Explore Workflows

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

Graph Name Retrieved From View
workflow graph rnaseq-pe.cwl

RNA-Seq basic analysis workflow for paired-end experiment.

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

Path: workflows/rnaseq-pe.cwl

Branch/Commit ID: cf107bc24a37883ef01b959fd89c19456aaecc02
workflow graph allele-alignreads-se-pe.cwl

Workflow maps FASTQ files from `fastq_files` input into reference genome `reference_star_indices_folder` and insilico generated `insilico_star_indices_folder` genome (concatenated genome for both `strain1` and `strain2` strains). For both genomes STAR is run with `outFilterMultimapNmax` parameter set to 1 to discard all of the multimapped reads. For insilico genome SAM file is generated. Then it's splitted into two SAM files based on strain names and then sorted by coordinates into the BAM format. For reference genome output BAM file from STAR slignment is also coordinate sorted.

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

Path: subworkflows/allele-alignreads-se-pe.cwl

Branch/Commit ID: a9551ece898f619167db58e4b74a6cae2d7f7d13
workflow graph scatter-wf4.cwl#main

https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/scatter-wf4.cwl

Branch/Commit ID: 20d664eff23e59aa57908345bfdb1ceeab3438f2

Packed ID: main
workflow graph Nested workflow example

https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/nested.cwl

Branch/Commit ID: 4c905b830371eee45188a53510ba0ee9113fd4c8
workflow graph step-valuefrom4-wf.cwl

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

Path: v1.0/v1.0/step-valuefrom4-wf.cwl

Branch/Commit ID: 9a23706ec061c5d2c02ff60238d218aadf0b5db9
workflow graph count-lines10-wf.cwl

https://github.com/common-workflow-language/cwltool.git

Path: cwltool/schemas/v1.0/v1.0/count-lines10-wf.cwl

Branch/Commit ID: f997d13af87216e9b5048c732a511053c7ba714c
workflow graph unifiedgenotyper.cwl

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/variant_calling/unifiedgenotyper.cwl

Branch/Commit ID: 342c8a39d5823bbcf298d2f807ec235910e5f412
workflow graph default-dir5.cwl

https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/default-dir5.cwl

Branch/Commit ID: 1441c285e8a5afe399f5d52ca9059cb8bb513edb
workflow graph directory.cwl

Inspect provided directory and return filenames. Generate a new directory and return it (including content).

https://github.com/common-workflow-language/cwltool.git

Path: tests/wf/directory.cwl

Branch/Commit ID: 6003cbb94f16103241b562f2133e7c4acac6c621
workflow graph Genome conversion and annotation

Workflow for genome annotation from EMBL format

 https://git.wur.nl/unlock/cwl.git

Path: cwl/workflows/workflow_sapp_others.cwl

Branch/Commit ID: d944d61ddc34a5b24ebac6e1701efd6f8fdf54ae