Explore Workflows

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

Graph Name Retrieved From View
workflow graph atm-std-n2n.cwl

https://github.com/E3SM-Project/e3sm_to_cmip.git

Path: scripts/cwl_workflows/atm-unified/atm-std-n2n.cwl

Branch/Commit ID: c5607619b8aa560552333a8b16f5ad9cd93a2d42
workflow graph gather AML trio outputs

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

Path: definitions/pipelines/gathered_cle_aml_trio.cwl

Branch/Commit ID: e2a34d2b8c406db9aed8e49e8bdcf36f51444379
workflow graph 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 **strand specific 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-dutp.cwl

Branch/Commit ID: 5561f7ee11dd74848680351411a19aa87b13d27b
workflow graph count-lines8-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines8-wf.cwl

Branch/Commit ID: 6003cbb94f16103241b562f2133e7c4acac6c621
workflow graph Single-cell ATAC-Seq Dimensionality Reduction Analysis

Single-cell ATAC-Seq Dimensionality Reduction Analysis Integrates multiple single-cell ATAC-Seq datasets, reduces dimensionality using LSI.

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

Path: workflows/sc-atac-reduce.cwl

Branch/Commit ID: 7030da528559c7106d156284e50ff0ecedab0c4e
workflow graph count-lines2-wf.cwl

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

Path: cwltool/schemas/v1.0/v1.0/count-lines2-wf.cwl

Branch/Commit ID: f207d168f4e7eb4dd2279840d4062ba75d9c79c3
workflow graph pipeline.cwl

https://github.com/hubmapconsortium/azimuth-annotate.git

Path: pipeline.cwl

Branch/Commit ID: 50b1700646d114499a94c1297646db98a4223879
workflow graph taxonomy_check_16S

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

Path: task_types/tt_taxonomy_check_16S.cwl

Branch/Commit ID: 733ab7198a66a0153d0f03c3022ab53c17325ff8
workflow graph ST610106.cwl

https://github.com/Marco-Salvi/dtc61.git

Path: ST610106.cwl

Branch/Commit ID: 8c2621b1d757d890cbbd0dfe5b363ad014f0a684
workflow graph exome alignment and somatic variant detection

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

Path: definitions/pipelines/somatic_exome.cwl

Branch/Commit ID: ddb49a0951d9ad537269d7db3fe8f904495a8bf4