Explore Workflows

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

Graph Name Retrieved From View
workflow graph dynresreq-workflow.cwl

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

Path: v1.0/v1.0/dynresreq-workflow.cwl

Branch/Commit ID: 622134ebc48980676b7e53fe39405c428920c03e
workflow graph assm_assm_blastn_wnode

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

Path: task_types/tt_assm_assm_blastn_wnode.cwl

Branch/Commit ID: 656113dcac0de7cef6cff6c688f61441ee05872a
workflow graph Spelling subworkflow

Login to spell server and perform a spell.

 https://gitlab.com/0xBADCAFE/test-cwl.git

Path: workflows/subworkflow-1/swf-1.cwl

Branch/Commit ID: ceb83cf01b11ae20cd1b02d3a107be28eb4faa1d
workflow graph Q/A subworkflow

Some documentation

 https://gitlab.com/0xBADCAFE/test-cwl.git

Path: workflows/subworkflow-2/swf-2.cwl

Branch/Commit ID: ceb83cf01b11ae20cd1b02d3a107be28eb4faa1d
workflow graph Main Workflow

A description of the Main Workflow, its goals and methods.

 https://gitlab.com/0xBADCAFE/test-cwl.git

Path: workflows/main.cwl

Branch/Commit ID: ceb83cf01b11ae20cd1b02d3a107be28eb4faa1d
workflow graph Main Workflow

A description of the Main Workflow, its goals and methods.

 https://gitlab.com/0xBADCAFE/test-cwl.git

Path: workflows/main.cwl

Branch/Commit ID: 6466e7ff1834effa8dc72cd12a8942321bacbe59
workflow graph kmer_cache_store

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

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: a34f47d1e37af51e387ecdfa5c3047f106c1146b
workflow graph Spelling subworkflow

Login to spell server and perform a spell.

 https://gitlab.com/0xBADCAFE/test-cwl.git

Path: workflows/subworkflow-1/swf-1.cwl

Branch/Commit ID: 9883500868b391737b415497ea4e2fcfdbe7375f
workflow graph Main Workflow

A description of the Main Workflow, its goals and methods.

 https://gitlab.com/0xBADCAFE/test-cwl.git

Path: workflows/main.cwl

Branch/Commit ID: 9883500868b391737b415497ea4e2fcfdbe7375f
workflow graph Trim Galore 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 **pair-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 files 2. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 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 files 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-pe.cwl

Branch/Commit ID: a839eb6390974089e1a558c49fc07b4c66c50767