From 5ce552cb8965304e6b208066536503a1d054b556 Mon Sep 17 00:00:00 2001
From: "snakedeploy-bot[bot]"
 <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Date: Fri, 31 May 2024 06:52:59 +0000
Subject: [PATCH] perf: autobump bio/rasusa (#2967)

Automatic bump of bio/rasusa.

---------

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/rasusa/environment.linux-64.pin.txt |  6 +++---
 bio/rasusa/environment.yaml             |  2 +-
 bio/rasusa/meta.yaml                    |  4 ++--
 bio/rasusa/wrapper.py                   | 14 ++++++++------
 4 files changed, 14 insertions(+), 12 deletions(-)

diff --git a/bio/rasusa/environment.linux-64.pin.txt b/bio/rasusa/environment.linux-64.pin.txt
index 2e5cf4b5d97..1480bce84d7 100644
--- a/bio/rasusa/environment.linux-64.pin.txt
+++ b/bio/rasusa/environment.linux-64.pin.txt
@@ -3,7 +3,7 @@
 # platform: linux-64
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
-https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h807b86a_3.conda#7124cbb46b13d395bdde68f2d215c989
+https://conda.anaconda.org/conda-forge/linux-64/libgomp-13.2.0-h77fa898_7.conda#abf3fec87c2563697defa759dec3d639
 https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2#73aaf86a425cc6e73fcf236a5a46396d
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h807b86a_3.conda#23fdf1fef05baeb7eadc2aed5fb0011f
-https://conda.anaconda.org/bioconda/linux-64/rasusa-0.8.0-h031d066_0.tar.bz2#0e86b97fdc0c8ea60b8e5b7b5725eb04
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-13.2.0-h77fa898_7.conda#72ec1b1b04c4d15d4204ece1ecea5978
+https://conda.anaconda.org/bioconda/linux-64/rasusa-2.0.0-h031d066_0.tar.bz2#59ca5054e6ec09ee5e7ec23c8b010a14
diff --git a/bio/rasusa/environment.yaml b/bio/rasusa/environment.yaml
index 85cc9d99764..b7847cec468 100644
--- a/bio/rasusa/environment.yaml
+++ b/bio/rasusa/environment.yaml
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - rasusa =0.8.0
+  - rasusa =2.0.0
diff --git a/bio/rasusa/meta.yaml b/bio/rasusa/meta.yaml
index fd710ef64d5..4085559f4e3 100644
--- a/bio/rasusa/meta.yaml
+++ b/bio/rasusa/meta.yaml
@@ -19,5 +19,5 @@ params:
     Alternatively, a FASTA/Q index file can be provided and the genome size will be set
     to the sum of all reference sequences. |nl|
     If ``bases`` is not provided, this option and ``coverage`` are required
-  options: >
-    Any other options as listed in `the docs <https://github.com/mbhall88/rasusa#usage>`_.
+  extra: >
+    Additional program arguments.
diff --git a/bio/rasusa/wrapper.py b/bio/rasusa/wrapper.py
index a7e88deb741..901dd3a83db 100644
--- a/bio/rasusa/wrapper.py
+++ b/bio/rasusa/wrapper.py
@@ -6,12 +6,12 @@
 
 from snakemake.shell import shell
 
-
-options = snakemake.params.get("options", "")
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+extra = snakemake.params.get("extra", "")
 
 bases = snakemake.params.get("bases")
-if bases is not None:
-    options += " -b {}".format(bases)
+if bases:
+    extra += f" --bases {bases}"
 else:
     covg = snakemake.params.get("coverage")
     gsize = snakemake.params.get("genome_size")
@@ -19,6 +19,8 @@
         raise ValueError(
             "If `bases` is not given, then `coverage` and `genome_size` must be"
         )
-    options += " -g {gsize} -c {covg}".format(gsize=gsize, covg=covg)
+    extra += f" --genome-size {gsize} --coverage {covg}"
 
-shell("rasusa {options} -i {snakemake.input} -o {snakemake.output} 2> {snakemake.log}")
+shell(
+    "rasusa reads {extra} --output {snakemake.output[0]} --output {snakemake.output[1]} {snakemake.input} {log}"
+)