Explore Workflows

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

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

Path: definitions/subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl

Branch/Commit ID: 22fce2dbdada0c4135b6f0677f78535cf980cb07

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

Path: definitions/subworkflows/germline_filter_vcf.cwl

Branch/Commit ID: 6d03a918639a69ddf6a7b93fe9f72128ef37edc3

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

Path: definitions/subworkflows/gatk_haplotypecaller_iterator.cwl

Branch/Commit ID: 6d03a918639a69ddf6a7b93fe9f72128ef37edc3

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

Path: definitions/subworkflows/bgzip_and_index.cwl

Branch/Commit ID: da335d9963418f7bedd84cb2791a0df1b3165ffe

\"foldseek easy-search sub-workflow for plant2human workflow Step 1: listing files Step 2: foldseek easy-search process\"

https://github.com/yonesora56/plant2human.git

Path: Workflow/10_foldseek_easy_search_wf.cwl

Branch/Commit ID: 11b46d8d8c0db462edbd2657fc62cf31bc93ecee

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

Path: testdata/record-output-wf_v1_1.cwl

Branch/Commit ID: 7af75226f084349e401b1114f25bdcdee060e127