' },
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{ data: { id: 'p31', label: 'groupTuple'}, classes: 'OPERATOR' },
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{ data: { id: 'p32', label: 'groupTuple'}, classes: 'OPERATOR' },
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{ data: { id: 'p33', label: 'mergeMuTectOutputs'}, classes: 'PROCESS' },
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{ data: { id: 'p34'}, classes: 'NODE' },
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{ data: { id: 'p35'}, classes: 'NODE' },
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],
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edges: [
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{ data: { source: 'p0', target: 'p1'} },
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{ data: { source: 'p1', target: 'p2'} },
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{ data: { source: 'p2', target: 'p6', label: 'tumor_bams' } },
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{ data: { source: 'p3', target: 'p4'} },
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{ data: { source: 'p4', target: 'p5'} },
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{ data: { source: 'p5', target: 'p6', label: 'tumor_bais' } },
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{ data: { source: 'p6', target: 'p7'} },
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{ data: { source: 'p7', target: 'p16', label: 'tumor_bam_bai' } },
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{ data: { source: 'p8', target: 'p9'} },
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{ data: { source: 'p9', target: 'p10'} },
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{ data: { source: 'p10', target: 'p14', label: 'normal_bams' } },
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{ data: { source: 'p11', target: 'p12'} },
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{ data: { source: 'p12', target: 'p13'} },
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{ data: { source: 'p13', target: 'p14', label: 'normal_bais' } },
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{ data: { source: 'p14', target: 'p15'} },
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{ data: { source: 'p15', target: 'p16', label: 'normal_bam_bai' } },
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{ data: { source: 'p16', target: 'p17'} },
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{ data: { source: 'p17', target: 'p20', label: 'tn_bambai' } },
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{ data: { source: 'p18', target: 'p19', label: 'outbed' } },
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{ data: { source: 'p19', target: 'p20', label: 'split_bed' } },
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{ data: { source: 'p19', target: 'p29', label: 'count_split_bed' } },
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{ data: { source: 'p20', target: 'p28'} },
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{ data: { source: 'p21', target: 'p28', label: 'mutect_version' } },
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{ data: { source: 'p22', target: 'p28', label: 'dbsnp_option' } },
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{ data: { source: 'p23', target: 'p28', label: 'cosmic_option' } },
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{ data: { source: 'p24', target: 'p28', label: 'fasta_ref' } },
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{ data: { source: 'p25', target: 'p28', label: 'fasta_ref_fai' } },
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{ data: { source: 'p26', target: 'p28', label: 'fasta_ref_gzi' } },
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{ data: { source: 'p27', target: 'p28', label: 'fasta_ref_dict' } },
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{ data: { source: 'p28', target: 'p31', label: 'mutect_output1' } },
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{ data: { source: 'p28', target: 'p32', label: 'mutect_output2' } },
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{ data: { source: 'p29', target: 'p30'} },
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{ data: { source: 'p31', target: 'p33'} },
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{ data: { source: 'p32', target: 'p33'} },
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{ data: { source: 'p33', target: 'p35', label: 'res1' } },
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{ data: { source: 'p33', target: 'p34', label: 'res2' } },
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],
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},
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});
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});
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</script>
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</head>
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<body>
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<h1>Nextflow Cytoscape.js with Dagre</h1>
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<div id="cy"></div>
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</body>
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</html>

‎dag.png

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Loading

‎deploy.sh

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#!/bin/bash
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cd ~/mutect-nf/
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git config --global user.email "robitaillea@students.iarc.fr"
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git add dag.png
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git add dag.html
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git commit -m "Generated DAG [skip ci]"
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git push origin $CIRCLE_BRANCH
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curl -H "Content-Type: application/json" --data "{\"source_type\": \"Branch\", \"source_name\": \"$CIRCLE_BRANCH\"}" -X POST https://registry.hub.docker.com/u/iarcbioinfo/mutect-nf/trigger/848d00e1-4e32-498a-aaaa-4e17029cdf3c/

‎mutect.nf

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log.info ' --java PATH Name of the JAVA command (default: java).'
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log.info ''
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log.info ''
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exit 1
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exit 0
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}
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fasta_ref = file(params.ref)

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