fix: set container for create_circExplorer_merged_found_counts_table

resolves #124
CCBR · Oct 22, 2024 · eb936a5 · eb936a5
1 parent d8f9cf0
commit eb936a5
Showing 1 changed file with 13 additions and 12 deletions.
diff --git a/workflow/rules/post_findcircrna_processing.smk b/workflow/rules/post_findcircrna_processing.smk
@@ -278,20 +278,21 @@ rule create_circExplorer_merged_found_counts_table:
         ),
         outdir=join(WORKDIR, "results", "{sample}", "circExplorer"),
         tmpdir=f"{TEMPDIR}/{str(uuid.uuid4())}",
+    container: config['containers']['star_ucsc_cufflinks']
     shell:
         """
-set -exo pipefail
-mkdir -p {params.tmpdir}
-python3 {params.pythonscript} \\
-    -b {input.bsj_found_counts} \\
-    -l {input.linear_spliced_counts} \\
-    -o {output.found_counts_table}
-
-python3 {params.pythonscript2} \\
-    --annotationcounts {input.annotation_counts} \\
-    --allfoundcounts {output.found_counts_table} \\
-    --countstable {output.count_counts_table}
-"""
+        set -exo pipefail
+        mkdir -p {params.tmpdir}
+        python3 {params.pythonscript} \\
+            -b {input.bsj_found_counts} \\
+            -l {input.linear_spliced_counts} \\
+            -o {output.found_counts_table}
+
+        python3 {params.pythonscript2} \\
+            --annotationcounts {input.annotation_counts} \\
+            --allfoundcounts {output.found_counts_table} \\
+            --countstable {output.count_counts_table}
+        """
 
 
 if RUN_MAPSPLICE: