Explore Workflows

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

Graph Name Retrieved From View
workflow graph alignment for mouse with qc

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

Path: definitions/pipelines/alignment_wgs_mouse.cwl

Branch/Commit ID: c625e05eefb1754353c1bdfa46c01dc61e6233dd
workflow graph kmer_ref_compare_wnode

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

Path: task_types/tt_kmer_ref_compare_wnode.cwl

Branch/Commit ID: ef266744578e2dcbce57c110c6fa3b9eee91e316
workflow graph change_formats_and_names.cwl

https://github.com/EBI-Metagenomics/pipeline-v5.git

Path: workflows/subworkflows/assembly/change_formats_and_names.cwl

Branch/Commit ID: 4b98d8bf882bc96d924b5d2d4e6d9c188fa7b273
workflow graph trim-chipseq-se.cwl

Runs ChIP-Seq BioWardrobe basic analysis with single-end data file.

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

Path: workflows/trim-chipseq-se.cwl

Branch/Commit ID: 568da91bb1c6182ba4f146e2a729cac1c3d8783c
workflow graph RNA-Seq pipeline single-read stranded mitochondrial

Slightly changed 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. An additional steps were added to map data to mitochondrial chromosome only and then merge the output. Experiment files in [FASTQ](http://maq.sourceforge.net/fastq.shtml) format either compressed or not can be used. Current workflow should be used only with single-read strand specific RNA-Seq data. It performs the following steps: 1. `STAR` to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. `fastx_quality_stats` to analyze input FASTQ file and generate quality statistics file 3. `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-mitochondrial.cwl

Branch/Commit ID: 42dc4f70b117e78785b82865ec4c4b941ac1c259
workflow graph pindel parallel workflow

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

Path: definitions/subworkflows/pindel.cwl

Branch/Commit ID: b9e7392e72506cadd898a6ac4db330baf6535ab6
workflow graph canine_vardict_module.cwl

https://github.com/d3b-center/canine-dev.git

Path: subworkflows/canine_vardict_module.cwl

Branch/Commit ID: 462aaebbd442e84ea101b45b716df0174b88512e
workflow graph assm_assm_blastn_wnode

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

Path: task_types/tt_assm_assm_blastn_wnode.cwl

Branch/Commit ID: 8a8fffb78b1e327ba0da51840ac8acc0c218d611
workflow graph sec-wf-out.cwl

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

Path: tests/wf/sec-wf-out.cwl

Branch/Commit ID: cd1ba3df3745fba4b635f05c67ebeaf3b8a9f4ec
workflow graph rna annotation

RNAs - predict, cluster, identify, annotate

 https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/rna-annotation.workflow.cwl

Branch/Commit ID: 6a8727124baf77416ca797982fd4e0689c2a593a