Merge branch 'devel' of https://github.com/wtsi-npg/npg_irods into master to create release 2.31.1

Author: dkj

Changes

@@ -1,5 +1,9 @@
 Upcoming
 
+Release 2.31.1
+
+  - substitution_analyis filename fix
+
 Release 2.31.0
 
  - PacBio - ensure runfolders are writable for md5 files prior to iRODS

lib/WTSI/NPG/HTS/Illumina/ResultSet.pm

@@ -72,8 +72,8 @@ our %ILLUMINA_PART_PATTERNS =
        '[.]seqchksum',
        '[.]sha512primesums512[.]seqchksum',
        '[.]spatial_filter[.]stats',
-       '_substitution_analysis.txt',      # non-conforming file name
-       '_substitution_metrics.txt',       # non-conforming file name
+       '.substitution_analysis.txt',      # non-conforming file name
+       '.substitution_metrics.txt',       # non-conforming file name
        '_target[.]stats',                 # non-conforming file name
        '_target_autosome[.]stats',        # non-conforming file name
        '[.]stats',

t/data/illumina/sequence/190514_MS5_29467_A_MS8070734-300V2/Data/Intensities/BAM_basecalls_20190520-165319/no_cal/archive/lane1/29467_1#1_substitution_analysis.txt renamed to t/data/illumina/sequence/190514_MS5_29467_A_MS8070734-300V2/Data/Intensities/BAM_basecalls_20190520-165319/no_cal/archive/lane1/29467_1#1.substitution_analysis.txt

@@ -623,11 +623,11 @@ sub publish_plex_geno_sec_data_samplesheet : Test(73) {
                   "lane$lane/29467_1#1.seqchksum",
                   "lane$lane/29467_1#1.sha512primesums512.seqchksum",
                   "lane$lane/29467_1#1.spatial_filter.stats",
+                  "lane$lane/29467_1#1.substitution_analysis.txt",
+                  "lane$lane/29467_1#1.substitution_metrics.txt",
                   "lane$lane/29467_1#1.vcf",
                   "lane$lane/29467_1#1_F0x900.stats",
                   "lane$lane/29467_1#1_F0xB00.stats",
-                  "lane$lane/29467_1#1_substitution_analysis.txt",
-                  "lane$lane/29467_1#1_substitution_metrics.txt",
                   );
 
   is_deeply(\@observed, \@expected) or diag explain \@observed;