diff --git a/08-snakemake/Snakefile_apsimx b/08-snakemake/Snakefile_apsimx index 338c219..5fe66e1 100644 --- a/08-snakemake/Snakefile_apsimx +++ b/08-snakemake/Snakefile_apsimx @@ -44,7 +44,11 @@ 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: @@ -52,8 +56,8 @@ rule sort_db_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 index 113072b..aacaff2 100644 --- 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}" \ No newline at end of file + "mkdir -p {output}"