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* modified affy/justrma to allow the user get the unlog data when --keep.log2 FALSE * after prettier * trailing whitespace * added final newline * fix issue * updated snapshot * corrected md5sum issues with inconsistent decimals * corrected round matrix method * . * copied pytest_modules.yml * . * updated container version and added reproducible test for fdr
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name: propr_propr | ||
channels: | ||
- conda-forge | ||
- bioconda | ||
- defaults | ||
dependencies: | ||
- conda-forge::r-propr=5.0.3 |
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process PROPR_PROPR { | ||
tag "$meta.id" | ||
label 'process_medium' | ||
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conda "${moduleDir}/environment.yml" | ||
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
'https://depot.galaxyproject.org/singularity/r-propr:5.0.3': | ||
'biocontainers/r-propr:5.0.3' }" | ||
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input: | ||
tuple val(meta), path(count) | ||
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output: | ||
tuple val(meta), path("*.propr.rds"), emit: propr | ||
tuple val(meta), path("*.propr.tsv"), emit: matrix | ||
tuple val(meta), path("*.fdr.tsv"), emit: fdr , optional:true | ||
path "*.R_sessionInfo.log", emit: session_info | ||
path "versions.yml", emit: versions | ||
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when: | ||
task.ext.when == null || task.ext.when | ||
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script: | ||
template 'propr.R' | ||
} |
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name: "propr_propr" | ||
description: | | ||
Perform logratio-based correlation analysis -> get proportionality & basis shrinkage partial correlation coefficients. | ||
One can also compute standard correlation coefficients, if required. | ||
keywords: | ||
- coexpression | ||
- correlation | ||
- proportionality | ||
- logratio | ||
- propr | ||
- corpcor | ||
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tools: | ||
- "propr": | ||
description: "Logratio methods for omics data" | ||
homepage: "https://github.com/tpq/propr" | ||
documentation: "https://rdrr.io/cran/propr/man/propr.html" | ||
tool_dev_url: "https://github.com/tpq/propr" | ||
doi: "10.1038/s41598-017-16520-0" | ||
licence: ["GPL-2"] | ||
- "corpcor": | ||
description: "Efficient Estimation of Covariance and (Partial) Correlation" | ||
homepage: "https://cran.r-project.org/web/packages/corpcor/index.html" | ||
documentation: "https://cran.r-project.org/web/packages/corpcor/corpcor.pdf" | ||
doi: "10.2202/1544-6115.1175" | ||
licence: ["GPL >=3"] | ||
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input: | ||
- meta: | ||
type: map | ||
description: | | ||
Groovy Map containing sample information. | ||
This can be used at the workflow level to pass optional parameters to the module. | ||
[id: 'test', ...] | ||
- count: | ||
type: file | ||
description: | | ||
Count matrix, where rows = variables or genes, columns = samples or cells. | ||
This matrix should not contain zeros. Otherwise, they will be replaced by the minimun number. | ||
It is recommended to handle the zeros beforehand with the method of preference. | ||
pattern: "*.{csv,tsv}" | ||
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output: | ||
- meta: | ||
type: map | ||
description: | | ||
Groovy Map containing sample information. | ||
This can be used at the workflow level to pass optional parameters to the module. | ||
[id: 'test', ...] | ||
- propr: | ||
type: file | ||
description: R propr object | ||
pattern: "*.propr.rds" | ||
- matrix: | ||
type: file | ||
description: Coefficient matrix | ||
pattern: "*.propr.tsv" | ||
- fdr: | ||
type: file | ||
description: (optional) propr fdr table | ||
pattern: "*.fdr.tsv" | ||
- session_info: | ||
type: file | ||
description: dump of R SessionInfo | ||
pattern: "*.R_sessionInfo.log" | ||
- versions: | ||
type: file | ||
description: File containing software versions | ||
pattern: "versions.yml" | ||
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authors: | ||
- "@suzannejin" |
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