Explore Workflows

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Graph Name Retrieved From View
workflow graph 04-quantification-pe-unstranded.cwl

RNA-seq 04 quantification

 https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/RNA-seq_pipeline/04-quantification-pe-unstranded.cwl

Branch/Commit ID: dd2241dbbbc23abd91b5e6a18c139530e7ef8d2b
workflow graph bam-bedgraph-bigwig.cwl

Workflow converts input BAM file into bigWig and bedGraph files

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

Path: subworkflows/bam-bedgraph-bigwig.cwl

Branch/Commit ID: 8d7ba680b7904da84ad611d184caf247da4a5dc7
workflow graph secret_wf.cwl

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

Path: tests/wf/secret_wf.cwl

Branch/Commit ID: 478c2ffc09fb189c4f36ccb82aad945b3db5f9b3
workflow graph Exome QC workflow

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

Path: definitions/subworkflows/qc_exome.cwl

Branch/Commit ID: 8cee1920920ed73384fb3ab74272da9c92a20cf2
workflow graph iwdr_with_nested_dirs.cwl

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

Path: cwltool/schemas/v1.0/v1.0/iwdr_with_nested_dirs.cwl

Branch/Commit ID: 478c2ffc09fb189c4f36ccb82aad945b3db5f9b3
workflow graph 02-trim-pe.cwl

ChIP-seq 02 trimming - reads: PE

 https://github.com/alexbarrera/GGR-cwl.git

Path: v1.0/ChIP-seq_pipeline/02-trim-pe.cwl

Branch/Commit ID: 7696e7eb27a9251fba53ef4ccacc84cc8f8b0685
workflow graph step-valuefrom-wf.cwl

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

Path: v1.0/v1.0/step-valuefrom-wf.cwl

Branch/Commit ID: a062055fddcc7d7d9dbc53d28288e3ccb9a800d8
workflow graph unix_align_workflow.cwl

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

Path: workflows/unix/unix_align_workflow.cwl

Branch/Commit ID: 0d3fdddeae5a398e476d91aa98766965866d8eae
workflow graph module-1-2-chunk

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

Path: setup/cwl/module-1-2.chunk.cwl

Branch/Commit ID: 08e592a521057cef4982c1d4111d2e3b30ea3f2f
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: e9a24699d8b5ffe64412b1ba0af8448c281b223a