nf-sourmash

Nextflow workflow running sourmash

Inputs

--samplesheet

Simple CSV with columns sample and file. Everything in the file column should be a FASTQ. All of the FASTQ files with the same sample label will be combined.

--k

Value of k used for sketching the input data.

The value of k must match the database used

--db

Database file used for searching

--tax_db

Taxonomy database -- can be compiled from CSV with (docs):

sourmash tax prepare --taxonomy file1.csv file2.csv -o tax.db

--output

Folder for all output files. Example structure:

output
├── [ 128]  gather
│   ├── [9.9K]  SRR8859675_1.gather.csv
│   └── [9.9K]  SRR8859675_2.gather.csv
├── [ 288]  logs
│   ├── [2.1K]  SRR8859675_1.gather.log
│   ├── [7.9K]  SRR8859675_1.sketch.log
│   ├── [4.2K]  SRR8859675_1.tax.metagenome.log
│   ├── [2.1K]  SRR8859675_2.gather.log
│   ├── [7.9K]  SRR8859675_2.sketch.log
│   ├── [4.2K]  SRR8859675_2.tax.metagenome.log
│   └── [4.9K]  all.tax.metagenome.log
├── [ 128]  matches
│   ├── [423K]  SRR8859675_1.matches.zip
│   └── [423K]  SRR8859675_2.matches.zip
├── [ 128]  sketch
│   ├── [1.3M]  SRR8859675_1.sig.gz
│   └── [1.5M]  SRR8859675_2.sig.gz
└── [ 832]  tax_metagenome
    ├── [ 631]  SRR8859675_1.tax.metagenome.class.krona.tsv
    ├── [ 942]  SRR8859675_1.tax.metagenome.family.krona.tsv
    ├── [1.4K]  SRR8859675_1.tax.metagenome.genus.krona.tsv
    ├── [2.5K]  SRR8859675_1.tax.metagenome.human.txt
    ├── [2.3K]  SRR8859675_1.tax.metagenome.kreport.txt
    ├── [ 788]  SRR8859675_1.tax.metagenome.order.krona.tsv
    ├── [ 436]  SRR8859675_1.tax.metagenome.phylum.krona.tsv
    ├── [2.4K]  SRR8859675_1.tax.metagenome.species.krona.tsv
    ├── [ 13K]  SRR8859675_1.tax.metagenome.summarized.csv
    ├── [ 632]  SRR8859675_2.tax.metagenome.class.krona.tsv
    ├── [ 943]  SRR8859675_2.tax.metagenome.family.krona.tsv
    ├── [1.4K]  SRR8859675_2.tax.metagenome.genus.krona.tsv
    ├── [2.5K]  SRR8859675_2.tax.metagenome.human.txt
    ├── [2.3K]  SRR8859675_2.tax.metagenome.kreport.txt
    ├── [ 789]  SRR8859675_2.tax.metagenome.order.krona.tsv
    ├── [ 438]  SRR8859675_2.tax.metagenome.phylum.krona.tsv
    ├── [2.4K]  SRR8859675_2.tax.metagenome.species.krona.tsv
    ├── [ 13K]  SRR8859675_2.tax.metagenome.summarized.csv
    ├── [ 796]  all.tax.metagenome.class.lineage_summary.tsv
    ├── [1.0K]  all.tax.metagenome.family.lineage_summary.tsv
    ├── [1.6K]  all.tax.metagenome.genus.lineage_summary.tsv
    ├── [ 934]  all.tax.metagenome.order.lineage_summary.tsv
    ├── [ 598]  all.tax.metagenome.phylum.lineage_summary.tsv
    └── [2.7K]  all.tax.metagenome.species.lineage_summary.tsv

--container

Docker container used to run the commands in the workflow.

Default: quay.io/biocontainers/sourmash:4.8.4--hdfd78af_0

--threshold_bp

Minimum number of basepairs required for a match (default: 50000)

--ranks

Taxonomic ranks over which results will be summarized.

Default: phylum class order family genus species strain