Explore Workflows

Input is a fasta file with n>1 samples, with sample id as sequence identifier prefix, and a sample id file. The workflow calls open reference otus and assigns taxa using greengenes. The output are taxa plots.

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

Path: CWL/Workflows/qiime/OPENrefcluster2plot.cwl

Branch/Commit ID: b8c2be41cd8805023a0d9e5916042b2557205d03

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

Path: task_types/tt_kmer_cache_store.cwl

Branch/Commit ID: 7e875f77b615b4f7ebfb23a1da30eb216cc52919

Workflow runs [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886) to build indices for reference genome provided in a single FASTA file as fasta_file input and GTF annotation file from annotation_gtf_file input. Generated indices are saved in a folder with the name that corresponds to the input genome.

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

Path: workflows/star-index.cwl

Branch/Commit ID: ebbf23764ede324cabc064bd50647c1f643726fa

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

Path: definitions/subworkflows/germline_filter_vcf.cwl

Branch/Commit ID: b7d9ace34664d3cedb16f2512c8a6dc6debfc8ca

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

Path: tests/wf/conditional_step_no_inputs.cwl

Branch/Commit ID: 2dce710246e091f0189fab41b589ee062ee94500

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

Path: tests/wf/cache_test_workflow.cwl

Branch/Commit ID: 2dce710246e091f0189fab41b589ee062ee94500

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: 664de58d95728edbf7d369d894f9037ebe2475fa

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

Path: tests/count-lines13-wf.cwl

Branch/Commit ID: 664835e83eb5e57eee18a04ce7b05fb9d70d77b7

The original [BioWardrobe's](https://biowardrobe.com) [PubMed ID:26248465](https://www.ncbi.nlm.nih.gov/pubmed/26248465) **RNA-Seq** basic analysis for a **single-read** 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-read RNA-Seq data. It performs the following steps: 1. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 2. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 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) 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.cwl

Branch/Commit ID: 12c29f88855329192bfff977f046990031f04931

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

Path: definitions/subworkflows/bisulfite_qc.cwl

Branch/Commit ID: 22fce2dbdada0c4135b6f0677f78535cf980cb07