modules/duckdb_table2parquet

Convert a delimited text table (CSV or TSV, gzipped or not) to Parquet. DuckDB types each column from the first 20480 rows and reads only the empty string as missing. Pass read_csv options through ext.args, for example nullstr=['NA',''] for tables written by R.

parquetcsvtsvconversion

https://github.com/nf-core/modules/[...]/modules/nf-core/duckdb/table2parquet

Description

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`table`
`:file`

A delimited text table to convert. The delimiter is picked from the filename – .tsv/.tsv.gz/.tsv.zst for tab, .csv/.csv.gz/.csv.zst for comma; any other suffix is an error.

*.{csv,csv.gz,csv.zst,tsv,tsv.gz,tsv.zst}

Output

name:type

description

pattern

`parquet`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:'sample1' ]

`*.parquet`
`:file`

The input table, converted to Parquet

*.parquet

`versions_duckdb`

`${task.process}`
`:string`

The name of the process

`duckdb`
`:string`

The name of the tool

`duckdb --version | sed 's/^v//; s/ .*//'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`duckdb`
`:string`

The name of the tool

`duckdb --version | sed 's/^v//; s/ .*//'`
`:eval`

The expression to obtain the version of the tool

Tools

duckdb
MIT

An in-process SQL OLAP database management system

duckdb.org duckdb.org/docs https://github.com/duckdb/duckdb

modules/duckdb_table2parquet

Description

Input

`meta`
`:map`

`table`
`:file`

Output

`parquet`

`meta`
`:map`

`*.parquet`
`:file`

`versions_duckdb`

`${task.process}`
`:string`

`duckdb`
`:string`

`duckdb --version | sed 's/^v//; s/ .*//'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`duckdb`
`:string`

`duckdb --version | sed 's/^v//; s/ .*//'`
`:eval`

Tools

duckdb
MIT

included in

maintainer

get in touch

modules/duckdb_table2parquet

Description

Input

meta :map

table :file

Output

parquet

meta :map

*.parquet :file

versions_duckdb

${task.process} :string

duckdb :string

duckdb --version | sed 's/^v//; s/ .*//' :eval

Topics

versions

${task.process} :string

duckdb :string

duckdb --version | sed 's/^v//; s/ .*//' :eval

Tools

duckdbMIT

included in

maintainer

get in touch

`meta`
`:map`

`table`
`:file`

`parquet`

`meta`
`:map`

`*.parquet`
`:file`

`versions_duckdb`

`${task.process}`
`:string`

`duckdb`
`:string`

`duckdb --version | sed 's/^v//; s/ .*//'`
`:eval`

`versions`

`${task.process}`
`:string`

`duckdb`
`:string`

`duckdb --version | sed 's/^v//; s/ .*//'`
`:eval`

duckdb
MIT