Explore Workflows

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

Graph Name Retrieved From View
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: c61af827113ebc41596aa839c65d21b4d2b0c8b6
workflow graph allele-vcf-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-vcf-alignreads-se-pe.cwl

Branch/Commit ID: 7f5ba081a98fccf9210623d4cef2b5feb7a55e5d
workflow graph schemadef-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/schemadef-wf.cwl

Branch/Commit ID: 10492acee927c177933160f6ad67085f9112b0d1
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: 509938802c5e42bb8084c6a5a26ab6425c60e69a
workflow graph selfcal_targ_lba.cwl

https://git.astron.nl/RD/LINC.git

Path: workflows/linc_target/selfcal_targ_lba.cwl

Branch/Commit ID: 0601b0801bc238c464e954803c16b48bd7e6b14e
workflow graph HBA_target.cwl

https://git.astron.nl/RD/LINC.git

Path: workflows/HBA_target.cwl

Branch/Commit ID: 16b52facea91f7ebd2200c471b69a8c6a49b9e66
workflow graph scatter-wf4.cwl#main

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

Path: tests/wf/scatter-wf4.cwl

Branch/Commit ID: 4a5fe26e32d244d95f9483c3edfc3df04f3e5f7b

Packed ID: main
workflow graph cond-wf-004.1.cwl

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

Path: testdata/cond-wf-004.1.cwl

Branch/Commit ID: 68843d2d829a337c7bb7dc51473f1ff68d6d59ca
workflow graph ethseq_from_pileup.cwl

Creates a genotype file based on the pileup of the SNPs and then runs EthSEQ.

 https://github.com/demichelislab/SPICE-pipeline-CWL.git

Path: cwl/workflows/ethseq_from_pileup.cwl

Branch/Commit ID: 06e4a6f868651c8e26a88db518af1974159ecba9
workflow graph packed_no_main.cwl#collision

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

Path: tests/wf/packed_no_main.cwl

Branch/Commit ID: 18b8fdf7d425d8e7d8986e08904ef09492798cf6

Packed ID: collision