Explore Workflows

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

Graph Name Retrieved From View
workflow graph SetMirrorPanelAlignment

Derive mirror panel alignment parameters from measurements of the optical point-spread functions.

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

Path: workflows/SetMirrorPanelAlignment.cwl

Branch/Commit ID: bf4d4a44a543bcc04f4508ce020751c71550acf5

workflow graph gcaccess_from_list

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

Path: task_types/tt_gcaccess_from_list.cwl

Branch/Commit ID: c64599f5db2437f9323d41cc3d8d9efb20a2667e

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: c64599f5db2437f9323d41cc3d8d9efb20a2667e

workflow graph trim-rnaseq-se-dutp.cwl

Runs RNA-Seq dUTP BioWardrobe basic analysis with strand specific single-end data file.

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

Path: workflows/trim-rnaseq-se-dutp.cwl

Branch/Commit ID: de847468843203ce92b6d19323c5fe77dc488e34

workflow graph WF6101.cwl

https://github.com/Marco-Salvi/dtc61.git

Path: WF6101.cwl

Branch/Commit ID: f435de822bbe32648738934700d340ba29dea215

workflow graph bact_get_kmer_reference

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

Path: task_types/tt_bact_get_kmer_reference.cwl

Branch/Commit ID: c64599f5db2437f9323d41cc3d8d9efb20a2667e

workflow graph Filter Protein Seeds; Find ProSplign Alignments

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

Path: protein_alignment/wf_compart_filter_prosplign.cwl

Branch/Commit ID: c64599f5db2437f9323d41cc3d8d9efb20a2667e

workflow graph record-output-wf_v1_0.cwl

https://github.com/common-workflow-language/cwl-utils.git

Path: testdata/record-output-wf_v1_0.cwl

Branch/Commit ID: 5759b4275906e6cfe13912c8426de2a2237cb4b0

workflow graph bacterial_kmer

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

Path: bacterial_kmer/wf_bacterial_kmer.cwl

Branch/Commit ID: a34f47d1e37af51e387ecdfa5c3047f106c1146b

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/Barski-lab/workflows.git

Path: tools/bam-bedgraph-bigwig.cwl

Branch/Commit ID: c4759ed88dcd40e96067685a345488414b6f88fb