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analysisRNAseq.xml
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analysisRNAseq.xml
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<configuration name='RNAseqAnalysis' description='paired end RNA seq analysis using STAR, feature counts, kallisto, arriba, RNAseQC and QualiMap2'
configurationType='analysis' class='de.dkfz.roddy.core.Analysis'
workflowClass='de.dkfz.b080.co.rnaseqworkflow.RNAseqWorkflow'
runtimeServiceClass='de.dkfz.b080.co.common.COProjectsRuntimeService'
listOfUsedTools=""
usedToolFolders="rnaseqworkflow,tools"
cleanupScript="cleanupScript">
<configurationvalues>
<!-- ## Imported from cofilenames -->
<cvalue name='sampleDirectory' value='${inputBaseDirectory}/${pid}/${sample}/${library}/${SEQUENCER_PROTOCOL}' type='path'/>
<cvalue name='sequenceDirectory' value='${sampleDirectory}/${run}/sequence' type='path'/>
<cvalue name='mergedBamSuffix_markDuplicatesShort' value='merged.mdup.bam' type="string" />
<cvalue name='mergedBamSuffixList' value='${mergedBamSuffix_markDuplicatesShort}' type="string" description="A list of all known suffixes for merged bam files. I.e. merged.dupmark.bam, merged.mdup.bam..." />
<cvalue name='defaultMergedBamSuffix' value='${mergedBamSuffix_markDuplicatesShort}' type="string" description="The default suffix for merged bam files when they are created by Roddy." />
<!-- ## Imported from cobase project -->
<cvalue name='possibleControlSampleNamePrefixes' value='( blood BLOOD normal control CONTROL buffy_coat GERMLINE )' type='bashArray'/>
<cvalue name='possibleTumorSampleNamePrefixes' value='( tumor TUMOR metastasis xenograft disease DISEASE relapse RELAPSE autopsy AUTOPSY metastasis METASTASIS )' type='bashArray'/>
<cvalue name="useCentralAnalysisArchive" value="true"/>
<cvalue name="enableJobProfiling" value="false"/>
<cvalue name='QUAL' value='phred' description="Default quality is phred, can be illumina."/>
<!-- ## Imported from commonCOWorkflowsSettings -->
<cvalue name='SEQUENCER_PROTOCOL' value='paired' type="string" description="only paired read sequencing is currently supported"/>
<!-- ## -->
<!-- ## SOME RUNTIME_CONFIG PARMS -->
<!-- ## -->
<cvalue name='CORES' value='8' type='string'/>
<cvalue name='FEATURE_COUNT_CORES' value='${CORES}' type='string'/>
<cvalue name='TEST_RUN' value='false' type='boolean' description="only print the commands and doesnt execute them"/>
<cvalue name='DO_FIRST' value='echo "Do something first"' type='string' description="increase something needs to be run at the start of the workflow"/>
<cvalue name='useSingleEndProcessing' value='false' type='boolean' description="flag for using single end mode"/>
<cvalue name='runSingleCellWorkflow' value='false' type='boolean'/>
<!-- ## DIRECTORIES -->
<cvalue name='trimmingOutputDirectory' value='trimming' type='string'/>
<cvalue name='alignmentOutputDirectory' value='alignment' type='string'/>
<cvalue name='qcOutputDirectory' value='qualitycontrol' type='string'/>
<cvalue name='ALIGNMENT_DIR' value='${outputAnalysisBaseDirectory}/${alignmentOutputDirectory}' type='string'/>
<cvalue name='SCRATCH' value='${outputAnalysisBaseDirectory}/temp' type='string'/>
<cvalue name='COUNT_DIR' value='${outputAnalysisBaseDirectory}/featureCounts' type='string'/>
<cvalue name='COUNT_DIR_EXON' value='${outputAnalysisBaseDirectory}/featureCounts_dexseq' type='string'/>
<cvalue name='KALLISTO_UN_DIR' value='${outputAnalysisBaseDirectory}/kallisto_un' type='string'/>
<cvalue name='KALLISTO_FR_DIR' value='${outputAnalysisBaseDirectory}/kallisto_fr' type='string'/>
<cvalue name='KALLISTO_RF_DIR' value='${outputAnalysisBaseDirectory}/kallisto_rf' type='string'/>
<cvalue name='QC_DIR' value='${outputAnalysisBaseDirectory}/${qcOutputDirectory}' type='string'/>
<cvalue name='RNASEQC_DIR' value='${QC_DIR}/RNAseQC' type='string'/>
<cvalue name='QUALIMAP_DIR' value='${QC_DIR}/QualiMap2' type='string'/>
<cvalue name='ARRIBA_DIR' value='${outputAnalysisBaseDirectory}/fusions_arriba' type='string'/>
<!-- # RUNTIME_CONFIG_OUTFILE DEFINITITIONS -->
<cvalue name='STAR_PREFIX' value='${SAMPLE}_${pid}_merged' type='string'/>
<cvalue name='STAR_TMPDIR' value='${RODDY_SCRATCH}/${SAMPLE}_${pid}_STAR'/>
<cvalue name='STAR_CHIMERA_PREFIX' value='${SAMPLE}_${pid}_chimeric_merged' type='string'/>
<cvalue name='STAR_NOTSORTED_BAM' value='${STAR_PREFIX}.Aligned.out.bam' type='string'/>
<cvalue name='STAR_SORTED_BAM' value='${STAR_PREFIX}.Aligned.sortedByCoord.out.bam' type='string'/>
<cvalue name='STAR_SORTED_MKDUP_BAM' value='${STAR_PREFIX}.mdup.bam' type='string'/>
<cvalue name='STAR_CHIMERA_SAM' value='${STAR_PREFIX}.Chimeric.out.sam' type='string'/>
<cvalue name='STAR_CHIMERA_BAM_PREF' value='${STAR_PREFIX}.Chimeric.out' type='string'/>
<cvalue name='STAR_CHIMERA_MKDUP_BAM' value='${STAR_CHIMERA_PREFIX}.mdup.bam' type='string'/>
<!-- ## -->
<!-- ## SOFTWARE STACK -->
<!-- ## -->
<cvalue name='PYTHON_VERSION' value='2.7.9' type='string'/>
<cvalue name='STAR_VERSION' value='2.7.10a' type='string'/>
<cvalue name='STAR_MODULE_NAME' value='star' type='string'/>
<cvalue name='SUBREAD_VERSION' value='1.6.5' type='string'/>
<cvalue name='SAMBAMBA_VERSION' value='0.6.5' type='string'/>
<cvalue name='SAMTOOLS_VERSION' value='1.9' type='string'/>
<cvalue name='HTSLIB_VERSION' value='1.9' type='string'/>
<cvalue name='RNASEQC_VERSION' value='1.1.8' type='string'/>
<cvalue name='KALLISTO_VERSION' value='0.46.0' type='string'/>
<cvalue name='QUALIMAP_VERSION' value='2.2.1' type='string'/>
<cvalue name='ARRIBA_VERSION' value='2.2.1' type='string'/>
<cvalue name='R_VERSION' value='3.4.2' type='string'/>
<cvalue name="workflowEnvironmentScript" value="workflowEnvironment_tbiCluster" type="string"/>
<!-- ## -->
<!-- ## Alternative environment script using a composite module definition -->
<!-- ## -->
<!--<cvalue name="workflowEnvironmentScript" value="workflowEnvironment_tbiClusterCompositeModule" type="string"/>-->
<!--<cvalue name='LOAD_MODULE' value='true' type='boolean'/>-->
<!--<cvalue name="MODULE_ENV" value="HIPO2_rna/v1" type="string"/>-->
<!-- ## -->
<!-- ## WHAT TO RUN -->
<!-- ## -->
<cvalue name='RUN_STAR' value='true' type='boolean'/>
<cvalue name='RUN_FEATURE_COUNTS' value='true' type='boolean'/>
<cvalue name='RUN_FEATURE_COUNTS_DEXSEQ' value='true' type='boolean'/>
<cvalue name='RUN_RNASEQC' value='true' type='boolean'/>
<cvalue name='RUN_QUALIMAP' value='false' type='boolean'/>
<cvalue name='RUN_KALLISTO' value='false' type='boolean'/>
<cvalue name='RUN_KALLISTO_FR' value='false' type='boolean'/>
<cvalue name='RUN_KALLISTO_RF' value='false' type='boolean'/>
<cvalue name='RUN_ARRIBA' value='true' type='boolean'/>
<cvalue name='RUN_QCJSON' value='true' type='boolean'/>
<cvalue name='RUN_CLEANUP' value='true' type='boolean'/>
<!-- ## -->
<!-- ## DATABASE/FILE STACK -->
<!-- ## -->
<cvalue name='hg19BaseDirectory'
value='/omics/odcf/reference_data/legacy/ngs_share/assemblies/hg19_GRCh37_1000genomes/'
type='path'/>
<cvalue name='hg19DatabaseDirectory' value='${hg19BaseDirectory}/databases' type='string'/>
<cvalue name='hg19IndexDirectory' value='${hg19BaseDirectory}/indexes/' type='string'/>
<cvalue name='mm10BaseDirectory' value='/omics/odcf/reference_data/legacy/ngs_share/assemblies/mm10' type='path'/>
<cvalue name='mm10DatabaseDirectory' value='${mm10BaseDirectory}/databases' type='string'/>
<cvalue name='mm10IndexDirectory' value='${mm10BaseDirectory}/indexes/' type='string'/>
<cvalue name='databaseDirectory' value='${hg19DatabaseDirectory}' type='string'/>
<cvalue name='indexDirectory' value='${hg19IndexDirectory}' type='string'/>
<cvalue name='GENOME_FA' value='${hg19IndexDirectory}/bwa/bwa06_1KGRef_Phix/hs37d5_PhiX.fa' type='string'/>
<cvalue name='GENOME_GATK_INDEX' value='${hg19IndexDirectory}/bwa/bwa06_1KGRef_Phix/hs37d5_PhiX.fa' type='string'/>
<cvalue name='GENE_MODELS' value='${hg19DatabaseDirectory}/gencode/gencode19/gencode.v19.annotation_plain.gtf' type='string'/>
<cvalue name='GENE_MODELS_NOGENE' value='${GENE_MODELS}' type='string'
description="Like GENE_MODELS, but without 'gene' features. Required for gencode update for hg38. Defaults (for hg19): $GENE_MODELS."/>
<cvalue name='GENE_MODELS_EXCLUDE' value='${hg19DatabaseDirectory}/gencode/gencode19/gencode.v19.annotation_plain.chrXYMT.rRNA.tRNA.gtf' type='string'/>
<cvalue name='GENE_MODELS_DEXSEQ' value='${hg19DatabaseDirectory}/gencode/gencode19/gencode.v19.annotation_plain.dexseq.gff' type='string'/>
<cvalue name='GENE_MODELS_GC' value='${hg19DatabaseDirectory}/gencode/gencode19/gencode.v19.annotation_plain.transcripts.autosomal_transcriptTypeProteinCoding_nonPseudo.1KGRef.gc' type='string'/>
<cvalue name='GENOME_STAR_INDEX_50' value='${hg19IndexDirectory}/STAR/STAR_2.5.2b_1KGRef_PhiX_Gencode19_50bp' type='string'/>
<cvalue name='GENOME_STAR_INDEX_100' value='${hg19IndexDirectory}/STAR/STAR_2.5.2b_1KGRef_PhiX_Gencode19_100bp' type='string'/>
<cvalue name='GENOME_STAR_INDEX_200' value='${hg19IndexDirectory}/STAR/STAR_2.5.2b_1KGRef_PhiX_Gencode19_200bp' type='string'/>
<cvalue name='GENOME_KALLISTO_INDEX' value='${hg19IndexDirectory}/kallisto/kallisto-0.43.0_1KGRef_Gencode19_k31/kallisto-0.43.0_1KGRef_Gencode19_k31.noGenes.index' type='string'/>
<cvalue name='ARRIBA_KNOWN_FUSIONS' value='${hg19BaseDirectory}/tools_data/arriba/known_fusions_hg19_hs37d5_GRCh37_v${ARRIBA_VERSION}.tsv.gz' type='string'/>
<cvalue name='ARRIBA_TAGS' value='${ARRIBA_KNOWN_FUSIONS}' type='string'/>
<cvalue name='ARRIBA_BLACKLIST' value='${hg19BaseDirectory}/tools_data/arriba/blacklist_hg19_hs37d5_GRCh37_v${ARRIBA_VERSION}.tsv.gz' type='string'/>
<cvalue name='ARRIBA_PROTEIN_DOMAINS' value='${hg19BaseDirectory}/tools_data/arriba/protein_domains_hg19_hs37d5_GRCh37_v${ARRIBA_VERSION}.gff3' type='string'/>
<cvalue name='ARRIBA_CYTOBANDS' value='${hg19BaseDirectory}/tools_data/arriba/cytobands_hg19_hs37d5_GRCh37_v${ARRIBA_VERSION}.tsv' type="string"/>
<!-- ## -->
<!-- ## SOFTWARE PARAMS -->
<!-- ## -->
<!-- ## STAR -->
<cvalue name='READ_COMMAND' value='${UNZIPTOOL} ${UNZIPTOOL_OPTIONS}' type='string'/>
<!-- ## Adapter sequence for 3' should be reverse compliment of the 5'sequencing adapter: https://support.illumina.com/bulletins/2016/12/what-sequences-do-i-use-for-adapter-trimming.html -->
<cvalue name='ADAPTER_SEQ_TRUSEQ_LT_HT' value="AGATCGGAAGAGCACACGTCTGAACTCCAGTCA AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT" type='string' description="TruSeq LT and TruSeq HT"/>
<cvalue name='ADAPTER_SEQ_TRUSEQ_DNAME' value="AGATCGGAAGAGCACACGTCTGAAC AGATCGGAAGAGCGTCGTGTAGGGA" type='string' description="ScriptSeq and TruSeq DNA Methylation"/>
<cvalue name='ADAPTER_SEQ_TRUSEQ_SRNA' value="TGGAATTCTCGGGTGCCAAGG" type='string' description="TruSeq Small RNA"/>
<cvalue name='ADAPTER_SEQ_TRUSEQ_RIBO' value="AGATCGGAAGAGCACACGTCT" type='string' description="TruSeq Ribo Profile"/>
<cvalue name='ADAPTER_SEQ_NEXTERA' value="CTGTCTCTTATACACATCT" type='string' description="Nextera, Nextera XT, Nextera Enrichment, Nextera Rapid Capture Enrichment, TruSight Enrichment, TruSight Rapid Capture Enrichment, TruSight HLA"/>
<cvalue name='ADAPTER_SEQ_NEXTERA_MP' value="CTGTCTCTTATACACATCT AGATGTGTATAAGAGACAG" type='string' description="Nextera Mate Pair"/>
<cvalue name='ADAPTER_SEQ' value='${ADAPTER_SEQ_TRUSEQ_LT_HT}' type='string'/>
<cvalue name='STAR_PARAMS_CLIP' value="--clip3pAdapterSeq ${ADAPTER_SEQ} --clip3pAdapterMMp 0.1 0.1" type='string'
description="Better not quote ${ADAPTER_SEQ}, because STAR can parse this correctly and the manual never uses quotes for parameter arguments."/>
<cvalue name='GENOME_STAR_INDEX' value='${GENOME_STAR_INDEX_200}' type='string'/>
<cvalue name='STAR_PARAMS_BASIC'
value='--sjdbOverhang 200 --runThreadN ${CORES} --outFileNamePrefix ${STAR_PREFIX}. --genomeDir ${GENOME_STAR_INDEX} --runRNGseed 1234 --outTmpDir ${SCRATCH}/${SAMPLE}_${pid}_STAR'
type='string'/>
<cvalue name='STAR_PARAMS_OUT'
value='--outSAMtype BAM Unsorted SortedByCoordinate --limitBAMsortRAM 100000000000 --outBAMsortingThreadN=1 --outSAMstrandField intronMotif --outSAMunmapped Within KeepPairs --outFilterMultimapNmax 1 --outFilterMismatchNmax 5 --outFilterMismatchNoverLmax 0.3'
type='string'/>
<cvalue name='STAR_PARAMS_2PASS' value='--twopassMode Basic --twopass1readsN -1 --genomeLoad NoSharedMemory' type='string'/>
<cvalue name='STAR_PARAMS_CHIMERIC' value='--chimSegmentMin 15 --chimScoreMin 1 --chimScoreJunctionNonGTAG 0 --chimJunctionOverhangMin 15 --chimSegmentReadGapMax 3 --alignSJstitchMismatchNmax 5 -1 5 5' type='string'/>
<cvalue name='STAR_PARAMS_INTRONS' value='--alignIntronMax 1100000 --alignMatesGapMax 1100000 --alignSJDBoverhangMin 3 --alignIntronMin 20' type='string'/>
<cvalue name='STAR_PARAMS_ADDITIONAL' value=' ' type='string'/>
<cvalue name='STAR_PARAMS' value='${STAR_PARAMS_BASIC} ${STAR_PARAMS_OUT} ${STAR_PARAMS_2PASS} ${STAR_PARAMS_CHIMERIC} ${STAR_PARAMS_INTRONS} ${STAR_PARAMS_CLIP} ${STAR_PARAMS_ADDITIONAL}' type='string'/>
<cvalue name='disableDoC_GATK' value='true' type='boolean'/>
<cvalue name='JSON_PREFIX' value='${SAMPLE}_${pid}_' type='string'/>
<!-- Fingerprinting -->
<cvalue name="runFingerprinting" value="true" type="boolean"/>
<cvalue name="fingerprintingSitesFile_hg37"
value="${databaseDirectory}/fingerprinting/hovestadt_v1.1/snp138Common.n1000.vh20140318.bed"
type="path"/>
<cvalue name="fingerprintingSitesFile" value="${fingerprintingSitesFile_hg37}" type="path"
description='BED file with the reference positions used for fingerprinting. Used by alignment workflow for fingerprinting individuals to discover swaps. Use runFingerprinting=true/false to toggle fingerprinting.'/>
<!-- ## Default file access -->
<cvalue name='outputFileGroup' value='B080'/>
<cvalue name='outputUMask' value='007' type='string'/>
<cvalue name='outputAccessRights' value='u+rw,g+rw,o-rwx'/>
<cvalue name='outputAccessRightsForDirectories' value='u+rwx,g+rwx,o-rwx'/>
<cvalue name='outputAllowAccessRightsModification' value='false' type="boolean"/>
</configurationvalues>
<processingTools>
<tool name="workflowEnvironment_tbiCluster" value="tbi-cluster.sh" basepath="rnaseqworkflow/environments"/>
<tool name="navLib" value="navBashLib.sh" basepath="rnaseqworkflow"/>
<!--<tool name="bashLib" value="bashLib.sh" basepath="rnaseqworkflow"/>-->
<!--<tool name="workflowLib" value="workflowLib.sh" basepath="rnaseqworkflow"/>-->
<tool name="cleanupScript" value="cleanupScript.sh" basepath="rnaseqworkflow">
<resourcesets>
<rset size="l" memory="0.1" cores="1" nodes="1" walltime="1"/>
</resourcesets>
</tool>
<tool name="countsToFpkmTpm" value="featureCounts_2_FpkmTpm" basepath="rnaseqworkflow"/>
<tool name="countsdexseqToFpkmTpm" value="featureCountsDexseq_2_FpkmTpm" basepath="rnaseqworkflow"/>
<tool name="kallistoRescale" value="kallistoRescaleTPM" basepath="rnaseqworkflow"/>
<tool name="createJsonFromOutput" value="qcJson" basepath="rnaseqworkflow"/>
<tool name='fingerprint' value="bsnp.py" basepath="qcPipeline"/>
<tool name="starAlignment" value="rnaseq_processing.sh" basepath="rnaseqworkflow">
<resourcesets>
<rset size="s" memory="37g" cores="4" nodes="1" walltime="3h" queue="devel"/>
<rset size="m" memory="50g" cores="4" nodes="1" walltime="120h"/>
<rset size="xl" memory="100g" cores="8" nodes="1" walltime="120h"/>
</resourcesets>
<input type="file" typeof="LaneFile" scriptparameter="FAKE_FILE"/>
<input type="string" setby="callingCode" scriptparameter="SAMPLE"/>
<input type="string" setby="callingCode" scriptparameter="sample"/>
<input type="string" setby="callingCode" scriptparameter="READS_STAR_LEFT"/>
<input type="string" setby="callingCode" scriptparameter="READS_STAR_RIGHT"/>
<input type="string" setby="callingCode" scriptparameter="READS_KALLISTO"/>
<input type="string" setby="callingCode" scriptparameter="PARM_READGROUPS"/>
<output type="file" typeof="BamFile" scriptparameter="STAR_SORTED_MKDUP_BAM2">
<!--<output type="file" variable="indexFile" typeof="BamIndexFile" scriptparameter="STAR_SORTED_MKDUP_BAM_INDEX"/>-->
</output>
</tool>
</processingTools>
<filenames package='de.dkfz.b080.co.files' filestagesbase='de.dkfz.b080.co.files.COFileStage'>
<filename class='BamFile' onTool="starAlignment" pattern='${outputAnalysisBaseDirectory}/${alignmentOutputDirectory}/${cvalue,name="STAR_PREFIX"}.mdup.bam'/>
<!--<filename class='BamFile' onTool="rna_processing" pattern='${outputAnalysisBaseDirectory}/${alignmentOutputDirectory}/${pid}.${sample}.sorted.mkdup.bam'/>-->
<!--<filename class='BasicBamFile' onTool="starAlignment" onScriptParameter="starAlignment:STAR_SORTED_MKDUP_BAM" pattern='${outputAnalysisBaseDirectory}/${alignmentOutputDirectory}/${pid}.${sample}.sorted.mkdup.bam' />-->
<filename class='BamIndexFile' derivedFrom='BamFile' pattern='${sourcefile}.bai'/>
</filenames>
</configuration>