Explore Workflows

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

Graph Name Retrieved From View
workflow graph Chipseq alignment for nonhuman with qc and creating homer tag directory

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

Path: definitions/pipelines/chipseq_alignment_nonhuman.cwl

Branch/Commit ID: 5fda2d9eb52a363bd51011b3851c2afb86318c0c
workflow graph chipseq-pe.cwl

Runs ChIP-Seq BioWardrobe basic analysis with paired-end input data files.

https://github.com/Barski-lab/workflows.git

Path: workflows/chipseq-pe.cwl

Branch/Commit ID: 8587882f145d3eb8e258e7bf819a94f8dd666dbf
workflow graph helloworld-htcondorcern.cwl

https://github.com/reanahub/reana-demo-helloworld.git

Path: workflow/cwl/helloworld-htcondorcern.cwl

Branch/Commit ID: 39d64e14294db8ccf9fe0b256231d0a819f53cd4
workflow graph FASTQ Download

FASTQ Download Downloads FASTQ files from the provided SRR identifiers

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

Path: workflows/fastq-download.cwl

Branch/Commit ID: 12e5256de1b680c551c87fd5db6f3bc65428af67
workflow graph Cell Ranger ARC Count Gene Expression + ATAC

Cell Ranger ARC Count Gene Expression + ATAC ============================================

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

Path: workflows/cellranger-arc-count.cwl

Branch/Commit ID: 12e5256de1b680c551c87fd5db6f3bc65428af67
workflow graph STAR-RNA-Seq alignment and transcript/gene abundance workflow

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

Path: definitions/pipelines/rnaseq_star_fusion.cwl

Branch/Commit ID: 97572e3a088d79f6a4166385f79e79ea77b11470
workflow graph RNA-Seq pipeline single-read strand specific

Note: should be updated The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for **strand specific single-read** experiment. A corresponded input [FASTQ](http://maq.sourceforge.net/fastq.shtml) file has to be provided. Current workflow should be used only with the single-read RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 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) 5. Generate BigWig file on the base of sorted BAM file 6. Map input FASTQ file to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 7. 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-se-dutp.cwl

Branch/Commit ID: 12e5256de1b680c551c87fd5db6f3bc65428af67
workflow graph fail-unconnected.cwl

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/fail-unconnected.cwl

Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733
workflow graph gatk4.2.4.1_mutect2_workflow.cwl

GATK4.2.4.1 Mutect2 workflow

https://github.com/nci-gdc/gatk4_mutect2_cwl.git

Path: subworkflows/gatk4.2.4.1_mutect2_workflow.cwl

Branch/Commit ID: 138d484362084dfc97d9fb7d839855b4bc2c5599
workflow graph count-lines11-null-step-wf.cwl

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/count-lines11-null-step-wf.cwl

Branch/Commit ID: b1d4a69df86350059bd49aa127c02be0c349f7de