feat: add "qualimap bamqc" wrapper (#533)

* first commit of bamqc wrapper

* first commit of bamqc wrapper

* remove annoation, not used for bamqc

* make clear what the output is

* state target in call

* use only minor version

* use snakemake wrapper utils for JAVA OPTS

* Update bio/qualimap/bamqc/meta.yaml

Co-authored-by: Filipe G. Vieira <fgarrettvieira@gmail.com>

* Removed URL and added extra

Co-authored-by: Fritjof Lammers <f.lammers@dkfz-heidelberg.de>
Co-authored-by: Filipe G. Vieira <fgarrettvieira@gmail.com>

bio/qualimap/bamqc/environment.yaml

@@ -0,0 +1,7 @@
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - qualimap =2.2
+  - snakemake-wrapper-utils =0.4

bio/qualimap/bamqc/meta.yaml

@@ -0,0 +1,14 @@
+name: qualimap rnaseq
+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.
+url: http://qualimap.conesalab.org/doc_html/analysis.html#bam-qc
+authors:
+  - Fritjof Lammers
+  - Brett Copeland
+input:
+  - BAM file of data aligned to genome
+output:
+  - QC report in TXT format (genome_results.txt)
+notes: |
+  * The `extra` param allows for additional program arguments.

bio/qualimap/bamqc/test/Snakefile

@@ -0,0 +1,14 @@
+rule qualimap:
+    input:
+        # BAM aligned, splicing-aware, to reference genome
+        bam="mapped/a.bam",
+    output:
+        directory("qc/a"),
+    log:
+        "logs/qualimap/bamqc/a.log",
+    # optional specification of memory usage of the JVM that snakemake will respect with global
+    # resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
+    # and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
+    # https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
+    wrapper:
+        "master/bio/qualimap/bamqc"

bio/qualimap/bamqc/wrapper.py

@@ -0,0 +1,31 @@
+__author__ = "Fritjof Lammers"
+__copyright__ = "Copyright 2022, Fritjof Lammers"
+__email__ = "f.lammers@dkfz.de"
+
+__license__ = "MIT"
+
+
+import os
+
+from snakemake.shell import shell
+from snakemake_wrapper_utils.java import get_java_opts
+
+java_opts = get_java_opts(snakemake)
+
+if java_opts:
+    java_opts_str = f'JAVA_OPTS="{java_opts}"'
+else:
+    java_opts_str = ""
+
+# unset DISPLAY environment variable to avoid X11 error message issued by qualimap
+if os.environ.get("DISPLAY"):
+    del os.environ["DISPLAY"]
+
+extra = snakemake.params.get("extra", "")
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+shell(
+    "{java_opts_str} qualimap bamqc {extra} "
+    "-bam {snakemake.input.bam} "
+    "-outdir {snakemake.output} "
+    "{log}"
+)

test.py

@@ -4629,6 +4629,12 @@ def test_qualimaprnaseq():
         ["snakemake", "--cores", "1", "--use-conda", "-F"],
     )
 
+@skip_if_not_modified
+def test_qualimapbamqc():
+    run(
+        "bio/qualimap/bamqc",
+        ["snakemake", "--cores", "1", "qc/a", "--use-conda", "-F"],
+    )
 
 @skip_if_not_modified
 def test_collectrnaseqmetrics():