Merge tag '3.5.6' into develop

* Adding parameters to "bcftools mpileup" call to resolve issue for samples using multiple wells
* Correcting code version

Author: Thomas Clarke

CHANGES.md

@@ -1,5 +1,9 @@
 # CHANGES
 
+## 3.5.6
+* Adding parameters to "bcftools mpileup" call to resolve issue for samples using multiple wells
+* Correcting code version
+
 ## 3.5.5
 * Fix bugs in nanoseq result plotter
 * Fix bugs in indel caller

LSF/nextflow.config

@@ -14,4 +14,4 @@ profiles {
     executor.perJobMemLimit = true
     executor.queueSize = 200
   }
-}
+}

perl/indelCaller_step2.pl

@@ -212,7 +212,7 @@ sub runCmd {
 
   print STDOUT "Step 3...\n";
   #`samtools mpileup --no-BAQ  -d 250 -m 2 -F 0.5 -r $chr:$start-$end --BCF --output-tags DP,DV,DP4,SP -f $ref_genome -o $tempdir/$out_name.bcf $tempdir/$out_name.tmp.bam`;
-  &runCmd("bcftools mpileup --no-BAQ  -L 250 -m 2 -F 0.5 -r \"$chr:$start-$end\" -O b -a DP,DV,DP4,SP -f $ref_genome -o $tempdir/$out_name.bcf $tempdir/$out_name.tmp.bam");
+  &runCmd("bcftools mpileup --no-BAQ --ignore-RG -L 250 -m 2 -F 0.5 -r \"$chr:$start-$end\" -O b -a DP,DV,DP4,SP -f $ref_genome -o $tempdir/$out_name.bcf $tempdir/$out_name.tmp.bam");
 
   print STDOUT "Step 4...\n";
   &runCmd( "bcftools index -f $tempdir/$out_name.bcf $tempdir/$out_name.indexed.bcf");
@@ -267,7 +267,7 @@ sub runCmd {
         }
         #clean up these lines so no tmp files appear
         if (/^##bcftoolsCommand=mpileup/) {
-          $_ ="##bcftoolsCommand=mpileup --no-BAQ -L 250 -m 2 -F 0.5 -O b -a DP,DV,DP4,SP\n";
+          $_ ="##bcftoolsCommand=mpileup --no-BAQ --ignore-RG -L 250 -m 2 -F 0.5 -O b -a DP,DV,DP4,SP\n";
         }
         if (/^##bcftools_callCommand=call/) {
           $_ ="##bcftools_callCommand=call --ploidy 1 --skip-variants snps --multiallelic-caller --variants-only -O v\n";

perl/post_process_discarded_variants.pl

@@ -1,4 +1,35 @@
-#!/usr/bin/perl -w
+#!/usr/bin/env perl
+
+########## LICENCE ##########
+# Copyright (c) 2022 Genome Research Ltd
+# 
+# Author: CASM/Cancer IT <[email protected]>
+# 
+# This file is part of NanoSeq.
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+# 
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU Affero General Public License for more details.
+# 
+# You should have received a copy of the GNU Affero General Public License
+# along with this program.  If not, see <https://www.gnu.org/licenses/>.
+# 
+# 1. The usage of a range of years within a copyright statement contained within
+# this distribution should be interpreted as being equivalent to a list of years
+# including the first and last year specified and all consecutive years between
+# them. For example, a copyright statement that reads ‘Copyright (c) 2005, 2007-
+# 2009, 2011-2012’ should be interpreted as being identical to a statement that
+# reads ‘Copyright (c) 2005, 2007, 2008, 2009, 2011, 2012’ and a copyright
+# statement that reads ‘Copyright (c) 2005-2012’ should be interpreted as being
+# identical to a statement that reads ‘Copyright (c) 2005, 2006, 2007, 2008,
+# 2009, 2010, 2011, 2012’.
+###########################
 
 use strict;
 use List::Util qw(min);

python/runNanoSeq.py

@@ -47,7 +47,7 @@
 import tempfile
 import copy
 
-version = '3.5.4'
+version = '3.5.6'
 
 parser = argparse.ArgumentParser()
 # arguments for all subcommands