Explore Workflows

Water bodies detection based on NDWI and otsu threshold applied to a single Sentinel-2 COG STAC item

https://github.com/eoap/quickwin.git

Path: cwl-workflow/app-water-body-cloud-native.cwl

Branch/Commit ID: a7d87a9978b546cbc708bf2792edeea9945d0033

Packed ID: main

https://github.com/nigyta/bact_genome.git

Path: cwl/workflow/dfastqc-filelist-outputdir.cwl

Branch/Commit ID: e316f37f502005165ebd7f22b5257900c7c712ac

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

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl

Branch/Commit ID: 0db1a5f1ceedd4416ac550787c27b99c87dbe985

https://github.com/common-workflow-language/cwl-v1.1.git

Path: tests/scatter-valuefrom-wf3.cwl

Branch/Commit ID: 3e90671b25f7840ef2926ad2bacbf447772dda94

Packed ID: main

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

Path: tests/env-wf2.cwl

Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **paired-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 paired-end RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ files according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ files and generate quality statistics files 3. Use samtools sort to generate coordinate sorted BAM(+BAI) file pair from the unsorted BAM file obtained on the step 1 (after running STAR) 4. Generate BigWig file on the base of sorted BAM file 5. Map input FASTQ files to predefined rRNA reference indices using Bowtie to define the level of rRNA contamination; export resulted statistics to file 6. 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-pe.cwl

Branch/Commit ID: 261c0232a7a40880f2480b811ed2d7e89c463869

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

Path: tests/scatter-valuefrom-wf4.cwl

Branch/Commit ID: 57baec040c99d7edef8242ef51b5470b1c82d733

Packed ID: main

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

Path: definitions/pipelines/somatic_exome_cle_gathered.cwl

Branch/Commit ID: 9cbf2a483e1b9e4cdb8e2564be27a9e64fc1169e

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: 42dc4f70b117e78785b82865ec4c4b941ac1c259

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

Path: protein_alignment/wf_protein_alignment.cwl

Branch/Commit ID: 551493f5c24b757a46cd22821a05e6ac6dcceb7f