minor changes from current version in qiita

Author: antgonza

src/sequence_processing_pipeline/Commands.py

@@ -106,7 +106,13 @@ def demux(id_map, fp, out_d, task, maxtask):
             fullname_r1 = outdir + sep + r1 + ext
             fullname_r2 = outdir + sep + r2 + ext
 
-            os.makedirs(outdir, exist_ok=True)
+            # we have seen in lustre that sometime this line
+            # can have a raise condition; making sure it doesn't brake
+            # things
+            try:
+                os.makedirs(outdir, exist_ok=True)
+            except FileExistsError:
+                pass
             current_fp_r1 = gzip.open(fullname_r1, mode)
             current_fp_r2 = gzip.open(fullname_r2, mode)
             current_fp = {'1': current_fp_r1, '2': current_fp_r2}

src/sequence_processing_pipeline/Pipeline.py

@@ -267,8 +267,8 @@ def __init__(self, configuration_file_path, run_id, input_file_path,
         required_files = ['RTAComplete.txt', 'RunInfo.xml']
         for some_file in required_files:
             if not exists(join(self.run_dir, some_file)):
-                raise PipelineError("required file '%s' is not present." %
-                                    some_file)
+                raise PipelineError(f"required file '{some_file}' is not "
+                                    f"present {self.run_dir}.")
 
         # verify that RunInfo.xml file is readable.
         try:

src/sequence_processing_pipeline/templates/multiqc_job.sh

@@ -4,7 +4,8 @@
 #SBATCH -N {{node_count}}
 #SBATCH -n {{nprocs}}
 #SBATCH --time {{wall_time_limit}}
-#SBATCH --mem {{mem_in_gb}}G
+# fastqc/multiqc use the same mem value in the templates (2gb); however multiqc requires ~12.
+#SBATCH --mem 1{{mem_in_gb}}G
 #SBATCH --array {{array_params}}
 set -x
 set +e