Explore Workflows

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

Graph Name Retrieved From View
workflow graph Running cellranger count and lineage inference

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

Path: definitions/subworkflows/single_cell_rnaseq.cwl

Branch/Commit ID: b7d9ace34664d3cedb16f2512c8a6dc6debfc8ca
workflow graph get_spike_in_counts.cwl

https://github.com/CompEpigen/ChIPseq_workflows.git

Path: CWL/workflow_modules/get_spike_in_counts.cwl

Branch/Commit ID: 12aba268a55088a0350b7475a255a9713c78f8ff
workflow graph Transcripts annotation workflow

https://github.com/mscheremetjew/workflow-is-cwl.git

Path: workflows/TranscriptsAnnotation-i5only-wf.cwl

Branch/Commit ID: 4c860f3356b3a94b07f620d5e11aa1607d3c36e1
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