Nextflow Registry | nf-core/parsesdrf/convert@0.0.0-4b801f9

nf-core/parsesdrf/convert @ 0.0.0-4b801f9

Convert an SDRF (Sample and Data Relationship Format) file into a pipeline-specific samplesheet/configuration using the parse_sdrf convert-<format> subcommands of the sdrf-pipelines package. The chosen format selects the subcommand; the module owns the output filenames and emits one tuple per supported format (mhcquant, openms, maxquant, msstats, normalyzerde, diann).

sdrf sdrf-pipelines samplesheet proteomics immunopeptidomics mhcquant openms maxquant msstats normalyzerde diann metadata

Latest version: 0.0.0-4b801f9

Total downloads: 0

Source: nf-core/modules

Authors: @jonasscheid

Maintainers: @jonasscheid

Summary

Get started

Add the following snippet to your workflow script to include this module.

include { PARSESDRF_CONVERT } from 'nf-core/parsesdrf/convert'

License

MIT License

Process

`Name`	`PARSESDRF_CONVERT`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample/run information e.g. `[ id:'PXD009752' ]`
`sdrf` file	SDRF file describing the experimental design and sample metadata. `*.{tsv,sdrf.tsv}`
`fasta` file	Protein database FASTA. Required when `format == 'maxquant'` (passed to `-f`); pass `[]` otherwise. `*.{fasta,fa,fasta.gz,fa.gz}`
`raw_folder` string	Directory prefix embedded as a literal string into the `<filePaths>` block of the generated MaxQuant `mqpar.xml`; must resolve on the host that later runs MaxQuant. Required when `format == 'maxquant'`; pass `''` otherwise.

`format` string	Target converter. One of: `mhcquant`, `openms`, `maxquant`, `msstats`, `normalyzerde`, `diann`. Selects the `parse_sdrf convert-<format>` subcommand.

Output 7 channels

#1 diann tuple

`meta` map	Groovy Map containing sample/run information
`${prefix}.cfg` file	DIA-NN config (renamed from `diann_config.cfg`). `*.cfg`
`${prefix}_design.tsv` file	DIA-NN experimental design TSV (renamed from `diann_design.tsv`). `*_design.tsv`

#2 openms tuple

`meta` map	Groovy Map containing sample/run information
`${prefix}_samplesheet.tsv` file	OpenMS samplesheet TSV (renamed from `openms.tsv`). `*_samplesheet.tsv`
`${prefix}_experimental_design.tsv` file	OpenMS experimental design TSV. `*_experimental_design.tsv`

#3 msstats tuple

`meta` map	Groovy Map containing sample/run information
`${prefix}.csv` file	MSstats annotation CSV (`-o`). `*.csv`

#4 maxquant tuple

`meta` map	Groovy Map containing sample/run information
`${prefix}.xml` file	MaxQuant `mqpar.xml` (`-o1`). `*.xml`
`${prefix}_design.txt` file	MaxQuant experimental design TXT (`-o2`). `*_design.txt`

#5 mhcquant tuple

`meta` map	Groovy Map containing sample/run information
`${prefix}_samplesheet.tsv` file	MHCquant samplesheet TSV (`-os`). `*_samplesheet.tsv`
`${prefix}_presets.tsv` file	MHCquant search-preset TSV (`-op`). `*_presets.tsv`

#6 normalyzerde tuple

`meta` map	Groovy Map containing sample/run information
`${prefix}_design.csv` file	NormalyzerDE design CSV (`-o`). `*_design.csv`
`${prefix}_comparisons.csv` file	NormalyzerDE comparisons CSV (`-oc`). `*_comparisons.csv`

#7 versions_sdrfpipelines tuple

`${task.process}` string