Explore Workflows

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

Graph Name Retrieved From View
workflow graph extract_readgroups_bam.cwl

https://github.com/nci-gdc/gdc-dnaseq-cwl.git

Path: workflows/bamfastq_align/extract_readgroups_bam.cwl

Branch/Commit ID: 2f7c0e92e7b88b57b86602f11c595661c374008a
workflow graph rnaseq-header.cwl

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

Path: metadata/rnaseq-header.cwl

Branch/Commit ID: 0ddfca10c41f83bb120c7633e0db9dba7441bca0
workflow graph exome alignment and germline variant detection

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

Path: definitions/pipelines/germline_exome.cwl

Branch/Commit ID: 5f120e5bc3c0f75bfbc636ea2c6f4393f5d45ca1
workflow graph amplicon_metrics.cwl

https://github.com/nci-gdc/gdc-dnaseq-cwl.git

Path: workflows/bamfastq_align/amplicon_metrics.cwl

Branch/Commit ID: a3eec6c1081d28efe00a0d269fb41303acc4ccdd
workflow graph etl.cwl

https://github.com/nci-gdc/gdc-dnaseq-cwl.git

Path: workflows/bamfastq_align/etl.cwl

Branch/Commit ID: 2f7c0e92e7b88b57b86602f11c595661c374008a
workflow graph Unaligned to aligned BAM

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

Path: definitions/subworkflows/align.cwl

Branch/Commit ID: 6a55118f915e24d2ad008c93a02d9de5643f5511
workflow graph Xenbase ChIP-Seq pipeline single-read

1. Convert input SRA file into FASTQ file (run fastq-dump) 2. Analyze quality of FASTQ file (run fastqc) 3. If any of the following fields in fastqc generated report is marked as failed: \"Per base sequence quality\", \"Per sequence quality scores\", \"Overrepresented sequences\", \"Adapter Content\", - trim adapters (run trimmomatic) 4. Align original or trimmed FASTQ file to reference genome (run Bowtie2) 5. Sort and index generated by Bowtie2 BAM file (run samtools sort, samtools index) 6. Remove duplicates in sorted BAM file (run picard) 7. Sort and index BAM file after duplicates removing (run samtools sort, samtools index) 8. Count mapped reads number in sorted BAM file (run bamtools stats) 9. Generate genome coverage BED file (run bedtools genomecov) 10. Sort genearted BED file (run sort) 11. Generate genome coverage bigWig file from BED file (run bedGraphToBigWig)

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

Path: workflows/xenbase-chipseq-se.cwl

Branch/Commit ID: ae2b231562822ed66b8e35e5452ae7f012416b2a
workflow graph 1st-workflow.cwl

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

Path: _includes/cwl/21-1st-workflow/1st-workflow.cwl

Branch/Commit ID: ac6a278bb10779972716271c8d583850c1faf744
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: d64178072bc4fc9700ab80cdf90146890b96587e
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: 8cee1920920ed73384fb3ab74272da9c92a20cf2