From 85955368144c7290c7471fdfad8ecbe384f45524 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Mon, 18 Dec 2023 22:00:32 +0000 Subject: [PATCH] Improved documentation as advised by @jmtcsngr --- bin/npg_samplesheet_generator_NovaSeqXSeries | 6 ++++++ lib/npg/samplesheet/novaseq_xseries.pm | 12 +++++++----- 2 files changed, 13 insertions(+), 5 deletions(-) diff --git a/bin/npg_samplesheet_generator_NovaSeqXSeries b/bin/npg_samplesheet_generator_NovaSeqXSeries index d759b0cc..3bf9ee5f 100755 --- a/bin/npg_samplesheet_generator_NovaSeqXSeries +++ b/bin/npg_samplesheet_generator_NovaSeqXSeries @@ -57,6 +57,12 @@ npg_samplesheet_generator_NovaSeqXSeries DRAGEN analysis can deal with a limited number of distinct configurations. Set this attribute if processing off-board. + C - + DRAGEN software version to use, optional + + C - + name of the samplesheet CSV file, optional + =head1 DESCRIPTION Generates a samplesheet for the NovaSeq Series X Illumina instrument and diff --git a/lib/npg/samplesheet/novaseq_xseries.pm b/lib/npg/samplesheet/novaseq_xseries.pm index 39faf030..27fb6853 100755 --- a/lib/npg/samplesheet/novaseq_xseries.pm +++ b/lib/npg/samplesheet/novaseq_xseries.pm @@ -201,7 +201,7 @@ has 'read_length' => ( 'is' => 'ro', 'lazy_build' => 1, 'required' => 0, - 'documentation' => 'An array containing the length of the forward and the ' . + 'documentation' => 'An array containing the length of the forward and ' . 'reverse read', ); sub _build_read_length { @@ -585,15 +585,17 @@ used when processing the sequencing data. Must adhere to the following requirements: - Must be same number of fields (delimited by semicolon) as sequencing and - indexing reads specified in RunInfo.xml or Reads section. + indexing reads specified in RunInfo.xml or 'Reads' section. -- Indexing reads are specified with I, sequencing reads are specified with - Y, UMI cycles are specified with U, and trimmed reads are specified with N. +- Indexing reads are specified with 'I', + sequencing reads are specified with 'Y', + UMI cycles are specified with 'U', + and trimmed reads are specified with 'N'. - The number of cycles specified for each read must equal the number of cycles specified for that read in the RunInfo.xml file. -- Only one Y or I sequence can be specified per read. +- Only one 'Y' or 'I' sequence can be specified per read. =cut