taf-csvtk

taf-csvtk packages csvtk 0.37.0-r1, a fast command-line toolkit for reproducible CSV/TSV table processing.

Package identity:

• name: csvtk
• command: taf-csvtk
• kind: tool
• TAFFISH version: 0.37.0-r1
• container image: ghcr.io/taffish/csvtk:0.37.0-r1
• upstream release: v0.37.0
• runtime version string: csvtk v0.37.0
• upstream license: MIT
• Linux amd64 archive SHA256: f6d09493b7ad1ba8c5ee79e6904de9499f7411ca97fcfcd8cf6b816e9c967411
• Linux arm64 archive SHA256: 7f481b8ee1948b14c3d7a1c9c6c8cdf36d3f537c5a51f07af7f243e4ee31b708

What Is Included

This app installs the official upstream static Linux binary for the target container architecture. csvtk itself is a single executable and does not require external databases, models, interpreters, or office suites for its ordinary command-line operation.

csvtk supports common table work including:

• inspecting headers and dimensions with headers, dim, nrow, and ncol
• summary statistics with summary and correlation with corr
• format conversion with csv2tab, tab2csv, csv2json, csv2md, csv2rst, csv2xlsx, and xlsx2csv
• row and field operations with cut, grep, filter, filter2, uniq, freq, inter, join, sample, and concat
• table editing with fix, fix-quotes, add-header, rename, replace, round, mutate, and related commands
• reshaping with transpose, sep, gather, spread, unfold, and fold
• sorting and shuffling with sort and shuf
• common upstream plot subcommands through csvtk plot
• compressed input/output including gzip, xz, zstd, bzip2, and LZ4 where supported by upstream csvtk

Command Mode

taf-csvtk --help prints this TAFFISH app help. Use -- only when passing option-leading arguments to the default upstream command:

taf-csvtk -- --help

csvtk is a subcommand-based CLI. Because this TAFFISH app keeps command_mode = true, use the upstream executable name when running csvtk subcommands:

taf-csvtk csvtk --version
taf-csvtk csvtk dim table.csv
taf-csvtk csvtk summary -f count:sum -g group table.csv
taf-csvtk csvtk join -f id samples.csv values.csv > joined.csv

Avoid ambiguous forms such as taf-csvtk cut -f sample table.csv; TAFFISH may treat cut as a container command rather than as csvtk cut.

Common Workflows

Inspect dimensions and headers:

taf-csvtk csvtk dim table.csv
taf-csvtk csvtk headers table.csv

Convert between CSV and TSV:

taf-csvtk csvtk csv2tab table.csv > table.tsv
taf-csvtk csvtk -t tab2csv table.tsv > table.csv

Select columns and filter rows:

taf-csvtk csvtk cut -f sample,count table.csv > selected.csv
taf-csvtk csvtk filter2 -f '$count >= 10' table.csv > filtered.csv

Summarize by group:

taf-csvtk csvtk summary -f count:sum,count:mean -g group table.csv > summary.csv

Join two tables:

taf-csvtk csvtk join -f id samples.csv values.csv > joined.csv

Convert to and from XLSX:

taf-csvtk csvtk csv2xlsx table.csv -o table.xlsx
taf-csvtk csvtk xlsx2csv table.xlsx > table.csv

Use compressed streams:

taf-csvtk csvtk cat table.csv -o table.csv.lz4
taf-csvtk csvtk headers table.csv.lz4

Boundaries

This app exposes the upstream csvtk executable and its built-in subcommands. It does not bundle spreadsheet GUI tools, office suites, database servers, R/Python notebook environments, or tutorial datasets.

The upstream plot command group is included because it is part of csvtk. The normal smoke tests focus on table inspection, filtering, summary, joining, conversion, XLSX, compression, help, and version paths; they do not exhaustively validate every plot style or every subcommand combination.

The upstream version subcommand is documented as checking for updates. For offline validation and smoke tests, this app uses the global csvtk --version output instead of invoking update-checking behavior.

Platform

The image uses official upstream static Linux binaries and is intended for native linux/amd64 and linux/arm64 container platforms.

License Boundary

The TAFFISH app packaging files are licensed under Apache-2.0. The packaged upstream csvtk software is covered by: MIT. Bundled third-party components, datasets, models, and external resources keep their own license terms.

Upstream

• Upstream repository: https://github.com/shenwei356/csvtk
• Upstream documentation: https://bioinf.shenwei.me/csvtk/
• Upstream usage: https://bioinf.shenwei.me/csvtk/usage/
• Upstream release: https://github.com/shenwei356/csvtk/releases/tag/v0.37.0
• Upstream license: MIT

No dedicated csvtk paper was found in the upstream README at packaging time. Cite the upstream project, version, and documentation URL when reporting workflows that depend on csvtk.