Explore Workflows

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Graph Name Retrieved From View
workflow graph kmer_cache_retrieve

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

Path: task_types/tt_kmer_cache_retrieve.cwl

Branch/Commit ID: cabb1a9a95244e93294727be8cf5816c38992cb0
workflow graph kmer_cache_store

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

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: c28cfb9882dedd3c522160f933cff1050ae24100
workflow graph Kallisto transcript quant pipeline paired end

This workflow runs paired end RNA-Seq reads using the kallisto quant tool against a kallisto index reference genome (see \"Kallisto index pipeline\"). The kallisto transcript-level quantified samples are then compatible with the DESeq and GSEA downstream workflows. ### __Inputs__ - Kallisto index sample (of experimental organism) - R1/R2 FASTQ files of RNA-Seq read data - number of threads to use for multithreading processes ### __Outputs__ - kallisto quant file (transcript estimate tsv) ### __Data Analysis Steps__ 1. cwl calls dockercontainer robertplayer/scidap-kallisto to pseudo align reads using `kallisto quant`. 2. abundance tsv is formatted, and additional files are produced for gene and common TSS counts for use in differential expression analysis 3. read and alignment metrics are calculated for the sample piechart, and output to the overview.md 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-quant-pe.cwl

Branch/Commit ID: 261c0232a7a40880f2480b811ed2d7e89c463869
workflow graph env-wf1.cwl

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

Path: v1.0/v1.0/env-wf1.cwl

Branch/Commit ID: 4fd45edb9531a03223c18a586e32d0baf0d5acb2
workflow graph cache_asnb_entries

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

Path: task_types/tt_cache_asnb_entries.cwl

Branch/Commit ID: cabb1a9a95244e93294727be8cf5816c38992cb0
workflow graph timelimit3-wf.cwl

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

Path: tests/timelimit3-wf.cwl

Branch/Commit ID: 664835e83eb5e57eee18a04ce7b05fb9d70d77b7
workflow graph FASTQ to BQSR

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

Path: definitions/subworkflows/fastq_to_bqsr.cwl

Branch/Commit ID: da335d9963418f7bedd84cb2791a0df1b3165ffe
workflow graph directory.cwl

Inspect provided directory and return filenames. Generate a new directory and return it (including content).

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

Path: tests/wf/directory.cwl

Branch/Commit ID: dbc4c4c2ad30ed31367b4fbcc3bb4084fdcabaa2
workflow graph scatter-valuefrom-wf4.cwl#main

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

Path: v1.0/v1.0/scatter-valuefrom-wf4.cwl

Branch/Commit ID: 22490926651174c6cbe01c76c2ded3c9e8d0ee6f

Packed ID: main
workflow graph dynresreq-workflow.cwl

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

Path: cwltool/schemas/v1.0/v1.0/dynresreq-workflow.cwl

Branch/Commit ID: b82ce7ae901a54c7a062fd5eefd8d5ceb5a4d684