Explore Workflows

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

Graph Name Retrieved From View
workflow graph bam to trimmed fastqs

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

Path: definitions/subworkflows/bam_to_trimmed_fastq.cwl

Branch/Commit ID: 43c790e2ee6a0f3f42e40fb4d9a9005eb8de747a
workflow graph wf_rescue_ratio_1input.cwl

Calculates the rescue ratio (see Gabe's protocols paper), given two eCLIP IP samples and 2 size-matched input samples. Also returns the reproducible peaks given these two samples. This is different from the 1input workflow in that each INPUT is first merged together and is used downstream instead of the 1input version, which remains unmodified. Merged inputs are NOT used in calculating true reproducible peaks.

https://github.com/YeoLab/merge_peaks.git

Path: cwl/wf_rescue_ratio_1input.cwl

Branch/Commit ID: aedc0a14d4ba109ee65678a3201a52c5bb6ad473
workflow graph super-enhancer.cwl

Both `islands_file` and `islands_control_file` should be produced by the same cwl tool (iaintersect.cwl or macs2-callpeak-biowardrobe-only.cwl)

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

Path: workflows/super-enhancer.cwl

Branch/Commit ID: cf84038de256c7ca98657ad81734d1aca1dad8c1
workflow graph pipeline-pe.cwl

ATAC-seq pipeline - reads: PE

 https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/ATAC-seq_pipeline/pipeline-pe.cwl

Branch/Commit ID: 1a0dd34d59ec983d1f7ad77bff35da2f016e3134
workflow graph adapter for sequence_align_and_tag

Some workflow engines won't stage files in our nested structure, so parse it out here

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

Path: definitions/subworkflows/sequence_align_and_tag_adapter.cwl

Branch/Commit ID: 9cbf2a483e1b9e4cdb8e2564be27a9e64fc1169e
workflow graph scatter2.cwl

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

Path: tests/wf/scatter2.cwl

Branch/Commit ID: c7c379948c02ba8f048d157f06eb903b1bda9894
workflow graph helloworld-slurmcern.cwl

https://github.com/reanahub/reana-demo-helloworld.git

Path: workflow/cwl/helloworld-slurmcern.cwl

Branch/Commit ID: 0fc7939aca1c3dd336abe5886d40b07bf8a7b329
workflow graph pcr-bottleneck-coef.cwl

ChIP-seq - map - PCR Bottleneck Coefficients

 https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/map/pcr-bottleneck-coef.cwl

Branch/Commit ID: 1a0dd34d59ec983d1f7ad77bff35da2f016e3134
workflow graph md_launch.cwl

https://github.com/douglowe/biobb_hpc_cwl_md_list.git

Path: md_launch.cwl

Branch/Commit ID: 97122f21048a5ac4a12b21059b751d1d07050cbd
workflow graph extract_gencoll_ids

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

Path: task_types/tt_extract_gencoll_ids.cwl

Branch/Commit ID: 75ea689c0a8c9902b4598b453455857cb08e885a