Explore Workflows

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

Graph Name Retrieved From View
workflow graph cram_to_bam workflow

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

Path: definitions/subworkflows/cram_to_bam_and_index.cwl

Branch/Commit ID: 97572e3a088d79f6a4166385f79e79ea77b11470
workflow graph process VCF workflow

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

Path: definitions/subworkflows/strelka_process_vcf.cwl

Branch/Commit ID: 480c438a6a7e78c624712aec01bc4214d2bc179c
workflow graph cluster_blastp_wnode and gpx_qdump combined

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

Path: task_types/tt_cluster_and_qdump.cwl

Branch/Commit ID: be465ad19b07378f3f863f2c4e0019b420c859f2
workflow graph umi molecular alignment workflow

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

Path: definitions/subworkflows/molecular_alignment.cwl

Branch/Commit ID: 844c10a4466ab39c02e5bfa7a210c195b8efa77a
workflow graph assm_assm_blastn_wnode

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

Path: task_types/tt_assm_assm_blastn_wnode.cwl

Branch/Commit ID: be5ae41801b19ebc69a2889d8fdb39e8e2359611
workflow graph Per-region pindel

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

Path: definitions/subworkflows/pindel_cat.cwl

Branch/Commit ID: 77ec4f26eb14ed82481828bd9f6ef659cfd8b40f
workflow graph mosdepth_to_coverage_QC.cwl

https://github.com/YinanWang16/tso500-ctdna-post-processing.git

Path: cwl/workflows/mosdepth_to_coverage_QC.cwl

Branch/Commit ID: 08f855a08ca02b15c8d3540b28bb17b4f85a371a
workflow graph 02-trim-se.cwl

RNA-seq 02 trimming - reads: SE

 https://github.com/Duke-GCB/GGR-cwl.git

Path: v1.0/RNA-seq_pipeline/02-trim-se.cwl

Branch/Commit ID: ebd63f705d0fde7290e42c8300d5420c25cfbfe3
workflow graph 04-quantification-se-revstranded.cwl

RNA-seq 04 quantification

 https://github.com/Duke-GCB/GGR-cwl.git

Path: v1.0/RNA-seq_pipeline/04-quantification-se-revstranded.cwl

Branch/Commit ID: ebd63f705d0fde7290e42c8300d5420c25cfbfe3
workflow graph bam-bedgraph-bigwig.cwl

Workflow converts input BAM file into bigWig and bedGraph files. Input BAM file should be sorted by coordinates (required by `bam_to_bedgraph` step). If `split` input is not provided use true by default. Default logic is implemented in `valueFrom` field of `split` input inside `bam_to_bedgraph` step to avoid possible bug in cwltool with setting default values for workflow inputs. `scale` has higher priority over the `mapped_reads_number`. The last one is used to calculate `-scale` parameter for `bedtools genomecov` (step `bam_to_bedgraph`) only in a case when input `scale` is not provided. All logic is implemented inside `bedtools-genomecov.cwl`. `bigwig_filename` defines the output name only for generated bigWig file. `bedgraph_filename` defines the output name for generated bedGraph file and can influence on generated bigWig filename in case when `bigwig_filename` is not provided. All workflow inputs and outputs don't have `format` field to avoid format incompatibility errors when workflow is used as subworkflow.

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

Path: tools/bam-bedgraph-bigwig.cwl

Branch/Commit ID: e0a30aa1ad516dd2ec0e9ce006428964b840daf4