Explore Workflows

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

Graph Name Retrieved From View
workflow graph downsample unaligned BAM and align

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

Path: definitions/subworkflows/downsampled_alignment.cwl

Branch/Commit ID: e59c77629936fad069007ba642cad49fef7ad29f
workflow graph Per-chromosome pindel

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

Path: definitions/subworkflows/pindel_cat.cwl

Branch/Commit ID: 0a9a4ce83b49ed4e7eee5bcc09d83725136a36b0
workflow graph count-lines16-wf.cwl

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

Path: tests/count-lines16-wf.cwl

Branch/Commit ID: ea9f8634e41824ac3f81c3dde698d5f0eef54f1b
workflow graph stdout-wf_v1_1.cwl

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

Path: testdata/stdout-wf_v1_1.cwl

Branch/Commit ID: 0ad6983898f0d9001fe0f416f97c4d8b940e384a
workflow graph timelimit2-wf.cwl

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

Path: tests/timelimit2-wf.cwl

Branch/Commit ID: ea9f8634e41824ac3f81c3dde698d5f0eef54f1b
workflow graph Trim Galore 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 a **single-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 single-end RNA-Seq data. It performs the following steps: 1. Trim adapters from input FASTQ file 2. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 4. 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/trim-rnaseq-se-dutp.cwl

Branch/Commit ID: ce058d892d330125cd03d0a0d5fb3b321cda0be3
workflow graph Build STAR indices

Workflow runs [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886) to build indices for reference genome provided in a single FASTA file as fasta_file input and GTF annotation file from annotation_gtf_file input. Generated indices are saved in a folder with the name that corresponds to the input genome.

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

Path: workflows/star-index.cwl

Branch/Commit ID: a68821bf3a9ceadc3b2ffbb535d601d9a645b377
workflow graph Varscan Workflow

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

Path: definitions/subworkflows/varscan_pre_and_post_processing.cwl

Branch/Commit ID: e0b3c76e38630fb6234414b5adebfb6a4fb23117
workflow graph count-lines9-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines9-wf.cwl

Branch/Commit ID: e9c83739a93fa0b18f8dea2f98b632a9e32725c9
workflow graph chipseq-se.cwl

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

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

Path: workflows/chipseq-se.cwl

Branch/Commit ID: b4b7b2e7e508be5eac639f9e323d141daf714c0d