Explore Workflows

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

Graph Name Retrieved From View
workflow graph merge and annotate svs with population allele freq and vep

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

Path: definitions/subworkflows/merge_svs.cwl

Branch/Commit ID: a9133c999502acf94b433af8d39897e6c2cdf65f
workflow graph Subworkflow that runs cnvkit in single sample mode and returns a vcf file

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

Path: definitions/subworkflows/cnvkit_single_sample.cwl

Branch/Commit ID: a9133c999502acf94b433af8d39897e6c2cdf65f
workflow graph SV filtering workflow

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

Path: definitions/subworkflows/filter_sv_vcf.cwl

Branch/Commit ID: a9133c999502acf94b433af8d39897e6c2cdf65f
workflow graph psortedDefaultParams.cwl

https://github.com/hubmapconsortium/spatial-transcriptomics-pipeline.git

Path: steps/psortedDefaultParams.cwl

Branch/Commit ID: 5b866e480fb557cf53d619a22068c73548e337d5
workflow graph transform_pack.cwl#bwa_se.cwl

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

Path: workflows/bamfastq_align/transform_pack.cwl

Branch/Commit ID: 0c1a40ea1efb1656644ccec0b7abe659539340e7

Packed ID: bwa_se.cwl
workflow graph js_output_workflow.cwl

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

Path: tests/wf/js_output_workflow.cwl

Branch/Commit ID: d5f7fa162611243f0c66dd3e933c16a4964a09ca
workflow graph tt_blastn_wnode

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

Path: task_types/tt_blastn_wnode.cwl

Branch/Commit ID: 6d04f5d65d1d4893706d9ae7e27341633333054f
workflow graph 816_wf.cwl

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

Path: tests/wf/816_wf.cwl

Branch/Commit ID: d5f7fa162611243f0c66dd3e933c16a4964a09ca
workflow graph Apply filters to VCF file

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

Path: definitions/subworkflows/filter_vcf.cwl

Branch/Commit ID: ae57b60e9b01e3f0f02f4e828042748409dff5a3
workflow graph RNA-Seq pipeline single-read

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-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.cwl

Branch/Commit ID: f3e44d3b0f198cf5245c49011124dc3b6c2b06fd