Try to fix unselected files cleaning on GH

friendsofstrandseq · Jun 24, 2024 · 11c1985 · 11c1985
1 parent 397e170
commit 11c1985
Show file tree

Hide file tree

Showing 2 changed files with 23 additions and 1 deletion.
diff --git a/workflow/rules/count.smk b/workflow/rules/count.smk
@@ -147,7 +147,17 @@ rule remove_unselected_bam:
         "../envs/mc_base.yaml"
     shell:
         """
-        rm {input.bam} {input.bai}
+        # Show labels
+        cat {input.labels}
+        # echo bam
+        echo {input.bam}
+        # Show bai
+        echo {input.bai}
+        # Remove unselected bam & bai
+        # Check if bam and bai are not empty, then remove them
+        if [ -s {input.bam} ] && [ -s {input.bai} ]; then
+            rm {input.bam} {input.bai}
+        fi
         """
 
 

diff --git a/workflow/rules/utils.smk b/workflow/rules/utils.smk
@@ -159,6 +159,8 @@ rule save_config:
 rule save_conda_versions_mc_base:
     output:
         "{folder}/{sample}/config/conda_export/mc_base.yaml",
+    log:
+        "{folder}/log/save_conda_versions/{sample}/mc_base.log",
     conda:
         "../envs/mc_base.yaml"
     shell:
@@ -168,6 +170,8 @@ rule save_conda_versions_mc_base:
 rule save_conda_versions_mc_bioinfo_tools:
     output:
         "{folder}/{sample}/config/conda_export/mc_bioinfo_tools.yaml",
+    log:
+        "{folder}/log/save_conda_versions/{sample}/mc_bioinfo_tools.log",
     conda:
         "../envs/mc_bioinfo_tools.yaml"
     shell:
@@ -177,6 +181,8 @@ rule save_conda_versions_mc_bioinfo_tools:
 rule save_conda_versions_rtools:
     output:
         "{folder}/{sample}/config/conda_export/rtools.yaml",
+    log:
+        "{folder}/log/save_conda_versions/{sample}/rtools.log",
     conda:
         "../envs/rtools.yaml"
     shell:
@@ -186,6 +192,8 @@ rule save_conda_versions_rtools:
 rule save_conda_versions_scNOVA_bioinfo_tools:
     output:
         "{folder}/{sample}/config/conda_export/scNOVA_bioinfo_tools.yaml",
+    log:
+        "{folder}/log/save_conda_versions/{sample}/scNOVA_bioinfo_tools.log",
     conda:
         "../envs/scNOVA/scNOVA_bioinfo_tools.yaml"
     shell:
@@ -195,6 +203,8 @@ rule save_conda_versions_scNOVA_bioinfo_tools:
 rule save_conda_versions_scNOVA_DL:
     output:
         "{folder}/{sample}/config/conda_export/scNOVA_DL.yaml",
+    log:
+        "{folder}/log/save_conda_versions/{sample}/scNOVA_DL.log",
     conda:
         "../envs/scNOVA/scNOVA_DL.yaml"
     shell:
@@ -204,6 +214,8 @@ rule save_conda_versions_scNOVA_DL:
 rule save_conda_versions_scNOVA_R:
     output:
         "{folder}/{sample}/config/conda_export/scNOVA_R.yaml",
+    log:
+        "{folder}/log/save_conda_versions/{sample}/scNOVA_R.log",
     conda:
         "../envs/scNOVA/scNOVA_R.yaml"
     shell: