Explore Workflows

View already parsed workflows here or click here to add your own

Graph	Name	Retrieved From	View
	final_filtering Final filtering	https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git Path: structuralvariants/cwl/abstract_operations/subworkflows/final_filtering.cwl Branch/Commit ID: 3f6a871f81f343cf81a345f73ff2eeac70804b8c
	count-lines1-wf.cwl	https://github.com/common-workflow-language/cwl-v1.1.git Path: tests/count-lines1-wf.cwl Branch/Commit ID: 0e37d46e793e72b7c16b5ec03e22cb3ce1f55ba3
	Merge, annotate, and generate a TSV for SVs	https://github.com/genome/analysis-workflows.git Path: definitions/subworkflows/merge_svs.cwl Branch/Commit ID: da335d9963418f7bedd84cb2791a0df1b3165ffe
	Build Bowtie indices Workflow runs [Bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016) to build indices for reference genome provided in a single FASTA file as fasta_file input. Generated indices are saved in a folder with the name that corresponds to the input genome	https://github.com/datirium/workflows.git Path: workflows/bowtie-index.cwl Branch/Commit ID: 09267e79fd867aa68a219c69e6db7d8e2e877be2
	ani_top_n	https://github.com/ncbi/pgap.git Path: task_types/tt_ani_top_n.cwl Branch/Commit ID: 8fb4ac7f5a66897206c7469101a471108b06eada
	facets-workflow.cwl Workflow for running Facets-suite on a set of tumor normal pairs This workflow scatters over all the pairs in the input JSON to run all samples in parallel Input JSON format ----------------- { \"pairs\": [ { \"tumor_bam\": { \"class\": \"File\", \"path\": \"/test_data/bam/Tumor1.rg.md.abra.printreads.bam\" }, \"normal_bam\": { \"class\": \"File\", \"path\": \"/test_data/bam/Normal1.rg.md.abra.printreads.bam\" }, \"pair_maf\": { \"class\": \"File\", \"path\": \"/test_data/bam/Tumor1.Normal1.maf\" }, \"pair_id\": \"Tumor1.Normal1\" }, { \"tumor_bam\": { \"class\": \"File\", \"path\": \"/test_data/bam/Tumor2.rg.md.abra.printreads.bam\" }, \"normal_bam\": { \"class\": \"File\", \"path\": \"/test_data/bam/Normal2.rg.md.abra.printreads.bam\" }, \"pair_maf\": { \"class\": \"File\", \"path\": \"/test_data/bam/Tumor2.Normal2.maf\" }, \"pair_id\": \"Tumor2.Normal2\" } ] } Output format ------------- output └── facets-suite ├── Tumor1.Normal1.arm_level.txt ├── Tumor1.Normal1.gene_level.txt ├── Tumor1.Normal1_hisens.ccf.maf ├── Tumor1.Normal1_hisens.rds ├── Tumor1.Normal1_hisens.seg ├── Tumor1.Normal1_purity.rds ├── Tumor1.Normal1_purity.seg ├── Tumor1.Normal1.qc.txt ├── Tumor1.Normal1.snp_pileup.gz ├── Tumor1.Normal1.txt ├── Tumor2.Normal2.arm_level.txt ├── Tumor2.Normal2.gene_level.txt ├── Tumor2.Normal2_hisens.ccf.maf ├── Tumor2.Normal2_hisens.rds ├── Tumor2.Normal2_hisens.seg ├── Tumor2.Normal2_purity.rds ├── Tumor2.Normal2_purity.seg ├── Tumor2.Normal2.qc.txt ├── Tumor2.Normal2.snp_pileup.gz ├── Tumor2.Normal2.txt └── logs ├── success └── failed	https://github.com/mskcc/pluto-cwl.git Path: cwl/facets-workflow.cwl Branch/Commit ID: 45604eaeea15030c7302941c761464ce392abf74
	RNASelector as a CWL workflow https://doi.org/10.1007/s12275-011-1213-z	https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git Path: workflows/rna-selector.cwl Branch/Commit ID: 7bb76f33bf40b5cd2604001cac46f967a209c47f
	SPRM pipeline	https://github.com/hubmapconsortium/sprm.git Path: pipeline.cwl Branch/Commit ID: 2ddb0cefffd0fc05b897695c20d897fd080871ba
	workflow.cwl	https://github.com/nal-i5k/organism_onboarding.git Path: flow_apollo2_data_processing/processing/workflow.cwl Branch/Commit ID: b1e1b906fcfb2c0fad8811fb8ab03009282c1d19
	Detect Variants workflow for WGS pipeline	https://github.com/genome/analysis-workflows.git Path: definitions/pipelines/detect_variants_wgs.cwl Branch/Commit ID: 061d3a2fbcd8a1c39c0b38c549e528deb24a9d54