Explore Workflows

https://github.com/NAL-i5K/Organism_Onboarding.git

Path: CreateSymlink-workflow.cwl

Branch/Commit ID: 096a9feffe292a1aeb329552661d27bb579e084c

Outputs a message using echo

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

Path: tests/wf/hello-workflow.cwl

Branch/Commit ID: 83038feb2a6fc3bab952e1ecc2a11bfbc8c557b4

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

Path: task_types/tt_kmer_top_n_extract.cwl

Branch/Commit ID: 7f9cfcbda5998b164bd1d8f1f6006aefda0f47f3

This workflow indexes the input reference FASTA with bwa, and generates faidx and dict file using samtools. This index sample can then be used as input into the germline variant calling workflow, or others that may include this workflow as an upstream source. ### __Inputs__ - FASTA file of the reference genome that will be indexed. ### __Outputs__ - Directory containing the original FASTA, faidx, dict, and bwa index files. - stdout log file (output in Overview tab as well) - stderr log file ### __Data Analysis Steps__ 1. cwl calls dockercontainer robertplayer/scidap-gatk4 to index reference FASTA with bwa, and generates faidx and dict files using samtools ### __References__ - Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 25(14), 1754–1760.

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

Path: workflows/bwa-index.cwl

Branch/Commit ID: 22880e0f41d0420a17d643e8a6e8ee18165bbfbf

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

Path: task_types/tt_hmmsearch_wnode.cwl

Branch/Commit ID: ac387721a55fd91df3dcdf16e199354618b136d1

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf4.cwl

Branch/Commit ID: 2ae8117360a3cd4909d9d3f2b35c30bfffb25d0a

Packed ID: main

Note: should be updated 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-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 file 2. Use STAR to align reads from input FASTQ file according to the predefined reference indices; generate unsorted BAM file and alignment statistics file 3. Use fastx_quality_stats to analyze input FASTQ file and generate quality statistics file 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 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/trim-rnaseq-se-dutp.cwl

Branch/Commit ID: 36fd18f11e939d3908b1eca8d2939402f7a99b0f

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf1.cwl

Branch/Commit ID: 2ae8117360a3cd4909d9d3f2b35c30bfffb25d0a

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

Path: definitions/pipelines/gathered_cle_aml_trio.cwl

Branch/Commit ID: 4bc0a4577d626b65a4b44683e5a1ab2f7d7faf4c

Workflow runs [Bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016) to build indices for reference genome provided in a single FASTA file as fasta_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/bowtie-index.cwl

Branch/Commit ID: c0ca7b140d776eec223ceb1c620eda17281860c4