Explore Workflows

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

Graph Name Retrieved From View
workflow graph STAR-RNA-Seq alignment and transcript/gene abundance workflow with Xenosplit

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

Path: definitions/pipelines/rnaseq_star_fusion_with_xenosplit.cwl

Branch/Commit ID: 8da2b1cd6fa379b2c22baf9dad762d39630e6f46
workflow graph qc-assembled.workflow.cwl

https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/qc-assembled.workflow.cwl

Branch/Commit ID: 932da3abed7166bd5a962871386ba2c31d47b85c
workflow graph Unaligned to aligned BAM

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

Path: definitions/subworkflows/align.cwl

Branch/Commit ID: e7e888df9e7d44f036c4c7985e474016ee9e6525
workflow graph revsort.cwl

Reverse the lines in a document, then sort those lines.

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

Path: tests/wf/revsort.cwl

Branch/Commit ID: 6300a49ec29be956ab451311fe9781522f461aee
workflow graph default-wf5.cwl

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

Path: tests/wf/default-wf5.cwl

Branch/Commit ID: 1397d96ad97fe8abfd1184675d728a8a04699d67
workflow graph Xenbase RNA-Seq pipeline paired-end

1. Convert input SRA file into pair of upsrtream and downstream FASTQ files (run fastq-dump) 2. Analyze quality of FASTQ files (run fastqc with each of the FASTQ files) 3. If any of the following fields in fastqc generated report is marked as failed for at least one of input FASTQ files: \"Per base sequence quality\", \"Per sequence quality scores\", \"Overrepresented sequences\", \"Adapter Content\", - trim adapters (run trimmomatic) 4. Align original or trimmed FASTQ files to reference genome, calculate genes and isoforms expression (run RSEM) 5. Count mapped reads number in sorted BAM file (run bamtools stats) 6. Generate genome coverage BED file (run bedtools genomecov) 7. Sort genearted BED file (run sort) 8. Generate genome coverage bigWig file from BED file (run bedGraphToBigWig)

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

Path: workflows/xenbase-rnaseq-pe.cwl

Branch/Commit ID: d6f58c383d0676269afb519399061191a1144a6a
workflow graph wgs alignment and germline variant detection

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

Path: definitions/pipelines/germline_wgs_gvcf.cwl

Branch/Commit ID: 00df82a529a58d362158110581e1daa28b4d7ecb
workflow graph workflow1.cwl

https://github.com/process-project/PREFACTOR-XENON-CWL.git

Path: workflow1.cwl

Branch/Commit ID: 55fde09d37cb68efafca77ec8d59f2b4428e0d3e
workflow graph cond-wf-010.cwl

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/conditionals/cond-wf-010.cwl

Branch/Commit ID: a5073143db4155e05df8d2e7eb59d9e62acd65a5
workflow graph Create Genomic Collection for Bacterial Pipeline

https://github.com/ncbi/pgap.git

Path: genomic_source/wf_genomic_source.cwl

Branch/Commit ID: 5b498b4c4f17bb8f17e6886aa4c5661d7aba34fc