├── .dockstore.yml ├── .dockstore ├── arriba-pipeline │ └── 2.5.0 │ │ └── arriba-pipeline__2.5.0.packed.cwl.json ├── bclconvert-interop-qc │ ├── 1.3.1--1.21 │ │ └── bclconvert-interop-qc__1.3.1--1.21.packed.cwl.json │ ├── 1.3.1--1.25.2 │ │ └── bclconvert-interop-qc__1.3.1--1.25.2.packed.cwl.json │ └── 1.5.0--1.31 │ │ └── bclconvert-interop-qc__1.5.0--1.31.packed.cwl.json ├── dragen-alignment-pipeline │ ├── 4.2.4 │ │ └── dragen-alignment-pipeline__4.2.4.packed.cwl.json │ └── 4.3.6 │ │ └── dragen-alignment-pipeline__4.3.6.packed.cwl.json ├── dragen-build-reference-tarball-pipeline │ └── 4.2.4 │ │ └── dragen-build-reference-tarball-pipeline__4.2.4.packed.cwl.json ├── dragen-germline-pipeline │ ├── 4.2.4 │ │ └── dragen-germline-pipeline__4.2.4.packed.cwl.json │ └── 4.3.6 │ │ └── dragen-germline-pipeline__4.3.6.packed.cwl.json ├── dragen-instrument-run-fastq-to-ora-pipeline │ └── 4.2.4 │ │ └── dragen-instrument-run-fastq-to-ora-pipeline__4.2.4.packed.cwl.json ├── dragen-somatic-with-germline-pipeline │ ├── 4.2.4 │ │ └── dragen-somatic-with-germline-pipeline__4.2.4.packed.cwl.json │ └── 4.3.6 │ │ └── dragen-somatic-with-germline-pipeline__4.3.6.packed.cwl.json ├── dragen-transcriptome-pipeline │ ├── 4.2.4 │ │ └── dragen-transcriptome-pipeline__4.2.4.packed.cwl.json │ └── 4.3.6 │ │ └── dragen-transcriptome-pipeline__4.3.6.packed.cwl.json ├── dragen-wgts-dna-pipeline │ ├── 4.4.4 │ │ └── dragen-wgts-dna-pipeline__4.4.4.packed.cwl.json │ └── 4.4.6 │ │ └── dragen-wgts-dna-pipeline__4.4.6.packed.cwl.json ├── dragen-wgts-rna-pipeline │ └── 4.4.4 │ │ └── dragen-wgts-rna-pipeline__4.4.4.packed.cwl.json ├── dragen-wts-qc-pipeline │ └── 4.2.4 │ │ └── dragen-wts-qc-pipeline__4.2.4.packed.cwl.json ├── rnasum-pipeline │ ├── 1.0.0 │ │ └── rnasum-pipeline__1.0.0.packed.cwl.json │ ├── 1.1.0 │ │ └── rnasum-pipeline__1.1.0.packed.cwl.json │ ├── 1.1.5 │ │ └── rnasum-pipeline__1.1.5.packed.cwl.json │ └── 2.0.0 │ │ └── rnasum-pipeline__2.0.0.packed.cwl.json └── umccrise-pipeline │ └── 2.3.1--1 │ └── umccrise-pipeline__2.3.1--1.packed.cwl.json ├── .github ├── actions │ ├── decrypt_token │ │ └── action.yml │ ├── encrypt_token │ │ └── action.yml │ └── get_ica_access_token │ │ └── action.yml ├── catalogue │ ├── docs │ │ ├── expressions │ │ │ ├── create-contig-obj-for-hla-chr6-region │ │ │ │ └── 1.0.0 │ │ │ │ │ └── create-contig-obj-for-hla-chr6-region__1.0.0.md │ │ │ ├── create-predefined-mount-paths-and-umccrise-row-from-umccrise-schema │ │ │ │ ├── 1.2.1--0 │ │ │ │ │ └── create-predefined-mount-paths-and-umccrise-row-from-umccrise-schema__1.2.1--0.md │ │ │ │ └── 1.2.2--0 │ │ │ │ │ └── create-predefined-mount-paths-and-umccrise-row-from-umccrise-schema__1.2.2--0.md │ │ │ ├── create-single-directory-from-directories-array │ │ │ │ └── 1.0.0 │ │ │ │ │ └── create-single-directory-from-directories-array__1.0.0.md │ │ │ ├── flatten-array-fastq-list │ │ │ │ └── 1.0.0 │ │ │ │ │ └── flatten-array-fastq-list__1.0.0.md │ │ │ ├── get-bam-file-from-directory │ │ │ │ └── 1.0.0 │ │ │ │ │ └── get-bam-file-from-directory__1.0.0.md │ │ │ ├── get-compressed-vcf-file-from-directory │ │ │ │ └── 1.0.0 │ │ │ │ │ └── get-compressed-vcf-file-from-directory__1.0.0.md │ │ │ ├── get-custom-output-dir-entry-for-tso500-post-processing │ │ │ │ ├── 1.0.0 │ │ │ │ │ └── get-custom-output-dir-entry-for-tso500-post-processing__1.0.0.md │ │ │ │ └── 2.0.1 │ │ │ │ │ └── get-custom-output-dir-entry-for-tso500-post-processing__2.0.1.md │ │ │ ├── get-custom-output-dir-entry-for-tso500-with-post-processing │ │ │ │ └── 2.0.1 │ │ │ │ │ └── get-custom-output-dir-entry-for-tso500-with-post-processing__2.0.1.md │ │ │ ├── get-faidx-file-from-reference-file │ │ │ │ └── 1.0.0 │ │ │ │ │ └── get-faidx-file-from-reference-file__1.0.0.md │ │ │ ├── get-samplesheet-midfix-regex │ │ │ │ └── 1.0.0 │ │ │ │ │ └── get-samplesheet-midfix-regex__1.0.0.md │ │ │ ├── parse-file │ │ │ │ └── 1.0.0 │ │ │ │ │ └── parse-file__1.0.0.md │ │ │ ├── parse-int-array │ │ │ │ └── 1.0.0 │ │ │ │ │ └── parse-int-array__1.0.0.md │ │ │ └── parse-int │ │ │ │ └── 1.0.0 │ │ │ │ └── parse-int__1.0.0.md │ │ ├── tools │ │ │ ├── arriba-drawing │ │ │ │ ├── 2.0.0 │ │ │ │ │ └── arriba-drawing__2.0.0.md │ │ │ │ ├── 2.3.0 │ │ │ │ │ └── arriba-drawing__2.3.0.md │ │ │ │ └── 2.4.0 │ │ │ │ │ └── arriba-drawing__2.4.0.md │ │ │ ├── arriba-fusion-calling │ │ │ │ ├── 2.0.0 │ │ │ │ │ └── arriba-fusion-calling__2.0.0.md │ │ │ │ ├── 2.3.0 │ │ │ │ │ └── arriba-fusion-calling__2.3.0.md │ │ │ │ └── 2.4.0 │ │ │ │ │ └── arriba-fusion-calling__2.4.0.md │ │ │ ├── bamtofastq │ │ │ │ └── 2.0.183 │ │ │ │ │ └── bamtofastq__2.0.183.md │ │ │ ├── bcftools-view │ │ │ │ └── 1.13.0 │ │ │ │ │ └── bcftools-view__1.13.0.md │ │ │ ├── bcl-convert │ │ │ │ └── 4.0.3 │ │ │ │ │ └── bcl-convert__4.0.3.md │ │ │ ├── bclConvert │ │ │ │ └── 3.7.5 │ │ │ │ │ └── bclConvert__3.7.5.md │ │ │ ├── bedops │ │ │ │ └── 2.4.39 │ │ │ │ │ └── bedops__2.4.39.md │ │ │ ├── bgzip │ │ │ │ └── 1.12.0 │ │ │ │ │ └── bgzip__1.12.0.md │ │ │ ├── calculate-coverage │ │ │ │ └── 1.0.0 │ │ │ │ │ └── calculate-coverage__1.0.0.md │ │ │ ├── create-dummy-file │ │ │ │ └── 1.0.0 │ │ │ │ │ └── create-dummy-file__1.0.0.md │ │ │ ├── custom-create-directory │ │ │ │ ├── 1.0.0 │ │ │ │ │ └── custom-create-directory__1.0.0.md │ │ │ │ ├── 1.0.1 │ │ │ │ │ └── custom-create-directory__1.0.1.md │ │ │ │ ├── 2.0.0 │ │ │ │ │ └── custom-create-directory__2.0.0.md │ │ │ │ └── 2.0.1 │ │ │ │ │ └── custom-create-directory__2.0.1.md │ │ │ ├── custom-create-tso500-samplesheet │ │ │ │ └── 1.0.0 │ │ │ │ │ └── custom-create-tso500-samplesheet__1.0.0.md │ │ │ ├── custom-create-umccr-dragen-refdata-tarball-from-illumina-tar │ │ │ │ └── 1.0.0 │ │ │ │ │ └── custom-create-umccr-dragen-refdata-tarball-from-illumina-tar__1.0.0.md │ │ │ ├── custom-create-umccrise-tsv │ │ │ │ ├── 1.2.1--0 │ │ │ │ │ └── custom-create-umccrise-tsv__1.2.1--0.md │ │ │ │ └── 1.2.2--0 │ │ │ │ │ └── custom-create-umccrise-tsv__1.2.2--0.md │ │ │ ├── custom-gzip-file │ │ │ │ └── 1.0.0 │ │ │ │ │ └── custom-gzip-file__1.0.0.md │ │ │ ├── custom-hla-bed-from-faidx │ │ │ │ └── 1.0.0 │ │ │ │ │ └── custom-hla-bed-from-faidx__1.0.0.md │ │ │ ├── custom-samplesheet-split-by-settings │ │ │ │ └── 1.0.0 │ │ │ │ │ └── custom-samplesheet-split-by-settings__1.0.0.md │ │ │ ├── custom-stats-qc │ │ │ │ ├── 1.0.0 │ │ │ │ │ └── custom-stats-qc__1.0.0.md │ │ │ │ └── 1.0.1 │ │ │ │ │ └── custom-stats-qc__1.0.1.md │ │ │ ├── custom-subset-bam │ │ │ │ └── 1.12.0 │ │ │ │ │ └── custom-subset-bam__1.12.0.md │ │ │ ├── custom-tar-file-list │ │ │ │ └── 1.0.0 │ │ │ │ │ └── custom-tar-file-list__1.0.0.md │ │ │ ├── custom-tar-vcf-file-list │ │ │ │ └── 1.0.0 │ │ │ │ │ └── custom-tar-vcf-file-list__1.0.0.md │ │ │ ├── custom-tso500-align-collapse-fusion-caller-csv-metrics-to-json │ │ │ │ └── 1.0.0 │ │ │ │ │ └── custom-tso500-align-collapse-fusion-caller-csv-metrics-to-json__1.0.0.md │ │ │ ├── custom-tso500-cnv-caller-bin-counts-to-json │ │ │ │ └── 1.0.0 │ │ │ │ │ └── custom-tso500-cnv-caller-bin-counts-to-json__1.0.0.md │ │ │ ├── custom-tso500-make-exon-coverage-qc │ │ │ │ └── 1.0.0 │ │ │ │ │ └── custom-tso500-make-exon-coverage-qc__1.0.0.md │ │ │ ├── custom-tso500-make-region-coverage-qc │ │ │ │ └── 1.0.0 │ │ │ │ │ └── custom-tso500-make-region-coverage-qc__1.0.0.md │ │ │ ├── custom-tsv-to-json │ │ │ │ └── 1.0.0 │ │ │ │ │ └── custom-tsv-to-json__1.0.0.md │ │ │ ├── dragen-alignment │ │ │ │ ├── 3.7.5 │ │ │ │ │ └── dragen-alignment__3.7.5.md │ │ │ │ ├── 3.9.3 │ │ │ │ │ └── dragen-alignment__3.9.3.md │ │ │ │ ├── 4.0.3 │ │ │ │ │ └── dragen-alignment__4.0.3.md │ │ │ │ └── 4.2.4 │ │ │ │ │ └── dragen-alignment__4.2.4.md │ │ │ ├── dragen-build-reference-tarball │ │ │ │ ├── 3.7.5 │ │ │ │ │ └── dragen-build-reference-tarball__3.7.5.md │ │ │ │ ├── 3.8.4 │ │ │ │ │ └── dragen-build-reference-tarball__3.8.4.md │ │ │ │ ├── 4.0.3 │ │ │ │ │ └── dragen-build-reference-tarball__4.0.3.md │ │ │ │ └── 4.2.4 │ │ │ │ │ └── dragen-build-reference-tarball__4.2.4.md │ │ │ ├── dragen-germline │ │ │ │ ├── 3.7.5 │ │ │ │ │ └── dragen-germline__3.7.5.md │ │ │ │ ├── 3.9.3 │ │ │ │ │ └── dragen-germline__3.9.3.md │ │ │ │ ├── 4.0.3 │ │ │ │ │ └── dragen-germline__4.0.3.md │ │ │ │ └── 4.2.4 │ │ │ │ │ └── dragen-germline__4.2.4.md │ │ │ ├── dragen-instrument-run-fastq-to-ora │ │ │ │ └── 4.2.4 │ │ │ │ │ └── dragen-instrument-run-fastq-to-ora__4.2.4.md │ │ │ ├── dragen-somatic │ │ │ │ ├── 3.7.5 │ │ │ │ │ └── dragen-somatic__3.7.5.md │ │ │ │ ├── 3.9.3 │ │ │ │ │ └── dragen-somatic__3.9.3.md │ │ │ │ ├── 4.0.3 │ │ │ │ │ └── dragen-somatic__4.0.3.md │ │ │ │ └── 4.2.4 │ │ │ │ │ └── dragen-somatic__4.2.4.md │ │ │ ├── dragen-transcriptome │ │ │ │ ├── 3.7.5 │ │ │ │ │ └── dragen-transcriptome__3.7.5.md │ │ │ │ ├── 3.8.4 │ │ │ │ │ └── dragen-transcriptome__3.8.4.md │ │ │ │ ├── 3.9.3 │ │ │ │ │ └── dragen-transcriptome__3.9.3.md │ │ │ │ ├── 4.0.3 │ │ │ │ │ └── dragen-transcriptome__4.0.3.md │ │ │ │ └── 4.2.4 │ │ │ │ │ └── dragen-transcriptome__4.2.4.md │ │ │ ├── dragen-umi │ │ │ │ ├── 3.8.4 │ │ │ │ │ └── dragen-umi__3.8.4.md │ │ │ │ └── 3.9.3 │ │ │ │ │ └── dragen-umi__3.9.3.md │ │ │ ├── illumina-interop │ │ │ │ └── 1.2.0 │ │ │ │ │ └── illumina-interop__1.2.0.md │ │ │ ├── map_resource_requirements │ │ │ │ └── 0.1.0 │ │ │ │ │ └── map_resource_requirements__0.1.0.md │ │ │ ├── mosdepth │ │ │ │ └── 0.3.1 │ │ │ │ │ └── mosdepth__0.3.1.md │ │ │ ├── multiqc-interop │ │ │ │ ├── 1.14.0--1.2.0 │ │ │ │ │ └── multiqc-interop__1.14.0--1.2.0.md │ │ │ │ └── 1.2.1 │ │ │ │ │ └── multiqc-interop__1.2.1.md │ │ │ ├── multiqc │ │ │ │ ├── 1.10.1 │ │ │ │ │ └── multiqc__1.10.1.md │ │ │ │ ├── 1.11.0 │ │ │ │ │ └── multiqc__1.11.0.md │ │ │ │ ├── 1.12.0 │ │ │ │ │ └── multiqc__1.12.0.md │ │ │ │ ├── 1.14.0 │ │ │ │ │ └── multiqc__1.14.0.md │ │ │ │ ├── 1.15.0 │ │ │ │ │ └── multiqc__1.15.0.md │ │ │ │ ├── 1.19.0 │ │ │ │ │ └── multiqc__1.19.0.md │ │ │ │ ├── 1.21.0 │ │ │ │ │ └── multiqc__1.21.0.md │ │ │ │ └── 1.25.2 │ │ │ │ │ └── multiqc__1.25.2.md │ │ │ ├── optitype │ │ │ │ └── 1.3.5 │ │ │ │ │ └── optitype__1.3.5.md │ │ │ ├── qualimap │ │ │ │ └── 2.2.2 │ │ │ │ │ └── qualimap__2.2.2.md │ │ │ ├── rnasum │ │ │ │ ├── 0.4.1 │ │ │ │ │ └── rnasum__0.4.1.md │ │ │ │ ├── 0.4.2 │ │ │ │ │ └── rnasum__0.4.2.md │ │ │ │ ├── 0.4.3 │ │ │ │ │ └── rnasum__0.4.3.md │ │ │ │ ├── 0.4.4 │ │ │ │ │ └── rnasum__0.4.4.md │ │ │ │ ├── 0.4.5 │ │ │ │ │ └── rnasum__0.4.5.md │ │ │ │ ├── 0.4.7 │ │ │ │ │ └── rnasum__0.4.7.md │ │ │ │ ├── 0.4.8 │ │ │ │ │ └── rnasum__0.4.8.md │ │ │ │ ├── 0.4.9 │ │ │ │ │ └── rnasum__0.4.9.md │ │ │ │ ├── 0.5.0 │ │ │ │ │ └── rnasum__0.5.0.md │ │ │ │ ├── 0.6.5 │ │ │ │ │ └── rnasum__0.6.5.md │ │ │ │ ├── 1.0.0 │ │ │ │ │ └── rnasum__1.0.0.md │ │ │ │ ├── 1.1.0 │ │ │ │ │ └── rnasum__1.1.0.md │ │ │ │ └── 1.1.5 │ │ │ │ │ └── rnasum__1.1.5.md │ │ │ ├── sambamba-merge-and-index │ │ │ │ └── 0.8.0 │ │ │ │ │ └── sambamba-merge-and-index__0.8.0.md │ │ │ ├── sambamba-slice-and-index │ │ │ │ └── 0.8.0 │ │ │ │ │ └── sambamba-slice-and-index__0.8.0.md │ │ │ ├── sambamba-sort-and-index │ │ │ │ └── 0.8.0 │ │ │ │ │ └── sambamba-sort-and-index__0.8.0.md │ │ │ ├── sambamba-view-and-index │ │ │ │ └── 0.8.0 │ │ │ │ │ └── sambamba-view-and-index__0.8.0.md │ │ │ ├── samtools-merge │ │ │ │ └── 1.12.0 │ │ │ │ │ └── samtools-merge__1.12.0.md │ │ │ ├── samtools-stats │ │ │ │ └── 1.13.0 │ │ │ │ │ └── samtools-stats__1.13.0.md │ │ │ ├── star │ │ │ │ └── 2.7.10 │ │ │ │ │ └── star__2.7.10.md │ │ │ ├── tabix │ │ │ │ └── 0.2.6 │ │ │ │ │ └── tabix__0.2.6.md │ │ │ ├── tso500-ctdna-analysis-workflow │ │ │ │ └── 1.1.0--120 │ │ │ │ │ └── tso500-ctdna-analysis-workflow__1.1.0--120.md │ │ │ ├── tso500-ctdna-demultiplex-workflow │ │ │ │ └── 1.1.0--120 │ │ │ │ │ └── tso500-ctdna-demultiplex-workflow__1.1.0--120.md │ │ │ ├── tso500-ctdna-reporting-workflow │ │ │ │ └── 1.1.0--120 │ │ │ │ │ └── tso500-ctdna-reporting-workflow__1.1.0--120.md │ │ │ └── umccrise │ │ │ │ ├── 1.2.1--0 │ │ │ │ └── umccrise__1.2.1--0.md │ │ │ │ ├── 1.2.2--0 │ │ │ │ └── umccrise__1.2.2--0.md │ │ │ │ ├── 2.0.0--0 │ │ │ │ └── umccrise__2.0.0--0.md │ │ │ │ ├── 2.0.1--0 │ │ │ │ └── umccrise__2.0.1--0.md │ │ │ │ ├── 2.0.2--0 │ │ │ │ └── umccrise__2.0.2--0.md │ │ │ │ ├── 2.1.0--0 │ │ │ │ └── umccrise__2.1.0--0.md │ │ │ │ ├── 2.1.1--0 │ │ │ │ └── umccrise__2.1.1--0.md │ │ │ │ ├── 2.2.0--0 │ │ │ │ └── umccrise__2.2.0--0.md │ │ │ │ ├── 2.2.1--0 │ │ │ │ └── umccrise__2.2.1--0.md │ │ │ │ ├── 2.3.0--0 │ │ │ │ └── umccrise__2.3.0--0.md │ │ │ │ └── 2.3.1--1 │ │ │ │ └── umccrise__2.3.1--1.md │ │ └── workflows │ │ │ ├── bcl-conversion │ │ │ └── 3.7.5 │ │ │ │ └── bcl-conversion__3.7.5.md │ │ │ ├── bclconvert-interop-qc │ │ │ ├── 1.3.1--1.19 │ │ │ │ └── bclconvert-interop-qc__1.3.1--1.19.md │ │ │ ├── 1.3.1--1.21 │ │ │ │ └── bclconvert-interop-qc__1.3.1--1.21.md │ │ │ └── 1.3.1--1.25.2 │ │ │ │ └── bclconvert-interop-qc__1.3.1--1.25.2.md │ │ │ ├── bclconvert-scatter │ │ │ └── 4.0.3 │ │ │ │ └── bclconvert-scatter__4.0.3.md │ │ │ ├── bclconvert-with-qc-pipeline │ │ │ └── 4.0.3 │ │ │ │ └── bclconvert-with-qc-pipeline__4.0.3.md │ │ │ ├── bclconvert │ │ │ └── 4.0.3 │ │ │ │ └── bclconvert__4.0.3.md │ │ │ ├── dragen-alignment-pipeline │ │ │ ├── 3.7.5 │ │ │ │ └── dragen-alignment-pipeline__3.7.5.md │ │ │ ├── 3.9.3 │ │ │ │ └── dragen-alignment-pipeline__3.9.3.md │ │ │ ├── 4.0.3 │ │ │ │ └── dragen-alignment-pipeline__4.0.3.md │ │ │ ├── 4.2.4 │ │ │ │ └── dragen-alignment-pipeline__4.2.4.md │ │ │ └── 4.3.6 │ │ │ │ └── dragen-alignment-pipeline__4.3.6.md │ │ │ ├── dragen-germline-pipeline │ │ │ ├── 3.7.5 │ │ │ │ └── dragen-germline-pipeline__3.7.5.md │ │ │ ├── 3.9.3 │ │ │ │ └── dragen-germline-pipeline__3.9.3.md │ │ │ ├── 4.0.3 │ │ │ │ └── dragen-germline-pipeline__4.0.3.md │ │ │ ├── 4.2.4 │ │ │ │ └── dragen-germline-pipeline__4.2.4.md │ │ │ └── 4.3.6 │ │ │ │ └── dragen-germline-pipeline__4.3.6.md │ │ │ ├── dragen-instrument-run-fastq-to-ora-pipeline │ │ │ └── 4.2.4 │ │ │ │ └── dragen-instrument-run-fastq-to-ora-pipeline__4.2.4.md │ │ │ ├── dragen-pon-qc │ │ │ └── 3.9.3 │ │ │ │ └── dragen-pon-qc__3.9.3.md │ │ │ ├── dragen-qc-hla-pipeline │ │ │ └── 3.7.5--1.3.5 │ │ │ │ └── dragen-qc-hla-pipeline__3.7.5--1.3.5.md │ │ │ ├── dragen-somatic-pipeline │ │ │ ├── 3.7.5 │ │ │ │ └── dragen-somatic-pipeline__3.7.5.md │ │ │ ├── 3.9.3 │ │ │ │ └── dragen-somatic-pipeline__3.9.3.md │ │ │ ├── 4.0.3 │ │ │ │ └── dragen-somatic-pipeline__4.0.3.md │ │ │ └── 4.2.4 │ │ │ │ └── dragen-somatic-pipeline__4.2.4.md │ │ │ ├── dragen-somatic-with-germline-pipeline │ │ │ ├── 3.9.3 │ │ │ │ └── dragen-somatic-with-germline-pipeline__3.9.3.md │ │ │ ├── 4.0.3 │ │ │ │ └── dragen-somatic-with-germline-pipeline__4.0.3.md │ │ │ ├── 4.2.4 │ │ │ │ └── dragen-somatic-with-germline-pipeline__4.2.4.md │ │ │ └── 4.3.6 │ │ │ │ └── dragen-somatic-with-germline-pipeline__4.3.6.md │ │ │ ├── dragen-transcriptome-pipeline │ │ │ ├── 3.7.5 │ │ │ │ └── dragen-transcriptome-pipeline__3.7.5.md │ │ │ ├── 3.8.4 │ │ │ │ └── dragen-transcriptome-pipeline__3.8.4.md │ │ │ ├── 3.9.3 │ │ │ │ └── dragen-transcriptome-pipeline__3.9.3.md │ │ │ ├── 4.0.3 │ │ │ │ └── dragen-transcriptome-pipeline__4.0.3.md │ │ │ ├── 4.2.4 │ │ │ │ └── dragen-transcriptome-pipeline__4.2.4.md │ │ │ └── 4.3.6 │ │ │ │ └── dragen-transcriptome-pipeline__4.3.6.md │ │ │ ├── dragen-wgs-qc-pipeline │ │ │ ├── 3.7.5 │ │ │ │ └── dragen-wgs-qc-pipeline__3.7.5.md │ │ │ └── 3.9.3 │ │ │ │ └── dragen-wgs-qc-pipeline__3.9.3.md │ │ │ ├── dragen-wts-qc-pipeline │ │ │ ├── 3.9.3 │ │ │ │ └── dragen-wts-qc-pipeline__3.9.3.md │ │ │ ├── 4.0.3 │ │ │ │ └── dragen-wts-qc-pipeline__4.0.3.md │ │ │ └── 4.2.4 │ │ │ │ └── dragen-wts-qc-pipeline__4.2.4.md │ │ │ ├── get-hla-regions-bed │ │ │ └── 1.0.0 │ │ │ │ └── get-hla-regions-bed__1.0.0.md │ │ │ ├── ghif-qc │ │ │ ├── 1.0.0 │ │ │ │ └── ghif-qc__1.0.0.md │ │ │ └── 1.0.1 │ │ │ │ └── ghif-qc__1.0.1.md │ │ │ ├── illumina-interop-qc │ │ │ └── 1.2.0--1.14.0 │ │ │ │ └── illumina-interop-qc__1.2.0--1.14.0.md │ │ │ ├── optitype-pipeline │ │ │ └── 1.3.5 │ │ │ │ └── optitype-pipeline__1.3.5.md │ │ │ ├── rnasum-pipeline │ │ │ ├── 0.4.5 │ │ │ │ └── rnasum-pipeline__0.4.5.md │ │ │ ├── 1.0.0 │ │ │ │ └── rnasum-pipeline__1.0.0.md │ │ │ ├── 1.1.0 │ │ │ │ └── rnasum-pipeline__1.1.0.md │ │ │ └── 1.1.5 │ │ │ │ └── rnasum-pipeline__1.1.5.md │ │ │ ├── tabix-workflow │ │ │ └── 0.2.6 │ │ │ │ └── tabix-workflow__0.2.6.md │ │ │ ├── tso500-ctdna-post-processing-pipeline │ │ │ └── 1.0.0 │ │ │ │ └── tso500-ctdna-post-processing-pipeline__1.0.0.md │ │ │ ├── tso500-ctdna-with-post-processing-pipeline │ │ │ ├── 1.1.0--1.0.0 │ │ │ │ └── tso500-ctdna-with-post-processing-pipeline__1.1.0--1.0.0.md │ │ │ └── 1.2.0--1.0.0 │ │ │ │ └── tso500-ctdna-with-post-processing-pipeline__1.2.0--1.0.0.md │ │ │ ├── tso500-ctdna │ │ │ ├── 1.1.0--120 │ │ │ │ └── tso500-ctdna__1.1.0--120.md │ │ │ └── 1.2.0--1 │ │ │ │ └── tso500-ctdna__1.2.0--1.md │ │ │ ├── umccrise-pipeline │ │ │ ├── 1.2.1--0 │ │ │ │ └── umccrise-pipeline__1.2.1--0.md │ │ │ ├── 1.2.2--0 │ │ │ │ └── umccrise-pipeline__1.2.2--0.md │ │ │ ├── 2.2.0--0 │ │ │ │ └── umccrise-pipeline__2.2.0--0.md │ │ │ ├── 2.2.1--0 │ │ │ │ └── umccrise-pipeline__2.2.1--0.md │ │ │ ├── 2.3.0--0 │ │ │ │ └── umccrise-pipeline__2.3.0--0.md │ │ │ └── 2.3.1--1 │ │ │ │ └── umccrise-pipeline__2.3.1--1.md │ │ │ ├── umccrise-with-dragen-germline-pipeline │ │ │ ├── 2.0.0--3.9.3 │ │ │ │ └── umccrise-with-dragen-germline-pipeline__2.0.0--3.9.3.md │ │ │ ├── 2.0.1--3.9.3 │ │ │ │ └── umccrise-with-dragen-germline-pipeline__2.0.1--3.9.3.md │ │ │ ├── 2.0.2--3.9.3 │ │ │ │ └── umccrise-with-dragen-germline-pipeline__2.0.2--3.9.3.md │ │ │ ├── 2.1.0--3.9.3 │ │ │ │ └── umccrise-with-dragen-germline-pipeline__2.1.0--3.9.3.md │ │ │ ├── 2.1.1--3.9.3 │ │ │ │ └── umccrise-with-dragen-germline-pipeline__2.1.1--3.9.3.md │ │ │ ├── 2.2.0--3.9.3 │ │ │ │ └── umccrise-with-dragen-germline-pipeline__2.2.0--3.9.3.md │ │ │ └── 2.2.1--3.9.3 │ │ │ │ └── umccrise-with-dragen-germline-pipeline__2.2.1--3.9.3.md │ │ │ └── validate-bclconvert-samplesheet │ │ │ └── 4.0.3 │ │ │ └── validate-bclconvert-samplesheet__4.0.3.md │ └── images │ │ ├── runs │ │ ├── tools │ │ │ ├── custom-create-umccr-dragen-refdata-tarball-from-illumina-tar │ │ │ │ └── 1.0.0 │ │ │ │ │ ├── create-dragen-v8-GRCh37-cnv-anchored-reference__wfr.f0f2f6f602e54d3ebcbc1837d1fc7074.svg │ │ │ │ │ └── create-dragen-v8-hg38-altaware-cnv-anchored-reference__wfr.3bf2bc688d0d442489cadfcdb2bf9842.svg │ │ │ ├── dragen-somatic │ │ │ │ └── 3.9.3 │ │ │ │ │ ├── InlineCSV-pipeline-test2Mar__wfr.63351b7bd8f9431db0a58c27d5538f0e.svg │ │ │ │ │ ├── InlineCSV-test-TO__wfr.4aef0ef9d4154f7a9a3a8138c12dbd6f.svg │ │ │ │ │ └── InlineCSV-test__wfr.2661494f42d045fe80ab8229dfcd8245.svg │ │ │ ├── dragen-umi │ │ │ │ └── 3.8.4 │ │ │ │ │ ├── Dragen3.8-NO-SBJ00471__wfr.96ea5cf11b2843c9b9b7a88070b48e3e.svg │ │ │ │ │ ├── Dragen3.8-TN-SBJ00471_plasma__wfr.affca1fb24e34cbca115844c3f9f6c57.svg │ │ │ │ │ └── Dragen3.8-TO-SBJ00471_plasma__wfr.d068fc090a204a08823974db7b255f88.svg │ │ │ ├── rnasum │ │ │ │ └── 0.4.1 │ │ │ │ │ └── Dragen-RNAsum__wfr.dce6425b60044757a78bb545c627c58a.svg │ │ │ └── samtools-stats │ │ │ │ └── 1.13.0 │ │ │ │ └── samtools-stats__wfr.32ff48e48bce4d4e8d70efe6fbf92040.svg │ │ └── workflows │ │ │ ├── bcl-conversion │ │ │ └── 3.7.5 │ │ │ │ └── umccr__automated__bcl_convert__210708_A00130_0166_AH7KTJDSX2__r.E92UIDDiCUKQS5joVDO6Gg__1626253458__wfr.d9ddc8eb7d544d32bdbe285fd45a4365.svg │ │ │ ├── dragen-germline-pipeline │ │ │ └── 3.9.3 │ │ │ │ ├── Dragen3.9-germline-workflow-test__wfr.4759b2ccf6234141b06d5aab5b932dbb.svg │ │ │ │ └── Dragen3.9-germline-workflow__wfr.d058e5f7be4b4683a9b1a59b8f67f91b.svg │ │ │ ├── dragen-pon-qc │ │ │ └── 3.9.3 │ │ │ │ └── PON-GHIF-QC__wfr.e0cccb29cf44482182507bd33579270c.svg │ │ │ ├── dragen-somatic-pipeline │ │ │ ├── 3.7.5 │ │ │ │ ├── umccr__automated__tumor_normal__SBJ00910__1626338884__wfr.58436856778e4f70ae7856869571470c.svg │ │ │ │ └── umccr__automated__tumor_normal__SBJ00913__1626338891__wfr.e3c6b8ce7e4447cbbd321b5c96ef7670.svg │ │ │ └── 3.9.3 │ │ │ │ ├── Dragen-3.9-somatic-pipeline__wfr.b19291caab384e78b7661a85c3f82003.svg │ │ │ │ ├── InlineCSV-pipeline-test2Mar__wfr.72d2a10d54ca472a96d4023556932b8e.svg │ │ │ │ ├── InlineCSV-pipeline-test__wfr.46c3b2a719864bf1bab827449e64f28c.svg │ │ │ │ ├── InlineCSV-test-TO__wfr.7241dd632c0f40df88236e210e257bd1.svg │ │ │ │ └── test-run__wfr.128790246e9c48f39e14d8f8ef7d868e.svg │ │ │ ├── dragen-transcriptome-pipeline │ │ │ ├── 3.7.5 │ │ │ │ └── Dragen-WTS-MDX210147__wfr.f0fa0ea3972f405aa5af5003e1427428.svg │ │ │ └── 3.9.3 │ │ │ │ ├── Dragen-3.9.3-PTC-test__wfr.f75bddad9d4740d3873fce5ceb782bc7.svg │ │ │ │ ├── Dragen-3.9.3-WTS-QC1.12dev__wfr.784173de5b4342b797f04259ebd04df6.svg │ │ │ │ └── Dragen-3.9.3-inlinecsv-multiQC__wfr.491f5fd1b5e74f6e87113d964675504e.svg │ │ │ ├── dragen-wgs-qc-pipeline │ │ │ ├── 3.7.5 │ │ │ │ └── umccr__automated__dragen_wgs_qc__210708_A00130_0166_AH7KTJDSX2__r.E92UIDDiCUKQS5joVDO6Gg__L2100746__1626290650__wfr.1fd8c32d79c34e179a4c0d6754edd3a2.svg │ │ │ └── 3.9.3 │ │ │ │ └── Dragen-3.9-WGS-QC__wfr.8bb7083dc6e74a2f9c21edd65e627a2e.svg │ │ │ ├── ghif-qc │ │ │ └── 1.0.1 │ │ │ │ ├── qc-ghif-1.0.1__wfr.10176db758d94e56833422dfd60d0f90.svg │ │ │ │ └── qc-ghif-1.0.1__wfr.f6adb13c92e340f89317c337674b18a6.svg │ │ │ ├── tso500-ctdna-with-post-processing-pipeline │ │ │ └── 1.1.0--1.0.0 │ │ │ │ ├── tso500-ctdna-full-start-end-workflow-test__wfr.c419c549d0c349538ba811f65c8ed684.svg │ │ │ │ ├── tso500-ctdna-full-start-end-workflow-test__wfr.d92a2d28bbfe46fe878f6513fdb06723.svg │ │ │ │ └── tso500-ctdna-tiny-start-end-workflow-test__wfr.332cf48caff84cdba27eb6c11526432a.svg │ │ │ └── umccrise-pipeline │ │ │ └── 1.2.2--0 │ │ │ └── umccrise-v1.2.2-test-run__wfr.070e013822304c0191e8195ce10a3b2b.svg │ │ └── workflows │ │ ├── bcl-conversion │ │ └── 3.7.5 │ │ │ └── bcl-conversion__3.7.5.svg │ │ ├── bclconvert-interop-qc │ │ ├── 1.3.1--1.19 │ │ │ └── bclconvert-interop-qc__1.3.1--1.19.svg │ │ ├── 1.3.1--1.21 │ │ │ └── bclconvert-interop-qc__1.3.1--1.21.svg │ │ └── 1.3.1--1.25.2 │ │ │ └── bclconvert-interop-qc__1.3.1--1.25.2.svg │ │ ├── bclconvert-scatter │ │ └── 4.0.3 │ │ │ └── bclconvert-scatter__4.0.3.svg │ │ ├── bclconvert-with-qc-pipeline │ │ └── 4.0.3 │ │ │ └── bclconvert-with-qc-pipeline__4.0.3.svg │ │ ├── bclconvert │ │ └── 4.0.3 │ │ │ └── bclconvert__4.0.3.svg │ │ ├── dragen-alignment-pipeline │ │ ├── 3.7.5 │ │ │ └── dragen-alignment-pipeline__3.7.5.svg │ │ ├── 3.9.3 │ │ │ └── dragen-alignment-pipeline__3.9.3.svg │ │ ├── 4.0.3 │ │ │ └── dragen-alignment-pipeline__4.0.3.svg │ │ ├── 4.2.4 │ │ │ └── dragen-alignment-pipeline__4.2.4.svg │ │ └── 4.3.6 │ │ │ └── dragen-alignment-pipeline__4.3.6.svg │ │ ├── dragen-germline-pipeline │ │ ├── 3.7.5 │ │ │ └── dragen-germline-pipeline__3.7.5.svg │ │ ├── 3.9.3 │ │ │ └── dragen-germline-pipeline__3.9.3.svg │ │ ├── 4.0.3 │ │ │ └── dragen-germline-pipeline__4.0.3.svg │ │ ├── 4.2.4 │ │ │ └── dragen-germline-pipeline__4.2.4.svg │ │ └── 4.3.6 │ │ │ └── dragen-germline-pipeline__4.3.6.svg │ │ ├── dragen-instrument-run-fastq-to-ora-pipeline │ │ └── 4.2.4 │ │ │ └── dragen-instrument-run-fastq-to-ora-pipeline__4.2.4.svg │ │ ├── dragen-pon-qc │ │ └── 3.9.3 │ │ │ └── dragen-pon-qc__3.9.3.svg │ │ ├── dragen-qc-hla-pipeline │ │ └── 3.7.5--1.3.5 │ │ │ └── dragen-qc-hla-pipeline__3.7.5--1.3.5.svg │ │ ├── dragen-somatic-pipeline │ │ ├── 3.7.5 │ │ │ └── dragen-somatic-pipeline__3.7.5.svg │ │ ├── 3.9.3 │ │ │ └── dragen-somatic-pipeline__3.9.3.svg │ │ ├── 4.0.3 │ │ │ └── dragen-somatic-pipeline__4.0.3.svg │ │ └── 4.2.4 │ │ │ └── dragen-somatic-pipeline__4.2.4.svg │ │ ├── dragen-somatic-with-germline-pipeline │ │ ├── 3.9.3 │ │ │ └── dragen-somatic-with-germline-pipeline__3.9.3.svg │ │ ├── 4.0.3 │ │ │ └── dragen-somatic-with-germline-pipeline__4.0.3.svg │ │ ├── 4.2.4 │ │ │ └── dragen-somatic-with-germline-pipeline__4.2.4.svg │ │ └── 4.3.6 │ │ │ └── dragen-somatic-with-germline-pipeline__4.3.6.svg │ │ ├── dragen-transcriptome-pipeline │ │ ├── 3.7.5 │ │ │ └── dragen-transcriptome-pipeline__3.7.5.svg │ │ ├── 3.8.4 │ │ │ └── dragen-transcriptome-pipeline__3.8.4.svg │ │ ├── 3.9.3 │ │ │ └── dragen-transcriptome-pipeline__3.9.3.svg │ │ ├── 4.0.3 │ │ │ └── dragen-transcriptome-pipeline__4.0.3.svg │ │ ├── 4.2.4 │ │ │ └── dragen-transcriptome-pipeline__4.2.4.svg │ │ └── 4.3.6 │ │ │ └── dragen-transcriptome-pipeline__4.3.6.svg │ │ ├── dragen-wgs-qc-pipeline │ │ ├── 3.7.5 │ │ │ └── dragen-wgs-qc-pipeline__3.7.5.svg │ │ └── 3.9.3 │ │ │ └── dragen-wgs-qc-pipeline__3.9.3.svg │ │ ├── dragen-wts-qc-pipeline │ │ ├── 3.9.3 │ │ │ └── dragen-wts-qc-pipeline__3.9.3.svg │ │ ├── 4.0.3 │ │ │ └── dragen-wts-qc-pipeline__4.0.3.svg │ │ └── 4.2.4 │ │ │ └── dragen-wts-qc-pipeline__4.2.4.svg │ │ ├── get-hla-regions-bed │ │ └── 1.0.0 │ │ │ └── get-hla-regions-bed__1.0.0.svg │ │ ├── ghif-qc │ │ ├── 1.0.0 │ │ │ └── ghif-qc__1.0.0.svg │ │ └── 1.0.1 │ │ │ └── ghif-qc__1.0.1.svg │ │ ├── illumina-interop-qc │ │ └── 1.2.0--1.14.0 │ │ │ └── illumina-interop-qc__1.2.0--1.14.0.svg │ │ ├── optitype-pipeline │ │ └── 1.3.5 │ │ │ └── optitype-pipeline__1.3.5.svg │ │ ├── rnasum-pipeline │ │ ├── 0.4.5 │ │ │ └── rnasum-pipeline__0.4.5.svg │ │ ├── 1.0.0 │ │ │ └── rnasum-pipeline__1.0.0.svg │ │ ├── 1.1.0 │ │ │ └── rnasum-pipeline__1.1.0.svg │ │ └── 1.1.5 │ │ │ └── rnasum-pipeline__1.1.5.svg │ │ ├── tabix-workflow │ │ └── 0.2.6 │ │ │ └── tabix-workflow__0.2.6.svg │ │ ├── tso500-ctdna-post-processing-pipeline │ │ └── 1.0.0 │ │ │ └── tso500-ctdna-post-processing-pipeline__1.0.0.svg │ │ ├── tso500-ctdna-with-post-processing-pipeline │ │ ├── 1.1.0--1.0.0 │ │ │ └── tso500-ctdna-with-post-processing-pipeline__1.1.0--1.0.0.svg │ │ └── 1.2.0--1.0.0 │ │ │ └── tso500-ctdna-with-post-processing-pipeline__1.2.0--1.0.0.svg │ │ ├── tso500-ctdna │ │ ├── 1.1.0--120 │ │ │ └── tso500-ctdna__1.1.0--120.svg │ │ └── 1.2.0--1 │ │ │ └── tso500-ctdna__1.2.0--1.svg │ │ ├── umccrise-pipeline │ │ ├── 1.2.1--0 │ │ │ └── umccrise-pipeline__1.2.1--0.svg │ │ ├── 1.2.2--0 │ │ │ └── umccrise-pipeline__1.2.2--0.svg │ │ ├── 2.2.0--0 │ │ │ └── umccrise-pipeline__2.2.0--0.svg │ │ ├── 2.2.1--0 │ │ │ └── umccrise-pipeline__2.2.1--0.svg │ │ ├── 2.3.0--0 │ │ │ └── umccrise-pipeline__2.3.0--0.svg │ │ └── 2.3.1--1 │ │ │ └── umccrise-pipeline__2.3.1--1.svg │ │ ├── umccrise-with-dragen-germline-pipeline │ │ ├── 2.0.0--3.9.3 │ │ │ └── umccrise-with-dragen-germline-pipeline__2.0.0--3.9.3.svg │ │ ├── 2.0.1--3.9.3 │ │ │ └── umccrise-with-dragen-germline-pipeline__2.0.1--3.9.3.svg │ │ ├── 2.0.2--3.9.3 │ │ │ └── umccrise-with-dragen-germline-pipeline__2.0.2--3.9.3.svg │ │ ├── 2.1.0--3.9.3 │ │ │ └── umccrise-with-dragen-germline-pipeline__2.1.0--3.9.3.svg │ │ ├── 2.1.1--3.9.3 │ │ │ └── umccrise-with-dragen-germline-pipeline__2.1.1--3.9.3.svg │ │ ├── 2.2.0--3.9.3 │ │ │ └── umccrise-with-dragen-germline-pipeline__2.2.0--3.9.3.svg │ │ └── 2.2.1--3.9.3 │ │ │ └── umccrise-with-dragen-germline-pipeline__2.2.1--3.9.3.svg │ │ └── validate-bclconvert-samplesheet │ │ └── 4.0.3 │ │ └── validate-bclconvert-samplesheet__4.0.3.svg ├── releases │ ├── arriba-pipeline__2.5.0__20251004075334 │ │ └── workflow.svg │ ├── bclconvert-interop-qc__1.3.1--1.21__20240627051309 │ │ └── workflow.svg │ ├── bclconvert-interop-qc__1.3.1--1.21__20241119001529 │ │ └── workflow.svg │ ├── bclconvert-interop-qc__1.3.1--1.25.2__20241120234352 │ │ └── workflow.svg │ ├── bclconvert-interop-qc__1.3.1--1.25.2__20250414112602 │ │ └── workflow.svg │ ├── bclconvert-interop-qc__1.3.1--1.25.2__20250629065755 │ │ └── workflow.svg │ ├── bclconvert-interop-qc__1.3.1--1.25.2__20250629070033 │ │ └── workflow.svg │ ├── bclconvert-interop-qc__1.3.1--1.25.2__20250805060609 │ │ └── workflow.svg │ ├── bclconvert-interop-qc__1.5.0--1.31__20251015011608 │ │ └── workflow.svg │ ├── bclconvert-interop-qc__1.5.0--1.31__20251015012615 │ │ └── workflow.svg │ ├── bclconvert-interop-qc__1.5.0--1.31__20251015013928 │ │ └── workflow.svg │ ├── dragen-alignment-pipeline__4.2.4__20240627051848 │ │ └── workflow.svg │ ├── dragen-alignment-pipeline__4.2.4__20240708034912 │ │ └── workflow.svg │ ├── dragen-alignment-pipeline__4.2.4__20240801063352 │ │ └── workflow.svg │ ├── dragen-alignment-pipeline__4.2.4__20240803074610 │ │ └── workflow.svg │ ├── dragen-alignment-pipeline__4.2.4__20240830041127 │ │ └── workflow.svg │ ├── dragen-alignment-pipeline__4.3.6__20241106102650 │ │ └── workflow.svg │ ├── dragen-build-reference-tarball-pipeline__4.2.4__20241210071831 │ │ └── workflow.svg │ ├── dragen-build-reference-tarball-pipeline__4.2.4__20241210072731 │ │ └── workflow.svg │ ├── dragen-germline-pipeline__4.2.4__20250205035322 │ │ └── workflow.svg │ ├── dragen-germline-pipeline__4.3.6__20241106102657 │ │ └── workflow.svg │ ├── dragen-germline-pipeline__4.3.6__20250207031159 │ │ └── workflow.svg │ ├── dragen-instrument-run-fastq-to-ora-pipeline__4.2.4__20241030041958 │ │ └── workflow.svg │ ├── dragen-instrument-run-fastq-to-ora-pipeline__4.2.4__20241115044412 │ │ └── workflow.svg │ ├── dragen-instrument-run-fastq-to-ora-pipeline__4.2.4__20241115064819 │ │ └── workflow.svg │ ├── dragen-instrument-run-fastq-to-ora-pipeline__4.2.4__20241120224050 │ │ └── workflow.svg │ ├── dragen-instrument-run-fastq-to-ora-pipeline__4.2.4__20241122070556 │ │ └── workflow.svg │ ├── dragen-somatic-with-germline-pipeline__4.2.4__20240627054304 │ │ └── workflow.svg │ ├── dragen-somatic-with-germline-pipeline__4.2.4__20240801063441 │ │ └── workflow.svg │ ├── dragen-somatic-with-germline-pipeline__4.2.4__20240803080024 │ │ └── workflow.svg │ ├── dragen-somatic-with-germline-pipeline__4.2.4__20240830041201 │ │ └── workflow.svg │ ├── dragen-somatic-with-germline-pipeline__4.2.4__20241107061831 │ │ └── workflow.svg │ ├── dragen-somatic-with-germline-pipeline__4.2.4__20241114110541 │ │ └── workflow.svg │ ├── dragen-somatic-with-germline-pipeline__4.2.4__20241210230846 │ │ └── workflow.svg │ ├── dragen-somatic-with-germline-pipeline__4.3.6__20241106102705 │ │ └── workflow.svg │ ├── dragen-somatic-with-germline-pipeline__4.3.6__20241107061820 │ │ └── workflow.svg │ ├── dragen-somatic-with-germline-pipeline__4.3.6__20241115045341 │ │ └── workflow.svg │ ├── dragen-somatic-with-germline-pipeline__4.3.6__20241115073817 │ │ └── workflow.svg │ ├── dragen-transcriptome-pipeline__4.2.4__20240627052945 │ │ └── workflow.svg │ ├── dragen-transcriptome-pipeline__4.2.4__20240708054448 │ │ └── workflow.svg │ ├── dragen-transcriptome-pipeline__4.2.4__20240801063424 │ │ └── workflow.svg │ ├── dragen-transcriptome-pipeline__4.2.4__20240803074622 │ │ └── workflow.svg │ ├── dragen-transcriptome-pipeline__4.2.4__20240830041834 │ │ └── workflow.svg │ ├── dragen-transcriptome-pipeline__4.2.4__20241210230924 │ │ └── workflow.svg │ ├── dragen-transcriptome-pipeline__4.2.4__20250330232251 │ │ └── workflow.svg │ ├── dragen-transcriptome-pipeline__4.2.4__20250331013709 │ │ └── workflow.svg │ ├── dragen-transcriptome-pipeline__4.3.6__20241106102659 │ │ └── workflow.svg │ ├── dragen-wgts-dna-pipeline__4.4.4__20250617224149 │ │ ├── dragen-create-aligner-options-object__4.4.4.svg │ │ ├── dragen-create-mapper-options-object__4.4.4.svg │ │ ├── dragen-create-wgts-alignment-options-object__4.4.4.svg │ │ ├── dragen-create-wgts-dna-variant-calling-options-object__4.4.4.svg │ │ ├── dragen-wgts-alignment-stage__4.4.4.svg │ │ └── workflow.svg │ ├── dragen-wgts-dna-pipeline__4.4.4__20251015010222 │ │ ├── dragen-create-aligner-options-object__4.4.4.svg │ │ ├── dragen-create-mapper-options-object__4.4.4.svg │ │ ├── dragen-create-wgts-alignment-options-object__4.4.4.svg │ │ ├── dragen-create-wgts-dna-variant-calling-options-object__4.4.4.svg │ │ ├── dragen-parse-fastq-list-rows-input__2.0.0.svg │ │ ├── dragen-parse-sequence-data__1.0.0.svg │ │ ├── dragen-wgts-dna-variant-calling-stage__4.4.4.svg │ │ └── workflow.svg │ ├── dragen-wgts-rna-pipeline__4.4.4__20250822040654 │ │ ├── dragen-create-aligner-options-object__4.4.4.svg │ │ ├── dragen-create-mapper-options-object__4.4.4.svg │ │ ├── dragen-create-wgts-alignment-options-object__4.4.4.svg │ │ ├── dragen-create-wgts-rna-variant-calling-options-object__4.4.4.svg │ │ ├── dragen-wgts-rna-variant-calling-stage__4.4.4.svg │ │ └── workflow.svg │ ├── dragen-wts-qc-pipeline__4.2.4__20240830041140 │ │ └── workflow.svg │ ├── rnasum-pipeline__1.0.0__20240627054519 │ │ └── workflow.svg │ ├── rnasum-pipeline__1.0.0__20240627060107 │ │ └── workflow.svg │ ├── rnasum-pipeline__1.1.0__20240901053225 │ │ └── workflow.svg │ ├── rnasum-pipeline__1.1.5__20241112044604 │ │ └── workflow.svg │ ├── rnasum-pipeline__2.0.0__20251004080109 │ │ └── workflow.svg │ ├── rnasum-pipeline__2.0.0__20251007042648 │ │ └── workflow.svg │ ├── umccrise-pipeline__2.3.1--1__20240627054449 │ │ └── workflow.svg │ ├── umccrise-pipeline__2.3.1--1__20240627233816 │ │ └── workflow.svg │ └── umccrise-pipeline__2.3.1--1__20240820075836 │ │ └── workflow.svg ├── scripts │ ├── create_catalogue.sh │ ├── create_workflow_release_asset.sh │ └── run_sync-tools_and_sync-workflows.sh └── workflows │ ├── create_workflow_release_asset.yml │ ├── get_ica_access_token.yml │ ├── get_tenant_icav2_access_token.yml │ └── sync-tools_and_sync-workflows.yml ├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE ├── Readme.md ├── config ├── category.yaml ├── expression.yaml ├── icav2.yaml ├── project.yaml ├── run.yaml ├── schema.yaml ├── tenant.yaml ├── tool.yaml ├── user.yaml └── workflow.yaml ├── cwl-ica-catalogue.md ├── dragen-instrument-run-fastq-to-ora-pipeline__4.2.4.zip ├── expressions ├── add-run-info-and-samplesheet-to-bclconvert-run-configuration │ └── 2.0.0--4.0.3 │ │ └── add-run-info-and-samplesheet-to-bclconvert-run-configuration__2.0.0--4.0.3.cwl ├── assert-true │ └── 1.0.0 │ │ └── assert-true__1.0.0.cwl ├── create-contig-obj-for-hla-chr6-region │ └── 1.0.0 │ │ └── create-contig-obj-for-hla-chr6-region__1.0.0.cwl ├── create-directory │ └── 1.0.0 │ │ └── create-directory__1.0.0.cwl ├── create-file │ └── 1.0.0 │ │ └── create-file__1.0.0.cwl ├── create-predefined-mount-paths-and-umccrise-row-from-umccrise-schema │ ├── 1.2.1--0 │ │ └── create-predefined-mount-paths-and-umccrise-row-from-umccrise-schema__1.2.1--0.cwl │ └── 1.2.2--0 │ │ └── create-predefined-mount-paths-and-umccrise-row-from-umccrise-schema__1.2.2--0.cwl ├── create-single-directory-from-directories-array │ └── 1.0.0 │ │ └── create-single-directory-from-directories-array__1.0.0.cwl ├── dragen-parse-aligner-schema │ ├── 4.4.0 │ │ └── dragen-parse-aligner-schema__4.4.0.cwl │ └── 4.4.4 │ │ └── dragen-parse-aligner-schema__4.4.4.cwl ├── dragen-parse-bam-input │ └── 1.0.0 │ │ └── dragen-parse-bam-input__1.0.0.cwl ├── dragen-parse-cram-input │ └── 1.0.0 │ │ └── dragen-parse-cram-input__1.0.0.cwl ├── dragen-parse-fastq-list-row │ └── 2.0.0 │ │ └── dragen-parse-fastq-list-row__2.0.0.cwl ├── dragen-parse-fastq-list-rows │ └── 2.0.0 │ │ └── dragen-parse-fastq-list-rows__2.0.0.cwl ├── dragen-parse-mapper-schema │ ├── 4.4.0 │ │ └── dragen-parse-mapper-schema__4.4.0.cwl │ └── 4.4.4 │ │ └── dragen-parse-mapper-schema__4.4.4.cwl ├── dragen-parse-qc-coverage │ └── 1.0.0 │ │ └── dragen-parse-qc-coverage__1.0.0.cwl ├── dragen-parse-rna-gene-expression-quantification-schema │ └── 4.4.0 │ │ └── dragen-parse-rna-gene-expression-quantification-schema__4.4.0.cwl ├── dragen-parse-sequence-data │ └── 1.0.0 │ │ └── dragen-parse-sequence-data__1.0.0.cwl ├── dragen-parse-snv-variant-caller-schema │ ├── 4.4.0 │ │ └── dragen-parse-snv-variant-caller-schema__4.4.0.cwl │ └── 4.4.4 │ │ └── dragen-parse-snv-variant-caller-schema__4.4.4.cwl ├── dragen-parse-sv-caller-schema │ ├── 4.4.0 │ │ └── dragen-parse-sv-caller-schema__4.4.0.cwl │ └── 4.4.4 │ │ └── dragen-parse-sv-caller-schema__4.4.4.cwl ├── dragen-wgts-parse-alignment-schema │ ├── 4.4.0 │ │ └── dragen-wgts-parse-alignment-schema__4.4.0.cwl │ └── 4.4.4 │ │ └── dragen-wgts-parse-alignment-schema__4.4.4.cwl ├── ensure-all-samples-have-passed-all-tso500-ctdna-steps │ └── 1.0.0 │ │ └── ensure-all-samples-have-passed-all-tso500-ctdna-steps__1.0.0.cwl ├── flatten-array-fastq-list │ └── 1.0.0 │ │ └── flatten-array-fastq-list__1.0.0.cwl ├── get-attr-from-tso500-sample-object │ ├── 1.0.0 │ │ └── get-attr-from-tso500-sample-object__1.0.0.cwl │ └── 1.2.0 │ │ └── get-attr-from-tso500-sample-object__1.2.0.cwl ├── get-bam-file-from-directory │ ├── 1.0.0 │ │ └── get-bam-file-from-directory__1.0.0.cwl │ ├── 1.0.1-rabix │ │ ├── get-bam-file-from-directory__1.0.1-rabix.cwl │ │ └── typescript-expressions │ │ │ ├── get-bam-file-from-directory__1.0.1-rabix.cwljs │ │ │ ├── get-bam-file-from-directory__1.0.1-rabix.js │ │ │ ├── get-bam-file-from-directory__1.0.1-rabix.ts │ │ │ ├── jest.config.js │ │ │ ├── package.json │ │ │ ├── tests │ │ │ ├── get-bam-file-from-directory__1.0.1-rabix.test.js │ │ │ ├── get-bam-file-from-directory__1.0.1-rabix.test.ts │ │ │ └── summary.txt │ │ │ ├── tsconfig.json │ │ │ └── yarn.lock │ └── 1.0.1 │ │ ├── get-bam-file-from-directory__1.0.1.cwl │ │ └── typescript-expressions │ │ ├── get-bam-file-from-directory__1.0.1.cwljs │ │ ├── get-bam-file-from-directory__1.0.1.js │ │ ├── get-bam-file-from-directory__1.0.1.ts │ │ ├── jest.config.js │ │ ├── package.json │ │ ├── tests │ │ ├── get-bam-file-from-directory__1.0.1.test.js │ │ ├── get-bam-file-from-directory__1.0.1.test.ts │ │ └── summary.txt │ │ ├── tsconfig.json │ │ └── yarn.lock ├── get-compressed-vcf-file-from-directory │ └── 1.0.0 │ │ └── get-compressed-vcf-file-from-directory__1.0.0.cwl ├── get-custom-output-dir-entry-for-tso500-post-processing │ ├── 1.0.0 │ │ └── get-custom-output-dir-entry-for-tso500-post-processing__1.0.0.cwl │ └── 2.0.1 │ │ └── get-custom-output-dir-entry-for-tso500-post-processing__2.0.1.cwl ├── get-custom-output-dir-entry-for-tso500-with-post-processing │ ├── 1.0.0 │ │ └── get-custom-output-dir-entry-for-tso500-with-post-processing__1.0.0.cwl │ └── 2.0.1 │ │ └── get-custom-output-dir-entry-for-tso500-with-post-processing__2.0.1.cwl ├── get-faidx-file-from-reference-file │ └── 1.0.0 │ │ └── get-faidx-file-from-reference-file__1.0.0.cwl ├── get-file-from-directory-with-regex │ └── 1.0.0 │ │ └── get-file-from-directory-with-regex__1.0.0.cwl ├── get-file-from-directory │ ├── 1.0.0 │ │ └── get-file-from-directory__1.0.0.cwl │ └── 1.0.1 │ │ └── get-file-from-directory__1.0.1.cwl ├── get-files-from-directory │ └── 1.0.0 │ │ └── get-files-from-directory__1.0.0.cwl ├── get-first-non-null-bam-file │ └── 1.0.0 │ │ └── get-first-non-null-bam-file__1.0.0.cwl ├── get-samplesheet-midfix-regex │ └── 1.0.0 │ │ └── get-samplesheet-midfix-regex__1.0.0.cwl ├── get-subdirectory-from-directory │ └── 1.0.0 │ │ └── get-subdirectory-from-directory__1.0.0.cwl ├── get-tso500-outputs-per-sample │ ├── 1.0.0 │ │ └── get-tso500-outputs-per-sample__1.0.0.cwl │ └── 1.2.0 │ │ └── get-tso500-outputs-per-sample__1.2.0.cwl ├── parse-bclconvert-run-configuration-object │ └── 2.0.0--4.0.3 │ │ └── parse-bclconvert-run-configuration-object__2.0.0--4.0.3.cwl ├── parse-file │ └── 1.0.0 │ │ └── parse-file__1.0.0.cwl ├── parse-int-array │ └── 1.0.0 │ │ └── parse-int-array__1.0.0.cwl ├── parse-int │ └── 1.0.0 │ │ └── parse-int__1.0.0.cwl ├── parse-samplesheet │ └── 2.0.0--4.0.3 │ │ └── parse-samplesheet__2.0.0--4.0.3.cwl ├── parse-string-array │ └── 1.0.0 │ │ └── parse-string-array__1.0.0.cwl ├── parse-string │ └── 1.0.0 │ │ └── parse-string__1.0.0.cwl └── validate-dsdm-json │ └── 1.0.0 │ └── validate-dsdm-json__1.0.0.cwl ├── package.json ├── schemas ├── bam-input │ └── 1.0.0 │ │ ├── bam-input__1.0.0.ts │ │ └── bam-input__1.0.0.yaml ├── bam-output │ └── 1.0.0 │ │ ├── bam-output__1.0.0.ts │ │ └── bam-output__1.0.0.yaml ├── bclconvert-data-row │ └── 4.0.3 │ │ ├── bclconvert-data-row__4.0.3.ts │ │ └── bclconvert-data-row__4.0.3.yaml ├── bclconvert-run-configuration │ └── 2.0.0--4.0.3 │ │ ├── bclconvert-run-configuration__2.0.0--4.0.3.ts │ │ └── bclconvert-run-configuration__2.0.0--4.0.3.yaml ├── bclconvert-settings │ └── 4.0.3 │ │ ├── bclconvert-settings__4.0.3.ts │ │ └── bclconvert-settings__4.0.3.yaml ├── contig │ └── 1.0.0 │ │ └── contig__1.0.0.yaml ├── cram-input │ └── 1.0.0 │ │ ├── cram-input__1.0.0.ts │ │ └── cram-input__1.0.0.yaml ├── cram-output │ └── 1.0.0 │ │ ├── cram-output__1.0.0.ts │ │ └── cram-output__1.0.0.yaml ├── custom-output-dir-entry │ ├── 2.0.0 │ │ └── custom-output-dir-entry__2.0.0.yaml │ └── 2.0.1 │ │ └── custom-output-dir-entry__2.0.1.yaml ├── dragen-aligner-options │ └── 4.4.0 │ │ ├── dragen-aligner-options__4.4.0.ts │ │ └── dragen-aligner-options__4.4.0.yaml ├── dragen-cnv-caller-options │ └── 4.4.0 │ │ ├── dragen-cnv-caller-options__4.4.0.ts │ │ └── dragen-cnv-caller-options__4.4.0.yaml ├── dragen-maf-conversion-options │ └── 4.4.0 │ │ ├── dragen-maf-conversion-options__4.4.0.ts │ │ └── dragen-maf-conversion-options__4.4.0.yaml ├── dragen-mapper-options │ └── 4.4.0 │ │ ├── dragen-mapper-options__4.4.0.ts │ │ └── dragen-mapper-options__4.4.0.yaml ├── dragen-mrjd-options │ └── 4.4.0 │ │ ├── dragen-mrjd-options__4.4.0.ts │ │ └── dragen-mrjd-options__4.4.0.yaml ├── dragen-msi-options │ └── 4.4.0 │ │ ├── dragen-msi-options__4.4.0.ts │ │ └── dragen-msi-options__4.4.0.yaml ├── dragen-nirvana-annotation-options │ └── 4.4.0 │ │ ├── dragen-nirvana-annotation-options__4.4.0.ts │ │ └── dragen-nirvana-annotation-options__4.4.0.yaml ├── dragen-qc-coverage │ └── 1.0.0 │ │ ├── dragen-qc-coverage__1.0.0.ts │ │ └── dragen-qc-coverage__1.0.0.yaml ├── dragen-reference │ └── 1.0.0 │ │ ├── dragen-reference__1.0.0.ts │ │ └── dragen-reference__1.0.0.yaml ├── dragen-rna-gene-expression-quantification-options │ └── 4.4.0 │ │ ├── dragen-rna-gene-expression-quantification-options__4.4.0.ts │ │ └── dragen-rna-gene-expression-quantification-options__4.4.0.yaml ├── dragen-rna-gene-fusion-detection-options │ └── 4.4.0 │ │ ├── dragen-rna-gene-fusion-detection-options__4.4.0.ts │ │ └── dragen-rna-gene-fusion-detection-options__4.4.0.yaml ├── dragen-rna-splice-variant-caller-options │ └── 4.4.0 │ │ ├── dragen-rna-splice-variant-caller-options__4.4.0.ts │ │ └── dragen-rna-splice-variant-caller-options__4.4.0.yaml ├── dragen-snv-variant-caller-options │ └── 4.4.0 │ │ ├── dragen-snv-variant-caller-options__4.4.0.ts │ │ └── dragen-snv-variant-caller-options__4.4.0.yaml ├── dragen-sv-caller-options │ └── 4.4.0 │ │ ├── dragen-sv-caller-options__4.4.0.ts │ │ └── dragen-sv-caller-options__4.4.0.yaml ├── dragen-targeted-caller-options │ └── 4.4.0 │ │ ├── dragen-targeted-caller-options__4.4.0.ts │ │ └── dragen-targeted-caller-options__4.4.0.yaml ├── dragen-tmb-options │ └── 4.4.0 │ │ ├── dragen-tmb-options__4.4.0.ts │ │ └── dragen-tmb-options__4.4.0.yaml ├── dragen-wgts-alignment-options │ └── 4.4.0 │ │ ├── dragen-wgts-alignment-options__4.4.0.ts │ │ └── dragen-wgts-alignment-options__4.4.0.yaml ├── dragen-wgts-dna-options-variant-calling-stage │ └── 4.4.0 │ │ ├── dragen-wgts-dna-options-variant-calling-stage__4.4.0.ts │ │ └── dragen-wgts-dna-options-variant-calling-stage__4.4.0.yaml ├── dragen-wgts-options-alignment-stage │ └── 4.4.0 │ │ ├── dragen-wgts-options-alignment-stage__4.4.0.ts │ │ └── dragen-wgts-options-alignment-stage__4.4.0.yaml ├── dragen-wgts-rna-options-variant-calling-stage │ └── 4.4.0 │ │ ├── dragen-wgts-rna-options-variant-calling-stage__4.4.0.ts │ │ └── dragen-wgts-rna-options-variant-calling-stage__4.4.0.yaml ├── fastq-list-row │ ├── 1.0.0 │ │ ├── fastq-list-row__1.0.0.ts │ │ └── fastq-list-row__1.0.0.yaml │ └── 2.0.0 │ │ ├── fastq-list-row__2.0.0.ts │ │ └── fastq-list-row__2.0.0.yaml ├── fastq-list-rows-input │ └── 2.0.0 │ │ ├── fastq-list-rows-input__2.0.0.ts │ │ └── fastq-list-rows-input__2.0.0.yaml ├── predefined-mount-path │ └── 1.0.0 │ │ └── predefined-mount-path__1.0.0.yaml ├── samplesheet-header │ └── 2.0.0 │ │ ├── samplesheet-header__2.0.0.ts │ │ └── samplesheet-header__2.0.0.yaml ├── samplesheet-reads │ └── 2.0.0 │ │ ├── samplesheet-reads__2.0.0.ts │ │ └── samplesheet-reads__2.0.0.yaml ├── samplesheet │ └── 2.0.0--4.0.3 │ │ ├── samplesheet__2.0.0--4.0.3.ts │ │ └── samplesheet__2.0.0--4.0.3.yaml ├── settings-by-samples │ └── 1.0.0 │ │ └── settings-by-samples__1.0.0.yaml ├── tso500-outputs-by-sample │ └── 1.0.0 │ │ └── tso500-outputs-by-sample__1.0.0.yaml ├── tso500-sample │ ├── 1.0.0 │ │ ├── tso500-sample__1.0.0.ts │ │ └── tso500-sample__1.0.0.yaml │ └── 1.2.0 │ │ ├── tso500-sample__1.2.0.ts │ │ └── tso500-sample__1.2.0.yaml └── umccrise-input │ ├── 1.2.1--0 │ └── umccrise-input__1.2.1--0.yaml │ └── 1.2.2--0 │ └── umccrise-input__1.2.2--0.yaml ├── tests ├── __init__.py └── subcommands │ ├── __init__.py │ ├── configure │ ├── __init__.py │ ├── test_configure_repo.py │ ├── test_configure_tenant.py │ └── test_configure_user.py │ ├── creators │ └── test_create_tool_from_template.py │ ├── ica_initialisers │ ├── __init__.py │ ├── test_category_init.py │ └── test_project_init.py │ └── set_defaults │ ├── __init__.py │ ├── test_set_default_project.py │ ├── test_set_default_tenant.py │ └── test_set_default_user.py ├── tools ├── arriba-drawing │ ├── 2.0.0 │ │ └── arriba-drawing__2.0.0.cwl │ ├── 2.3.0 │ │ └── arriba-drawing__2.3.0.cwl │ ├── 2.4.0 │ │ └── arriba-drawing__2.4.0.cwl │ └── 2.5.0 │ │ └── arriba-drawing__2.5.0.cwl ├── arriba-fusion-calling │ ├── 2.0.0 │ │ └── arriba-fusion-calling__2.0.0.cwl │ ├── 2.3.0 │ │ └── arriba-fusion-calling__2.3.0.cwl │ ├── 2.4.0 │ │ └── arriba-fusion-calling__2.4.0.cwl │ └── 2.5.0 │ │ └── arriba-fusion-calling__2.5.0.cwl ├── bamtofastq │ └── 2.0.183 │ │ └── bamtofastq__2.0.183.cwl ├── bcftools-view │ └── 1.13.0 │ │ └── bcftools-view__1.13.0.cwl ├── bcl-convert │ └── 4.0.3 │ │ └── bcl-convert__4.0.3.cwl ├── bclConvert │ └── 3.7.5 │ │ └── bclConvert__3.7.5.cwl ├── bedops │ └── 2.4.39 │ │ └── bedops__2.4.39.cwl ├── bgzip │ └── 1.12.0 │ │ └── bgzip__1.12.0.cwl ├── calculate-coverage │ └── 1.0.0 │ │ └── calculate-coverage__1.0.0.cwl ├── create-dummy-directory │ └── 1.0.0 │ │ └── create-dummy-directory__1.0.0.cwl ├── create-dummy-file │ └── 1.0.0 │ │ └── create-dummy-file__1.0.0.cwl ├── custom-convert-multiqc-json-data-to-qlims-import-csv │ └── 1.0.0 │ │ └── custom-convert-multiqc-json-data-to-qlims-import-csv__1.0.0.cwl ├── custom-create-csv-from-fastq-list-rows │ └── 1.0.0 │ │ └── custom-create-csv-from-fastq-list-rows__1.0.0.cwl ├── custom-create-directory │ ├── 1.0.0 │ │ └── custom-create-directory__1.0.0.cwl │ ├── 1.0.1 │ │ └── custom-create-directory__1.0.1.cwl │ ├── 2.0.0 │ │ └── custom-create-directory__2.0.0.cwl │ └── 2.0.1 │ │ └── custom-create-directory__2.0.1.cwl ├── custom-create-regions-bed-from-contigs-list │ └── 1.0.0 │ │ └── custom-create-regions-bed-from-contigs-list__1.0.0.cwl ├── custom-create-tso500-samplesheet │ ├── 1.0.0 │ │ └── custom-create-tso500-samplesheet__1.0.0.cwl │ └── 1.2.0 │ │ └── custom-create-tso500-samplesheet__1.2.0.cwl ├── custom-create-umccr-dragen-refdata-tarball-from-illumina-tar │ └── 1.0.0 │ │ └── custom-create-umccr-dragen-refdata-tarball-from-illumina-tar__1.0.0.cwl ├── custom-create-umccrise-tsv │ ├── 1.2.1--0 │ │ └── custom-create-umccrise-tsv__1.2.1--0.cwl │ └── 1.2.2--0 │ │ └── custom-create-umccrise-tsv__1.2.2--0.cwl ├── custom-get-sample-name-from-bam-header │ └── 1.0.0 │ │ └── custom-get-sample-name-from-bam-header__1.0.0.cwl ├── custom-gzip-file │ └── 1.0.0 │ │ └── custom-gzip-file__1.0.0.cwl ├── custom-hla-bed-from-faidx │ └── 1.0.0 │ │ └── custom-hla-bed-from-faidx__1.0.0.cwl ├── custom-samplesheet-split-by-settings │ └── 1.0.0 │ │ └── custom-samplesheet-split-by-settings__1.0.0.cwl ├── custom-stats-qc │ ├── 1.0.0 │ │ └── custom-stats-qc__1.0.0.cwl │ └── 1.0.1 │ │ └── custom-stats-qc__1.0.1.cwl ├── custom-subset-bam │ └── 1.12.0 │ │ └── custom-subset-bam__1.12.0.cwl ├── custom-tar-file-list │ └── 1.0.0 │ │ └── custom-tar-file-list__1.0.0.cwl ├── custom-tar-vcf-file-list │ └── 1.0.0 │ │ └── custom-tar-vcf-file-list__1.0.0.cwl ├── custom-touch-file │ └── 1.0.0 │ │ └── custom-touch-file__1.0.0.cwl ├── custom-tso500-align-collapse-fusion-caller-csv-metrics-to-json │ └── 1.0.0 │ │ └── custom-tso500-align-collapse-fusion-caller-csv-metrics-to-json__1.0.0.cwl ├── custom-tso500-cnv-caller-bin-counts-to-json │ └── 1.0.0 │ │ └── custom-tso500-cnv-caller-bin-counts-to-json__1.0.0.cwl ├── custom-tso500-make-exon-coverage-qc │ └── 1.0.0 │ │ └── custom-tso500-make-exon-coverage-qc__1.0.0.cwl ├── custom-tso500-make-region-coverage-qc │ └── 1.0.0 │ │ └── custom-tso500-make-region-coverage-qc__1.0.0.cwl ├── custom-tsv-to-json │ └── 1.0.0 │ │ └── custom-tsv-to-json__1.0.0.cwl ├── dragen-alignment-step │ └── 4.4.0 │ │ └── dragen-alignment-step__4.4.0.cwl ├── dragen-alignment │ ├── 3.7.5 │ │ └── dragen-alignment__3.7.5.cwl │ ├── 3.9.3 │ │ └── dragen-alignment__3.9.3.cwl │ ├── 4.0.3 │ │ └── dragen-alignment__4.0.3.cwl │ ├── 4.2.4 │ │ └── dragen-alignment__4.2.4.cwl │ └── 4.3.6 │ │ └── dragen-alignment__4.3.6.cwl ├── dragen-build-reference-tarball │ ├── 3.7.5 │ │ └── dragen-build-reference-tarball__3.7.5.cwl │ ├── 3.8.4 │ │ └── dragen-build-reference-tarball__3.8.4.cwl │ ├── 4.0.3 │ │ └── dragen-build-reference-tarball__4.0.3.cwl │ └── 4.2.4 │ │ └── dragen-build-reference-tarball__4.2.4.cwl ├── dragen-germline │ ├── 3.7.5 │ │ └── dragen-germline__3.7.5.cwl │ ├── 3.9.3 │ │ └── dragen-germline__3.9.3.cwl │ ├── 4.0.3 │ │ └── dragen-germline__4.0.3.cwl │ ├── 4.2.4 │ │ └── dragen-germline__4.2.4.cwl │ └── 4.3.6 │ │ └── dragen-germline__4.3.6.cwl ├── dragen-instrument-run-fastq-to-ora │ └── 4.2.4 │ │ └── dragen-instrument-run-fastq-to-ora__4.2.4.cwl ├── dragen-nirvana-downloader │ └── 4.4.4 │ │ └── dragen-nirvana-downloader__4.4.4.cwl ├── dragen-somatic │ ├── 3.7.5 │ │ └── dragen-somatic__3.7.5.cwl │ ├── 3.9.3 │ │ └── dragen-somatic__3.9.3.cwl │ ├── 4.0.3 │ │ └── dragen-somatic__4.0.3.cwl │ ├── 4.2.4 │ │ └── dragen-somatic__4.2.4.cwl │ └── 4.3.6 │ │ └── dragen-somatic__4.3.6.cwl ├── dragen-transcriptome │ ├── 3.7.5 │ │ └── dragen-transcriptome__3.7.5.cwl │ ├── 3.8.4 │ │ └── dragen-transcriptome__3.8.4.cwl │ ├── 3.9.3 │ │ └── dragen-transcriptome__3.9.3.cwl │ ├── 4.0.3 │ │ └── dragen-transcriptome__4.0.3.cwl │ ├── 4.2.4 │ │ └── dragen-transcriptome__4.2.4.cwl │ └── 4.3.6 │ │ └── dragen-transcriptome__4.3.6.cwl ├── dragen-umi │ ├── 3.8.4 │ │ └── dragen-umi__3.8.4.cwl │ └── 3.9.3 │ │ └── dragen-umi__3.9.3.cwl ├── dragen-wgts-alignment-step │ └── 4.4.4 │ │ └── dragen-wgts-alignment-step__4.4.4.cwl ├── dragen-wgts-dna-variant-calling-step │ ├── 4.4.4 │ │ └── dragen-wgts-dna-variant-calling-step__4.4.4.cwl │ └── 4.4.6 │ │ └── dragen-wgts-dna-variant-calling-step__4.4.6.cwl ├── dragen-wgts-parse-alignment-schema │ └── 4.4.4 │ │ └── dragen-wgts-parse-alignment-schema__4.4.4.cwl ├── dragen-wgts-rna-variant-calling-step │ └── 4.4.4 │ │ └── dragen-wgts-rna-variant-calling-step__4.4.4.cwl ├── get-dragen-default-configuration-json │ ├── 4.4.4 │ │ └── get-dragen-default-configuration-json__4.4.4.cwl │ └── 4.4.6 │ │ └── get-dragen-default-configuration-json__4.4.6.cwl ├── illumina-interop │ ├── 1.2.0 │ │ └── illumina-interop__1.2.0.cwl │ ├── 1.3.1 │ │ └── illumina-interop__1.3.1.cwl │ └── 1.5.0 │ │ └── illumina-interop__1.5.0.cwl ├── map_resource_requirements │ └── 0.1.0 │ │ └── map_resource_requirements__0.1.0.cwl ├── mosdepth │ └── 0.3.1 │ │ └── mosdepth__0.3.1.cwl ├── multiqc-interop │ ├── 1.14.0--1.2.0 │ │ └── multiqc-interop__1.14.0--1.2.0.cwl │ └── 1.2.1 │ │ └── multiqc-interop__1.2.1.cwl ├── multiqc │ ├── 1.10.1 │ │ └── multiqc__1.10.1.cwl │ ├── 1.11.0 │ │ └── multiqc__1.11.0.cwl │ ├── 1.12.0 │ │ └── multiqc__1.12.0.cwl │ ├── 1.14.0 │ │ └── multiqc__1.14.0.cwl │ ├── 1.15.0 │ │ └── multiqc__1.15.0.cwl │ ├── 1.19.0 │ │ └── multiqc__1.19.0.cwl │ ├── 1.21.0 │ │ └── multiqc__1.21.0.cwl │ ├── 1.25.1 │ │ └── multiqc__1.25.1.cwl │ ├── 1.25.2 │ │ └── multiqc__1.25.2.cwl │ └── 1.31.0 │ │ └── multiqc__1.31.0.cwl ├── nirvana-downloader │ └── 4.4.4 │ │ └── nirvana-downloader__4.4.4.cwl ├── optitype │ └── 1.3.5 │ │ └── optitype__1.3.5.cwl ├── qualimap │ └── 2.2.2 │ │ └── qualimap__2.2.2.cwl ├── rename-rgsm-in-alignment-header │ └── 1.0.0 │ │ └── rename-rgsm-in-alignment-header__1.0.0.cwl ├── rnasum │ ├── 0.4.1 │ │ └── rnasum__0.4.1.cwl │ ├── 0.4.2 │ │ └── rnasum__0.4.2.cwl │ ├── 0.4.3 │ │ └── rnasum__0.4.3.cwl │ ├── 0.4.4 │ │ └── rnasum__0.4.4.cwl │ ├── 0.4.5 │ │ └── rnasum__0.4.5.cwl │ ├── 0.4.7 │ │ └── rnasum__0.4.7.cwl │ ├── 0.4.8 │ │ └── rnasum__0.4.8.cwl │ ├── 0.4.9 │ │ └── rnasum__0.4.9.cwl │ ├── 0.5.0 │ │ └── rnasum__0.5.0.cwl │ ├── 0.6.5 │ │ └── rnasum__0.6.5.cwl │ ├── 1.0.0 │ │ └── rnasum__1.0.0.cwl │ ├── 1.1.0 │ │ └── rnasum__1.1.0.cwl │ ├── 1.1.5 │ │ └── rnasum__1.1.5.cwl │ └── 2.0.0 │ │ └── rnasum__2.0.0.cwl ├── sambamba-merge-and-index │ └── 0.8.0 │ │ └── sambamba-merge-and-index__0.8.0.cwl ├── sambamba-slice-and-index │ └── 0.8.0 │ │ └── sambamba-slice-and-index__0.8.0.cwl ├── sambamba-sort-and-index │ └── 0.8.0 │ │ └── sambamba-sort-and-index__0.8.0.cwl ├── sambamba-view-and-index │ └── 0.8.0 │ │ └── sambamba-view-and-index__0.8.0.cwl ├── samtools-fastq │ └── 1.12.0 │ │ └── samtools-fastq__1.12.0.cwl ├── samtools-merge │ └── 1.12.0 │ │ └── samtools-merge__1.12.0.cwl ├── samtools-reheader │ └── 1.21.0 │ │ └── samtools-reheader__1.21.0.cwl ├── samtools-stats │ └── 1.13.0 │ │ └── samtools-stats__1.13.0.cwl ├── somalier-extract │ └── 0.2.13 │ │ └── somalier-extract__0.2.13.cwl ├── star │ └── 2.7.10 │ │ └── star__2.7.10.cwl ├── tabix │ └── 0.2.6 │ │ └── tabix__0.2.6.cwl ├── tso500-ctdna-analysis-workflow │ ├── 1.1.0--120 │ │ └── tso500-ctdna-analysis-workflow__1.1.0--120.cwl │ └── 1.2.0--1 │ │ └── tso500-ctdna-analysis-workflow__1.2.0--1.cwl ├── tso500-ctdna-demultiplex-workflow │ ├── 1.1.0--120 │ │ └── tso500-ctdna-demultiplex-workflow__1.1.0--120.cwl │ └── 1.2.0--1 │ │ └── tso500-ctdna-demultiplex-workflow__1.2.0--1.cwl ├── tso500-ctdna-reporting-workflow │ ├── 1.1.0--120 │ │ └── tso500-ctdna-reporting-workflow__1.1.0--120.cwl │ └── 1.2.0--1 │ │ └── tso500-ctdna-reporting-workflow__1.2.0--1.cwl └── umccrise │ ├── 1.2.1--0 │ └── umccrise__1.2.1--0.cwl │ ├── 1.2.2--0 │ └── umccrise__1.2.2--0.cwl │ ├── 2.0.0--0 │ └── umccrise__2.0.0--0.cwl │ ├── 2.0.1--0 │ └── umccrise__2.0.1--0.cwl │ ├── 2.0.2--0 │ └── umccrise__2.0.2--0.cwl │ ├── 2.1.0--0 │ └── umccrise__2.1.0--0.cwl │ ├── 2.1.1--0 │ └── umccrise__2.1.1--0.cwl │ ├── 2.2.0--0 │ └── umccrise__2.2.0--0.cwl │ ├── 2.2.1--0 │ └── umccrise__2.2.1--0.cwl │ ├── 2.3.0--0 │ └── umccrise__2.3.0--0.cwl │ └── 2.3.1--1 │ └── umccrise__2.3.1--1.cwl ├── typescript-expressions ├── bclconvert-run-configuration-expressions │ └── 2.0.0--4.0.3 │ │ ├── bclconvert-run-configuration-expressions__2.0.0--4.0.3.cwljs │ │ ├── bclconvert-run-configuration-expressions__2.0.0--4.0.3.js │ │ ├── bclconvert-run-configuration-expressions__2.0.0--4.0.3.ts │ │ ├── jest.config.js │ │ ├── package.json │ │ ├── tests │ │ ├── bclconvert-run-configuration-expressions__2.0.0--4.0.3.test.js │ │ ├── bclconvert-run-configuration-expressions__2.0.0--4.0.3.test.ts │ │ └── summary.txt │ │ ├── tsconfig.json │ │ └── yarn.lock ├── dragen-tools │ ├── 4.0.3 │ │ ├── dragen-tools__4.0.3.cwljs │ │ ├── dragen-tools__4.0.3.js │ │ ├── dragen-tools__4.0.3.ts │ │ ├── jest.config.js │ │ ├── package.json │ │ ├── tests │ │ │ ├── data │ │ │ │ ├── fastq_list.csv │ │ │ │ ├── fastq_list.ora.csv │ │ │ │ ├── fastq_list.reordered.csv │ │ │ │ ├── generate-new-fastq-list-csv.sh │ │ │ │ ├── mv-ora.sh │ │ │ │ └── tumor_fastq_list.csv │ │ │ ├── dragen-tools__4.0.3.test.js │ │ │ ├── dragen-tools__4.0.3.test.ts │ │ │ └── summary.txt │ │ ├── tsconfig.json │ │ └── yarn.lock │ └── 4.4.0 │ │ ├── dragen-tools__4.4.0.cwljs │ │ ├── dragen-tools__4.4.0.js │ │ ├── dragen-tools__4.4.0.ts │ │ ├── dragen-tools_custom_input_interfaces.cwljs │ │ ├── dragen-tools_custom_input_interfaces.js │ │ ├── dragen-tools_custom_input_interfaces.ts │ │ ├── dragen-tools_function_interfaces.cwljs │ │ ├── dragen-tools_function_interfaces.js │ │ ├── dragen-tools_function_interfaces.ts │ │ ├── jest.config.js │ │ ├── package.json │ │ ├── tests │ │ ├── data │ │ │ ├── dragen_alignment_options_input.json │ │ │ ├── dragen_default_config.cfg │ │ │ ├── dragen_default_config.json │ │ │ ├── dragen_default_config.thin.cfg │ │ │ ├── fastq_list_row.json │ │ │ └── fastq_list_row_expected.csv │ │ ├── dragen-tools__4.4.0.test.js │ │ ├── dragen-tools__4.4.0.test.ts │ │ └── summary.txt │ │ ├── tsconfig.json │ │ └── yarn.lock ├── get-fastq-list-rows-from-fastq-list-csv │ └── 1.0.0 │ │ ├── get-fastq-list-rows-from-fastq-list-csv__1.0.0.cwljs │ │ ├── get-fastq-list-rows-from-fastq-list-csv__1.0.0.js │ │ ├── get-fastq-list-rows-from-fastq-list-csv__1.0.0.ts │ │ ├── jest.config.js │ │ ├── package.json │ │ ├── tests │ │ ├── data │ │ │ └── fastq_list.csv │ │ ├── get-fastq-list-rows-from-fastq-list-csv__1.0.0.test.js │ │ ├── get-fastq-list-rows-from-fastq-list-csv__1.0.0.test.ts │ │ └── summary.txt │ │ ├── tsconfig.json │ │ └── yarn.lock ├── get-file-from-directory │ └── 1.0.0 │ │ ├── get-file-from-directory__1.0.0.cwljs │ │ ├── get-file-from-directory__1.0.0.js │ │ ├── get-file-from-directory__1.0.0.ts │ │ ├── jest.config.js │ │ ├── package.json │ │ ├── tests │ │ ├── get-file-from-directory__1.0.0.test.js │ │ ├── get-file-from-directory__1.0.0.test.ts │ │ └── summary.txt │ │ ├── tsconfig.json │ │ └── yarn.lock ├── multiqc-tools │ └── 1.0.0 │ │ ├── jest.config.js │ │ ├── multiqc-tools__1.0.0.cwljs │ │ ├── multiqc-tools__1.0.0.js │ │ ├── multiqc-tools__1.0.0.ts │ │ ├── package.json │ │ ├── tests │ │ ├── multiqc-tools__1.0.0.test.js │ │ ├── multiqc-tools__1.0.0.test.ts │ │ └── summary.txt │ │ ├── tsconfig.json │ │ └── yarn.lock ├── samplesheet-builder │ └── 2.0.0--4.0.3 │ │ ├── jest.config.js │ │ ├── package.json │ │ ├── samplesheet-builder__2.0.0--4.0.3.cwljs │ │ ├── samplesheet-builder__2.0.0--4.0.3.js │ │ ├── samplesheet-builder__2.0.0--4.0.3.ts │ │ ├── tests │ │ ├── samplesheet-builder__2.0.0--4.0.3.test.js │ │ ├── samplesheet-builder__2.0.0--4.0.3.test.ts │ │ └── summary.txt │ │ ├── tsconfig.json │ │ └── yarn.lock ├── tso500-ctdna │ └── 1.2.0--1 │ │ ├── jest.config.js │ │ ├── package.json │ │ ├── tests │ │ ├── summary.txt │ │ ├── tso500-ctdna__1.2.0--1.test.js │ │ └── tso500-ctdna__1.2.0--1.test.ts │ │ ├── tsconfig.json │ │ ├── tso500-ctdna__1.2.0--1.cwljs │ │ ├── tso500-ctdna__1.2.0--1.js │ │ ├── tso500-ctdna__1.2.0--1.ts │ │ └── yarn.lock ├── umccrise │ └── 2.0.0 │ │ ├── jest.config.js │ │ ├── package.json │ │ ├── tests │ │ ├── summary.txt │ │ ├── umccrise__2.0.0.test.js │ │ └── umccrise__2.0.0.test.ts │ │ ├── tsconfig.json │ │ ├── umccrise__2.0.0.cwljs │ │ ├── umccrise__2.0.0.js │ │ ├── umccrise__2.0.0.ts │ │ └── yarn.lock └── utils │ └── 1.0.0 │ ├── jest.config.js │ ├── package.json │ ├── tests │ ├── summary.txt │ ├── utils__1.0.0.test.js │ └── utils__1.0.0.test.ts │ ├── tsconfig.json │ ├── utils__1.0.0.cwljs │ ├── utils__1.0.0.js │ ├── utils__1.0.0.ts │ └── yarn.lock ├── workflows ├── arriba-pipeline │ └── 2.5.0 │ │ └── arriba-pipeline__2.5.0.cwl ├── bcl-conversion │ └── 3.7.5 │ │ └── bcl-conversion__3.7.5.cwl ├── bclconvert-interop-qc │ ├── 1.3.1--1.19 │ │ └── bclconvert-interop-qc__1.3.1--1.19.cwl │ ├── 1.3.1--1.21 │ │ └── bclconvert-interop-qc__1.3.1--1.21.cwl │ ├── 1.3.1--1.25.2 │ │ └── bclconvert-interop-qc__1.3.1--1.25.2.cwl │ └── 1.5.0--1.31 │ │ └── bclconvert-interop-qc__1.5.0--1.31.cwl ├── bclconvert-scatter │ └── 4.0.3 │ │ └── bclconvert-scatter__4.0.3.cwl ├── bclconvert-with-qc-pipeline │ └── 4.0.3 │ │ └── bclconvert-with-qc-pipeline__4.0.3.cwl ├── bclconvert │ └── 4.0.3 │ │ └── bclconvert__4.0.3.cwl ├── dragen-alignment-pipeline │ ├── 3.7.5 │ │ └── dragen-alignment-pipeline__3.7.5.cwl │ ├── 3.9.3 │ │ └── dragen-alignment-pipeline__3.9.3.cwl │ ├── 4.0.3 │ │ └── dragen-alignment-pipeline__4.0.3.cwl │ ├── 4.2.4 │ │ └── dragen-alignment-pipeline__4.2.4.cwl │ └── 4.3.6 │ │ └── dragen-alignment-pipeline__4.3.6.cwl ├── dragen-alignment-stage │ └── 4.4.0 │ │ └── dragen-alignment-stage__4.4.0.cwl ├── dragen-build-reference-tarball-pipeline │ ├── 4.2.4 │ │ └── dragen-build-reference-tarball-pipeline__4.2.4.cwl │ └── 4.3.6 │ │ └── dragen-build-reference-tarball-pipeline__4.3.6.cwl ├── dragen-create-aligner-options-object │ └── 4.4.0 │ │ └── dragen-create-aligner-options-object__4.4.0.cwl ├── dragen-create-mapper-options-object │ └── 4.4.0 │ │ └── dragen-create-mapper-options-object__4.4.0.cwl ├── dragen-create-wgts-alignment-options-object │ └── 4.4.0 │ │ └── dragen-create-wgts-alignment-options-object__4.4.0.cwl ├── dragen-create-wgts-dna-variant-calling-options-object │ └── 4.4.0 │ │ └── dragen-create-wgts-dna-variant-calling-options-object__4.4.0.cwl ├── dragen-create-wgts-rna-variant-calling-options-object │ └── 4.4.4 │ │ └── dragen-create-wgts-rna-variant-calling-options-object__4.4.4.cwl ├── dragen-germline-pipeline │ ├── 3.7.5 │ │ └── dragen-germline-pipeline__3.7.5.cwl │ ├── 3.9.3 │ │ └── dragen-germline-pipeline__3.9.3.cwl │ ├── 4.0.3 │ │ └── dragen-germline-pipeline__4.0.3.cwl │ ├── 4.2.4 │ │ └── dragen-germline-pipeline__4.2.4.cwl │ └── 4.3.6 │ │ └── dragen-germline-pipeline__4.3.6.cwl ├── dragen-instrument-run-fastq-to-ora-pipeline │ └── 4.2.4 │ │ └── dragen-instrument-run-fastq-to-ora-pipeline__4.2.4.cwl ├── dragen-parse-fastq-list-rows-input │ └── 2.0.0 │ │ └── dragen-parse-fastq-list-rows-input__2.0.0.cwl ├── dragen-parse-sequence-data │ └── 1.0.0 │ │ └── dragen-parse-sequence-data__1.0.0.cwl ├── dragen-pon-qc │ └── 3.9.3 │ │ └── dragen-pon-qc__3.9.3.cwl ├── dragen-qc-hla-pipeline │ └── 3.7.5--1.3.5 │ │ └── dragen-qc-hla-pipeline__3.7.5--1.3.5.cwl ├── dragen-somatic-pipeline │ ├── 3.7.5 │ │ └── dragen-somatic-pipeline__3.7.5.cwl │ ├── 3.9.3 │ │ └── dragen-somatic-pipeline__3.9.3.cwl │ ├── 4.0.3 │ │ └── dragen-somatic-pipeline__4.0.3.cwl │ └── 4.2.4 │ │ └── dragen-somatic-pipeline__4.2.4.cwl ├── dragen-somatic-with-germline-pipeline │ ├── 3.9.3 │ │ └── dragen-somatic-with-germline-pipeline__3.9.3.cwl │ ├── 4.0.3 │ │ └── dragen-somatic-with-germline-pipeline__4.0.3.cwl │ ├── 4.2.4 │ │ └── dragen-somatic-with-germline-pipeline__4.2.4.cwl │ └── 4.3.6 │ │ └── dragen-somatic-with-germline-pipeline__4.3.6.cwl ├── dragen-transcriptome-pipeline │ ├── 3.7.5 │ │ └── dragen-transcriptome-pipeline__3.7.5.cwl │ ├── 3.8.4 │ │ └── dragen-transcriptome-pipeline__3.8.4.cwl │ ├── 3.9.3 │ │ └── dragen-transcriptome-pipeline__3.9.3.cwl │ ├── 4.0.3 │ │ └── dragen-transcriptome-pipeline__4.0.3.cwl │ ├── 4.2.4 │ │ └── dragen-transcriptome-pipeline__4.2.4.cwl │ └── 4.3.6 │ │ └── dragen-transcriptome-pipeline__4.3.6.cwl ├── dragen-wgs-qc-pipeline │ ├── 3.7.5 │ │ └── dragen-wgs-qc-pipeline__3.7.5.cwl │ └── 3.9.3 │ │ └── dragen-wgs-qc-pipeline__3.9.3.cwl ├── dragen-wgts-alignment-stage │ └── 4.4.4 │ │ └── dragen-wgts-alignment-stage__4.4.4.cwl ├── dragen-wgts-dna-pipeline │ ├── 4.4.4 │ │ └── dragen-wgts-dna-pipeline__4.4.4.cwl │ └── 4.4.6 │ │ └── dragen-wgts-dna-pipeline__4.4.6.cwl ├── dragen-wgts-dna-variant-calling-stage │ ├── 4.4.4 │ │ └── dragen-wgts-dna-variant-calling-stage__4.4.4.cwl │ └── 4.4.6 │ │ └── dragen-wgts-dna-variant-calling-stage__4.4.6.cwl ├── dragen-wgts-rna-pipeline │ └── 4.4.4 │ │ └── dragen-wgts-rna-pipeline__4.4.4.cwl ├── dragen-wgts-rna-variant-calling-stage │ └── 4.4.4 │ │ └── dragen-wgts-rna-variant-calling-stage__4.4.4.cwl ├── dragen-wts-qc-pipeline │ ├── 3.9.3 │ │ └── dragen-wts-qc-pipeline__3.9.3.cwl │ ├── 4.0.3 │ │ └── dragen-wts-qc-pipeline__4.0.3.cwl │ └── 4.2.4 │ │ └── dragen-wts-qc-pipeline__4.2.4.cwl ├── get-hla-regions-bed │ └── 1.0.0 │ │ └── get-hla-regions-bed__1.0.0.cwl ├── ghif-qc │ ├── 1.0.0 │ │ └── ghif-qc__1.0.0.cwl │ └── 1.0.1 │ │ └── ghif-qc__1.0.1.cwl ├── illumina-interop-qc │ └── 1.2.0--1.14.0 │ │ └── illumina-interop-qc__1.2.0--1.14.0.cwl ├── optitype-pipeline │ └── 1.3.5 │ │ └── optitype-pipeline__1.3.5.cwl ├── rnasum-pipeline │ ├── 0.4.5 │ │ └── rnasum-pipeline__0.4.5.cwl │ ├── 1.0.0 │ │ └── rnasum-pipeline__1.0.0.cwl │ ├── 1.1.0 │ │ └── rnasum-pipeline__1.1.0.cwl │ ├── 1.1.5 │ │ └── rnasum-pipeline__1.1.5.cwl │ └── 2.0.0 │ │ └── rnasum-pipeline__2.0.0.cwl ├── tabix-workflow │ └── 0.2.6 │ │ └── tabix-workflow__0.2.6.cwl ├── tso500-ctdna-post-processing-pipeline │ └── 1.0.0 │ │ └── tso500-ctdna-post-processing-pipeline__1.0.0.cwl ├── tso500-ctdna-with-post-processing-pipeline │ ├── 1.1.0--1.0.0 │ │ └── tso500-ctdna-with-post-processing-pipeline__1.1.0--1.0.0.cwl │ └── 1.2.0--1.0.0 │ │ └── tso500-ctdna-with-post-processing-pipeline__1.2.0--1.0.0.cwl ├── tso500-ctdna │ ├── 1.1.0--120 │ │ └── tso500-ctdna__1.1.0--120.cwl │ └── 1.2.0--1 │ │ └── tso500-ctdna__1.2.0--1.cwl ├── umccrise-pipeline │ ├── 1.2.1--0 │ │ └── umccrise-pipeline__1.2.1--0.cwl │ ├── 1.2.2--0 │ │ └── umccrise-pipeline__1.2.2--0.cwl │ ├── 2.2.0--0 │ │ └── umccrise-pipeline__2.2.0--0.cwl │ ├── 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