Explore Workflows

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

Graph Name Retrieved From View
workflow graph wgs alignment with qc

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

Path: definitions/pipelines/wgs_alignment.cwl

Branch/Commit ID: aba52e94b6d7470132d3c092c26d67e29d615300
workflow graph Trim Galore RNA-Seq pipeline paired-end strand specific

Modified 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-dutp.cwl

Branch/Commit ID: 7eef0294395d83ff0765fce61726a59d71126422
workflow graph Immunotherapy Workflow

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

Path: definitions/pipelines/immuno.cwl

Branch/Commit ID: 00df82a529a58d362158110581e1daa28b4d7ecb
workflow graph allele-process-strain.cwl

https://github.com/Barski-lab/workflows.git

Path: subworkflows/allele-process-strain.cwl

Branch/Commit ID: afbec98437a7796a509fffbad8c3370aa099f059
workflow graph blast_extratc_aligned_seq_ids

This workflow screening a Fasta file and extract aligned reads

 https://github.com/ncbi/cwl-ngs-workflows-cbb.git

Path: workflows/Blast/blast-extratc-aligned-seq-ids.cwl

Branch/Commit ID: 3247592a89deafaa0d9c5910a1cb1d000ef9b098
workflow graph count-lines11-null-step-wf-noET.cwl

https://github.com/common-workflow-language/cwl-v1.2.git

Path: tests/count-lines11-null-step-wf-noET.cwl

Branch/Commit ID: 1f3ef888d9ef2306c828065c460c1800604f0de4
workflow graph kmer_cache_store

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

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: ce433f771ebf5677c9f40858e2ae91b1a7e75d30
workflow graph exomeseq-01-preprocessing.cwl

https://github.com/Duke-GCB/bespin-cwl.git

Path: subworkflows/exomeseq-01-preprocessing.cwl

Branch/Commit ID: cb2c1423d635b2d8527103835b4918ffdf1f5b80
workflow graph rnaseq-pe-dutp.cwl

RNA-Seq basic analysis workflow for strand specific paired-end experiment.

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

Path: workflows/rnaseq-pe-dutp.cwl

Branch/Commit ID: cb5e5b8563be4977e9f2babc14fe084faa234847
workflow graph HS Metrics workflow

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

Path: definitions/subworkflows/hs_metrics.cwl

Branch/Commit ID: 51724b44c96e5fd849ae55b752865b80bc47d66c