diff --git a/accessory_files/MyeloseqHD.16462-1615924889.CoverageQC.hg38.bed b/accessory_files/MyeloseqHD.16462-1615924889.CoverageQC.hg38.bed index fd46259..f7f6ed3 100644 --- a/accessory_files/MyeloseqHD.16462-1615924889.CoverageQC.hg38.bed +++ b/accessory_files/MyeloseqHD.16462-1615924889.CoverageQC.hg38.bed @@ -138,7 +138,7 @@ chr7 102227364 102227671 CUX1_exon_21 + CUX1 307 ENSG00000257923 ENST00000292535 chr7 102234049 102234242 CUX1_exon_22 + CUX1 193 ENSG00000257923 ENST00000292535 102234051 102234240 3434 1145 chr7 102239317 102239586 CUX1_exon_23 + CUX1 269 ENSG00000257923 ENST00000292535 102239319 102239584 3623 1208 chr7 102248409 102249043 CUX1_exon_24 + CUX1 634 ENSG00000257923 ENST00000292535 102248411 102249042 3888 1296 -chr7 140753272 140753395 BRAF_exon_16 - BRAF 123 ENSG00000157764 ENST00000644969 140753274 140753393 1862 621 +chr7 140753272 140753395 BRAF_exon_15 - BRAF 123 ENSG00000157764 ENST00000646891 140753274 140753393 1742 581 chr7 148807644 148807708 EZH2_exon_20 - EZH2 64 ENSG00000106462 ENST00000320356 148807645 148807706 2196 732 chr7 148809068 148809157 EZH2_exon_19 - EZH2 89 ENSG00000106462 ENST00000320356 148809070 148809155 2111 704 chr7 148809307 148809392 EZH2_exon_18 - EZH2 85 ENSG00000106462 ENST00000320356 148809309 148809390 2030 677 diff --git a/scripts/launcher.pl b/scripts/launcher.pl index ff5285d..41bed7c 100755 --- a/scripts/launcher.pl +++ b/scripts/launcher.pl @@ -70,7 +70,14 @@ die "Lane number is expected, Check sample sheet spreadsheet"; } my ($lane, $flowcell, $lib, $index_str, $exception) = @$row; - $exception =~ s/\s+/_/g if $exception; + + if ($exception) { + $exception =~ s/^\s+//; + $exception =~ s/\s+$//; + $exception =~ s/,\s+/,/g; + $exception =~ s/\s+,/,/g; + $exception =~ s/\s+/_/g; + } if ($exception and $exception =~ /NOTRANSFER/ and $exception =~ /RESEQ/) { die "$lib has both NOTRANSFER and RESEQ as exception and only one is allowed."; @@ -81,7 +88,7 @@ #my $id = $lib =~ /^H_|Research/ ? 'NONE' : $mrn.'_'.$accession; my $id = ($exception and $exception =~ /RESEQ|RESEARCH|NOTRANSFER/) ? 'NONE' : $mrn.'_'.$accession; - ($sample) = $lib =~ /^(\S+)\-lib/ if $lib =~ /^H_|Research/; + ($sample) = $lib =~ /^(\S+)\-lib/ if $lib =~ /^H_|Research|Positive\-Control/; unless ($id eq 'NONE') { unless ($mrn and $accession) {