Explore Workflows

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

Graph Name Retrieved From View
workflow graph fp_filter workflow

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

Path: definitions/subworkflows/fp_filter.cwl

Branch/Commit ID: b7d9ace34664d3cedb16f2512c8a6dc6debfc8ca
workflow graph Single-Cell RNA-Seq Filtering Analysis

Single-Cell RNA-Seq Filtering Analysis Removes low-quality cells from the outputs of the “Cell Ranger Count (RNA)”, “Cell Ranger Count (RNA+VDJ)”, and “Cell Ranger Aggregate (RNA, RNA+VDJ)” pipelines. The results of this workflow are used in the “Single-Cell RNA-Seq Dimensionality Reduction Analysis” pipeline.

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

Path: workflows/sc-rna-filter.cwl

Branch/Commit ID: 69643d8c15f5357a320aa7e2f6adb2e71302fd20
workflow graph align_merge_sas

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

Path: task_types/tt_align_merge_sas.cwl

Branch/Commit ID: 4ea5956bb97ea2eb6de124bc9b6a6a81a14fd2e7
workflow graph mut2.cwl

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

Path: tests/wf/mut2.cwl

Branch/Commit ID: 20d664eff23e59aa57908345bfdb1ceeab3438f2
workflow graph collect_pair_files.cwl

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

Path: modules/pair/collect_pair_files.cwl

Branch/Commit ID: 0b9721d7d512352c7f80b27f42b3192a585ed5f6
workflow graph BWA index pipeline

This workflow indexes the input reference FASTA with bwa, and generates faidx and dict file using samtools. This index sample can then be used as input into the germline variant calling workflow, or others that may include this workflow as an upstream source. ### __Inputs__ - FASTA file of the reference genome that will be indexed. ### __Outputs__ - Directory containing the original FASTA, faidx, dict, and bwa index files. - stdout log file (output in Overview tab as well) - stderr log file ### __Data Analysis Steps__ 1. cwl calls dockercontainer robertplayer/scidap-gatk4 to index reference FASTA with bwa, and generates faidx and dict files using samtools ### __References__ - Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25(14), 1754–1760.

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

Path: workflows/bwa-index.cwl

Branch/Commit ID: 69643d8c15f5357a320aa7e2f6adb2e71302fd20
workflow graph heatmap.cwl

Generates ATDP heatmap centered on TSS from an array of input BAM files and genelist TSV file. Returns array of heatmap JSON files with the names that have the same basenames as input BAM files, but with .json extension

https://github.com/Barski-lab/workflows.git

Path: workflows/heatmap.cwl

Branch/Commit ID: ca2dbb71d0537b1d93a8bd44719250cf8949b157
workflow graph kmer_ref_compare_wnode

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

Path: task_types/tt_kmer_ref_compare_wnode.cwl

Branch/Commit ID: 72804b6506c9f54ec75627f82aafe6a28d7a49fa
workflow graph count-lines11-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines11-wf.cwl

Branch/Commit ID: 665141f319e6b23bd9924b14844f2e979f141944
workflow graph Immunotherapy Workflow

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

Path: definitions/pipelines/immuno.cwl

Branch/Commit ID: 22fce2dbdada0c4135b6f0677f78535cf980cb07