Explore Workflows

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

Graph Name Retrieved From View
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/Barski-lab/workflows.git

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

Branch/Commit ID: fb355eda4555a7e7182a91ce045212b0a087d73f
workflow graph varscan somatic workflow

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

Path: definitions/subworkflows/varscan.cwl

Branch/Commit ID: d57c2af01a3cb6016e5a264f60641eafd2e5aa05
workflow graph Per-region pindel

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

Path: definitions/subworkflows/pindel_cat.cwl

Branch/Commit ID: d57c2af01a3cb6016e5a264f60641eafd2e5aa05
workflow graph varscan somatic workflow

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

Path: definitions/subworkflows/varscan.cwl

Branch/Commit ID: 5be54bf09092c53e6c7797a875f64a360d511d7f
workflow graph process VCF workflow

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

Path: definitions/subworkflows/strelka_process_vcf.cwl

Branch/Commit ID: 5be54bf09092c53e6c7797a875f64a360d511d7f
workflow graph bqsr_workflow.cwl

https://github.com/mskcc/ACCESS-Pipeline.git

Path: workflows/BQSR/bqsr_workflow.cwl

Branch/Commit ID: 0a30dee7a8e16ec336fabf62a987042d4a0fba22
workflow graph pangenome-generate.cwl

https://github.com/arvados/bh20-seq-resource.git

Path: workflows/pangenome-generate/pangenome-generate.cwl

Branch/Commit ID: 39eca644ed4a0a86510ae0b8afb8da9207d9750a
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: d6ec0dee61ef65a110e10141bde1a79332a64ab0
workflow graph group-isoforms-batch.cwl

Workflow runs group-isoforms.cwl tool using scatter for isoforms_file input. genes_filename and common_tss_filename inputs are ignored.

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

Path: tools/group-isoforms-batch.cwl

Branch/Commit ID: 2cad55523d1b4ee7fd9e64df0f6263c6545e4b0e
workflow graph gaps_or_not.cwl

https://github.com/nal-i5k/organism_onboarding.git

Path: gaps_or_not.cwl

Branch/Commit ID: f7894707dd30a0edd199d3b67c4c8678f64c90b3