Explore Workflows

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

Graph Name Retrieved From View
workflow graph preprocess_vcf.cwl

This workflow will perform preprocessing steps on VCFs for the OxoG/Variantbam/Annotation workflow.

https://github.com/svonworl/OxoG-Dockstore-Tools.git

Path: preprocess_vcf.cwl

Branch/Commit ID: b38a8a4785746b8267913ea5389e21ae6dc921a3
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_microbes.cwl

Branch/Commit ID: d944d61ddc34a5b24ebac6e1701efd6f8fdf54ae
workflow graph fireprot.cwl

https://github.com/CERIT-SC/fireprot.git

Path: fireprot.cwl

Branch/Commit ID: a2b0c18f117dcf2b0d7e33c59c0f180b6a9bf709
workflow graph js-expr-req-wf.cwl#wf

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

Path: cwltool/schemas/v1.0/v1.0/js-expr-req-wf.cwl

Branch/Commit ID: fc6ca8b1498926f705dcfde7ab0a365bd09a9675

Packed ID: wf
workflow graph io-int-optional-wf.cwl

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

Path: v1.0/v1.0/io-int-optional-wf.cwl

Branch/Commit ID: 1f501e38ff692a408e16b246ac7d64d32f0822c2
workflow graph cnv_manta

CNV Manta calling

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/cwl/abstract_operations/subworkflows/cnv_manta.cwl

Branch/Commit ID: de9cb009f8fe0c8d5a94db5c882cf21ddf372452
workflow graph RNA-seq alelle specific pipeline for single-read data

Allele specific RNA-Seq single-read workflow

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

Path: workflows/allele-rnaseq-se.cwl

Branch/Commit ID: 6bf56698c6fe6e781723dea32bc922b91ef49cf3
workflow graph Transcripts annotation workflow

https://github.com/EBI-Metagenomics/workflow-is-cwl.git

Path: workflows/TranscriptsAnnotation-wf.cwl

Branch/Commit ID: 26dad276bac124f89086268bcbca962a5c0caca6
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