Explore Workflows
View already parsed workflows here or click here to add your own
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Workflow that executes the Sounder SIPS end-to-end L1a processing
Cognito credentials to access the U-DS services are retrieved from the AWS Parameter Store with the supplied keys. |
https://github.com/unity-sds/unity-sps-workflows.git
Path: sounder_sips/ssips_L1a_workflow.cwl Branch/Commit ID: a4fd2d3f33c94071241dcfc7a868aa6facd59dd6 |
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gp_makeblastdb
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https://github.com/ncbi/pgap.git
Path: progs/gp_makeblastdb.cwl Branch/Commit ID: 8c21035bff3cbffccf5682bd0357a6d71f3bdb81 |
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Bacterial Annotation, pass 4, blastp-based functional annotation (second pass)
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https://github.com/ncbi/pgap.git
Path: bacterial_annot/wf_bacterial_annot_pass4.cwl Branch/Commit ID: a1f39f21670be28427ceb91ceaeb9339545c18fc |
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extract_gencoll_ids
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https://github.com/ncbi/pgap.git
Path: task_types/tt_extract_gencoll_ids.cwl Branch/Commit ID: d40ef1462a4c210be3184609dbb3467ff61fc017 |
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STAR-Alignment-PE-circRNA
This workflow aligns the fastq files using STAR for paired-end samples to be used in circRNA pipeline |
https://github.com/ncbi/cwl-ngs-workflows-cbb.git
Path: workflows/Alignments/star-alignment-circRNA-default.cwl Branch/Commit ID: b5a440939ac6022ee81aeeb0dd7daf3983228a61 |
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tt_fscr_calls_pass1
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https://github.com/ncbi/pgap.git
Path: task_types/tt_fscr_calls_pass1.cwl Branch/Commit ID: d40ef1462a4c210be3184609dbb3467ff61fc017 |
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03-map-pe.cwl
ATAC-seq 03 mapping - reads: PE |
https://github.com/Duke-GCB/GGR-cwl.git
Path: v1.0/ATAC-seq_pipeline/03-map-pe.cwl Branch/Commit ID: 6e68bda2cb45e8dc8e4d067c4220d65acfa53065 |
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pipeline-pe-blacklist-removal.cwl
ATAC-seq pipeline - reads: PE - with blacklist removal |
https://github.com/Duke-GCB/GGR-cwl.git
Path: v1.0/ATAC-seq_pipeline/pipeline-pe-blacklist-removal.cwl Branch/Commit ID: 7696e7eb27a9251fba53ef4ccacc84cc8f8b0685 |
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CUTnRUN.cwl
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https://github.com/CompEpigen/ChIPseq_workflows.git
Path: CWL/workflows/CUTnRUN.cwl Branch/Commit ID: 6a2df36b7c019ecb91bd1b7ed9eb7c62ccbe112d |
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scRNA-seq pipeline using Salmon and Alevin
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https://github.com/hubmapconsortium/salmon-rnaseq.git
Path: pipeline.cwl Branch/Commit ID: 41c6490b9249bb793428a62fcbfe6006f20e2c06 |
