feat: Enhanced-volcano (#1521)

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### Description

This PR adds
[EnhancedVolcano](https://bioconductor.org/packages/3.17/bioc/html/EnhancedVolcano.html)
to the list of available wrappers

### QC
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* [x] I confirm that:

For all wrappers added by this PR, 

* there is a test case which covers any introduced changes,
* `input:` and `output:` file paths in the resulting rule can be changed
arbitrarily,
* either the wrapper can only use a single core, or the example rule
contains a `threads: x` statement with `x` being a reasonable default,
* rule names in the test case are in
[snake_case](https://en.wikipedia.org/wiki/Snake_case) and somehow tell
what the rule is about or match the tools purpose or name (e.g.,
`map_reads` for a step that maps reads),
* all `environment.yaml` specifications follow [the respective best
practices](https://stackoverflow.com/a/64594513/2352071),
* wherever possible, command line arguments are inferred and set
automatically (e.g. based on file extensions in `input:` or `output:`),
* all fields of the example rules in the `Snakefile`s and their entries
are explained via comments (`input:`/`output:`/`params:` etc.),
* `stderr` and/or `stdout` are logged correctly (`log:`), depending on
the wrapped tool,
* temporary files are either written to a unique hidden folder in the
working directory, or (better) stored where the Python function
`tempfile.gettempdir()` points to (see
[here](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir);
this also means that using any Python `tempfile` default behavior
works),
* the `meta.yaml` contains a link to the documentation of the respective
tool or command,
* `Snakefile`s pass the linting (`snakemake --lint`),
* `Snakefile`s are formatted with
[snakefmt](https://github.com/snakemake/snakefmt),
* Python wrapper scripts are formatted with
[black](https://black.readthedocs.io).
* Conda environments use a minimal amount of channels, in recommended
ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as
conda-forge should have highest priority and defaults channels are
usually not needed because most packages are in conda-forge nowadays).

---------

Co-authored-by: tdayris <tdayris@gustaveroussy.fr>
Co-authored-by: tdayris <thibault.dayris@gustaveroussy.fr>
Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Co-authored-by: Felix Mölder <felix.moelder@uni-due.de>
Co-authored-by: Christopher Schröder <christopher.schroeder@tu-dortmund.de>

bio/enhancedvolcano/environment.yaml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - bioconductor-enhancedvolcano =1.18.0

bio/enhancedvolcano/meta.yaml

@@ -0,0 +1,16 @@
+name: Enhanced Volcano
+url: https://bioconductor.org/packages/3.17/bioc/html/EnhancedVolcano.html
+authors:
+  - Thibault Dayris
+description: |
+  Build Volcano-plots with EnhancedVolcano
+input:
+  - Path to a TSV/CSV table (separator are inferred from file extension) or a RDS formatted object convertible into a `data.frame`.
+output:
+  - Path to SVG or PNG formatted Volcano plot
+params:
+  - extra: additional parameters besides `toptable`
+  - height: plot default height (in `grDevices::svg`)
+  - width: plot default width (in `grDevices::svg`)
+notes: |
+  * Input table requires at least the following: column for variable names; a column for log2 fold changes; a column for nominal or adjusted p-value.

bio/enhancedvolcano/test/Snakefile

@@ -0,0 +1,46 @@
+rule test_enhanced_volcano_tsv:
+    input:
+        "table.tsv",
+    output:
+        "volcano_tsv.png",
+    threads: 1
+    log:
+        "logs/enhanced-volcano/tsv.log",
+    params:
+        extra="lab='Gene_id', x='ShrinkedFC', y='adjusted_pvalues'",
+        width=1024,  # Optional PNG width
+        height=768,  # Optional PNG height
+    wrapper:
+        "master/bio/enhancedvolcano"
+
+
+rule test_enhanced_volcano_csv:
+    input:
+        "table.csv",
+    output:
+        "volcano_csv.svg",
+    threads: 1
+    log:
+        "logs/enhanced-volcano/csv.log",
+    params:
+        extra="lab='Gene_id', x='ShrinkedFC', y='adjusted_pvalues'",
+        # width=7,  # Optional PNG width
+        # height=7,  # Optional PNG height
+    wrapper:
+        "master/bio/enhancedvolcano"
+
+
+rule test_enhanced_volcano_rds:
+    input:
+        "table.RDS",
+    output:
+        "volcano_rds.svg",
+    threads: 1
+    log:
+        "logs/enhanced-volcano/rds.log",
+    params:
+        extra="lab='Gene_id', x='ShrinkedFC', y='adjusted_pvalues'",
+        # width=7,  # Optional PNG width
+        # height=7,  # Optional PNG height
+    wrapper:
+        "master/bio/enhancedvolcano"

bio/enhancedvolcano/test/table.csv

@@ -0,0 +1,5 @@
+Gene_id,ShrinkedFC,adjusted_pvalues
+G1,12.05,0.006
+G2,0,1
+G3,17,0.7
+G4,0.01,0.003

bio/enhancedvolcano/test/table.tsv

@@ -0,0 +1,5 @@
+Gene_id	ShrinkedFC	adjusted_pvalues
+G1	12.05	0.006
+G2	0	1
+G3	17	0.7
+G4	0.01	0.003

bio/enhancedvolcano/wrapper.R

@@ -0,0 +1,110 @@
+# __author__ = "Thibault Dayris"
+# __copyright__ = "Copyright 2023, Thibault Dayris"
+# __email__ = "thibault.dayris@gustaveroussy.fr"
+# __license__ = "MIT"
+
+# This script builds a Volcano plot from a table or
+# a RDS object that can be casted into a data.frame
+
+# Sink the stderr and stdout to the snakemake log file
+# https://stackoverflow.com/a/48173272
+log.file <- base::file(snakemake@log[[1]], open = "wt")
+base::sink(log.file)
+base::sink(log.file, type = "message")
+
+# Loading Libraries and input data
+base::library(package = "EnhancedVolcano", character.only = TRUE)
+base::message("Library loaded")
+
+save_png <- function(output_path, width, height) {
+  grDevices::png(
+    filename = output_path,
+    width = width,
+    height = height,
+  )
+
+  base::print(base::eval(base::parse(text = cmd)))
+
+  grDevices::dev.off()
+}
+
+save_svg <- function(output_path, width, height) {
+  grDevices::svg(
+    filename = output_path,
+    width = width,
+    height = height
+  )
+
+  base::print(base::eval(base::parse(text = cmd)))
+
+  grDevices::dev.off()
+}
+
+input_path <- base::as.character(x = snakemake@input[[1]])
+toptable <- NULL
+if (base::endsWith(x = input_path, suffix = ".tsv")) {
+  toptable <- utils::read.table(
+    file = input_path,
+    header = TRUE,
+    sep = "\t",
+    stringsAsFactors = FALSE,
+  )
+} else if (base::endsWith(x = input_path, suffix = ".csv")) {
+  toptable <- utils::read.table(
+    file = input_path,
+    header = TRUE,
+    sep = ",",
+    stringsAsFactors = FALSE,
+  )
+} else if (base::endsWith(x = input_path, suffix = ".RDS")) {
+  toptable <- base::readRDS(file = input_path)
+} else {
+  base::stop(
+    "Input file format unknown. Expected either '.tsv', '.csv', or 'RDS'"
+  )
+}
+base::message("Data loaded")
+base::print(toptable)
+
+# Building command line
+extra <- "toptable = toptable"
+if ("extra" %in% base::names(snakemake@params)) {
+  extra <- base::paste(
+    extra,
+    base::as.character(x = snakemake@params[["extra"]]),
+    sep = ","
+  )
+}
+
+width <- 7
+if ("width" %in% base::names(snakemake@params)) {
+  width <- base::as.numeric(x = snakemake@params[["width"]])
+}
+height <- 7
+if ("height" %in% base::names(snakemake@params)) {
+  height <- base::as.numeric(x = snakemake@params[["height"]])
+}
+
+
+cmd <- base::paste0(
+  "EnhancedVolcano::EnhancedVolcano(",
+  extra,
+  ")"
+)
+base::message("Command line: ")
+base::message(cmd)
+
+
+# Run EnhancedVolcano
+outfile <- base::as.character(x = snakemake@output[[1]])
+if (base::endsWith(x = outfile, suffix = ".png")) {
+  save_png(output_path = outfile, width = width, height = height)
+} else {
+  save_svg(output_path = outfile, width = width, height = height)
+}
+base::message("Process over")
+
+# Proper syntax to close the connection for the log file
+# but could be optional for Snakemake wrapper
+base::sink(type = "message")
+base::sink()

test.py

@@ -1181,6 +1181,42 @@ def test_bwa_mapping_meta():
     )
 
 
+@skip_if_not_modified
+def test_enhanced_volcano():
+    run(
+        "bio/enhancedvolcano",
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "--use-conda",
+            "volcano_tsv.png",
+        ],
+    )
+
+    run(
+        "bio/enhancedvolcano",
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "--use-conda",
+            "volcano_csv.svg",
+        ],
+    )
+
+    run(
+        "bio/enhancedvolcano",
+        [
+            "snakemake",
+            "--cores",
+            "1",
+            "--use-conda",
+            "volcano_rds.svg",
+        ],
+    )
+
+
 @skip_if_not_modified
 def test_gridss_call():
     run(