Explore Workflows

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

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

Path: tests/wf/811-12.cwl

Branch/Commit ID: a67c898958f6affc8cb9de05fe87c9228a4fc63e

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

Path: tests/wf/scatterfail.cwl

Branch/Commit ID: a67c898958f6affc8cb9de05fe87c9228a4fc63e

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

Path: bacterial_annot/wf_bacterial_annot_pass4.cwl

Branch/Commit ID: 1e16653514fd5629a704516eb447043c9fd0a53b

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

Path: tests/wf/paramref_arguments_self.cwl

Branch/Commit ID: a67c898958f6affc8cb9de05fe87c9228a4fc63e

Wrapped in a workflow SoupX tool for easy access to Cell Ranger pipeline compressed outputs.

https://github.com/Barski-lab/workflows.git

Path: tools/soupx-subworkflow.cwl

Branch/Commit ID: 9a03dbe8829ca649814d9c8bd11fe3a673750a95