From ab4bdff451297b847369265e8a95b09de14e224b Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Wed, 8 Jul 2020 15:47:07 +0200
Subject: [PATCH] Trying to fix featureCounts wrapper.
---
smwrappers/feature_count_reads/wrapper.py | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/smwrappers/feature_count_reads/wrapper.py b/smwrappers/feature_count_reads/wrapper.py
index 6cc52ef..9fdb16a 100644
--- a/smwrappers/feature_count_reads/wrapper.py
+++ b/smwrappers/feature_count_reads/wrapper.py
@@ -13,7 +13,9 @@
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
from snakemake.shell import shell
-from libworkflows import run_with_modules
+from libworkflows import run_with_modules, SHELL_FUNCTIONS
+
+shell.prefix(SHELL_FUNCTIONS)
load_modules = snakemake.config.get("load_modules", False)
if load_modules:
@@ -30,9 +32,7 @@ if not hasattr(snakemake.params, "other_opts"):
shell_commands = """
tmpdir=$(mktemp --tmpdir -d {snakemake.params.tmpdir_prefix})
-cmd="niceload --noswap featureCounts \\
- {snakemake.params.min_mapq} \\
- {snakemake.params.other_opts} \\
+cmd="niceload --noswap featureCounts {snakemake.params.min_mapq} {snakemake.params.other_opts} \\
-a {snakemake.params.annot} -o {snakemake.output.counts} \\
-t {snakemake.wildcards.feature_type} -g {snakemake.params.gene_id_name} \\
-O -s {snakemake.params.stranded} {snakemake.params.overlap} \\
--
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