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pipeline.xml
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pipeline.xml
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<?xml version="1.0" encoding="UTF-8"?>
<pipeline xmlns="http://www.sing-group.org/compi/pipeline-1.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<version>1.1.0</version>
<params>
<param name="workingDir" shortName="wd" global="true" defaultValue="/working_dir">The working directory of the project.</param>
<param name="fastqDir" shortName="dd" global="true" defaultValue="input/fastq">The directory containing the fastq files (default is relative to workingDir).</param>
<param name="outDir" shortName="o" global="true" defaultValue="output">The directory containing the pipeline outputs (relative to workingDir).</param>
<param name="organism" shortName="ogn" global="true" defaultValue="Homo sapiens">The organism from which the data was obtained, needed for the functional enrichment analysis.</param>
<param name="adapter" shortName="adp" global="true" defaultValue="NA">The sequence of the adapter to remove.</param>
<param name="genome" shortName="genome" global="true" defaultValue="">The directory path to the genome to align.</param>
<param name="bwtIndex" shortName="bwti" global="true" defaultValue="">The absolute path to the rootname of the Bowtie index.</param>
<param name="gffFile" shortName="gff">The path to the .gff file of the reference genome.</param>
<param name="gffFeature" shortName="gfft" defaultValue="miRNA">Feature of the .gff file to use for the annotations (eg.: miRNA, gene, transcript...), default miRNA.</param>
<param name="gffAttribute" shortName="gffa" defaultValue="Name">Attribute of the .gff to use in the annotations (eg.: Name, gene_id, transcript_id...), default Name.</param>
<param name="conditions" shortName="cond">The path to the .tsv file with the rootnames of the samples, conditions and labels.</param>
<param name="contrast" shortName="cont">The path to the .tsv file with the contrast DESeq2 has to perform.</param>
<param name="qvalue" shortName="qval" global="true" defaultValue="0.05">FDR-corrected pvalue used to filter miRNAs after the differential expression analysis.</param>
<param name="log2FC" shortName="logfc" global="true" defaultValue="0.5">Absolute value of the log2FC, used to filter miRNAs after the differential expression analysis.</param>
<param name="distance_method" shortName="dmt" global="true" defaultValue="euclidean">Method used to compute distances on the hierarchical clustering step, default euclidean.</param>
<param name="vennFormat" shortName="venf" global="true" defaultValue="png">The file format of the Venn diagram (png/svg/tiff), default png.</param>
<param name="fqcOut" shortName="fqco" global="true" defaultValue="1_fastqc">The relative path to the directory containing the FastQC results.</param>
<param name="ctdOut" shortName="ctdo" global="true" defaultValue="2_cutadapt">The relative path to the directory containing the Cutadapt results.</param>
<param name="bwtOut" shortName="bwto" global="true" defaultValue="3_bowtie">The relative path to the directory containing the Bowtie results.</param>
<param name="bamstOut" shortName="bsto" global="true" defaultValue="4_bam_stats">The relative path to the directory containing the Samtools stats and Plot-bamstats results.</param>
<param name="ftqOut" shortName="ftqo" global="true" defaultValue="5_feature_counts">The relative path to the directory containing the FeatureCounts results.</param>
<param name="dsqOut" shortName="dsqo" global="true" defaultValue="6_deseq2">The relative path to the directory containing the DESeq2 results.</param>
<param name="edgOut" shortName="edgo" global="true" defaultValue="6_edger">The relative path to the directory containing the EdgeR results.</param>
<param name="deaIntOut" shortName="dinto" global="true" defaultValue="6_deseq2+edger">The relative path to the directory containing the results of the DESeq2 and EdgeR integration.</param>
<param name="mqcOut" shortName="mqco" global="true" defaultValue="7_multiqc">The relative path to the directory containing the MultiQC report.</param>
<param name="scriptsDir" shortName="sd" global="true" defaultValue="/scripts/">The relative path to the directory containing the R scripts.</param>
<param name="testAdapterBashScript" shortName="tabs" global="true" defaultValue="test_isadapter.sh">The relative path to the directory containing the R script to get the path of the aligned/unaligned data.</param>
<param name="deSeq2Rscript" shortName="rdes" global="true" defaultValue="run_deseq2.R">The relative path to the directory containing the R script to run the DESeq2 analysis.</param>
<param name="filterCtsRscript" shortName="fcrs" global="true" defaultValue="filter_counts.R">The relative path to the directory containing the R script used to filter all-counts.txt and conditions_file.</param>
<param name="edgerRscript" shortName="reds" global="true" defaultValue="run_edger_exact-test.R">The relative path to the directory containing the R script to run the EdgeR analysis.</param>
<param name="enhancedVolcanoRscript" shortName="evrs" global="true" defaultValue="run_enhanced-volcano.R">The relative path to the directory containing the R script to build the Volcano plot.</param>
<param name="deaIntRscript" shortName="deais" global="true" defaultValue="run_dea-integration.R">The relative path to the directory containing the R script to run the DESeq-EdgeR results integration.</param>
<param name="vennRscript" shortName="rven" global="true" defaultValue="run_venn-diagram.R">The relative path to the directory containing the R script to run the DESeq-EdgeR results integration.</param>
<param name="deseq2NormalizationRscript" shortName="dnrs" global="true" defaultValue="run_deseq2_normalization.R">The relative path to the directory containing the R script for the creation of the hclust table.</param>
<param name="hclustMakeTableRscript" shortName="hmk" global="true" defaultValue="run_make_hclust_table.R">The relative path to the directory containing the R script for the creation of the hclust table.</param>
<param name="hclustRscript" shortName="hcr" global="true" defaultValue="run_hierarchical-clustering.R">The relative path to the directory containing the R script for the hierarchical clustering analysis.</param>
<param name="functionalEnrichmentRscript" shortName="fers" global="true" defaultValue="run_functional-enrichment-analysis.R">The relative path to the directory containing the R script for the functional enrichment analysis.</param>
<param name="networkRscript" shortName="nrs" global="true" defaultValue="run_network_plot.R">The relative path to the directory containing the R script for the network creation.</param>
<param name="databasesDir" shortName="db" global="true" defaultValue="/databases/">The relative path to the directory containing the TarBase and Reactome databases.</param>
<param name="tarbaseDB" shortName="tbdb" global="true" defaultValue="TarBase_v8_download.txt">The relative path to the TarBase file.</param>
<param name="reactomeDB" shortName="rcdb" global="true" defaultValue="Ensembl2Reactome.txt">The relative path to a Reactome file with Ensembl IDs and Reactome IDs.</param>
<param name="reactomeInteractionsDB" shortName="rcidb" global="true" defaultValue="reactome.all_species.interactions.tab-delimited.txt">The relative path to a the Reactome file downloaded from https://reactome.org/download/current/interactors/reactome.all_species.interactions.tab-delimited.txt and renamed as ReactomeInteractions.txt.</param>
<param name="rDeseq2Version" shortName="rdv" defaultValue="1.32.0_v2" global="true">Version of the pegi3s/r_deseq2 Docker image to use.</param>
<param name="rEdgerVersion" shortName="redv" defaultValue="3.36.0" global="true">Version of the pegi3s/r_edger Docker image to use.</param>
<param name="rEnhancedVolcanoVersion" shortName="revv" defaultValue="1.12.0" global="true">Version of the pegi3s/r_enhanced-volcano Docker image to use.</param>
<param name="cutadaptVersion" shortName="cdv" defaultValue="1.16" global="true">Version of the pegi3s/cutadapt Docker image to use.</param>
<param name="fastqcVersion" shortName="fqcv" defaultValue="0.11.9" global="true">Version of the pegi3s/fastqc Docker image to use.</param>
<param name="bowtieVersion" shortName="bwv" defaultValue="1.2.3" global="true">Version of the pegi3s/bowtie1 Docker image to use.</param>
<param name="featureCountsVersion" shortName="fqv" defaultValue="2.0.0" global="true">Version of the pegi3s/feature-counts Docker image to use.</param>
<param name="samtoolsVersion" shortName="stv" defaultValue="1.9" global="true">Version of the pegi3s/samtools_bcftools Docker image to use.</param>
<param name="samtoolsBamstatsVersion" shortName="spb" defaultValue="1.10" global="true">Version of the pegi3s/samtools_bcftools Docker image to use for bam analysis.</param>
<param name="rdatanalysisVersion" shortName="rdav" defaultValue="4.1.1_v3" global="true">Version of the pegi3s/r_data-analysis Docker image to use.</param>
<param name="rVennVersion" shortName="rvv" defaultValue="1.7.0" global="true">Version of the pegi3s/r_venn-diagram Docker image to use.</param>
<param name="rNetworkVersion" shortName="rntv" defaultValue="4.1.1_v2_v3" global="true">Version of the pegi3s/r_network Docker image to use.</param>
<param name="multiqcVersion" shortName="mqv" defaultValue="1.14.0" global="true">Version of the pegi3s/multiqc Docker image to use.</param>
<flag name="skipPullDockerImages" shortName="sdi">Use this flag to skip the pull-docker-images task.</flag>
<flag name="deseqNormalizationHclust" shortName="dnh">Use this flag to perform a global count normalization with DESeq2 before the hierarchical clustering.</flag>
<param name="selectDEAsoftware" shortName="dea" defaultValue="both" global="true">Use this param to select the differential expression analysis software (deseq, edger or both).</param>
</params>
<tasks>
<!--Pull the docker images of the software used for the analysis-->
<task id="pull-docker-images" params="skipPullDockerImages" if="[ -v ${skipPullDockerImages} ]">
${scriptsDir}/pull-docker-images.sh
</task>
<!--Creates the output directories-->
<task id="initialization" after="pull-docker-images">
${scriptsDir}/initialization.sh
</task>
<!--Bowtie genome index build-->
<task id="build-genome-index" after="initialization" params="bwtOut genome" if="[ ! -z ${genome} ]"> #if user sets a value for genome, then this task is executed
${scriptsDir}/build-genome-index.sh
</task>
<!--Quality control with FastQC-->
<foreach id="fastqc-qc" after="initialization" of="command" in="ls -1 ${fastqDir} | grep .*\.fastq" as="file">
${scriptsDir}/fastqc-qc.sh
</foreach>
<!--Adapter removal with cutadapt-->
<foreach id="cut-sequences" after="fastqc-qc" of="command" in="ls -1 ${fastqDir} | grep .*\.fastq" as="file" params="adapter">
${scriptsDir}/cut-sequences.sh
</foreach>
<!--Alignment with Bowtie-->
<foreach id="bowtie-alignment" after="build-genome-index cut-sequences" of="command" in="bash ${scriptsDir}/${testAdapterBashScript} ${adapter} ${workingDir}/${outDir}/${ctdOut}/ ${fastqDir}" as="file" params="bwtIndex adapter fastqDir">
${scriptsDir}/bowtie-alignment.sh
</foreach>
<!--Converts the sam files to bam format-->
<foreach id="sam-to-bam" after="bowtie-alignment" of="command" in="ls -1 ${workingDir}/${outDir}/${bwtOut}/ | grep .*.\fastq.*\.sam" as="file">
${scriptsDir}/sam-to-bam.sh
</foreach>
<!--Performs the quality control with QualiMap-->
<foreach id="bam-stats" after="sam-to-bam" of="command" in="ls -1 ${workingDir}/${outDir}/${bwtOut}/ | grep .*.\fastq.*\.bam" as="bamFile">
${scriptsDir}/bam-stats.sh
</foreach>
<!--Performs the quantification with featureCounts-->
<task id="feature-counts" after="bam-stats" params="gffFile gffFeature gffAttribute">
${scriptsDir}/feature-counts.sh
</task>
<!--Performs the differential expression analysis with DESeq2-->
<foreach id="deseq" after="feature-counts" of="command" in="tail -n+2 ${contrast}" as="comparison" params="conditions contrast deSeq2Rscript" if="[ ${selectDEAsoftware} = deseq ] || [ ${selectDEAsoftware} = both ]">
${scriptsDir}/deseq.sh
</foreach>
<!--Performs the differential expression analysis with EdgeR-->
<foreach id="edger" after="feature-counts" of="command" in="tail -n+2 ${contrast}" as="comparison" params="conditions contrast edgerRscript" if="[ ${selectDEAsoftware} = edger ] || [ ${selectDEAsoftware} = both ]">
${scriptsDir}/edger.sh
</foreach>
<!--Compares the results of DESeq2 and EdgeR and builds a result file with the coincidences-->
<foreach id="dea-integration" after="deseq edger" of="command" in="tail -n+2 ${contrast}" as="comparison" params="conditions contrast" if="[ ${selectDEAsoftware} = both ]">
${scriptsDir}/dea-integration.sh
</foreach>
<!--Build the Venn diagram with the DESeq2+EdgeR results-->
<foreach id="venn" after="deseq edger dea-integration" of="command" in="tail -n+2 ${contrast}" as="comparison" params="vennFormat contrast" if="[ -s "${workingDir}/${outDir}/${deaIntOut}/$(echo ${comparison} | cut -d '"' -f 2)"/pipel/*_venn.\tsv ]">
${scriptsDir}/venn.sh
</foreach>
<!--Build the Volcano Plot with the DESeq2/EdgeR results-->
<foreach id="volcano" after="deseq edger dea-integration" of="command" in="tail -n+2 ${contrast}" as="comparison" params="conditions contrast">
${scriptsDir}/volcano.sh
</foreach>
<!--Build a Hierarchical Clustering using the DESeq2/EdgeR results-->
<foreach id="hclust" after="deseq edger dea-integration" of="command" in="tail -n+2 ${contrast}" as="comparison" params="conditions contrast deseqNormalizationHclust">
${scriptsDir}/hclust.sh deseqNormalizationHclust
</foreach>
<!--Performs a Functional Enrichment Analysis using the DESeq2/EdgeR results-->
<foreach id="functional-enrichment" after="hclust" of="command" in="tail -n+2 ${contrast}" as="comparison" params="conditions contrast">
${scriptsDir}/functional-enrichment.sh
</foreach>
<!--Build the network of interactions with the most enriched pathway of the functional-enrichment task-->
<foreach id="network" after="functional-enrichment" of="command" in="tail -n+2 ${contrast}" as="comparison" params="conditions contrast">
${scriptsDir}/network.sh
</foreach>
<!--Create a MultiQC report with the results-->
<task id="multiqc" after="network">
${scriptsDir}/multiqc.sh
</task>
</tasks>
<metadata>
<task-description id="pull-docker-images">Pull the docker images of the software used for the analysis.</task-description>
<task-description id="initialization">Creates the output directories.</task-description>
<task-description id="fastqc-qc">Quality control with FastQC.</task-description>
<task-description id="cut-sequences">Adapter removal with cutadapt.</task-description>
<task-description id="build-genome-index">Builds a genome index if the genome parameter is passed in compi.parameters.</task-description>
<task-description id="bowtie-alignment">Alignment with Bowtie.</task-description>
<task-description id="sam-to-bam">Converts the sam files to bam format.</task-description>
<task-description id="bam-stats">Performs the quality control of the bam files with SAMtools.</task-description>
<task-description id="feature-counts">Performs the quantification with featureCounts.</task-description>
<task-description id="deseq">Performs the differential expression analysis with DESeq2.</task-description>
<task-description id="edger">Performs the differential expression analysis with EdgeR.</task-description>
<task-description id="dea-integration">Compares the results of DESeq2 and EdgeR and builds a result file with the coincidences.</task-description>
<task-description id="venn">Build the Venn diagram with the DESeq2+EdgeR results.</task-description>
<task-description id="volcano">Build the Volcano Plot with the DESeq2/EdgeR results.</task-description>
<task-description id="hclust">Build a Hierarchical Clustering using the DESeq2/EdgeR results.</task-description>
<task-description id="functional-enrichment">Performs a Functional Enrichment Analysis using the DESeq2/EdgeR results.</task-description>
<task-description id="network">Build the network of interactions with the most enriched pathway of the functional-enrichment task.</task-description>
<task-description id="multiqc">Create a MultiQC report with the results.</task-description>
</metadata>
</pipeline>