Explore Workflows

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Graph Name Retrieved From View
workflow graph 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: 84ecf33903c453db1228ed372ac676ac771136ef
workflow graph Bismark Methylation PE

Sequence reads are first cleaned from adapters and transformed into fully bisulfite-converted forward (C->T) and reverse read (G->A conversion of the forward strand) versions, before they are aligned to similarly converted versions of the genome (also C->T and G->A converted). Sequence reads that produce a unique best alignment from the four alignment processes against the bisulfite genomes (which are running in parallel) are then compared to the normal genomic sequence and the methylation state of all cytosine positions in the read is inferred. A read is considered to align uniquely if an alignment has a unique best alignment score (as reported by the AS:i field). If a read produces several alignments with the same number of mismatches or with the same alignment score (AS:i field), a read (or a read-pair) is discarded altogether. On the next step we extract the methylation call for every single C analysed. The position of every single C will be written out to a new output file, depending on its context (CpG, CHG or CHH), whereby methylated Cs will be labelled as forward reads (+), non-methylated Cs as reverse reads (-). The output of the methylation extractor is then transformed into a bedGraph and coverage file. The bedGraph counts output is then used to generate a genome-wide cytosine report which reports the number on every single CpG (optionally every single cytosine) in the genome, irrespective of whether it was covered by any reads or not. As this type of report is informative for cytosines on both strands the output may be fairly large (~46mn CpG positions or >1.2bn total cytosine positions in the human genome).

 https://github.com/datirium/workflows.git

Path: workflows/bismark-methylation-pe.cwl

Branch/Commit ID: b4d578c2ba4713a5a22163d9f8c7105acda1f22e
workflow graph kfdrc_star_diploid_wf.cwl

https://github.com/kids-first/kf-rnaseq-workflow.git

Path: workflow/kfdrc_star_diploid_wf.cwl

Branch/Commit ID: 65161d6565c436a7b1e0b3be56efb433a994ed9d
workflow graph step-valuefrom3-wf_v1_2.cwl

https://github.com/common-workflow-language/cwl-utils.git

Path: testdata/step-valuefrom3-wf_v1_2.cwl

Branch/Commit ID: e949503ac0dd7e22ba9b04ac51926d13780f9cee
workflow graph bacterial_orthology_cond

https://github.com/ncbi/pgap.git

Path: bacterial_orthology/wf_bacterial_orthology_conditional.cwl

Branch/Commit ID: 1e16653514fd5629a704516eb447043c9fd0a53b
workflow graph PGAP Pipeline

PGAP pipeline for external usage, powered via containers

 https://github.com/ncbi/pgap.git

Path: wf_common.cwl

Branch/Commit ID: 1e16653514fd5629a704516eb447043c9fd0a53b
workflow graph project-workflow.cwl

https://github.com/mskcc/argos-cwl.git

Path: project-workflow.cwl

Branch/Commit ID: 82a391eb588505a87e2f549b662fa68214076dd4
workflow graph Get Proteins

https://github.com/ncbi/pgap.git

Path: wf_bacterial_prot_src.cwl

Branch/Commit ID: 1e16653514fd5629a704516eb447043c9fd0a53b
workflow graph umi molecular alignment fastq workflow

https://github.com/genome/analysis-workflows.git

Path: definitions/pipelines/alignment_umi_molecular.cwl

Branch/Commit ID: a59a803e1809a8fbfabca6b8962a8ad66dd01f1d
workflow graph secret_wf.cwl

https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/secret_wf.cwl

Branch/Commit ID: 63f539ba60e91f0cb3ce7cda2c5da5c65525c375