Explore Workflows

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

Path: v1.0/v1.0/search.cwl

Branch/Commit ID: 4fd45edb9531a03223c18a586e32d0baf0d5acb2

Packed ID: main

Runs ChIP-Seq BioWardrobe basic analysis with single-end data file.

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

Path: workflows/chipseq-se.cwl

Branch/Commit ID: ca2dbb71d0537b1d93a8bd44719250cf8949b157

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

Path: tests/io-any-wf-1.cwl

Branch/Commit ID: 664835e83eb5e57eee18a04ce7b05fb9d70d77b7

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

Path: task_types/tt_format_rrnas_from_seq_entry.cwl

Branch/Commit ID: 6d04f5d65d1d4893706d9ae7e27341633333054f

This workflow taxonomically classifies paired-end sequencing reads in FASTQ format, that have been optionally adapter trimmed with trimgalore, using Kraken2 and a user-selected pre-built database from a list of [genomic index files](https://benlangmead.github.io/aws-indexes/k2). ### __Inputs__ Kraken2 database for taxonomic classification: - [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) Read 1 file: - FASTA/Q input R1 from a paired end library Read 2 file: - FASTA/Q input R2 from a paired end library Number of threads for steps that support multithreading: - Number of threads for steps that support multithreading - default set to `4` Advanced Inputs Tab (Optional): - Number of bases to clip from the 3p end - Number of bases to clip from the 5p end ### __Outputs__ - k2db, an upstream database used by kraken2 classifier ### __Data Analysis Steps__ 1. Trimming the adapters with TrimGalore. - This step is particularly important when the reads are long and the fragments are short - resulting in sequencing adapters at the ends of reads. If adapter is not removed the read will not map. TrimGalore can recognize standard adapters, such as Illumina or Nextera/Tn5 adapters. 2. Generate quality control statistics of trimmed, unmapped sequence data 3. (Optional) Clipping of 5' and/or 3' end by the specified number of bases. 4. Mapping reads to primary genome index with Bowtie. ### __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-classify-pe.cwl

Branch/Commit ID: 7030da528559c7106d156284e50ff0ecedab0c4e

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

Path: cwltool/schemas/v1.0/v1.0/iwdr_with_nested_dirs.cwl

Branch/Commit ID: 7dec97bb8f0bc2d9e9eb710faf41f2e98cc7cdda

https://github.com/bespin-workflows/exomeseq-gatk4.git

Path: subworkflows/exomeseq-gatk4-00-prepare-reference-data.cwl

Branch/Commit ID: 5438ab97697f9a9b246719302bedc79f305a98f5

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

Path: testdata/js-expr-req-wf.cwl

Branch/Commit ID: 7af75226f084349e401b1114f25bdcdee060e127

Packed ID: wf

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

Path: task_types/tt_bact_get_kmer_reference.cwl

Branch/Commit ID: 4a44218a713aecc488359be275409414ae8c1434

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

Path: tests/echo-wf-default.cwl

Branch/Commit ID: 664835e83eb5e57eee18a04ce7b05fb9d70d77b7