Explore Workflows

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

Graph Name Retrieved From View
workflow graph transform.cwl

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

Path: workflows/fastq_readgroup_stats/transform.cwl

Branch/Commit ID: 2f7c0e92e7b88b57b86602f11c595661c374008a
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: ae2b231562822ed66b8e35e5452ae7f012416b2a
workflow graph sample-workflow.cwl

https://github.com/mskcc/roslin-variant.git

Path: setup/cwl/workflows/sample-workflow.cwl

Branch/Commit ID: 8766def7f70f329e2a4c56239f141685a873599b
workflow graph transform_mirna.cwl

https://github.com/NCI-GDC/gdc-dnaseq-cwl.git

Path: workflows/mirnaseq/transform_mirna.cwl

Branch/Commit ID: 2f7c0e92e7b88b57b86602f11c595661c374008a
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