Explore Workflows

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

Graph Name Retrieved From View
workflow graph Tumor-Only Detect Variants workflow

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

Path: definitions/pipelines/tumor_only_detect_variants.cwl

Branch/Commit ID: a59a803e1809a8fbfabca6b8962a8ad66dd01f1d
workflow graph Bacterial Annotation, pass 3, structural annotation, functional annotation: ab initio GeneMark, by WP, by HMM (second pass)

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

Path: bacterial_annot/wf_bacterial_annot_pass3.cwl

Branch/Commit ID: 807fe40bca1fbd18ede6250851b9f71de98da69b
workflow graph Subworkflow to allow calling cnvkit with cram instead of bam files

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

Path: definitions/subworkflows/cram_to_cnvkit.cwl

Branch/Commit ID: 18600518ce6539a2e29c1707392a4c5da5687fa3
workflow graph Align reference proteins plane complete workflow

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

Path: protein_alignment/wf_protein_alignment.cwl

Branch/Commit ID: 41d14ec5e2dfa0fac7eebeefda1f26ccea14c9a0
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: 3a311af320e65271f3efb4f27a6ed10aa5d50a0e
workflow graph checkm

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

Path: checkm/wf_checkm.cwl

Branch/Commit ID: c64599f5db2437f9323d41cc3d8d9efb20a2667e
workflow graph exome alignment and somatic variant detection

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

Path: definitions/pipelines/somatic_exome_mouse.cwl

Branch/Commit ID: 22fce2dbdada0c4135b6f0677f78535cf980cb07
workflow graph varscan somatic workflow

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

Path: definitions/subworkflows/varscan.cwl

Branch/Commit ID: 1437aed13d240fd624f78df2c7efb096c5079d73
workflow graph env-wf1.cwl

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

Path: cwltool/schemas/v1.0/v1.0/env-wf1.cwl

Branch/Commit ID: c6cced7a2e6389d2eb43342e702677ccb7c7497c
workflow graph cache_asnb_entries

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

Path: task_types/tt_cache_asnb_entries.cwl

Branch/Commit ID: 72804b6506c9f54ec75627f82aafe6a28d7a49fa