Explore Workflows

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

Graph Name Retrieved From View
workflow graph Generate genome indices for Bismark

Copy input fasta file to the folder and run bismark_genome_preparation script to prepare indices for Bismark Methylation Analysis. Bowtie2 aligner is used by default. The name of the output indices folder is equal to the fasta file basename without extension.

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

Path: workflows/bismark-indices.cwl

Branch/Commit ID: bfa3843bcf36125ff258d6314f64b41336f06e6b
workflow graph hmmsearch_wnode and gpx_qdump combined workflow to apply scatter/gather

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

Path: task_types/tt_hmmsearch_wnode_plus_qdump.cwl

Branch/Commit ID: a3affd1b9e3e16f0644a25fee1a7b87b99df57b0
workflow graph wf_trim_partial_and_map_se_scatter.cwl

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

Path: cwl/wf_trim_partial_and_map_se_scatter.cwl

Branch/Commit ID: c0fffc4979a92371dc0667a03e3d957bf7f77600
workflow graph forome_vcf_upload_archive.cwl

https://github.com/ForomePlatform/vcf-upload-cwl-pipeline.git

Path: forome_vcf_upload_archive.cwl

Branch/Commit ID: 30114fc1643733f5a3cc8ca6ee956e33290c6022
workflow graph Cell Ranger Count Gene Expression

Cell Ranger Count Gene Expression =================================

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

Path: workflows/single-cell-preprocess-cellranger.cwl

Branch/Commit ID: 7ae3b75bbe614e59cdeaba06047234a6c40c0fe9
workflow graph Sort and merge input bed file and generate a .sorted.merged.bed file

https://github.com/swamyuma/cwl-tools.git

Path: sort_merge.cwl

Branch/Commit ID: 14be112d65ebb76f0368747099b5778f35d0387f
workflow graph waltz_workflow_all_bams.cwl

https://github.com/mskcc/ACCESS-Pipeline.git

Path: workflows/waltz/waltz_workflow_all_bams.cwl

Branch/Commit ID: 9998da2da694af2edad7c2135f6995e2282794a3
workflow graph waltz-workflow.cwl

https://github.com/mskcc/Innovation-Pipeline.git

Path: workflows/waltz/waltz-workflow.cwl

Branch/Commit ID: 9998da2da694af2edad7c2135f6995e2282794a3
workflow graph allele-process-strain.cwl

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

Path: subworkflows/allele-process-strain.cwl

Branch/Commit ID: 6e09b4bf1ff0eb3dd1294f5578624c5a2a2b0b37
workflow graph qc_workflow_wo_waltz.cwl

This workflow is intended to be used to test the QC module, without having to run the long waltz step

https://github.com/mskcc/ACCESS-Pipeline.git

Path: workflows/QC/qc_workflow_wo_waltz.cwl

Branch/Commit ID: 9998da2da694af2edad7c2135f6995e2282794a3