Merge pull request #794 from mgcam/novaseqx_ssheet_generator_refactor

Improved samplesheet generation for NovaSeqX.
wtsi-npg · Dec 19, 2023 · dbf9dd5 · dbf9dd5
2 parents e63a39e + 8595536
commit dbf9dd5
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diff --git a/bin/npg_samplesheet_generator_NovaSeqXSeries b/bin/npg_samplesheet_generator_NovaSeqXSeries
@@ -27,26 +27,46 @@ npg_samplesheet_generator_NovaSeqXSeries
 
   C<help>     - displays help message and exists
 
-  C<varcall>  - variant calling mode, defaults to C<None>, other valid options
-                C<SmallVariantCaller> and C<AllVariantCallers>
 
   C<batch_id> - LIMS batch identifier, optional
 
   C<id_run>   - NPG run ID, optional; if supplied, the record for this run
                 should exists in the run tracking database
+
+  C<read_length> -
+                an optional list of read lengths, forward first, reverse
+                second; currently both default to 151
+
+  C<index_read_length> -
+                an optional list of index read lengths for the first and,
+                optionally, second index read; if not given, computed from
+                the length of barcodes recorded in LIMS
+
   C<align>    - a boolean option, false by default; if set, the DRAGEN
                 germline analysis section is added to the file if suitable
                 samples are present
-  C<keep_fastq> - an option to keep FASTQ files for aligned data, false
-                  default
-  C<dragen_max_number_of_configs> - DRAGEN analysis can deal with a limited
-                  number of distinct configurations. Set this attribute if
-                  processing not on-board.
+
+  C<varcall>  - variant calling mode, defaults to C<None>, other valid options
+                C<SmallVariantCaller> and C<AllVariantCallers>
+
+  C<keep_fastq> -
+                an option to keep FASTQ files for aligned data, false by
+                default
+
+  C<dragen_max_number_of_configs> -
+                DRAGEN analysis can deal with a limited number of distinct
+                configurations. Set this attribute if processing off-board.
+
+  C<dragen_software_version> -
+                DRAGEN software version to use, optional
+
+  C<file_name> -
+                name of the samplesheet CSV file, optional
 
 =head1 DESCRIPTION
 
-Samplesheet generation to initiate DRAGEN analysis of data sequenced
-on the NovaSeq Series X Illumina instrument.
+Generates a samplesheet for the NovaSeq Series X Illumina instrument and
+DRAGEN analysis.
 
 =head1 EXIT STATUS
 
@@ -56,37 +76,13 @@ on the NovaSeq Series X Illumina instrument.
 
 =head1 CONFIGURATION
 
-Access to the ml warehouse database is required.
+Access to both ml warehouse and npg tracking  database is required.
 
 =head1 DEPENDENCIES
 
 =over
 
-=item strict
-
-=item warnings
-
-=item Carp
-
-=item Text::CSV
-
-=item Readonly
-
-=item List::MoreUtils
-
-=item List::Util
-
-=item Getopt::Long
-
-=item Pod::Usage
-
-=item DateTime
-
-=item Data::UUID
-
-=item st::api::lims
-
-=item npg_tracking::Schema
+=item npg::samplesheet::novaseq_xseries
 
 =back