Supressed keeping interim fastq files

wtsi-npg · Dec 19, 2023 · 3f960da · 3f960da
1 parent 474a510
commit 3f960da
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Showing 2 changed files with 8 additions and 4 deletions.
diff --git a/lib/npg/samplesheet/auto.pm b/lib/npg/samplesheet/auto.pm
@@ -150,13 +150,15 @@ sub process {
     my $ss;
     if ($self->instrument_format eq $MISEQ_INSTRUMENT_FORMAT) {
       $ss = npg::samplesheet->new(
-        run => $r, mlwh_schema => $self->mlwh_schema
+        run => $r,
+        mlwh_schema => $self->mlwh_schema
       );
     } else {
       $ss = npg::samplesheet::novaseq_xseries->new(
-        run => $r, id_run => $id_run,
+        id_run => $id_run,
+        run => $r,
         mlwh_schema => $self->mlwh_schema,
-        align => 1, keep_fastq => 1
+        align => 1
       );
     }
 

diff --git a/t/47-npg_samplesheet_auto.t b/t/47-npg_samplesheet_auto.t
@@ -93,7 +93,9 @@ my $schema = $util->create_test_db(q[npg_tracking::Schema],
   is (@files, 1, 'one NovaSeqX samplesheet file is generated');
   my $compare_file = 't/data/samplesheet/dragen/' .
                      '231206_47995_NVX1_A_ssbatch98292_align.csv';
-  is (slurp($files[0]), slurp($compare_file),
+  my $expected = slurp($compare_file);
+  $expected =~ s/KeepFastq,TRUE,,,/KeepFastq,FALSE,,,/;
+  is (slurp($files[0]), $expected,
     'the NovaSeqX samplesheet is generated correctly');
 }