Downloading nextflow dependencies. It may require a few seconds, please wait .. NOTE: Nextflow is not tested with Java 1.8.0_292 -- It's recommended the use of version 11 up to 19  Downloading nextflow dependencies. It may require a few seconds, please wait .. Error: A JNI error has occurred, please check your installation and try again Exception in thread "main" java.lang.UnsupportedClassVersionError: nextflow/cli/Launcher has been compiled by a more recent version of the Java Runtime (class file version 55.0), this version of the Java Runtime only recognizes class file versions up to 52.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClass(ClassLoader.java:756) at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142) at java.net.URLClassLoader.defineClass(URLClassLoader.java:468) at java.net.URLClassLoader.access$100(URLClassLoader.java:74) at java.net.URLClassLoader$1.run(URLClassLoader.java:369) at java.net.URLClassLoader$1.run(URLClassLoader.java:363) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:362) at java.lang.ClassLoader.loadClass(ClassLoader.java:418) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352) at java.lang.ClassLoader.loadClass(ClassLoader.java:351) at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:601) N E X T F L O W ~ version 21.04.3 Launching `/gpfs/home/khodaa01/Tools/nextNEOpi/nextNEOpi.nf` [determined_bartik] - revision: 63197eaf5d NEXTFLOW ~ version 21.04.3 5560 ------------------------------------------------------------------------- Nextfow NeoAntigen Prediction Pipeline - nextNEOpi ------------------------------------------------------------------------- Features: - somatic variants from tumor + matched normal samples - CNV analysis - tumor muational burden - class I and class II HLA typing - gene fusion peptide prediction using RNAseq data - peptide MHC binding perdiction - clonality of neoantigens - expression of neoantigens ------------------------------------------------------------------------- C O N F I G U R A T I O N Command Line: nextflow run /gpfs/home/khodaa01/Tools/nextNEOpi/nextNEOpi.nf --batchFile 10samples.csv -config /gpfs/home/khodaa01/Tools/nextNEOpi/conf/params.config --outputDir results --trim_adapters false --trim_adapters_RNAseq false --use_NetChop false --tmpDir temp -profile singularity,cluster -resume --accept_license --TCR true --MIXCR_lic /gpfs/home/khodaa01/Tools/nextNEOpi/conf/mi.license Working Directory: /gpfs/home/khodaa01/Projects/Michelle_krogsgaardlab/NeoAnt/2023-03-21/10s Output Directory: results I N P U T batch file: 10samples.csv Please check --help for further instruction ------------------------------------------------------------------------- WARN: I have read and accept the licence terms IEDB_dir: /gpfs/data/khodadadilab/Tools/nextNEOpi/resources/databases/iedb MHCFLURRY_dir: /gpfs/data/khodadadilab/Tools/nextNEOpi/resources/databases/mhcflurry_data tmpDir: /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/temp Pipeline Name : icbi/nextNEOpi Pipeline Version : 1.0 Batch file : 10samples.csv Read length : 101 Exome capture kit : sureSelectV6 Fasta Ref : /gpfs/home/khodaa01/Tools/nextNEOpi/resources/references/hg38/gdc/GRCh38.d1.vd1/fasta/GRCh38.d1.vd1.fa MillsGold : /gpfs/home/khodaa01/Tools/nextNEOpi/resources/databases/GATKresourceBundle/Mills_and_1000G_gold_standard.indels.hg38.vcf hcSNPS1000G : /gpfs/home/khodaa01/Tools/nextNEOpi/resources/databases/GATKresourceBundle/1000G_phase1.snps.high_confidence.hg38.vcf.gz HapMap : /gpfs/home/khodaa01/Tools/nextNEOpi/resources/databases/GATKresourceBundle/hapmap_3.3.hg38.vcf.gz Cosmic : /gpfs/home/khodaa01/Tools/nextNEOpi/resources/databases/cosmic/hg38/v84/CosmicCodingMuts.hg38.v84.vcf DBSNP : /gpfs/home/khodaa01/Tools/nextNEOpi/resources/databases/GATKresourceBundle/Homo_sapiens_assembly38.dbsnp138.vcf GnomAD : /gpfs/home/khodaa01/Tools/nextNEOpi/resources/databases/GATKresourceBundle/Mutect2/GetPileupSummaries/small_exac_common_3.hg38.vcf GnomADfull : /gpfs/home/khodaa01/Tools/nextNEOpi/resources/databases/GATKresourceBundle/Mutect2/gnomAD/af-only-gnomad.hg38.vcf.gz KnownIndels : /gpfs/home/khodaa01/Tools/nextNEOpi/resources/databases/GATKresourceBundle/Homo_sapiens_assembly38.known_indels.vcf BlastDB : /gpfs/home/khodaa01/Tools/nextNEOpi/resources/references/blast/ priority variant Caller : M2 Mutect 1 and 2 minAD : 5 VarScan min_cov : 10 VarScan min_cov_tumor : 10 VarScan min_cov_normal : 10 VarScan min_freq_for_hom : 0.75 VarScan somatic_pvalue : 0.99 VarScan somatic_somaticpvalue : 0.05 VarScan strand_filter : 1 VarScan processSomatic_pvalue : 0.05 VarScan max_normal_freq : 0.05 VarScan min_tumor_freq : 0.1 VarScan min_map_q : 10 VarScan min_base_q : 20 VEP assembly : GRCh38 VEP species : homo_sapiens VEP options : --everything Number of scatters : 40 Output dir : results Working dir : /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work TMP dir : /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/temp Current home : /gpfs/home/khodaa01 Current user : khodaa01 Current path : /gpfs/home/khodaa01/Projects/Michelle_krogsgaardlab/NeoAnt/2023-03-21/10s JAVA_Xmx : -Xmx64G Picard maxRecordsInRam : 4194304 Script dir : /gpfs/home/khodaa01/Tools/nextNEOpi Config Profile : singularity,cluster ------------------------------------------------------------------------- Found /gpfs/home/khodaa01/Tools/hlahd.1.6.1/bin/hlahd.sh at: /gpfs/home/khodaa01/Tools/hlahd.1.6.1/bin/hlahd.sh Found /gpfs/home/khodaa01/Tools/nextNEOpi/conf/mi.license at: /gpfs/home/khodaa01/Tools/nextNEOpi/conf/mi.license [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList - [- ] process > BaitsBedToIntervalList - [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [- ] process > FastQC - [- ] process > make_uBAM - [- ] process > Bwa - [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - Pulling Singularity image https://apps-01.i-med.ac.at/images/singularity/nextNEOpi_1.3.2_18734d43.sif [cache /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity/apps-01.i-med.ac.at-images-singularity-nextNEOpi_1.3.2_18734d43.sif] WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList - [- ] process > BaitsBedToIntervalList - [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [- ] process > FastQC - [- ] process > make_uBAM - [- ] process > Bwa - [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [- ] process > install_conda_GATK3 - [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - Pulling Singularity image https://apps-01.i-med.ac.at/images/singularity/nextNEOpi_1.3.2_18734d43.sif [cache /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity/apps-01.i-med.ac.at-images-singularity-nextNEOpi_1.3.2_18734d43.sif] Pulling Singularity image https://depot.galaxyproject.org/singularity/gatk:3.8--hdfd78af_11 [cache /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity/depot.galaxyproject.org-singularity-gatk-3.8--hdfd78af_11.img] INFO: Mutect1 not available, skipping.... WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList - [- ] process > BaitsBedToIntervalList - [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [- ] process > FastQC - [- ] process > make_uBAM - [- ] process > Bwa - [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [- ] process > install_conda_GATK3 - [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [- ] process > make_CNVkit_access_file - [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA - [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [- ] process > install_mixMHC2pred - [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [- ] process > install_IGS - Pulling Singularity image https://apps-01.i-med.ac.at/images/singularity/nextNEOpi_1.3.2_18734d43.sif [cache /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity/apps-01.i-med.ac.at-images-singularity-nextNEOpi_1.3.2_18734d43.sif] Pulling Singularity image https://depot.galaxyproject.org/singularity/gatk:3.8--hdfd78af_11 [cache /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity/depot.galaxyproject.org-singularity-gatk-3.8--hdfd78af_11.img] INFO: Mutect1 not available, skipping.... Pulling Singularity image https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0 [cache /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity/depot.galaxyproject.org-singularity-cnvkit-0.9.9--pyhdfd78af_0.img] WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location executor > local (2) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList - [- ] process > BaitsBedToIntervalList - [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [- ] process > FastQC - [- ] process > make_uBAM - [- ] process > Bwa - [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [- ] process > install_conda_GATK3 [ 0%] 0 of 1 [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [- ] process > make_CNVkit_access_file - [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA - [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [ 0%] 0 of 1 [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [ 0%] 0 of 1 [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - Pulling Singularity image https://apps-01.i-med.ac.at/images/singularity/nextNEOpi_1.3.2_18734d43.sif [cache /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity/apps-01.i-med.ac.at-images-singularity-nextNEOpi_1.3.2_18734d43.sif] Pulling Singularity image https://depot.galaxyproject.org/singularity/gatk:3.8--hdfd78af_11 [cache /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity/depot.galaxyproject.org-singularity-gatk-3.8--hdfd78af_11.img] INFO: Mutect1 not available, skipping.... Pulling Singularity image https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0 [cache /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity/depot.galaxyproject.org-singularity-cnvkit-0.9.9--pyhdfd78af_0.img] WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location executor > local (2) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList - [- ] process > BaitsBedToIntervalList - [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [- ] process > FastQC - [- ] process > make_uBAM - [- ] process > Bwa - [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [- ] process > install_conda_GATK3 [ 0%] 0 of 1 [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [- ] process > make_CNVkit_access_file [ 0%] 0 of 1 [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA - [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [ 0%] 0 of 1 [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [ 0%] 0 of 1 [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - Pulling Singularity image https://apps-01.i-med.ac.at/images/singularity/nextNEOpi_1.3.2_18734d43.sif [cache /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity/apps-01.i-med.ac.at-images-singularity-nextNEOpi_1.3.2_18734d43.sif] Pulling Singularity image https://depot.galaxyproject.org/singularity/gatk:3.8--hdfd78af_11 [cache /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity/depot.galaxyproject.org-singularity-gatk-3.8--hdfd78af_11.img] INFO: Mutect1 not available, skipping.... Pulling Singularity image https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0 [cache /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity/depot.galaxyproject.org-singularity-cnvkit-0.9.9--pyhdfd78af_0.img] WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location executor > local (4) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList - [- ] process > BaitsBedToIntervalList - [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [- ] process > FastQC - [- ] process > make_uBAM - [- ] process > Bwa - [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [ 0%] 0 of 1 [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [ 0%] 0 of 1 [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA - [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [ 0%] 0 of 1 [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - Pulling Singularity image https://apps-01.i-med.ac.at/images/singularity/nextNEOpi_1.3.2_18734d43.sif [cache /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity/apps-01.i-med.ac.at-images-singularity-nextNEOpi_1.3.2_18734d43.sif] Pulling Singularity image https://depot.galaxyproject.org/singularity/gatk:3.8--hdfd78af_11 [cache /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity/depot.galaxyproject.org-singularity-gatk-3.8--hdfd78af_11.img] INFO: Mutect1 not available, skipping.... Pulling Singularity image https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0 [cache /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity/depot.galaxyproject.org-singularity-cnvkit-0.9.9--pyhdfd78af_0.img] WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location executor > local (4) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList - [- ] process > BaitsBedToIntervalList - [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [- ] process > FastQC - [- ] process > make_uBAM - [- ] process > Bwa - [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [ 0%] 0 of 1 [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [ 0%] 0 of 1 [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA - [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [ 0%] 0 of 1 [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - Pulling Singularity image https://apps-01.i-med.ac.at/images/singularity/nextNEOpi_1.3.2_18734d43.sif [cache /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity/apps-01.i-med.ac.at-images-singularity-nextNEOpi_1.3.2_18734d43.sif] Pulling Singularity image https://depot.galaxyproject.org/singularity/gatk:3.8--hdfd78af_11 [cache /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity/depot.galaxyproject.org-singularity-gatk-3.8--hdfd78af_11.img] INFO: Mutect1 not available, skipping.... Pulling Singularity image https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0 [cache /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity/depot.galaxyproject.org-singularity-cnvkit-0.9.9--pyhdfd78af_0.img] WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location executor > local (12) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [ 0%] 0 of 1 [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [6c/82a75f] process > FastQC (Sample5 : tumor_DNA) [ 0%] 0 of 30 [- ] process > make_uBAM [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [ 0%] 0 of 1 [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - Pulling Singularity image https://apps-01.i-med.ac.at/images/singularity/nextNEOpi_1.3.2_18734d43.sif [cache /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity/apps-01.i-med.ac.at-images-singularity-nextNEOpi_1.3.2_18734d43.sif] Pulling Singularity image https://depot.galaxyproject.org/singularity/gatk:3.8--hdfd78af_11 [cache /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity/depot.galaxyproject.org-singularity-gatk-3.8--hdfd78af_11.img] INFO: Mutect1 not available, skipping.... Pulling Singularity image https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0 [cache /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity/depot.galaxyproject.org-singularity-cnvkit-0.9.9--pyhdfd78af_0.img] WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location executor > local (12) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [ 0%] 0 of 1 [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [6c/82a75f] process > FastQC (Sample5 : tumor_DNA) [ 0%] 0 of 30 [- ] process > make_uBAM [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [ 0%] 0 of 1 [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - Pulling Singularity image https://apps-01.i-med.ac.at/images/singularity/nextNEOpi_1.3.2_18734d43.sif [cache /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity/apps-01.i-med.ac.at-images-singularity-nextNEOpi_1.3.2_18734d43.sif] Pulling Singularity image https://depot.galaxyproject.org/singularity/gatk:3.8--hdfd78af_11 [cache /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity/depot.galaxyproject.org-singularity-gatk-3.8--hdfd78af_11.img] INFO: Mutect1 not available, skipping.... Pulling Singularity image https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0 [cache /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity/depot.galaxyproject.org-singularity-cnvkit-0.9.9--pyhdfd78af_0.img] WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location executor > local (13) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [6c/82a75f] process > FastQC (Sample5 : tumor_DNA) [ 0%] 0 of 30 [f2/dfd4f8] process > make_uBAM (Sample7 : normal... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [ 0%] 0 of 1 [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - Pulling Singularity image https://apps-01.i-med.ac.at/images/singularity/nextNEOpi_1.3.2_18734d43.sif [cache /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity/apps-01.i-med.ac.at-images-singularity-nextNEOpi_1.3.2_18734d43.sif] Pulling Singularity image https://depot.galaxyproject.org/singularity/gatk:3.8--hdfd78af_11 [cache /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity/depot.galaxyproject.org-singularity-gatk-3.8--hdfd78af_11.img] INFO: Mutect1 not available, skipping.... Pulling Singularity image https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0 [cache /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity/depot.galaxyproject.org-singularity-cnvkit-0.9.9--pyhdfd78af_0.img] WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location executor > local (14) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [6c/82a75f] process > FastQC (Sample5 : tumor_DNA) [ 0%] 0 of 30 [80/2fd06b] process > make_uBAM (sample2 : normal... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - Pulling Singularity image https://apps-01.i-med.ac.at/images/singularity/nextNEOpi_1.3.2_18734d43.sif [cache /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity/apps-01.i-med.ac.at-images-singularity-nextNEOpi_1.3.2_18734d43.sif] Pulling Singularity image https://depot.galaxyproject.org/singularity/gatk:3.8--hdfd78af_11 [cache /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity/depot.galaxyproject.org-singularity-gatk-3.8--hdfd78af_11.img] INFO: Mutect1 not available, skipping.... Pulling Singularity image https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0 [cache /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity/depot.galaxyproject.org-singularity-cnvkit-0.9.9--pyhdfd78af_0.img] WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/singularity -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location executor > local (15) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [98/f78606] process > FastQC (Sample4 : tumor_RNA) [ 3%] 1 of 30 [80/2fd06b] process > make_uBAM (sample2 : normal... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (15) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [98/f78606] process > FastQC (Sample4 : tumor_RNA) [ 3%] 1 of 30 [80/2fd06b] process > make_uBAM (sample2 : normal... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (16) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [62/dee178] process > FastQC (Sample4 : normal_DNA) [ 7%] 2 of 30 [80/2fd06b] process > make_uBAM (sample2 : normal... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (16) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [62/dee178] process > FastQC (Sample4 : normal_DNA) [ 7%] 2 of 30 [80/2fd06b] process > make_uBAM (sample2 : normal... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (16) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [27/f804d2] process > FastQC (sample2 : tumor_RNA) [ 10%] 3 of 30 [80/2fd06b] process > make_uBAM (sample2 : normal... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (17) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [d2/44a6fd] process > FastQC (sample1 : normal_DNA) [ 10%] 3 of 30 [80/2fd06b] process > make_uBAM (sample2 : normal... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (18) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [95/0f857a] process > FastQC (Sample5 : tumor_RNA) [ 13%] 4 of 30 [80/2fd06b] process > make_uBAM (sample2 : normal... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (19) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [95/0f857a] process > FastQC (Sample5 : tumor_RNA) [ 17%] 5 of 30 [80/2fd06b] process > make_uBAM (sample2 : normal... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (19) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [95/0f857a] process > FastQC (Sample5 : tumor_RNA) [ 17%] 5 of 30 [80/2fd06b] process > make_uBAM (sample2 : normal... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (20) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [6c/82a75f] process > FastQC (Sample5 : tumor_DNA) [ 20%] 6 of 30 [80/2fd06b] process > make_uBAM (sample2 : normal... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (20) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [6c/82a75f] process > FastQC (Sample5 : tumor_DNA) [ 20%] 6 of 30 [80/2fd06b] process > make_uBAM (sample2 : normal... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (21) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [e4/8df8f3] process > FastQC (Sample6 : tumor_RNA) [ 23%] 7 of 30 [80/2fd06b] process > make_uBAM (sample2 : normal... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (22) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [b3/340897] process > FastQC (Sample7 : tumor_DNA) [ 27%] 8 of 30 [80/2fd06b] process > make_uBAM (sample2 : normal... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (22) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [b3/340897] process > FastQC (Sample7 : tumor_DNA) [ 27%] 8 of 30 [80/2fd06b] process > make_uBAM (sample2 : normal... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (23) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [8a/82dcd6] process > FastQC (Sample7 : tumor_RNA) [ 30%] 9 of 30 [80/2fd06b] process > make_uBAM (sample2 : normal... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (24) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [a7/886a41] process > FastQC (sample2 : tumor_DNA) [ 33%] 10 of 30 [80/2fd06b] process > make_uBAM (sample2 : normal... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (24) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [a7/886a41] process > FastQC (sample2 : tumor_DNA) [ 33%] 10 of 30 [80/2fd06b] process > make_uBAM (sample2 : normal... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (25) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [80/a6a7dc] process > FastQC (sample3 : normal_DNA) [ 37%] 11 of 30 [80/2fd06b] process > make_uBAM (sample2 : normal... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (26) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [a7/391cfd] process > FastQC (Sample5 : normal_DNA) [ 40%] 12 of 30 [80/2fd06b] process > make_uBAM (sample2 : normal... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (27) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [6b/b9df14] process > FastQC (Sample6 : tumor_DNA) [ 43%] 13 of 30 [80/2fd06b] process > make_uBAM (sample2 : normal... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (27) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [6b/b9df14] process > FastQC (Sample6 : tumor_DNA) [ 43%] 13 of 30 [80/2fd06b] process > make_uBAM (sample2 : normal... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (28) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [2b/54c836] process > FastQC (Sample6 : normal_DNA) [ 47%] 14 of 30 [80/2fd06b] process > make_uBAM (sample2 : normal... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (30) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [d2/44a6fd] process > FastQC (sample1 : normal_DNA) [ 50%] 15 of 30 [b0/7a59da] process > make_uBAM (Sample4 : normal... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (30) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [d2/44a6fd] process > FastQC (sample1 : normal_DNA) [ 50%] 15 of 30 [b0/7a59da] process > make_uBAM (Sample4 : normal... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (31) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [83/6c1721] process > FastQC (Sample9 : normal_DNA) [ 53%] 16 of 30 [b0/7a59da] process > make_uBAM (Sample4 : normal... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (31) [- ] process > merge_fastq - [- ] process > RegionsBedToIntervalList [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [83/6c1721] process > FastQC (Sample9 : normal_DNA) [ 53%] 16 of 30 [b0/7a59da] process > make_uBAM (Sample4 : normal... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (33) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [ 0%] 0 of 1 [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [a7/886a41] process > FastQC (sample2 : tumor_DNA) [ 57%] 17 of 30 [9e/91044b] process > make_uBAM (Sample7 : tumor_... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (34) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList - [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [a7/886a41] process > FastQC (sample2 : tumor_DNA) [ 57%] 17 of 30 [e2/0299a9] process > make_uBAM (Sample5 : tumor_... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (34) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList [ 0%] 0 of 1 [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [a7/886a41] process > FastQC (sample2 : tumor_DNA) [ 57%] 17 of 30 [e2/0299a9] process > make_uBAM (Sample5 : tumor_... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (35) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList [ 0%] 0 of 1 [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [a7/391cfd] process > FastQC (Sample5 : normal_DNA) [ 60%] 18 of 30 [e2/0299a9] process > make_uBAM (Sample5 : tumor_... [ 0%] 0 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (36) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList [ 0%] 0 of 1 [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [a7/391cfd] process > FastQC (Sample5 : normal_DNA) [ 60%] 18 of 30 [3c/c5d2c8] process > make_uBAM (Sample5 : normal... [ 5%] 1 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (36) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList [ 0%] 0 of 1 [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [a7/391cfd] process > FastQC (Sample5 : normal_DNA) [ 60%] 18 of 30 [3c/c5d2c8] process > make_uBAM (Sample5 : normal... [ 5%] 1 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (37) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList [ 0%] 0 of 1 [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [80/a6a7dc] process > FastQC (sample3 : normal_DNA) [ 63%] 19 of 30 [3c/c5d2c8] process > make_uBAM (Sample5 : normal... [ 5%] 1 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (38) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList [ 0%] 0 of 1 [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [bb/576664] process > FastQC (Sample7 : normal_DNA) [ 67%] 20 of 30 [3c/c5d2c8] process > make_uBAM (Sample5 : normal... [ 5%] 1 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (40) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList [ 0%] 0 of 1 [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [2b/54c836] process > FastQC (Sample6 : normal_DNA) [ 70%] 21 of 30 [af/d3f543] process > make_uBAM (sample1 : normal... [ 5%] 1 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (40) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList [ 0%] 0 of 1 [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [2b/54c836] process > FastQC (Sample6 : normal_DNA) [ 70%] 21 of 30 [af/d3f543] process > make_uBAM (sample1 : normal... [ 5%] 1 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (41) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList [ 0%] 0 of 1 [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [25/175f9d] process > FastQC (Sample8 : normal_DNA) [ 73%] 22 of 30 [af/d3f543] process > make_uBAM (sample1 : normal... [ 5%] 1 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (43) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList [ 0%] 0 of 1 [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [83/6c1721] process > FastQC (Sample9 : normal_DNA) [ 77%] 23 of 30 [a4/f91eab] process > make_uBAM (sample3 : tumor_... [ 5%] 1 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (43) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList [ 0%] 0 of 1 [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [83/6c1721] process > FastQC (Sample9 : normal_DNA) [ 77%] 23 of 30 [a4/f91eab] process > make_uBAM (sample3 : tumor_... [ 5%] 1 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (44) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList [ 0%] 0 of 1 [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [83/6c1721] process > FastQC (Sample9 : normal_DNA) [ 77%] 23 of 30 [0b/f49e7b] process > make_uBAM (sample2 : tumor_... [ 10%] 2 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (45) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList [ 0%] 0 of 1 [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [1e/e3db70] process > FastQC (Sample9 : tumor_DNA) [ 80%] 24 of 30 [0b/f49e7b] process > make_uBAM (sample2 : tumor_... [ 10%] 2 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (46) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList [ 0%] 0 of 1 [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [fb/e4bcc6] process > FastQC (Sample8 : tumor_RNA) [ 83%] 25 of 30 [0b/f49e7b] process > make_uBAM (sample2 : tumor_... [ 10%] 2 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (48) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList [ 0%] 0 of 1 [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [dc/33e36f] process > FastQC (Sample10 : tumor_RNA) [ 87%] 26 of 30 [c4/e094b9] process > make_uBAM (Sample8 : tumor_... [ 10%] 2 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (50) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList [ 0%] 0 of 1 [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [fb/e4bcc6] process > FastQC (Sample8 : tumor_RNA) [ 90%] 27 of 30 [df/857e10] process > make_uBAM (sample1 : tumor_... [ 10%] 2 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (50) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList [ 0%] 0 of 1 [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [fb/e4bcc6] process > FastQC (Sample8 : tumor_RNA) [ 90%] 27 of 30 [df/857e10] process > make_uBAM (sample1 : tumor_... [ 10%] 2 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (51) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList [ 0%] 0 of 1 [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [fb/e4bcc6] process > FastQC (Sample8 : tumor_RNA) [ 90%] 27 of 30 [fe/440411] process > make_uBAM (Sample8 : normal... [ 15%] 3 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (52) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList [ 0%] 0 of 1 [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [5d/e25259] process > FastQC (Sample9 : tumor_RNA) [ 93%] 28 of 30 [fe/440411] process > make_uBAM (Sample8 : normal... [ 15%] 3 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (52) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList [ 0%] 0 of 1 [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [5d/e25259] process > FastQC (Sample9 : tumor_RNA) [ 93%] 28 of 30 [fe/440411] process > make_uBAM (Sample8 : normal... [ 15%] 3 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (53) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList [ 0%] 0 of 1 [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [0a/e48350] process > FastQC (Sample10 : tumor_DNA) [ 97%] 29 of 30 [fe/440411] process > make_uBAM (Sample8 : normal... [ 15%] 3 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (54) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList [ 0%] 0 of 1 [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [0a/e48350] process > FastQC (Sample10 : tumor_DNA) [ 97%] 29 of 30 [20/7ab7fb] process > make_uBAM (Sample9 : tumor_... [ 20%] 4 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (55) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList [ 0%] 0 of 1 [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [0a/e48350] process > FastQC (Sample10 : tumor_DNA) [ 97%] 29 of 30 [1a/b9d691] process > make_uBAM (Sample10 : tumor... [ 25%] 5 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (56) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [- ] process > preprocessIntervalList [ 0%] 0 of 1 [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [0a/e48350] process > FastQC (Sample10 : tumor_DNA) [ 97%] 29 of 30 [81/dff970] process > make_uBAM (Sample10 : norma... [ 30%] 6 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (57) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [3c/7b0afb] process > preprocessIntervalList (pre... [ 0%] 0 of 1 [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [0a/e48350] process > FastQC (Sample10 : tumor_DNA) [100%] 30 of 30 ✔ [81/dff970] process > make_uBAM (Sample10 : norma... [ 30%] 6 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (57) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [3c/7b0afb] process > preprocessIntervalList (pre... [ 0%] 0 of 1 [- ] process > SplitIntervals - [- ] process > IntervalListToBed - [- ] process > ScatteredIntervalListToBed - [0a/e48350] process > FastQC (Sample10 : tumor_DNA) [100%] 30 of 30 ✔ [81/dff970] process > make_uBAM (Sample10 : norma... [ 30%] 6 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (57) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [3c/7b0afb] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [- ] process > SplitIntervals [ 0%] 0 of 1 [- ] process > IntervalListToBed [ 0%] 0 of 1 [- ] process > ScatteredIntervalListToBed - [0a/e48350] process > FastQC (Sample10 : tumor_DNA) [100%] 30 of 30 ✔ [81/dff970] process > make_uBAM (Sample10 : norma... [ 30%] 6 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (59) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [3c/7b0afb] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [d1/b6d43d] process > SplitIntervals (SplitInterv... [ 0%] 0 of 1 [2c/9df816] process > IntervalListToBed (BedFromI... [ 0%] 0 of 1 [- ] process > ScatteredIntervalListToBed - [0a/e48350] process > FastQC (Sample10 : tumor_DNA) [100%] 30 of 30 ✔ [81/dff970] process > make_uBAM (Sample10 : norma... [ 30%] 6 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (59) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [3c/7b0afb] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [d1/b6d43d] process > SplitIntervals (SplitInterv... [ 0%] 0 of 1 [2c/9df816] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [- ] process > ScatteredIntervalListToBed - [0a/e48350] process > FastQC (Sample10 : tumor_DNA) [100%] 30 of 30 ✔ [81/dff970] process > make_uBAM (Sample10 : norma... [ 30%] 6 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (59) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [3c/7b0afb] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [d1/b6d43d] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [2c/9df816] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [- ] process > ScatteredIntervalListToBed - [0a/e48350] process > FastQC (Sample10 : tumor_DNA) [100%] 30 of 30 ✔ [81/dff970] process > make_uBAM (Sample10 : norma... [ 30%] 6 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (59) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [3c/7b0afb] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [d1/b6d43d] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [2c/9df816] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [- ] process > ScatteredIntervalListToBed [ 0%] 0 of 40 [0a/e48350] process > FastQC (Sample10 : tumor_DNA) [100%] 30 of 30 ✔ [81/dff970] process > make_uBAM (Sample10 : norma... [ 30%] 6 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (61) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [3c/7b0afb] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [d1/b6d43d] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [2c/9df816] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [cd/f7436d] process > ScatteredIntervalListToBed ... [ 0%] 0 of 40 [0a/e48350] process > FastQC (Sample10 : tumor_DNA) [100%] 30 of 30 ✔ [81/dff970] process > make_uBAM (Sample10 : norma... [ 30%] 6 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (63) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [3c/7b0afb] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [d1/b6d43d] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [2c/9df816] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [6e/dac671] process > ScatteredIntervalListToBed ... [ 5%] 2 of 40 [0a/e48350] process > FastQC (Sample10 : tumor_DNA) [100%] 30 of 30 ✔ [81/dff970] process > make_uBAM (Sample10 : norma... [ 30%] 6 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (63) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [3c/7b0afb] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [d1/b6d43d] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [2c/9df816] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [6e/dac671] process > ScatteredIntervalListToBed ... [ 5%] 2 of 40 [0a/e48350] process > FastQC (Sample10 : tumor_DNA) [100%] 30 of 30 ✔ [81/dff970] process > make_uBAM (Sample10 : norma... [ 30%] 6 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (64) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [3c/7b0afb] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [d1/b6d43d] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [2c/9df816] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [6e/15f618] process > ScatteredIntervalListToBed ... [ 8%] 3 of 40 [0a/e48350] process > FastQC (Sample10 : tumor_DNA) [100%] 30 of 30 ✔ [81/dff970] process > make_uBAM (Sample10 : norma... [ 30%] 6 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (65) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [3c/7b0afb] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [d1/b6d43d] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [2c/9df816] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [87/1ee9e2] process > ScatteredIntervalListToBed ... [ 10%] 4 of 40 [0a/e48350] process > FastQC (Sample10 : tumor_DNA) [100%] 30 of 30 ✔ [81/dff970] process > make_uBAM (Sample10 : norma... [ 30%] 6 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (66) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [3c/7b0afb] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [d1/b6d43d] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [2c/9df816] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [08/7c0b76] process > ScatteredIntervalListToBed ... [ 13%] 5 of 40 [0a/e48350] process > FastQC (Sample10 : tumor_DNA) [100%] 30 of 30 ✔ [81/dff970] process > make_uBAM (Sample10 : norma... [ 30%] 6 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (67) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [3c/7b0afb] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [d1/b6d43d] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [2c/9df816] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [72/2a6c9d] process > ScatteredIntervalListToBed ... [ 15%] 6 of 40 [0a/e48350] process > FastQC (Sample10 : tumor_DNA) [100%] 30 of 30 ✔ [81/dff970] process > make_uBAM (Sample10 : norma... [ 30%] 6 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (69) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [3c/7b0afb] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [d1/b6d43d] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [2c/9df816] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [ea/665867] process > ScatteredIntervalListToBed ... [ 20%] 8 of 40 [0a/e48350] process > FastQC (Sample10 : tumor_DNA) [100%] 30 of 30 ✔ [81/dff970] process > make_uBAM (Sample10 : norma... [ 30%] 6 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (69) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [3c/7b0afb] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [d1/b6d43d] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [2c/9df816] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [ea/665867] process > ScatteredIntervalListToBed ... [ 20%] 8 of 40 [0a/e48350] process > FastQC (Sample10 : tumor_DNA) [100%] 30 of 30 ✔ [81/dff970] process > make_uBAM (Sample10 : norma... [ 30%] 6 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (70) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [3c/7b0afb] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [d1/b6d43d] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [2c/9df816] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [24/cf9916] process > ScatteredIntervalListToBed ... [ 23%] 9 of 40 [0a/e48350] process > FastQC (Sample10 : tumor_DNA) [100%] 30 of 30 ✔ [81/dff970] process > make_uBAM (Sample10 : norma... [ 30%] 6 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (71) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [3c/7b0afb] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [d1/b6d43d] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [2c/9df816] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [ee/d53435] process > ScatteredIntervalListToBed ... [ 25%] 10 of 40 [0a/e48350] process > FastQC (Sample10 : tumor_DNA) [100%] 30 of 30 ✔ [81/dff970] process > make_uBAM (Sample10 : norma... [ 30%] 6 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (72) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [3c/7b0afb] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [d1/b6d43d] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [2c/9df816] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [bc/32792d] process > ScatteredIntervalListToBed ... [ 28%] 11 of 40 [0a/e48350] process > FastQC (Sample10 : tumor_DNA) [100%] 30 of 30 ✔ [81/dff970] process > make_uBAM (Sample10 : norma... [ 30%] 6 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (73) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [3c/7b0afb] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [d1/b6d43d] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [2c/9df816] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [3a/3e5cd3] process > ScatteredIntervalListToBed ... [ 30%] 12 of 40 [0a/e48350] process > FastQC (Sample10 : tumor_DNA) [100%] 30 of 30 ✔ [81/dff970] process > make_uBAM (Sample10 : norma... [ 30%] 6 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (74) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [3c/7b0afb] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [d1/b6d43d] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [2c/9df816] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [44/d0f01d] process > ScatteredIntervalListToBed ... [ 30%] 12 of 40 [0a/e48350] process > FastQC (Sample10 : tumor_DNA) [100%] 30 of 30 ✔ [81/dff970] process > make_uBAM (Sample10 : norma... [ 30%] 6 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - executor > local (74) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [3c/7b0afb] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [d1/b6d43d] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [2c/9df816] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [44/d0f01d] process > ScatteredIntervalListToBed ... [ 30%] 12 of 40 [0a/e48350] process > FastQC (Sample10 : tumor_DNA) [100%] 30 of 30 ✔ [81/dff970] process > make_uBAM (Sample10 : norma... [ 30%] 6 of 20 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - Error executing process > 'make_uBAM (sample1 : normal_DNA)' Caused by: Process `make_uBAM (sample1 : normal_DNA)` terminated with an error exit status (247) Command executed: mkdir -p /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/temp gatk --java-options "-Xmx64G -XX:ParallelGCThreads=1" FastqToSam \ --TMP_DIR /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/temp \ --MAX_RECORDS_IN_RAM 4194304 \ -F1 10-101PBMC_S20_R1.fastq.gz -F2 10-101PBMC_S20_R2.fastq.gz \ --READ_GROUP_NAME sample1_normal \ --SAMPLE_NAME sample1_normal \ --LIBRARY_NAME sample1_normal \ --PLATFORM ILLUMINA \ -O sample1_normal_DNA_unaligned.bam Command exit status: 247 Command output: (empty) Command error: INFO 2023-04-13 16:21:31 FastqToSam Processed 122,000,000 records. Elapsed time: 00:21:20s. Time for last 1,000,000: 17s. Last read position: */* INFO 2023-04-13 16:21:37 FastqToSam Processed 123,000,000 records. Elapsed time: 00:21:26s. Time for last 1,000,000: 6s. Last read position: */* INFO 2023-04-13 16:21:41 FastqToSam Processed 124,000,000 records. Elapsed time: 00:21:30s. Time for last 1,000,000: 3s. Last read position: */* INFO 2023-04-13 16:21:45 FastqToSam Processed 125,000,000 records. Elapsed time: 00:21:34s. Time for last 1,000,000: 4s. Last read position: */* INFO 2023-04-13 16:22:00 FastqToSam Processed 126,000,000 records. Elapsed time: 00:21:49s. Time for last 1,000,000: 14s. Last read position: */* INFO 2023-04-13 16:22:06 FastqToSam Processed 127,000,000 records. Elapsed time: 00:21:54s. Time for last 1,000,000: 5s. Last read position: */* INFO 2023-04-13 16:22:09 FastqToSam Processed 128,000,000 records. Elapsed time: 00:21:58s. Time for last 1,000,000: 3s. Last read position: */* INFO 2023-04-13 16:22:15 FastqToSam Processed 129,000,000 records. Elapsed time: 00:22:04s. Time for last 1,000,000: 5s. Last read position: */* INFO 2023-04-13 16:22:19 FastqToSam Processed 130,000,000 records. Elapsed time: 00:22:08s. Time for last 1,000,000: 4s. Last read position: */* INFO 2023-04-13 16:22:38 FastqToSam Processed 131,000,000 records. Elapsed time: 00:22:27s. Time for last 1,000,000: 18s. Last read position: */* INFO 2023-04-13 16:22:42 FastqToSam Processed 132,000,000 records. Elapsed time: 00:22:30s. Time for last 1,000,000: 3s. Last read position: */* INFO 2023-04-13 16:22:46 FastqToSam Processed 133,000,000 records. Elapsed time: 00:22:35s. Time for last 1,000,000: 4s. Last read position: */* INFO 2023-04-13 16:22:50 FastqToSam Processed 134,000,000 records. Elapsed time: 00:22:39s. Time for last 1,000,000: 3s. Last read position: */* INFO 2023-04-13 16:23:09 FastqToSam Processed 135,000,000 records. Elapsed time: 00:22:58s. Time for last 1,000,000: 19s. Last read position: */* INFO 2023-04-13 16:23:13 FastqToSam Processed 136,000,000 records. Elapsed time: 00:23:01s. Time for last 1,000,000: 3s. Last read position: */* INFO 2023-04-13 16:24:39 FastqToSam Processed 137,000,000 records. Elapsed time: 00:24:28s. Time for last 1,000,000: 86s. Last read position: */* INFO 2023-04-13 16:24:46 FastqToSam Processed 138,000,000 records. Elapsed time: 00:24:35s. Time for last 1,000,000: 6s. Last read position: */* INFO 2023-04-13 16:25:04 FastqToSam Processed 139,000,000 records. Elapsed time: 00:24:52s. Time for last 1,000,000: 17s. Last read position: */* INFO 2023-04-13 16:25:12 FastqToSam Processed 140,000,000 records. Elapsed time: 00:25:00s. Time for last 1,000,000: 7s. Last read position: */* INFO 2023-04-13 16:25:15 FastqToSam Processed 141,000,000 records. Elapsed time: 00:25:04s. Time for last 1,000,000: 3s. Last read position: */* INFO 2023-04-13 16:25:21 FastqToSam Processed 142,000,000 records. Elapsed time: 00:25:10s. Time for last 1,000,000: 6s. Last read position: */* INFO 2023-04-13 16:25:37 FastqToSam Processed 143,000,000 records. Elapsed time: 00:25:25s. Time for last 1,000,000: 15s. Last read position: */* INFO 2023-04-13 16:25:43 FastqToSam Processed 144,000,000 records. Elapsed time: 00:25:32s. Time for last 1,000,000: 6s. Last read position: */* INFO 2023-04-13 16:25:46 FastqToSam Processed 145,000,000 records. Elapsed time: 00:25:35s. Time for last 1,000,000: 2s. Last read position: */* INFO 2023-04-13 16:25:51 FastqToSam Processed 146,000,000 records. Elapsed time: 00:25:40s. Time for last 1,000,000: 5s. Last read position: */* INFO 2023-04-13 16:26:08 FastqToSam Processed 147,000,000 records. Elapsed time: 00:25:57s. Time for last 1,000,000: 16s. Last read position: */* INFO 2023-04-13 16:26:17 FastqToSam Processed 148,000,000 records. Elapsed time: 00:26:06s. Time for last 1,000,000: 8s. Last read position: */* INFO 2023-04-13 16:26:22 FastqToSam Processed 149,000,000 records. Elapsed time: 00:26:11s. Time for last 1,000,000: 5s. Last read position: */* INFO 2023-04-13 16:26:27 FastqToSam Processed 150,000,000 records. Elapsed time: 00:26:16s. Time for last 1,000,000: 4s. Last read position: */* INFO 2023-04-13 16:26:44 FastqToSam Processed 151,000,000 records. Elapsed time: 00:26:32s. Time for last 1,000,000: 16s. Last read position: */* INFO 2023-04-13 16:26:48 FastqToSam Processed 152,000,000 records. Elapsed time: 00:26:37s. Time for last 1,000,000: 4s. Last read position: */* INFO 2023-04-13 16:26:55 FastqToSam Processed 153,000,000 records. Elapsed time: 00:26:43s. Time for last 1,000,000: 6s. Last read position: */* INFO 2023-04-13 16:26:57 FastqToSam Processed 154,000,000 records. Elapsed time: 00:26:46s. Time for last 1,000,000: 2s. Last read position: */* INFO 2023-04-13 16:27:02 FastqToSam Processed 155,000,000 records. Elapsed time: 00:26:51s. Time for last 1,000,000: 4s. Last read position: */* INFO 2023-04-13 16:27:18 FastqToSam Processed 156,000,000 records. Elapsed time: 00:27:06s. Time for last 1,000,000: 15s. Last read position: */* INFO 2023-04-13 16:27:24 FastqToSam Processed 157,000,000 records. Elapsed time: 00:27:13s. Time for last 1,000,000: 6s. Last read position: */* INFO 2023-04-13 16:27:28 FastqToSam Processed 158,000,000 records. Elapsed time: 00:27:16s. Time for last 1,000,000: 3s. Last read position: */* INFO 2023-04-13 16:27:35 FastqToSam Processed 159,000,000 records. Elapsed time: 00:27:23s. Time for last 1,000,000: 6s. Last read position: */* INFO 2023-04-13 16:27:52 FastqToSam Processed 160,000,000 records. Elapsed time: 00:27:40s. Time for last 1,000,000: 16s. Last read position: */* INFO 2023-04-13 16:27:57 FastqToSam Processed 161,000,000 records. Elapsed time: 00:27:45s. Time for last 1,000,000: 4s. Last read position: */* INFO 2023-04-13 16:28:00 FastqToSam Processed 162,000,000 records. Elapsed time: 00:27:49s. Time for last 1,000,000: 3s. Last read position: */* INFO 2023-04-13 16:28:07 FastqToSam Processed 163,000,000 records. Elapsed time: 00:27:56s. Time for last 1,000,000: 6s. Last read position: */* INFO 2023-04-13 16:28:27 FastqToSam Processed 164,000,000 records. Elapsed time: 00:28:16s. Time for last 1,000,000: 19s. Last read position: */* INFO 2023-04-13 16:28:30 FastqToSam Processed 165,000,000 records. Elapsed time: 00:28:19s. Time for last 1,000,000: 3s. Last read position: */* INFO 2023-04-13 16:28:37 FastqToSam Processed 166,000,000 records. Elapsed time: 00:28:26s. Time for last 1,000,000: 7s. Last read position: */* INFO 2023-04-13 16:28:40 FastqToSam Processed 167,000,000 records. Elapsed time: 00:28:29s. Time for last 1,000,000: 3s. Last read position: */* INFO 2023-04-13 16:28:57 FastqToSam Processed 168,000,000 records. Elapsed time: 00:28:46s. Time for last 1,000,000: 17s. Last read position: */* Using GATK jar /opt/conda/share/gatk4-4.2.6.1-1/gatk-package-4.2.6.1-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx64G -XX:ParallelGCThreads=1 -jar /opt/conda/share/gatk4-4.2.6.1-1/gatk-package-4.2.6.1-local.jar FastqToSam --TMP_DIR /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/temp --MAX_RECORDS_IN_RAM 4194304 -F1 10-101PBMC_S20_R1.fastq.gz -F2 10-101PBMC_S20_R2.fastq.gz --READ_GROUP_NAME sample1_normal --SAMPLE_NAME sample1_normal --LIBRARY_NAME sample1_normal --PLATFORM ILLUMINA -O sample1_normal_DNA_unaligned.bam Work dir: /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/af/d3f543a0c1ac70ce752658b87bc136 Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh` executor > local (74) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [3c/7b0afb] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [d1/b6d43d] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [2c/9df816] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [44/d0f01d] process > ScatteredIntervalListToBed ... [ 30%] 12 of 40 [0a/e48350] process > FastQC (Sample10 : tumor_DNA) [100%] 30 of 30 ✔ [af/d3f543] process > make_uBAM (sample1 : normal... [ 35%] 7 of 20, failed: 1 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - Execution cancelled -- Finishing pending tasks before exit Error executing process > 'make_uBAM (sample1 : normal_DNA)' Caused by: Process `make_uBAM (sample1 : normal_DNA)` terminated with an error exit status (247) Command executed: mkdir -p /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/temp gatk --java-options "-Xmx64G -XX:ParallelGCThreads=1" FastqToSam \ --TMP_DIR /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/temp \ --MAX_RECORDS_IN_RAM 4194304 \ -F1 10-101PBMC_S20_R1.fastq.gz -F2 10-101PBMC_S20_R2.fastq.gz \ --READ_GROUP_NAME sample1_normal \ --SAMPLE_NAME sample1_normal \ --LIBRARY_NAME sample1_normal \ --PLATFORM ILLUMINA \ -O sample1_normal_DNA_unaligned.bam Command exit status: 247 Command output: (empty) Command error: INFO 2023-04-13 16:21:31 FastqToSam Processed 122,000,000 records. Elapsed time: 00:21:20s. Time for last 1,000,000: 17s. Last read position: */* INFO 2023-04-13 16:21:37 FastqToSam Processed 123,000,000 records. Elapsed time: 00:21:26s. Time for last 1,000,000: 6s. Last read position: */* INFO 2023-04-13 16:21:41 FastqToSam Processed 124,000,000 records. Elapsed time: 00:21:30s. Time for last 1,000,000: 3s. Last read position: */* INFO 2023-04-13 16:21:45 FastqToSam Processed 125,000,000 records. Elapsed time: 00:21:34s. Time for last 1,000,000: 4s. Last read position: */* INFO 2023-04-13 16:22:00 FastqToSam Processed 126,000,000 records. Elapsed time: 00:21:49s. Time for last 1,000,000: 14s. Last read position: */* INFO 2023-04-13 16:22:06 FastqToSam Processed 127,000,000 records. Elapsed time: 00:21:54s. Time for last 1,000,000: 5s. Last read position: */* INFO 2023-04-13 16:22:09 FastqToSam Processed 128,000,000 records. Elapsed time: 00:21:58s. Time for last 1,000,000: 3s. Last read position: */* INFO 2023-04-13 16:22:15 FastqToSam Processed 129,000,000 records. Elapsed time: 00:22:04s. Time for last 1,000,000: 5s. Last read position: */* INFO 2023-04-13 16:22:19 FastqToSam Processed 130,000,000 records. Elapsed time: 00:22:08s. Time for last 1,000,000: 4s. Last read position: */* INFO 2023-04-13 16:22:38 FastqToSam Processed 131,000,000 records. Elapsed time: 00:22:27s. Time for last 1,000,000: 18s. Last read position: */* INFO 2023-04-13 16:22:42 FastqToSam Processed 132,000,000 records. Elapsed time: 00:22:30s. Time for last 1,000,000: 3s. Last read position: */* INFO 2023-04-13 16:22:46 FastqToSam Processed 133,000,000 records. Elapsed time: 00:22:35s. Time for last 1,000,000: 4s. Last read position: */* INFO 2023-04-13 16:22:50 FastqToSam Processed 134,000,000 records. Elapsed time: 00:22:39s. Time for last 1,000,000: 3s. Last read position: */* INFO 2023-04-13 16:23:09 FastqToSam Processed 135,000,000 records. Elapsed time: 00:22:58s. Time for last 1,000,000: 19s. Last read position: */* INFO 2023-04-13 16:23:13 FastqToSam Processed 136,000,000 records. Elapsed time: 00:23:01s. Time for last 1,000,000: 3s. Last read position: */* INFO 2023-04-13 16:24:39 FastqToSam Processed 137,000,000 records. Elapsed time: 00:24:28s. Time for last 1,000,000: 86s. Last read position: */* INFO 2023-04-13 16:24:46 FastqToSam Processed 138,000,000 records. Elapsed time: 00:24:35s. Time for last 1,000,000: 6s. Last read position: */* INFO 2023-04-13 16:25:04 FastqToSam Processed 139,000,000 records. Elapsed time: 00:24:52s. Time for last 1,000,000: 17s. Last read position: */* INFO 2023-04-13 16:25:12 FastqToSam Processed 140,000,000 records. Elapsed time: 00:25:00s. Time for last 1,000,000: 7s. Last read position: */* INFO 2023-04-13 16:25:15 FastqToSam Processed 141,000,000 records. Elapsed time: 00:25:04s. Time for last 1,000,000: 3s. Last read position: */* INFO 2023-04-13 16:25:21 FastqToSam Processed 142,000,000 records. Elapsed time: 00:25:10s. Time for last 1,000,000: 6s. Last read position: */* INFO 2023-04-13 16:25:37 FastqToSam Processed 143,000,000 records. Elapsed time: 00:25:25s. Time for last 1,000,000: 15s. Last read position: */* INFO 2023-04-13 16:25:43 FastqToSam Processed 144,000,000 records. Elapsed time: 00:25:32s. Time for last 1,000,000: 6s. Last read position: */* INFO 2023-04-13 16:25:46 FastqToSam Processed 145,000,000 records. Elapsed time: 00:25:35s. Time for last 1,000,000: 2s. Last read position: */* INFO 2023-04-13 16:25:51 FastqToSam Processed 146,000,000 records. Elapsed time: 00:25:40s. Time for last 1,000,000: 5s. Last read position: */* INFO 2023-04-13 16:26:08 FastqToSam Processed 147,000,000 records. Elapsed time: 00:25:57s. Time for last 1,000,000: 16s. Last read position: */* INFO 2023-04-13 16:26:17 FastqToSam Processed 148,000,000 records. Elapsed time: 00:26:06s. Time for last 1,000,000: 8s. Last read position: */* INFO 2023-04-13 16:26:22 FastqToSam Processed 149,000,000 records. Elapsed time: 00:26:11s. Time for last 1,000,000: 5s. Last read position: */* INFO 2023-04-13 16:26:27 FastqToSam Processed 150,000,000 records. Elapsed time: 00:26:16s. Time for last 1,000,000: 4s. Last read position: */* INFO 2023-04-13 16:26:44 FastqToSam Processed 151,000,000 records. Elapsed time: 00:26:32s. Time for last 1,000,000: 16s. Last read position: */* INFO 2023-04-13 16:26:48 FastqToSam Processed 152,000,000 records. Elapsed time: 00:26:37s. Time for last 1,000,000: 4s. Last read position: */* INFO 2023-04-13 16:26:55 FastqToSam Processed 153,000,000 records. Elapsed time: 00:26:43s. Time for last 1,000,000: 6s. Last read position: */* INFO 2023-04-13 16:26:57 FastqToSam Processed 154,000,000 records. Elapsed time: 00:26:46s. Time for last 1,000,000: 2s. Last read position: */* INFO 2023-04-13 16:27:02 FastqToSam Processed 155,000,000 records. Elapsed time: 00:26:51s. Time for last 1,000,000: 4s. Last read position: */* INFO 2023-04-13 16:27:18 FastqToSam Processed 156,000,000 records. Elapsed time: 00:27:06s. Time for last 1,000,000: 15s. Last read position: */* INFO 2023-04-13 16:27:24 FastqToSam Processed 157,000,000 records. Elapsed time: 00:27:13s. Time for last 1,000,000: 6s. Last read position: */* INFO 2023-04-13 16:27:28 FastqToSam Processed 158,000,000 records. Elapsed time: 00:27:16s. Time for last 1,000,000: 3s. Last read position: */* INFO 2023-04-13 16:27:35 FastqToSam Processed 159,000,000 records. Elapsed time: 00:27:23s. Time for last 1,000,000: 6s. Last read position: */* INFO 2023-04-13 16:27:52 FastqToSam Processed 160,000,000 records. Elapsed time: 00:27:40s. Time for last 1,000,000: 16s. Last read position: */* INFO 2023-04-13 16:27:57 FastqToSam Processed 161,000,000 records. Elapsed time: 00:27:45s. Time for last 1,000,000: 4s. Last read position: */* INFO 2023-04-13 16:28:00 FastqToSam Processed 162,000,000 records. Elapsed time: 00:27:49s. Time for last 1,000,000: 3s. Last read position: */* INFO 2023-04-13 16:28:07 FastqToSam Processed 163,000,000 records. Elapsed time: 00:27:56s. Time for last 1,000,000: 6s. Last read position: */* INFO 2023-04-13 16:28:27 FastqToSam Processed 164,000,000 records. Elapsed time: 00:28:16s. Time for last 1,000,000: 19s. Last read position: */* INFO 2023-04-13 16:28:30 FastqToSam Processed 165,000,000 records. Elapsed time: 00:28:19s. Time for last 1,000,000: 3s. Last read position: */* INFO 2023-04-13 16:28:37 FastqToSam Processed 166,000,000 records. Elapsed time: 00:28:26s. Time for last 1,000,000: 7s. Last read position: */* INFO 2023-04-13 16:28:40 FastqToSam Processed 167,000,000 records. Elapsed time: 00:28:29s. Time for last 1,000,000: 3s. Last read position: */* INFO 2023-04-13 16:28:57 FastqToSam Processed 168,000,000 records. Elapsed time: 00:28:46s. Time for last 1,000,000: 17s. Last read position: */* Using GATK jar /opt/conda/share/gatk4-4.2.6.1-1/gatk-package-4.2.6.1-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx64G -XX:ParallelGCThreads=1 -jar /opt/conda/share/gatk4-4.2.6.1-1/gatk-package-4.2.6.1-local.jar FastqToSam --TMP_DIR /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/temp --MAX_RECORDS_IN_RAM 4194304 -F1 10-101PBMC_S20_R1.fastq.gz -F2 10-101PBMC_S20_R2.fastq.gz --READ_GROUP_NAME sample1_normal --SAMPLE_NAME sample1_normal --LIBRARY_NAME sample1_normal --PLATFORM ILLUMINA -O sample1_normal_DNA_unaligned.bam Work dir: /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/af/d3f543a0c1ac70ce752658b87bc136 Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh` executor > local (74) [- ] process > merge_fastq - [b9/b5cfa8] process > RegionsBedToIntervalList (R... [100%] 1 of 1 ✔ [c3/5e7149] process > BaitsBedToIntervalList (Bai... [100%] 1 of 1 ✔ [3c/7b0afb] process > preprocessIntervalList (pre... [100%] 1 of 1 ✔ [d1/b6d43d] process > SplitIntervals (SplitInterv... [100%] 1 of 1 ✔ [2c/9df816] process > IntervalListToBed (BedFromI... [100%] 1 of 1 ✔ [44/d0f01d] process > ScatteredIntervalListToBed ... [ 33%] 13 of 40 [0a/e48350] process > FastQC (Sample10 : tumor_DNA) [100%] 30 of 30 ✔ [af/d3f543] process > make_uBAM (sample1 : normal... [ 35%] 7 of 20, failed: 1 [- ] process > Bwa [ 0%] 0 of 20 [- ] process > merge_uBAM_BAM - [- ] process > MarkDuplicates - [- ] process > alignmentMetrics - [- ] process > scatterBaseRecalGATK4 - [- ] process > gatherGATK4scsatteredBQSRta... - [- ] process > scatterGATK4applyBQSRS - [- ] process > GatherRecalBamFiles - [- ] process > GetPileup - [65/083136] process > install_conda_GATK3 (instal... [100%] 1 of 1 ✔ [- ] process > Mutect2 - [- ] process > gatherMutect2VCFs - [- ] process > FilterMutect2 - [- ] process > HaploTypeCaller - [- ] process > CNNScoreVariants - [- ] process > MergeHaploTypeCallerGermlin... - [- ] process > FilterGermlineVariantTranches - [- ] process > IndelRealignerIntervals - [- ] process > GatherRealignedBamFiles - [- ] process > VarscanSomaticScattered - [- ] process > gatherVarscanVCFs - [- ] process > ProcessVarscan - [- ] process > FilterVarscan - [- ] process > MergeAndRenameSamplesInVars... - [- ] process > MantaSomaticIndels - [- ] process > StrelkaSomatic - [- ] process > finalizeStrelkaVCF - [- ] process > mkHCsomaticVCF - [- ] process > VepTab - [- ] process > mkCombinedVCF - [- ] process > VEPvcf - [- ] process > ReadBackedphasing - [- ] process > AlleleCounter - [- ] process > ConvertAlleleCounts - [- ] process > Ascat - [- ] process > SequenzaUtils - [- ] process > gatherSequenzaInput - [- ] process > Sequenza - [3a/6e5011] process > make_CNVkit_access_file (mk... [100%] 1 of 1 ✔ [- ] process > CNVkit - [- ] process > Clonality - [- ] process > MutationalBurden - [- ] process > MutationalBurdenCoding - [- ] process > mhc_extract - [- ] process > pre_map_hla - [- ] process > OptiType - [- ] process > pre_map_hla_RNA [ 0%] 0 of 10 [- ] process > OptiType_RNA - [- ] process > run_hla_hd - [- ] process > get_vhla - [- ] process > Neofuse - [- ] process > publish_NeoFuse - [- ] process > add_geneID - [- ] process > gene_annotator - [- ] process > pVACseq - [- ] process > concat_pVACseq_files - [- ] process > aggregated_reports - [- ] process > pVACtools_generate_protein_seq - [- ] process > pepare_mixMHC2_seq - [5e/8b6324] process > install_mixMHC2pred (instal... [100%] 1 of 1 ✔ [- ] process > mixMHC2pred - [- ] process > addCCF - [- ] process > make_epitopes_fasta - [- ] process > blast_epitopes - [- ] process > add_blast_hits - [- ] process > csin - [6f/7d7b1a] process > install_IGS (install IGS) [100%] 1 of 1 ✔ [- ] process > immunogenicity_scoring - [- ] process > mixcr [ 0%] 0 of 30 [- ] process > collectSampleInfo - [- ] process > multiQC - Execution cancelled -- Finishing pending tasks before exit Error executing process > 'make_uBAM (sample1 : normal_DNA)' Caused by: Process `make_uBAM (sample1 : normal_DNA)` terminated with an error exit status (247) Command executed: mkdir -p /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/temp gatk --java-options "-Xmx64G -XX:ParallelGCThreads=1" FastqToSam \ --TMP_DIR /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/temp \ --MAX_RECORDS_IN_RAM 4194304 \ -F1 10-101PBMC_S20_R1.fastq.gz -F2 10-101PBMC_S20_R2.fastq.gz \ --READ_GROUP_NAME sample1_normal \ --SAMPLE_NAME sample1_normal \ --LIBRARY_NAME sample1_normal \ --PLATFORM ILLUMINA \ -O sample1_normal_DNA_unaligned.bam Command exit status: 247 Command output: (empty) Command error: INFO 2023-04-13 16:21:31 FastqToSam Processed 122,000,000 records. Elapsed time: 00:21:20s. Time for last 1,000,000: 17s. Last read position: */* INFO 2023-04-13 16:21:37 FastqToSam Processed 123,000,000 records. Elapsed time: 00:21:26s. Time for last 1,000,000: 6s. Last read position: */* INFO 2023-04-13 16:21:41 FastqToSam Processed 124,000,000 records. Elapsed time: 00:21:30s. Time for last 1,000,000: 3s. Last read position: */* INFO 2023-04-13 16:21:45 FastqToSam Processed 125,000,000 records. Elapsed time: 00:21:34s. Time for last 1,000,000: 4s. Last read position: */* INFO 2023-04-13 16:22:00 FastqToSam Processed 126,000,000 records. Elapsed time: 00:21:49s. Time for last 1,000,000: 14s. Last read position: */* INFO 2023-04-13 16:22:06 FastqToSam Processed 127,000,000 records. Elapsed time: 00:21:54s. Time for last 1,000,000: 5s. Last read position: */* INFO 2023-04-13 16:22:09 FastqToSam Processed 128,000,000 records. Elapsed time: 00:21:58s. Time for last 1,000,000: 3s. Last read position: */* INFO 2023-04-13 16:22:15 FastqToSam Processed 129,000,000 records. Elapsed time: 00:22:04s. Time for last 1,000,000: 5s. Last read position: */* INFO 2023-04-13 16:22:19 FastqToSam Processed 130,000,000 records. Elapsed time: 00:22:08s. Time for last 1,000,000: 4s. Last read position: */* INFO 2023-04-13 16:22:38 FastqToSam Processed 131,000,000 records. Elapsed time: 00:22:27s. Time for last 1,000,000: 18s. Last read position: */* INFO 2023-04-13 16:22:42 FastqToSam Processed 132,000,000 records. Elapsed time: 00:22:30s. Time for last 1,000,000: 3s. Last read position: */* INFO 2023-04-13 16:22:46 FastqToSam Processed 133,000,000 records. Elapsed time: 00:22:35s. Time for last 1,000,000: 4s. Last read position: */* INFO 2023-04-13 16:22:50 FastqToSam Processed 134,000,000 records. Elapsed time: 00:22:39s. Time for last 1,000,000: 3s. Last read position: */* INFO 2023-04-13 16:23:09 FastqToSam Processed 135,000,000 records. Elapsed time: 00:22:58s. Time for last 1,000,000: 19s. Last read position: */* INFO 2023-04-13 16:23:13 FastqToSam Processed 136,000,000 records. Elapsed time: 00:23:01s. Time for last 1,000,000: 3s. Last read position: */* INFO 2023-04-13 16:24:39 FastqToSam Processed 137,000,000 records. Elapsed time: 00:24:28s. Time for last 1,000,000: 86s. Last read position: */* INFO 2023-04-13 16:24:46 FastqToSam Processed 138,000,000 records. Elapsed time: 00:24:35s. Time for last 1,000,000: 6s. Last read position: */* INFO 2023-04-13 16:25:04 FastqToSam Processed 139,000,000 records. Elapsed time: 00:24:52s. Time for last 1,000,000: 17s. Last read position: */* INFO 2023-04-13 16:25:12 FastqToSam Processed 140,000,000 records. Elapsed time: 00:25:00s. Time for last 1,000,000: 7s. Last read position: */* INFO 2023-04-13 16:25:15 FastqToSam Processed 141,000,000 records. Elapsed time: 00:25:04s. Time for last 1,000,000: 3s. Last read position: */* INFO 2023-04-13 16:25:21 FastqToSam Processed 142,000,000 records. Elapsed time: 00:25:10s. Time for last 1,000,000: 6s. Last read position: */* INFO 2023-04-13 16:25:37 FastqToSam Processed 143,000,000 records. Elapsed time: 00:25:25s. Time for last 1,000,000: 15s. Last read position: */* INFO 2023-04-13 16:25:43 FastqToSam Processed 144,000,000 records. Elapsed time: 00:25:32s. Time for last 1,000,000: 6s. Last read position: */* INFO 2023-04-13 16:25:46 FastqToSam Processed 145,000,000 records. Elapsed time: 00:25:35s. Time for last 1,000,000: 2s. Last read position: */* INFO 2023-04-13 16:25:51 FastqToSam Processed 146,000,000 records. Elapsed time: 00:25:40s. Time for last 1,000,000: 5s. Last read position: */* INFO 2023-04-13 16:26:08 FastqToSam Processed 147,000,000 records. Elapsed time: 00:25:57s. Time for last 1,000,000: 16s. Last read position: */* INFO 2023-04-13 16:26:17 FastqToSam Processed 148,000,000 records. Elapsed time: 00:26:06s. Time for last 1,000,000: 8s. Last read position: */* INFO 2023-04-13 16:26:22 FastqToSam Processed 149,000,000 records. Elapsed time: 00:26:11s. Time for last 1,000,000: 5s. Last read position: */* INFO 2023-04-13 16:26:27 FastqToSam Processed 150,000,000 records. Elapsed time: 00:26:16s. Time for last 1,000,000: 4s. Last read position: */* INFO 2023-04-13 16:26:44 FastqToSam Processed 151,000,000 records. Elapsed time: 00:26:32s. Time for last 1,000,000: 16s. Last read position: */* INFO 2023-04-13 16:26:48 FastqToSam Processed 152,000,000 records. Elapsed time: 00:26:37s. Time for last 1,000,000: 4s. Last read position: */* INFO 2023-04-13 16:26:55 FastqToSam Processed 153,000,000 records. Elapsed time: 00:26:43s. Time for last 1,000,000: 6s. Last read position: */* INFO 2023-04-13 16:26:57 FastqToSam Processed 154,000,000 records. Elapsed time: 00:26:46s. Time for last 1,000,000: 2s. Last read position: */* INFO 2023-04-13 16:27:02 FastqToSam Processed 155,000,000 records. Elapsed time: 00:26:51s. Time for last 1,000,000: 4s. Last read position: */* INFO 2023-04-13 16:27:18 FastqToSam Processed 156,000,000 records. Elapsed time: 00:27:06s. Time for last 1,000,000: 15s. Last read position: */* INFO 2023-04-13 16:27:24 FastqToSam Processed 157,000,000 records. Elapsed time: 00:27:13s. Time for last 1,000,000: 6s. Last read position: */* INFO 2023-04-13 16:27:28 FastqToSam Processed 158,000,000 records. Elapsed time: 00:27:16s. Time for last 1,000,000: 3s. Last read position: */* INFO 2023-04-13 16:27:35 FastqToSam Processed 159,000,000 records. Elapsed time: 00:27:23s. Time for last 1,000,000: 6s. Last read position: */* INFO 2023-04-13 16:27:52 FastqToSam Processed 160,000,000 records. Elapsed time: 00:27:40s. Time for last 1,000,000: 16s. Last read position: */* INFO 2023-04-13 16:27:57 FastqToSam Processed 161,000,000 records. Elapsed time: 00:27:45s. Time for last 1,000,000: 4s. Last read position: */* INFO 2023-04-13 16:28:00 FastqToSam Processed 162,000,000 records. Elapsed time: 00:27:49s. Time for last 1,000,000: 3s. Last read position: */* INFO 2023-04-13 16:28:07 FastqToSam Processed 163,000,000 records. Elapsed time: 00:27:56s. Time for last 1,000,000: 6s. Last read position: */* INFO 2023-04-13 16:28:27 FastqToSam Processed 164,000,000 records. Elapsed time: 00:28:16s. Time for last 1,000,000: 19s. Last read position: */* INFO 2023-04-13 16:28:30 FastqToSam Processed 165,000,000 records. Elapsed time: 00:28:19s. Time for last 1,000,000: 3s. Last read position: */* INFO 2023-04-13 16:28:37 FastqToSam Processed 166,000,000 records. Elapsed time: 00:28:26s. Time for last 1,000,000: 7s. Last read position: */* INFO 2023-04-13 16:28:40 FastqToSam Processed 167,000,000 records. Elapsed time: 00:28:29s. Time for last 1,000,000: 3s. Last read position: */* INFO 2023-04-13 16:28:57 FastqToSam Processed 168,000,000 records. Elapsed time: 00:28:46s. Time for last 1,000,000: 17s. Last read position: */* Using GATK jar /opt/conda/share/gatk4-4.2.6.1-1/gatk-package-4.2.6.1-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx64G -XX:ParallelGCThreads=1 -jar /opt/conda/share/gatk4-4.2.6.1-1/gatk-package-4.2.6.1-local.jar FastqToSam --TMP_DIR /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/temp --MAX_RECORDS_IN_RAM 4194304 -F1 10-101PBMC_S20_R1.fastq.gz -F2 10-101PBMC_S20_R2.fastq.gz --READ_GROUP_NAME sample1_normal --SAMPLE_NAME sample1_normal --LIBRARY_NAME sample1_normal --PLATFORM ILLUMINA -O sample1_normal_DNA_unaligned.bam Work dir: /gpfs/data/sequence/results/krogsgaardlab/2023-03-21/10s/work/af/d3f543a0c1ac70ce752658b87bc136 Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh` slurmstepd-fn2-0002: error: *** JOB 21392618 ON fn2-0002 CANCELLED AT 2023-04-17T11:26:50 *** slurmstepd-fn2-0002: error: Detected 1 oom-kill event(s) in StepId=21392618.batch. Some of your processes may have been killed by the cgroup out-of-memory handler.