Explore Workflows

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

Graph Name Retrieved From View
workflow graph exome alignment and germline variant detection

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

Path: definitions/subworkflows/germline_detect_variants.cwl

Branch/Commit ID: 889a077a20c0fdb01f4ed97aa4bc40f920c37a1a
workflow graph Subworkflow to allow calling different SV callers which require bam files as inputs

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

Path: definitions/subworkflows/single_sample_sv_callers.cwl

Branch/Commit ID: 889a077a20c0fdb01f4ed97aa4bc40f920c37a1a
workflow graph workflow.cwl

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

Path: flow_dispatch/workflow.cwl

Branch/Commit ID: 677d79c721ad5f7a7e09b693d7f3fe2da70826e2
workflow graph readme-assembly-workflow.cwl

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

Path: flow_create_readme/readme-assembly-workflow.cwl

Branch/Commit ID: 677d79c721ad5f7a7e09b693d7f3fe2da70826e2
workflow graph readme-genePrediction-workflow.cwl

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

Path: flow_create_readme/readme-genePrediction-workflow.cwl

Branch/Commit ID: 677d79c721ad5f7a7e09b693d7f3fe2da70826e2
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: d06eaa0bd48987b4975257694a32200cfc8f5bea
workflow graph workflow.cwl

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

Path: flow_download/workflow.cwl

Branch/Commit ID: 677d79c721ad5f7a7e09b693d7f3fe2da70826e2
workflow graph RNA-Seq alignment and transcript/gene abundance workflow

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

Path: definitions/pipelines/rnaseq.cwl

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

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

Path: flow_md5checksums/workflow.cwl

Branch/Commit ID: 677d79c721ad5f7a7e09b693d7f3fe2da70826e2
workflow graph RNASelector as a CWL workflow

https://doi.org/10.1007/s12275-011-1213-z

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

Path: workflows/rna-selector.cwl

Branch/Commit ID: 5dc7c5ca618a248a99bd4bf5f3042cdb21947193