Explore Workflows

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

Path: task_types/tt_kmer_build_tree.cwl

Branch/Commit ID: ef266744578e2dcbce57c110c6fa3b9eee91e316

run diamond on mutlple DBs and merge-sort results

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

Path: CWL/Workflows/protein-diamond.workflow.cwl

Branch/Commit ID: 091374dc59a23966338638a668ae397d4ee20b2f

https://github.com/uc-cdis/genomel_pipelines.git

Path: genomel/cwl/workflows/variant_calling/aws_freebayes.cwl

Branch/Commit ID: 7504ead048c3acd64b9b92e44d044d558cb696f2

Motif Finding with HOMER with custom background regions --------------------------------------------------- HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. For more information please refer to: ------------------------------------- [Official documentation](http://homer.ucsd.edu/homer/motif/)

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

Path: workflows/homer-motif-analysis-bg.cwl

Branch/Commit ID: 935a78f1aff757f977de4e3672aefead3b23606b

Cell Ranger Aggregate =====================

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

Path: workflows/cellranger-aggr.cwl

Branch/Commit ID: 1a46cb0e8f973481fe5ae3ae6188a41622c8532e

The 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.cwl

Branch/Commit ID: 9850a859de1f42d3d252c50e15701928856fe774

RNA-seq 02 trimming - reads: SE

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

Path: v1.0/RNA-seq_pipeline/02-trim-se.cwl

Branch/Commit ID: 8aabde14169421a7115c5cd48c4740b3a7bd818f

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

Path: task_types/tt_kmer_cache_retrieve.cwl

Branch/Commit ID: 4533a5e930305c674057bc4cf5dda4f39d39b5df

This workflow compute library complexity

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

Path: workflows/File-formats/bedtools-bam-pbc.cwl

Branch/Commit ID: dde32ff6c8e653a4e6b93316f28737706d5ec367

Creates indices for: * [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886) * [bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016) It performs the following steps: 1. `STAR --runMode genomeGenerate` to generate indices, based on [FASTA](http://zhanglab.ccmb.med.umich.edu/FASTA/) and [GTF](http://mblab.wustl.edu/GTF2.html) input files, returns results as an array of files 2. Outputs indices as [Direcotry](http://www.commonwl.org/v1.0/CommandLineTool.html#Directory) data type 3. Separates *chrNameLength.txt* file from Directory output 4. `bowtie-build` to generate indices requires genome [FASTA](http://zhanglab.ccmb.med.umich.edu/FASTA/) file as input, returns results as a group of main and secondary files

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

Path: workflows/genome-indices.cwl

Branch/Commit ID: 935a78f1aff757f977de4e3672aefead3b23606b