Explore Workflows

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

Graph Name Retrieved From View
workflow graph Functional analyis of sequences that match the 16S SSU

https://github.com/ProteinsWebTeam/ebi-metagenomics-cwl.git

Path: workflows/16S_taxonomic_analysis.cwl

Branch/Commit ID: 5e8217435bcdd597b2ad236f3e847d13d4c21824
workflow graph test-data.cwl

https://github.com/kyusque/abmp_log_dump2pieda.git

Path: test-data.cwl

Branch/Commit ID: 36d894eed604a2ba8ccaeaa3449f25b4128d224d
workflow graph final-workflow.cwl

https://github.com/NAL-i5K/Organism_Onboarding.git

Path: final-workflow.cwl

Branch/Commit ID: 5910b4d88aca172252d9102ddb610a7dc9e1347f
workflow graph Bisulfite QC tools

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

Path: definitions/subworkflows/bisulfite_qc.cwl

Branch/Commit ID: 8da2b1cd6fa379b2c22baf9dad762d39630e6f46
workflow graph Compute average of average per cross-mapped famil(y)ies

Compute average structure for all averaged structures corresponding to UniProt domain instances cross-mapped from Pfam/CATH to a CATH/Pfam family. First computes average per UniProt domain instance and then average all averaged structures per Pfam family.

https://github.com/HrishiDhondge/CroMaSt.git

Path: Tools/other_avg_subwf.cwl

Branch/Commit ID: b5a9d4b025ec8e065bae97eeb96f10db2dd8e1e6
workflow graph HLA LA workflow

https://github.com/mdaya/hla_la_typing.git

Path: HLA_LA_workflow.cwl

Branch/Commit ID: f6d1debfd7fcaf203a38aad7ff57f689c2cbbbfd
workflow graph bam to trimmed fastqs and biscuit alignments

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

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl

Branch/Commit ID: 8da2b1cd6fa379b2c22baf9dad762d39630e6f46
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: 801f7b363e0599b9a28ecda696dfdb1c0e40ce71
workflow graph running cellranger mkfastq and count

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

Path: definitions/subworkflows/cellranger_mkfastq_and_count.cwl

Branch/Commit ID: ad65dc1dfff9afa5077f498b85e699716c47f6cb
workflow graph exome alignment with qc, no bqsr, no verify_bam_id

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

Path: definitions/pipelines/exome_alignment_mouse.cwl

Branch/Commit ID: a23f42ef49c10a588fd35a3afaad5de03e253533