Merge pull request #71 from nesi/dini-dev

update output directories for each snakefile
nesi · Oct 14, 2024 · bf73c1c · bf73c1c
2 parents f4ba466 + 5f6e6b4
commit bf73c1c
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Showing 2 changed files with 10 additions and 6 deletions.
diff --git a/08-snakemake/Snakefile_apsimx b/08-snakemake/Snakefile_apsimx
@@ -44,16 +44,20 @@ rule create_logdir:
     output:
         directory(config["slurm_logdir"])
     shell:
-        "mkdir -p {output}"
+	    """
+        mkdir -p {output}
+        mkdir -p PASSED_DB
+        mkdir -p FAILED_DB
+        """
 
 rule sort_db_files:
     input:
         expand("{file}.processed", file=[os.path.splitext(f)[0] for f in apsimx_files])
     output:
         "db_files_sorted"
     run:
-        passed_dir = "PASSED"
-        failed_dir = "FAILED"
+        passed_dir = "PASSED_DB"
+        failed_dir = "FAILED_DB"
         os.makedirs(passed_dir, exist_ok=True)
         os.makedirs(failed_dir, exist_ok=True)
 

diff --git a/08-snakemake/Snakefile_txt b/08-snakemake/Snakefile_txt
@@ -35,7 +35,7 @@ rule process_txt_files:
         export APPTAINER_BIND="{config[apptainer_bind]}"
         export APPTAINER_CMD="apptainer exec {config[apptainer_image]}"
 
-        mkdir -p FAILED
+        mkdir -p FAILED_CONFIG
         consecutive_failures=0
         max_consecutive_failures={config[max_consecutive_failures]}
 
@@ -45,7 +45,7 @@ rule process_txt_files:
                 consecutive_failures=0
             else
                 echo "Failed to process $file"
-                mv "$file" FAILED/
+                mv "$file" FAILED_CONFIG/
                 ((consecutive_failures++))
 
                 if [ $consecutive_failures -ge $max_consecutive_failures ]; then
@@ -62,4 +62,4 @@ rule create_logdir:
     output:
         directory(config["slurm_logdir"])
     shell:
-        "mkdir -p {output}"
+        "mkdir -p {output}"