Explore Workflows

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

Graph Name Retrieved From View
workflow graph extract_amplicon_kit.cwl

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

Path: workflows/bamfastq_align/extract_amplicon_kit.cwl

Branch/Commit ID: 0d3fdddeae5a398e476d91aa98766965866d8eae
workflow graph 03-map-pe-blacklist-removal.cwl

ATAC-seq 03 mapping - reads: PE - blacklist removal

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

Path: v1.0/ATAC-seq_pipeline/03-map-pe-blacklist-removal.cwl

Branch/Commit ID: 13826f526a99e151e9cf5f22e70bdcf4feea73f4
workflow graph Create Genomic Collection for Bacterial Pipeline, ASN.1 input

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

Path: genomic_source/wf_genomic_source_asn.cwl

Branch/Commit ID: 4b8d11048f1047140b337a2cac6503d80a22d683
workflow graph count-lines3-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines3-wf.cwl

Branch/Commit ID: 4a5fe26e32d244d95f9483c3edfc3df04f3e5f7b
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: 2f7c0e92e7b88b57b86602f11c595661c374008a
workflow graph Xenbase RNA-Seq pipeline single-read

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-se.cwl

Branch/Commit ID: 02ffbbd7eb8e06bfb759edea440f78bdc8bb2631
workflow graph cwlsite.cwl

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

Path: cwltool/schemas/site/cwlsite.cwl

Branch/Commit ID: 5c7799a145595323d0a8628be1fe0e24985e793a
workflow graph 01-qc-pe.cwl

ChIP-seq 01 QC - reads: PE

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

Path: v1.0/ChIP-seq_pipeline/01-qc-pe.cwl

Branch/Commit ID: 13826f526a99e151e9cf5f22e70bdcf4feea73f4
workflow graph echo-wf.cwl

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

Path: tests/override/echo-wf.cwl

Branch/Commit ID: 478c2ffc09fb189c4f36ccb82aad945b3db5f9b3
workflow graph echo-wf.cwl

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

Path: tests/override/echo-wf.cwl

Branch/Commit ID: 4c905b830371eee45188a53510ba0ee9113fd4c8