Adding separate coverge metrics per sequencing technology to JSON

bin/gabi_summary.pl

@@ -48,7 +48,8 @@
     "mlst" => [],
     "confindr" => [],
     "kraken" => {},
-    "serotype" => []
+    "serotype" => [],
+    "mosdepth" => {}
 );
 
 my @files = glob '*/*' ;
@@ -91,9 +92,23 @@
         my %data;
         $data{'Lissero'} = parse_lissero(\@lines);
         push( @{ $matrix{'serotype'} }, \%data );
+    } elsif ( $filename =~ /ILLUMINA.mosdepth.summary.txt/) {
+        my @data = parse_mosdepth(\@lines);
+        $matrix{'mosdepth'}{'illumina'} = \@data;
+    } elsif ( $filename =~ /NANOPORE.mosdepth.summary.txt/) {
+        my @data = parse_mosdepth(\@lines);
+        $matrix{'mosdepth'}{'nanopore'} = \@data;
+    } elsif ( $filename =~ /PACBIO.mosdepth.summary.txt/) {
+        my @data = parse_mosdepth(\@lines);
+        $matrix{'mosdepth'}{'pacbio'} = \@data;      
     } elsif ( $filename =~ /.*mosdepth.summary.txt/) {
         my @data = parse_mosdepth(\@lines);
-        $matrix{'mosdepth'} = \@data;
+        $matrix{'mosdepth'}{'total'} = \@data;
+    } elsif ( $filename =~ /.sistr.tab/) {
+        my %data ;
+
+        $data{'Sistr'}= parse_sistr(\@lines);
+        push( @{ $matrix{'serotype'} }, \%data );
     }
 
     close($FILE);
@@ -107,6 +122,27 @@
 # Tool-specific parsing methods
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
+sub parse_sistr {
+    my @lines = @{$_[0] };
+
+    my $h = shift @lines ;
+    my @header = split "\t" , $h ;
+
+    my %data;
+
+    my $this_line = shift @lines;
+
+    my @elements = split "\t", $this_line;
+
+    for my $i (0..$#header) {
+        my $column = @header[$i];
+        my $entry = @elements[$i];
+        $data{$column} = $entry 
+    }
+
+   return \%data ;
+}
+
 sub parse_mosdepth {
 
     my @lines = @{$_[0] };

conf/modules.config

@@ -151,6 +151,7 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
+
     withName: 'CONFINDR' {
         publishDir = [
             path: { "${params.outdir}/samples/${meta.sample_id}/qc" },

conf/multiqc_config.yaml

@@ -15,6 +15,10 @@ extra_fn_clean_exts:
     - _1.fastq_trimmed
     - _2.fastq_trimmed
     - .NanoStats.txt
+    - .ALL
+    - .ILLUMINA
+    - .PACBIO
+    - .NANOPORE
 
 kraken:
     top_n: 15

modules/mosdepth/main.nf

@@ -20,7 +20,7 @@ process MOSDEPTH {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.sample_id}"
+    def prefix = task.ext.prefix ?: "${meta.sample_id}.${meta.platform}"
 
     """
     mosdepth \\

subworkflows/coverage/main.nf

@@ -15,6 +15,7 @@ include { ALIGN_LONG_READS }    from './../align_long_reads'
 ch_bam      = Channel.from([])
 ch_qc       = Channel.from([])
 ch_versions = Channel.from([])
+ch_summary_by_platform = Channel.from([])
 
 workflow COVERAGE {
 
@@ -100,9 +101,12 @@ workflow COVERAGE {
         SAMTOOLS_INDEX.out.bam
     )
 
+
+
     emit:
     versions    = ch_versions
     report      = MOSDEPTH.out.global_txt
     summary     = MOSDEPTH.out.summary_txt
+    summary_by_platform = ch_summary_by_platform
 
 }

workflows/gabi.nf

@@ -242,6 +242,11 @@ workflow GABI {
     )
     ch_report = ch_report.mix(COVERAGE.out.summary)
 
+    ch_report = ch_report.mix(
+        COVERAGE.out.summary.filter {m,r ->
+            m.platform != "ALL"
+        }
+    )
     /*
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     SUB: Identify and analyse plasmids from draft assemblies