feat: Pyroe id-to-name (#1499)

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### Description

This PR adds the pyroe id-to-name sub-command to the list of available
wrappers

### QC
<!-- Make sure that you can tick the boxes below. -->

* [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/pyroe/idtoname/environment.yaml

@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - pyroe =0.9.3

bio/pyroe/idtoname/meta.yaml

@@ -0,0 +1,14 @@
+name: pyroe id-to-name
+url: https://pyroe.readthedocs.io/en/latest/geneid_to_name.html
+description: >
+  Create a 2-column tab-separated file mapping IDs to names
+author:
+  - Thibault Dayris
+input:
+  - Path to genome annotation (GTF or GFF3)
+output:
+  - Path to gene id <-> gene names mapping 
+params:
+  - extra: Optional parameters to be passed to pyroe
+notes: |
+  Format is automatically inferred from input files.

bio/pyroe/idtoname/test/Snakefile

@@ -0,0 +1,12 @@
+rule test_pyroe_idtoname:
+    input:
+        "annotation.{format}",
+    output:
+        "id2name.{format}.tsv",
+    threads: 1
+    log:
+        "logs/{format}.log",
+    params:
+        extra="",
+    wrapper:
+        "master/bio/pyroe/idtoname"

bio/pyroe/idtoname/test/annotation.gff3

@@ -0,0 +1,9 @@
+##gff-version 3
+#description: evidence-based annotation of the human genome (GRCh38), version 43 (Ensembl 109)
+#provider: GENCODE
+#contact: gencode-help@ebi.ac.uk
+#format: gff3
+#date: 2022-11-29
+##sequence-region chr1 1 248956422
+chr1	HAVANA	gene	11869	14409	.	+	.	ID=ENSG00000290825.1;gene_id=ENSG00000290825.1;gene_type=lncRNA;gene_name=DDX11L2;level=2;tag=overlaps_pseudogene
+chr1	HAVANA	transcript	11869	14409	.	+	.	ID=ENST00000456328.2;Parent=ENSG00000290825.1;gene_id=ENSG00000290825.1;transcript_id=ENST00000456328.2;gene_type=lncRNA;gene_name=DDX11L2;transcript_type=lncRNA;transcript_name=DDX11L2-202;level=2;transcript_support_level=1;tag=basic,Ensembl_canonical;havana_transcript=OTTHUMT00000362751.1

bio/pyroe/idtoname/test/annotation.gtf

@@ -0,0 +1,7 @@
+##description: evidence-based annotation of the human genome (GRCh38), version 43 (Ensembl 109)
+##provider: GENCODE
+##contact: gencode-help@ebi.ac.uk
+##format: gtf
+##date: 2022-11-29
+chr1	HAVANA	gene	11869	14409	.	+	.	gene_id "ENSG00000290825.1"; gene_type "lncRNA"; gene_name "DDX11L2"; level 2; tag "overlaps_pseudogene";
+chr1	HAVANA	transcript	11869	14409	.	+	.	gene_id "ENSG00000290825.1"; transcript_id "ENST00000456328.2"; gene_type "lncRNA"; gene_name "DDX11L2"; transcript_type "lncRNA"; transcript_name "DDX11L2-202"; level 2; transcript_support_level "1"; tag "basic"; tag "Ensembl_canonical"; havana_transcript "OTTHUMT00000362751.1";

bio/pyroe/idtoname/wrapper.py

@@ -0,0 +1,18 @@
+__author__ = "Thibault Dayris"
+__copyright__ = "Copyright 2023, Thibault Dayris"
+__email__ = "thibault.dayris@gustaveroussy.fr"
+__license__ = "MIT"
+
+
+from snakemake.shell import shell
+
+
+log = snakemake.log_fmt_shell(stdout=True, stderr=True, append=True)
+extra = snakemake.params.get("extra", "")
+
+if str(snakemake.input).endswith(("gtf", "gtf.gz")):
+    extra += " --format GTF "
+elif str(snakemake.input).endswith(("gff", "gff.gz", "gff3", "gff3.gz")):
+    extra += " --format GFF3 "
+
+shell("pyroe id-to-name {extra} {snakemake.input} {snakemake.output} {log}")

test.py

@@ -170,7 +170,6 @@ def test_nonpareil_plot():
             "--use-conda",
             "-F",
             "results/a.pdf",
-            "results/samples.pdf",
 # Test disabled due to bug in nonpareil (#62)
 #            "results/a.nomodel.pdf",
         ]
@@ -1392,6 +1391,18 @@ def test_art_profiler_illumina():
     )
 
 
+@skip_if_not_modified
+def test_pyroe_id_to_name():
+    run(
+        "bio/pyroe/idtoname",
+        ["snakemake", "--cores", "1", "--use-conda", "-F", "id2name.gtf.tsv"],
+    )
+    run(
+        "bio/pyroe/idtoname",
+        ["snakemake", "--cores", "1", "--use-conda", "-F", "id2name.gff3.tsv"],
+    )
+
+
 @skip_if_not_modified
 def test_pyroe_makesplicedunspliced():
     run(