Explore Workflows

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

Graph Name Retrieved From View
workflow graph exome alignment and germline variant detection

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

Path: definitions/pipelines/germline_exome.cwl

Branch/Commit ID: b9e7392e72506cadd898a6ac4db330baf6535ab6
workflow graph taxonomy_check_16S

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

Path: task_types/tt_taxonomy_check_16S.cwl

Branch/Commit ID: 61e3752f1f5e2ee498fa024c235226f8580be942
workflow graph allele-rnaseq-pe.cwl

Allele specific RNA-Seq paired-end workflow

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

Path: workflows/allele-rnaseq-pe.cwl

Branch/Commit ID: db6abb2735f87614b870fca9990d36ea786cbbce
workflow graph Water bodies detection based on NDWI and the otsu threshold

Water bodies detection based on NDWI and otsu threshold applied to a single Sentinel-2 COG STAC item

 https://github.com/eoap/quickwin.git

Path: cwl-workflow/app-water-body-cloud-native.cwl

Branch/Commit ID: a7d87a9978b546cbc708bf2792edeea9945d0033

Packed ID: main
workflow graph dfastqc-filelist-outputdir.cwl

https://github.com/nigyta/bact_genome.git

Path: cwl/workflow/dfastqc-filelist-outputdir.cwl

Branch/Commit ID: e316f37f502005165ebd7f22b5257900c7c712ac
workflow graph bam to trimmed fastqs and biscuit alignments

https://github.com/tmooney/cancer-genomics-workflow.git

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl

Branch/Commit ID: 0db1a5f1ceedd4416ac550787c27b99c87dbe985
workflow graph scatter-valuefrom-wf3.cwl#main

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

Path: tests/scatter-valuefrom-wf3.cwl

Branch/Commit ID: 3e90671b25f7840ef2926ad2bacbf447772dda94

Packed ID: main
workflow graph env-wf2.cwl

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

Path: tests/env-wf2.cwl

Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733
workflow graph Deprecated. RNA-Seq pipeline paired-end

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.cwl

Branch/Commit ID: 261c0232a7a40880f2480b811ed2d7e89c463869
workflow graph scatter-valuefrom-wf4.cwl#main

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

Path: tests/scatter-valuefrom-wf4.cwl

Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733

Packed ID: main