Explore Workflows

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

Path: tests/wf/count-lines1-wf.cwl

Branch/Commit ID: 3ed10d0ea7ac57550433a89a92bdbe756bdb0e40

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

Path: task_types/tt_ani_top_n.cwl

Branch/Commit ID: f390475a4e0898d4933f0a28dae278aa35803eb1

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

Path: tests/wf-loadContents.cwl

Branch/Commit ID: e515226f8ac0f7985cd94dae4a301150adae3050

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: c0ca7b140d776eec223ceb1c620eda17281860c4

ChIP-seq - Quantification - samples: treatment

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

Path: v1.0/ChIP-seq_pipeline/05-quantification.cwl

Branch/Commit ID: c50b80e9b0eaaf4613f9feca44b3463bbfd288d5

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

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

Branch/Commit ID: 1eb6bfe3c77aebaf69453a669d21ae7a5a78056f

Packed ID: main

This workflow downloads the user-selected pre-built kraken2 database from: https://benlangmead.github.io/aws-indexes/k2 ### __Inputs__ Select a pre-built Kraken2 database to download and use for metagenomic classification: - Available options comprised of various combinations of RefSeq reference genome sets: - [Viral (0.5 GB)](https://genome-idx.s3.amazonaws.com/kraken/k2_viral_20221209.tar.gz), all refseq viral genomes - [MinusB (8.7 GB)](https://genome-idx.s3.amazonaws.com/kraken/k2_minusb_20221209.tar.gz), standard minus bacteria (archaea, viral, plasmid, human1, UniVec_Core) - [PlusPFP-16 (15.0 GB)](https://genome-idx.s3.amazonaws.com/kraken/k2_pluspfp_16gb_20221209.tar.gz), standard (archaea, bacteria, viral, plasmid, human1, UniVec_Core) + (protozoa, fungi & plant) capped at 16 GB (shrunk via random kmer downselect) - [EuPathDB46 (34.1 GB)](https://genome-idx.s3.amazonaws.com/kraken/k2_eupathdb48_20201113.tar.gz), eukaryotic pathogen genomes with contaminants removed (https://veupathdb.org/veupathdb/app) - [16S_gg_13_5 (73 MB)](https://genome-idx.s3.amazonaws.com/kraken/16S_Greengenes13.5_20200326.tgz), Greengenes 16S rRNA database ([release 13.5](https://greengenes.secondgenome.com/?prefix=downloads/greengenes_database/gg_13_5/), 20200326)\n - [16S_silva_138 (112 MB)](https://genome-idx.s3.amazonaws.com/kraken/16S_Silva138_20200326.tgz), SILVA 16S rRNA database ([release 138.1](https://www.arb-silva.de/documentation/release-1381/), 20200827) ### __Outputs__ - k2db, an upstream database used by kraken2 classification tool - compressed_k2db_tar, compressed and tarred kraken2 database directory file for download and use outside of scidap ### __Data Analysis Steps__ 1. download selected pre-built kraken2 database. 2. make available as upstream source for kraken2 metagenomic taxonomic classification. ### __References__ - Wood, D.E., Lu, J. & Langmead, B. Improved metagenomic analysis with Kraken 2. Genome Biol 20, 257 (2019). https://doi.org/10.1186/s13059-019-1891-0

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

Path: workflows/kraken2-databases.cwl

Branch/Commit ID: b4d578c2ba4713a5a22163d9f8c7105acda1f22e

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

Path: task_types/tt_hmmsearch_wnode.cwl

Branch/Commit ID: 1e16653514fd5629a704516eb447043c9fd0a53b

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

Path: bacterial_noncoding/wf_gcmsearch.cwl

Branch/Commit ID: 1e16653514fd5629a704516eb447043c9fd0a53b

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

Path: tests/wf/scatter2.cwl

Branch/Commit ID: a67c898958f6affc8cb9de05fe87c9228a4fc63e