From 7cd77d7b15de62b00b1ae541f616196358dc262d Mon Sep 17 00:00:00 2001 From: Carol Scott Date: Fri, 29 Jun 2018 11:41:31 +0100 Subject: [PATCH 1/2] bwa to bwa0_6 for rna_seqc rRNA alignment --- Changes | 1 + lib/npg_qc/autoqc/checks/rna_seqc.pm | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/Changes b/Changes index d8641dcec..2737e75f6 100644 --- a/Changes +++ b/Changes @@ -22,6 +22,7 @@ release 65.0 - all C source code moved to https://github.com/wtsi-npg/npg_qc_utils, executables are built by Conda https://github.com/wtsi-npg/npg_conda/tree/devel/recipes/npg_qc_utils/65.0; Build.PL changed accordingly + - bwa to bwa0_6 for rna_seqc rRNA alignment release 64.6.3 - update parsing of spatial filter stats in spatial_filter QC check diff --git a/lib/npg_qc/autoqc/checks/rna_seqc.pm b/lib/npg_qc/autoqc/checks/rna_seqc.pm index ed44d6941..7cf7c7bb7 100644 --- a/lib/npg_qc/autoqc/checks/rna_seqc.pm +++ b/lib/npg_qc/autoqc/checks/rna_seqc.pm @@ -28,7 +28,7 @@ Readonly::Scalar my $CHILD_ERROR_SHIFT => 8; Readonly::Scalar my $MAX_READS => 100; Readonly::Scalar my $MIN_READS => 50; Readonly::Scalar my $PAIRED_FLAG => 0x1; -Readonly::Scalar my $RRNA_ALIGNER => q[bwa]; +Readonly::Scalar my $RRNA_ALIGNER => q[bwa0_6]; Readonly::Scalar my $RRNA_STRAIN => q[default_rRNA]; Readonly::Scalar my $METRICS_FILE_NAME => q[metrics.tsv]; Readonly::Scalar my $QUANT_FILE_NAME => q[quant.genes.sf]; From 2752add24d955856a1798c21597c648d0bbdf953 Mon Sep 17 00:00:00 2001 From: mgcam Date: Fri, 29 Jun 2018 13:46:00 +0100 Subject: [PATCH 2/2] Update Changes --- Changes | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/Changes b/Changes index 2737e75f6..730b258db 100644 --- a/Changes +++ b/Changes @@ -1,5 +1,8 @@ LIST OF CHANGES FOR NPG-QC PACKAGE +release 65.1 + - bwa to bwa0_6 for rna_seqc rRNA alignment + release 65.0 - adapter autoqc check - discard code for fastq input - add genotype_call_results_reporter script to report genotype_call @@ -22,7 +25,6 @@ release 65.0 - all C source code moved to https://github.com/wtsi-npg/npg_qc_utils, executables are built by Conda https://github.com/wtsi-npg/npg_conda/tree/devel/recipes/npg_qc_utils/65.0; Build.PL changed accordingly - - bwa to bwa0_6 for rna_seqc rRNA alignment release 64.6.3 - update parsing of spatial filter stats in spatial_filter QC check