Explore Workflows

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

Graph Name Retrieved From View
workflow graph wf-loadContents3.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/wf-loadContents3.cwl

Branch/Commit ID: 3e90671b25f7840ef2926ad2bacbf447772dda94
workflow graph Run genomic CMsearch

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

Path: bacterial_noncoding/wf_gcmsearch.cwl

Branch/Commit ID: 4ffbad9ffeab15ec8af5f6f91bd352ef96d1ef77
workflow graph io-int-optional-wf.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/io-int-optional-wf.cwl

Branch/Commit ID: 3e90671b25f7840ef2926ad2bacbf447772dda94
workflow graph echo-wf-default.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/echo-wf-default.cwl

Branch/Commit ID: 3e90671b25f7840ef2926ad2bacbf447772dda94
workflow graph Kallisto index pipeline

This workflow indexes the input reference FASTA with kallisto, and generates a kallisto index file (.kdx). This index sample can then be used as input into the kallisto transcript-level quantification workflow (kallisto-quant-pe.cwl), or others that may include this workflow as an upstream source. ### __Inputs__ - FASTA file of the reference genome that will be indexed - number of threads to use for multithreading processes ### __Outputs__ - kallisto index file (.kdx). - stdout log file (output in Overview tab as well) - stderr log file ### __Data Analysis Steps__ 1. cwl calls dockercontainer robertplayer/scidap-kallisto to index reference FASTA with `kallisto index`, generating a kallisto index file. ### __References__ - Bray, N. L., Pimentel, H., Melsted, P. & Pachter, L. Near-optimal probabilistic RNA-seq quantification, Nature Biotechnology 34, 525-527(2016), doi:10.1038/nbt.3519

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

Path: workflows/kallisto-index.cwl

Branch/Commit ID: d76110e0bfc40c874f82e37cef6451d74df4f908
workflow graph extract_gencoll_ids

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

Path: task_types/tt_extract_gencoll_ids.cwl

Branch/Commit ID: 5b498b4c4f17bb8f17e6886aa4c5661d7aba34fc
workflow graph conflict-wf.cwl#collision

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/conflict-wf.cwl

Branch/Commit ID: 7d7986a6e852ca6e3239c96d3a05dd536c76c903

Packed ID: collision
workflow graph variant-calling-pair.cwl

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

Path: modules/pair/variant-calling-pair.cwl

Branch/Commit ID: 7c694b51d9d593439cf8ab3e5006665f0bbe2149
workflow graph tt_kmer_top_n.cwl

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

Path: task_types/tt_kmer_top_n.cwl

Branch/Commit ID: 1cfd46014be8d867044cb10d1ddde0cb3068ee84
workflow graph wf-loadContents4.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/wf-loadContents4.cwl

Branch/Commit ID: 3e90671b25f7840ef2926ad2bacbf447772dda94