Explore Workflows

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

Graph Name Retrieved From View
workflow graph joint genotyping for trios or small cohorts

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

Path: definitions/subworkflows/joint_genotype.cwl

Branch/Commit ID: 4aba7c6591c2f1ebd827a36d325a58738c429bea
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: dda9e6e06a656b7b3fa7504156474b962fe3953c
workflow graph Running cellranger count and lineage inference

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

Path: definitions/subworkflows/single_cell_rnaseq.cwl

Branch/Commit ID: 31a179d7a2f2ac86bfd7fcc4dc79832c3739ae76
workflow graph Detect Variants workflow

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

Path: definitions/pipelines/detect_variants_nonhuman.cwl

Branch/Commit ID: b9e7392e72506cadd898a6ac4db330baf6535ab6
workflow graph Whole genome alignment and somatic variant detection

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

Path: definitions/pipelines/somatic_wgs.cwl

Branch/Commit ID: f615832615c3b41728df8e47b72ef11e37e6a9e5
workflow graph Detect Variants workflow

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

Path: definitions/pipelines/detect_variants_mouse.cwl

Branch/Commit ID: f615832615c3b41728df8e47b72ef11e37e6a9e5
workflow graph umi molecular alignment workflow

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

Path: definitions/subworkflows/molecular_alignment.cwl

Branch/Commit ID: 76a35e7d885790f30559beb31f3b58770e343afd
workflow graph kmer_top_n_extract

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

Path: task_types/tt_kmer_top_n_extract.cwl

Branch/Commit ID: f58bb8121e49a72cf7419a4a38c08f01b931dd37
workflow graph WGS and MT analysis for fastq files

rna / protein - qc, preprocess, filter, annotation, index, abundance

 https://github.com/MG-RAST/pipeline.git

Path: CWL/Workflows/wgs-noscreen-fastq.workflow.cwl

Branch/Commit ID: 6a8727124baf77416ca797982fd4e0689c2a593a
workflow graph cnv_codex

CNV CODEX2 calling

https://gitlab.bsc.es/lrodrig1/structuralvariants_poc.git

Path: structuralvariants/subworkflows/cnv_codex.cwl

Branch/Commit ID: 86f2f3fb64e916607637d93cf6715bab90b1f1d3