csvtk_join

Tags: utility table join merge csv tsv csvtk relational run-scope

Join two CSV or TSV files based on common fields.

Uses csvtk join to merge two tabular files horizontally by matching values in a specified key column (similar to a SQL JOIN). It supports inner, left, right, and outer joins via optional arguments.

Inputs

record (
    meta: Record,
    csv1: Path,
    csv2: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
csv1	Path	The first CSV/TSV file (Left table)
csv2	Path	The second CSV/TSV file (Right table)

in_format: String
out_format: String
key: String

Name	Type	Description
in_format	String	Input format string ('csv', 'tsv', or a specific delimiter character)
out_format	String	Output format string ('csv', 'tsv', or a specific delimiter character)
key	String	The column name(s) or index(es) to use as the join key (e.g., "sample_id" or "1")

Outputs

record (
    meta: Record,
    csv: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
csv	Path	The joined tabular file (*.csv or *.tsv)
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

Used By

Subworkflows

• teton - Perform taxonomic classification and estimate bacterial genome sizes.

Workflows

• teton - Taxonomic classification and abundance profiling of metagenomic reads.

Citations

If you use this in your analysis, please cite the following.

• Bactopia
  Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020)

• csvtk
  Shen, W csvtk: A cross-platform, efficient and practical CSV/TSV toolkit in Golang. (GitHub)

Source

View source on GitHub

Version

CSVTK_JOIN:
    - csvtk: 0.31.0