Trying to fix featureCounts wrapper.

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} \\