perf: autobump bio/fgbio/collectduplexseqmetrics (#1100)

Automatic update of bio/fgbio/collectduplexseqmetrics.

---------

Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com>

bio/fgbio/annotatebamwithumis/meta.yaml

@@ -1,4 +1,5 @@
 name: "fgbio AnnotateBamWithUmis"
 description: Annotates existing BAM files with UMIs (Unique Molecular Indices, aka Molecular IDs, Molecular barcodes) from a separate FASTQ file.
+url: https://fulcrumgenomics.github.io/fgbio/
 authors:
   - Patrik Smeds

bio/fgbio/annotatebamwithumis/wrapper.py

@@ -7,10 +7,7 @@
 from snakemake.shell import shell
 from snakemake_wrapper_utils.java import get_java_opts
 
-shell.executable("bash")
-
 log = snakemake.log_fmt_shell(stdout=False, stderr=True)
-
 extra_params = snakemake.params.get("extra", "")
 java_opts = get_java_opts(snakemake)
 

bio/fgbio/collectduplexseqmetrics/environment.yaml

@@ -1,8 +1,7 @@
 channels:
-  - r
   - conda-forge
   - bioconda
   - nodefaults
 dependencies:
-  - fgbio ==0.6.1
-  - r-ggplot2
+  - fgbio =2.1.0
+  - snakemake-wrapper-utils =0.5.2

bio/fgbio/collectduplexseqmetrics/meta.yaml

@@ -1,4 +1,5 @@
 name: "fgbio CollectDuplexSeqMetrics"
-description: Collects a suite of metrics to QC duplex sequencing data.g.
+description: Collects a suite of metrics to QC duplex sequencing data.
+url: https://fulcrumgenomics.github.io/fgbio/
 authors:
   - Patrik Smeds

bio/fgbio/collectduplexseqmetrics/wrapper.py

@@ -4,14 +4,14 @@
 __license__ = "MIT"
 
 
-from snakemake.shell import shell
 from os import path
+from snakemake.shell import shell
+from snakemake_wrapper_utils.java import get_java_opts
 
-shell.executable("bash")
 
 log = snakemake.log_fmt_shell(stdout=False, stderr=True)
-
 extra_params = snakemake.params.get("extra", "")
+java_opts = get_java_opts(snakemake)
 
 bam_input = snakemake.input[0]
 
@@ -74,7 +74,7 @@
     raise ValueError("Input bam should be one bam file: " + str(bam_input) + "!")
 
 shell(
-    "fgbio CollectDuplexSeqMetrics"
+    "fgbio {java_opts} CollectDuplexSeqMetrics"
     " -i {bam_input}"
     " -o {path_name_prefix}"
     " {duplex_umi_counts_flag}"