Explore Workflows

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

Graph Name Retrieved From View
workflow graph workflow.cwl

https://github.com/nal-i5k/organism_onboarding.git

Path: flow_dispatch/2blat/workflow.cwl

Branch/Commit ID: f7894707dd30a0edd199d3b67c4c8678f64c90b3
workflow graph abra_workflow.cwl

https://github.com/mskcc/ACCESS-Pipeline.git

Path: workflows/ABRA/abra_workflow.cwl

Branch/Commit ID: 09ddd9711fb550f56d52f1806cdefd4a8cd943b0
workflow graph RNA-Seq pipeline paired-end strand specific

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **paired-end** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the paired-end RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 3. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 4. Generate BigWig file on the base of sorted BAM file 5. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 6. Calculate isoform expression level for the sorted BAM file and GTF/TAB annotation file using GEEP reads-counting utility; export results to file

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

Path: workflows/rnaseq-pe-dutp.cwl

Branch/Commit ID: 104059e07a2964673e21d371763e33c0afeb2d03
workflow graph retrieve metadata from Zenodo community

For a given Zenodo community, retrieve its repository records as Zenodo JSON and (eventually) schema.org JSON-LD and DataCite v4 XML.

https://github.com/stain/ro-index-paper.git

Path: code/data-gathering/workflows/zenodo-records.cwl

Branch/Commit ID: 322f215ffb58ca5f735f8f4f6a0cdc96cbd0e0aa
workflow graph blastp_wnode_naming

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

Path: task_types/tt_blastp_wnode_naming.cwl

Branch/Commit ID: 22ffe27d9d4a899def7592d75d5871c1856adbdb
workflow graph nestedworkflows.cwl

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

Path: cwltool/schemas/v1.0/examples/nestedworkflows.cwl

Branch/Commit ID: 445f6b3a214f0c48317b25f7af278ae919ce5403
workflow graph gcaccess_from_list

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

Path: task_types/tt_gcaccess_from_list.cwl

Branch/Commit ID: 2353ee2550529ca5b0705c94b32022a21713db18
workflow graph process VCF workflow

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

Path: definitions/subworkflows/strelka_process_vcf.cwl

Branch/Commit ID: d57c2af01a3cb6016e5a264f60641eafd2e5aa05
workflow graph mpi_simple_wf.cwl

Simple 2 step workflow to check that workflow steps are independently picking up on the number of processes. First run the parallel get PIDs step (on the input num procs) then run (on a single proc) the line count. This should equal the input.

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

Path: tests/wf/mpi_simple_wf.cwl

Branch/Commit ID: 84939620c3eec1ab11369849c63237ebfa48da41
workflow graph bam to trimmed fastqs and HISAT alignments

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

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_hisat_alignments.cwl

Branch/Commit ID: 3bebaf9b70331de9f4845e2223c55082f5a812fb