Propr propr (#4817)

* 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

modules/nf-core/propr/propr/environment.yml

@@ -0,0 +1,7 @@
+name: propr_propr
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - conda-forge::r-propr=5.0.3

modules/nf-core/propr/propr/main.nf

@@ -0,0 +1,25 @@
+process PROPR_PROPR {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${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' }"
+
+    input:
+    tuple val(meta), path(count)
+
+    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
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    template 'propr.R'
+}

modules/nf-core/propr/propr/meta.yml

@@ -0,0 +1,72 @@
+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
+
+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"]
+
+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}"
+
+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"
+
+authors:
+  - "@suzannejin"