Add an output for read_entropy_csv, for #442.

cfe-lab · Dec 5, 2019 · 1228ac5 · 1228ac5
1 parent 67b2b49
commit 1228ac5
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Showing 3 changed files with 7 additions and 2 deletions.
diff --git a/Singularity b/Singularity
@@ -186,7 +186,7 @@ From: centos:7
         failed_csv cascade_csv nuc_csv amino_csv coord_ins_csv conseq_csv \
         conseq_region_csv failed_align_csv coverage_scores_csv \
         coverage_maps_tar aligned_csv g2p_aligned_csv genome_coverage_csv \
-        genome_coverage_svg contigs_csv
+        genome_coverage_svg contigs_csv read_entropy_csv
     KIVE_THREADS 2
     KIVE_MEMORY 6000
 

diff --git a/micall/monitor/kive_watcher.py b/micall/monitor/kive_watcher.py
@@ -56,7 +56,8 @@
                       'alignment_svg',
                       'alignment_png',
                       'assembly_fasta',
-                      'genome_coverage_svg']
+                      'genome_coverage_svg',
+                      'read_entropy_csv']
 
 # noinspection PyArgumentList
 FolderEventType = Enum('FolderEventType', 'ADD_SAMPLE FINISH_FOLDER')

diff --git a/micall_kive.py b/micall_kive.py
@@ -74,6 +74,9 @@ def parse_args():
     parser.add_argument('contigs_csv',
                         nargs='?',
                         help='CSV containing contigs built by de novo assembly')
+    parser.add_argument('read_entropy_csv',
+                        nargs='?',
+                        help='CSV containing read pair length counts')
 
     return parser.parse_args()
 
@@ -107,6 +110,7 @@ def load_sample(args):
                     contigs_csv=args.contigs_csv,
                     genome_coverage_csv=args.genome_coverage_csv,
                     genome_coverage_svg=args.genome_coverage_svg,
+                    read_entropy_csv=args.read_entropy_csv,
                     scratch_path=scratch_path)
     sample.name = None  # Since the file names are messy in Kive.
     return sample