Explore Workflows

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

Graph Name Retrieved From View
workflow graph Downsample and HaplotypeCaller

https://github.com/apaul7/cancer-genomics-workflow.git

Path: definitions/pipelines/downsample_and_recall.cwl

Branch/Commit ID: bfcb5ffbea3d00a38cc03595d41e53ea976d599d
workflow graph mutect parallel workflow

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

Path: definitions/subworkflows/mutect.cwl

Branch/Commit ID: 293dc7b83639d21a56efff2baf9dfe4e97b9b806
workflow graph RNA-Seq pipeline single-read stranded mitochondrial

Slightly changed 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. An additional steps were added to map data to mitochondrial chromosome only and then merge the output. Experiment files in [FASTQ](http://maq.sourceforge.net/fastq.shtml) format either compressed or not can be used. Current workflow should be used only with single-read strand specific RNA-Seq data. It performs the following steps: 1. `STAR` to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. `fastx_quality_stats` to analyze input FASTQ file and generate quality statistics file 3. `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-mitochondrial.cwl

Branch/Commit ID: 36fd18f11e939d3908b1eca8d2939402f7a99b0f
workflow graph ani_top_n

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

Path: task_types/tt_ani_top_n.cwl

Branch/Commit ID: 6d8d29a2156b93a75f1d1c6952738bd63f6bd98e
workflow graph Single-cell Manual Cell Type Assignment

Single-cell Manual Cell Type Assignment Assigns cell types for clusters based on the provided metadata file.

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

Path: workflows/sc-ctype-assign.cwl

Branch/Commit ID: 36fd18f11e939d3908b1eca8d2939402f7a99b0f
workflow graph scatter-wf4.cwl#main

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

Path: tests/wf/scatter-wf4.cwl

Branch/Commit ID: 10492acee927c177933160f6ad67085f9112b0d1

Packed ID: main
workflow graph default-wf5.cwl

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

Path: tests/wf/default-wf5.cwl

Branch/Commit ID: 63f539ba60e91f0cb3ce7cda2c5da5c65525c375
workflow graph alignment for mouse with qc

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

Path: definitions/pipelines/alignment_wgs_mouse.cwl

Branch/Commit ID: 3034168d652bfa930ba09af20e473a4564a8010d
workflow graph Alignment without BQSR

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

Path: definitions/subworkflows/sequence_to_bqsr_mouse.cwl

Branch/Commit ID: 049f4aeff4c4a1b8421cac9b1c1c1f0da5848315
workflow graph bulk_analysis.cwl

https://github.com/hubmapconsortium/sc-atac-seq-pipeline.git

Path: steps/bulk_analysis.cwl

Branch/Commit ID: ffcc84c3376c4bd10738e22b7daec6a0aaa37108