Explore Workflows

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

Graph Name Retrieved From View
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
workflow graph salmon_wf_pe.cwl

https://github.com/pitagora-network/pitagora-cwl.git

Path: workflows/salmon/paired_end/salmon_wf_pe.cwl

Branch/Commit ID: 3affcd5588e273779b8b4084839ed0582ba2ea18
workflow graph 1st-workflow.cwl

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

Path: cwltool/schemas/v1.0/examples/1st-workflow.cwl

Branch/Commit ID: fec7a10466a26e376b14181a88734983cfb1b8cb
workflow graph 02-trim-pe.cwl

ATAC-seq 02 trimming - reads: PE

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

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

Branch/Commit ID: dd2241dbbbc23abd91b5e6a18c139530e7ef8d2b
workflow graph echo-wf-default.cwl

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

Path: cwltool/schemas/v1.0/v1.0/echo-wf-default.cwl

Branch/Commit ID: 4a5fe26e32d244d95f9483c3edfc3df04f3e5f7b
workflow graph PGAP Pipeline

PGAP pipeline for external usage, powered via containers

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

Path: wf_common.cwl

Branch/Commit ID: 7edbf07405191db65a913e311a7f2260b076d36c
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: 4a5fe26e32d244d95f9483c3edfc3df04f3e5f7b
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: e627079d8431e4f1f1c7531af1ca2e7dcc684b90