From ee04ec22b24c8d380ef98f5cee677f4ff4730ad3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Christopher=20Schr=C3=B6der?=
 <christopher.schroeder@tu-dortmund.de>
Date: Fri, 20 Sep 2024 11:36:41 +0200
Subject: [PATCH] fix: name of bamqc (#1464)

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### Description

The subcommand name was wrong in the description. Additionally add a
region param fro target analyse.

### 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: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com>
---
 bio/qualimap/bamqc/meta.yaml  |  2 +-
 bio/qualimap/bamqc/wrapper.py | 24 +++++++++++++++---------
 2 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/bio/qualimap/bamqc/meta.yaml b/bio/qualimap/bamqc/meta.yaml
index d3f77cf2cd..70ce4cd58a 100644
--- a/bio/qualimap/bamqc/meta.yaml
+++ b/bio/qualimap/bamqc/meta.yaml
@@ -1,4 +1,4 @@
-name: qualimap rnaseq
+name: qualimap bamqc
 description: |
         Run qualimap bamqc to create a QC report for aligned NGS data data. It can be
         used for WGS, WES, RNA, ChIP-Seq, etc.
diff --git a/bio/qualimap/bamqc/wrapper.py b/bio/qualimap/bamqc/wrapper.py
index ebd49d19b0..6c41fcb50b 100644
--- a/bio/qualimap/bamqc/wrapper.py
+++ b/bio/qualimap/bamqc/wrapper.py
@@ -1,4 +1,4 @@
-__author__ = "Fritjof Lammers"
+__author__ = "Fritjof Lammers, Christopher Schröder"
 __copyright__ = "Copyright 2022, Fritjof Lammers"
 __email__ = "f.lammers@dkfz.de"
 
@@ -6,12 +6,14 @@
 
 
 import os
-
 from snakemake.shell import shell
 from snakemake_wrapper_utils.java import get_java_opts
 
-java_opts = get_java_opts(snakemake)
+extra = snakemake.params.get("extra", "")
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
 
+# Set JAVA options
+java_opts = get_java_opts(snakemake)
 if java_opts:
     java_opts_str = f'JAVA_OPTS="{java_opts}"'
 else:
@@ -21,11 +23,15 @@
 if os.environ.get("DISPLAY"):
     del os.environ["DISPLAY"]
 
-extra = snakemake.params.get("extra", "")
-log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+if target := snakemake.input.get("target", ""):
+    target = f"--feature-file {target}"
+
 shell(
-    "{java_opts_str} qualimap bamqc {extra} "
-    "-bam {snakemake.input.bam} "
-    "-outdir {snakemake.output} "
-    "{log}"
+    "{java_opts_str} qualimap bamqc"
+    " -nt {snakemake.threads}"
+    " -bam {snakemake.input.bam}"
+    " {target}"
+    " {extra}"
+    " -outdir {snakemake.output}"
+    " {log}"
 )