Explore Workflows

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

Graph Name Retrieved From View
workflow graph STAR-Alignment-PE

This workflow aligns the fastq files using STAR for paired-end samples

 https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/Alignments/star-alignment.cwl

Branch/Commit ID: master
workflow graph inspect_solutions.cwl

https://github.com/peijin94/LOFAR-Sun-tools.git

Path: utils/IM/LINC/lincSun/steps/inspect_solutions.cwl

Branch/Commit ID: master
workflow graph 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: master
workflow graph bwameth_align_merge_sort_dedup.cwl

https://github.com/ifishlin/Benchmarking_CWL.git

Path: workflows/bwameth/tools/bwameth_align_merge_sort_dedup.cwl

Branch/Commit ID: main
workflow graph orgaquant_wf.cwl

https://github.com/alexandersenf/orgaquant.git

Path: orgaquant_wf.cwl

Branch/Commit ID: 1.1
workflow graph extract_single_optional_file.cwl

https://github.com/NCI-GDC/aliquot-maf-cwl.git

Path: vcf-to-aliquot-maf/subworkflows/extract_single_optional_file.cwl

Branch/Commit ID: main
workflow graph exomeseq-01-preprocessing.cwl

https://github.com/Duke-GCB/bespin-cwl.git

Path: subworkflows/exomeseq-01-preprocessing.cwl

Branch/Commit ID: gatk4-fixes
workflow graph SSU-from-tablehits.cwl

https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git

Path: tools/SSU-from-tablehits.cwl

Branch/Commit ID: 708fd97
workflow graph alignment_workflow_md5checker.cwl

https://github.com/DataBiosphere/topmed-workflows.git

Path: aligner/topmed-cwl/workflow/alignment_workflow_md5checker.cwl

Branch/Commit ID: develop
workflow graph Atmopsheric Calibration

This workflow performs calibrates atmosphere and produces an atmospheric model and an extinction hypercube.

https://gitlab.cta-observatory.org/cta-computing/dpps/dpps-workflows.git

Path: workflows/calibpipe/AtmosphericCalibrations/uc-cp-100.cwl

Branch/Commit ID: main