Explore Workflows

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

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

Branch/Commit ID: 49cd284a8fc7884de763573075d3e1d6a4c1ffdd

Packed ID: main

https://github.com/apaul7/cancer-genomics-workflow.git

Path: definitions/pipelines/chipseq.cwl

Branch/Commit ID: bfcb5ffbea3d00a38cc03595d41e53ea976d599d

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

Path: definitions/pipelines/exome_alignment.cwl

Branch/Commit ID: ec45fad68ca10fb64d5c58e704991b146dc31d28

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

Path: cwltool/schemas/v1.0/v1.0/conflict-wf.cwl

Branch/Commit ID: a858bb4db58ef2df17b4856294ad7904643c5c6e

Packed ID: collision

This workflow taxonomically classifies paired-end sequencing reads in FASTQ format for a SINGLE sample. Reads are first adapter trimmed with trimgalore and filtered using kneaddata with a bmtagger database. The resulting cleaned reads are classified using Kraken2 and a user-selected pre-built database from a list of [genomic index files](https://benlangmead.github.io/aws-indexes/k2). Unaligned reads are then classified using metaphlan4 with the mpa_vJan21_CHOCOPhlAnSGB_202103 database. The kraken2 report is used to generate a krona plot visualization of the abundance profile. Cleaned reads are also run through HUMANN3 using the uniref90 diamond databaseto produce a gene abundance report and metabolic pathway file. The latter is used for abundance coverage and functional assignment. ### __Inputs__ Kraken2 database for taxonomic classification: - Standard is recommended 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__ - kraken2 report (abundance profile) - krona plot (hierarchical visualization of taxonomic classifications) - various log files - metabolic pathway file - functional assignment ### __Data Analysis Steps__ 1. QC raw FASTQ files with fastQC and trimmomatic - OUTPUT1: trimmed FASTQ files 2. Filter human reads out of OUTPUT1 with the KneadData tool () - OUTPUT2: filtered FASTQ files 3. Classify OUTPUT2 with kraken2 using “Standard” database (Refeq archaea, bacteria, viral, plasmid, human, UniVec_Core) - OUTPUT3: taxonomic abundance profile - OUTPUT4: FASTQ files of unclassified reads - VISUALIZATION1: krakenreport to kronaplot 4. Attempt to classify OUTPUT4 with MetaPhlAn using “latest” database - OUTPUT5: taxonomic abundance profile of unclassified kraken2 reads 5. Classify OUTPUT2 with MetaPhlAn using “latest” database - OUTPUT6: final computed taxon abundances (listed one clade per line, tab-separated from the clade's relative abundance in percent) - format: https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-Workshop-on-Genomics-2023#13-metaphlan-output-files - used in the multi-sample workflow (https://github.com/biobakery/MetaPhlAn/wiki/MetaPhlAn-Workshop-on-Genomics-2023#15-analyzing-multiple-samples) 6. Use OUTPUT2 in Metagenome functional profiling/assignment with HUMAnN using “uniref : uniref90_diamond” database - database link: http://huttenhower.sph.harvard.edu/humann_data/uniprot/uniref_annotated/uniref90_annotated_v201901b_full.tar.gz - OUTPUT7: *_genefamilies.tsv, contains the abundances of each gene family in the community in reads per kilobase (RPK) units - OUTPUT8: *_pathabundance.tsv, lists the abundances of each pathway in the community, also in RPK units as described for gene families - OUTPUT9: normalized_genefamilies-cpm.tsv, contains the normalized abundances of each gene family in counts per million (CPM) units - OUTPUT10: rxn-cpm.tsv, regroup our CPM-normalized gene family abundance values to MetaCyc reaction (RXN) abundances - https://github.com/biobakery/MetaPhlAn/wiki/HUMAnN-Workshop-on-Genomics-2023#3-manipulating-humann-output-tables ### __References__ - McIver LJ, Abu-Ali G, Franzosa EA, Schwager R, Morgan XC, Waldron L, Segata N, Huttenhower C. bioBakery: a meta'omic analysis environment. Bioinformatics. 2018 Apr 1;34(7):1235-1237. PMID: 29194469 - Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999; 27(2):573–580. doi:10.1093/nar/27.2.573 - [**Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4.**](https://doi.org/10.1038/s41587-023-01688-w) Aitor Blanco-Miguez, Francesco Beghini, Fabio Cumbo, Lauren J. McIver, Kelsey N. Thompson, Moreno Zolfo, Paolo Manghi, Leonard Dubois, Kun D. Huang, Andrew Maltez Thomas, Gianmarco Piccinno, Elisa Piperni, Michal Punčochář, Mireia Valles-Colomer, Adrian Tett, Francesca Giordano, Richard Davies, Jonathan Wolf, Sarah E. Berry, Tim D. Spector, Eric A. Franzosa, Edoardo Pasolli, Francesco Asnicar, Curtis Huttenhower, Nicola Segata. Nature Biotechnology (2023)

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

Path: workflows/wgs-metagenomics-pe.cwl

Branch/Commit ID: b4d578c2ba4713a5a22163d9f8c7105acda1f22e

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

Path: testdata/scatter-wf1_v1_1.cwl

Branch/Commit ID: 0ab1d42d10f7311bb4032956c4a6f3d2730d9507

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

Path: definitions/pipelines/germline_wgs.cwl

Branch/Commit ID: 038cb3617a1966a1057386adcde97ce55d9e1139

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

Path: cwltool/schemas/v1.0/v1.0/scatter-valuefrom-wf6.cwl

Branch/Commit ID: 4a31f2a1c1163492ae37bbc748a299e8318c462c

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

Path: definitions/pipelines/tumor_only_detect_variants.cwl

Branch/Commit ID: 5c49c5a53259d4c88a02750f1a16a3c02d711115

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

Path: definitions/subworkflows/varscan_pre_and_post_processing.cwl

Branch/Commit ID: ffab5424bb8b5905aecf6f8e2e6387da7f3df562