Merge dd98198 into e510305

Clinical-Genomics · Aug 22, 2021 · 2bc069d · 2bc069d
2 parents e510305 + dd98198
commit 2bc069d
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Showing 7 changed files with 465 additions and 34 deletions.
diff --git a/definitions/rd_dna_initiation_map.yaml b/definitions/rd_dna_initiation_map.yaml
@@ -18,6 +18,8 @@ CHAIN_ALL:
     - CHAIN_TCOV:
       - tiddit_coverage
       - chromograph_cov
+    - CHAIN_MTDEL:
+      - mitodel
     - CHAIN_SBCOV:
       - sambamba_depth
     - CHAIN_SMN:

diff --git a/definitions/rd_dna_parameters.yaml b/definitions/rd_dna_parameters.yaml
@@ -175,6 +175,7 @@ recipe_core_number:
     gzip_fastq: 0
     manta: 36
     markduplicates: 13
+    mitodel: 1
     mt_annotation: 1
     multiqc_ar: 1
     peddy_ar: 4
@@ -240,6 +241,7 @@ recipe_memory:
     gatk_variantrecalibration: 30
     glnexus_merge: 10
     markduplicates: 10
+    mitodel: 2
     mt_annotation: 2
     picardtools_collecthsmetrics: 8
     picardtools_collectmultiplemetrics: 8
@@ -295,6 +297,7 @@ recipe_time:
     gzip_fastq: 2
     manta: 30
     markduplicates: 20
+    mitodel: 2
     mt_annotation: 1
     multiqc_ar: 5
     peddy_ar: 1
@@ -1533,6 +1536,15 @@ bcftools_core:
     - bgzip
     - tabix
   type: recipe
+mitodel:
+  analysis_mode: sample
+  associated_recipe:
+    - mip
+  data_type: SCALAR
+  default: 1
+  outfile_suffix: ".txt"
+  file_tag: _mitodel
+  type: recipe
 mt_annotation:
   analysis_mode: case
   associated_recipe:

diff --git a/lib/MIP/Program/Samtools.pm b/lib/MIP/Program/Samtools.pm
@@ -325,11 +325,10 @@ sub samtools_faidx {
             store       => \$infile_path,
             strict_type => 1,
         },
-        outfile_path => { store => \$outfile_path, strict_type => 1, },
-        regions_ref => { default => [], store => \$regions_ref, strict_type => 1, },
-        stderrfile_path => { store => \$stderrfile_path, strict_type => 1, },
-        stderrfile_path_append =>
-          { store => \$stderrfile_path_append, strict_type => 1, },
+        outfile_path           => { store   => \$outfile_path, strict_type => 1, },
+        regions_ref            => { default => [], store => \$regions_ref, strict_type => 1, },
+        stderrfile_path        => { store   => \$stderrfile_path,        strict_type => 1, },
+        stderrfile_path_append => { store   => \$stderrfile_path_append, strict_type => 1, },
     };
 
     check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
@@ -412,10 +411,8 @@ sub samtools_flagstat {
 
     check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
 
-    my @commands = (
-        get_executable_base_command( { base_command => $BASE_COMMAND, } ),
-        qw{ flagstat }
-    );
+    my @commands =
+      ( get_executable_base_command( { base_command => $BASE_COMMAND, } ), qw{ flagstat } );
 
     push @commands, $infile_path;
 
@@ -484,10 +481,8 @@ sub samtools_idxstats {
 
     check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
 
-    my @commands = (
-        get_executable_base_command( { base_command => $BASE_COMMAND, } ),
-        qw{ idxstats }
-    );
+    my @commands =
+      ( get_executable_base_command( { base_command => $BASE_COMMAND, } ), qw{ idxstats } );
 
     push @commands, $infile_path;
 
@@ -541,10 +536,9 @@ sub samtools_index {
             store       => \$infile_path,
             strict_type => 1,
         },
-        stderrfile_path => { store => \$stderrfile_path, strict_type => 1, },
-        stderrfile_path_append =>
-          { store => \$stderrfile_path_append, strict_type => 1, },
-        stdoutfile_path => { store => \$stdoutfile_path, strict_type => 1, },
+        stderrfile_path        => { store => \$stderrfile_path,        strict_type => 1, },
+        stderrfile_path_append => { store => \$stderrfile_path_append, strict_type => 1, },
+        stdoutfile_path        => { store => \$stdoutfile_path,        strict_type => 1, },
     };
 
     check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
@@ -643,10 +637,9 @@ sub samtools_merge {
             store       => \$region,
             strict_type => 1,
         },
-        stderrfile_path => { store => \$stderrfile_path, strict_type => 1, },
-        stderrfile_path_append =>
-          { store => \$stderrfile_path_append, strict_type => 1, },
-        stdoutfile_path => {
+        stderrfile_path        => { store => \$stderrfile_path,        strict_type => 1, },
+        stderrfile_path_append => { store => \$stderrfile_path_append, strict_type => 1, },
+        stdoutfile_path        => {
             strict_type => 1,
             store       => \$stdoutfile_path,
         },
@@ -775,10 +768,9 @@ sub samtools_sort {
             store       => \$referencefile_path,
             strict_type => 1,
         },
-        stderrfile_path => { store => \$stderrfile_path, strict_type => 1, },
-        stderrfile_path_append =>
-          { store => \$stderrfile_path_append, strict_type => 1, },
-        stdoutfile_path => {
+        stderrfile_path        => { store => \$stderrfile_path,        strict_type => 1, },
+        stderrfile_path_append => { store => \$stderrfile_path_append, strict_type => 1, },
+        stdoutfile_path        => {
             strict_type => 1,
             store       => \$stdoutfile_path,
         },
@@ -855,6 +847,7 @@ sub samtools_stats {
 ##          : $auto_detect_input_format => Ignored (input format is auto-detected)
 ##          : $filehandle               => Sbatch filehandle to write to
 ##          : $infile_path              => Infile path
+##          : $insert_size              => Maximum insert size
 ##          : $outfile_path             => Outfile path
 ##          : $regions_ref              => Regions to process {REF}
 ##          : $remove_overlap           => Remove overlaps of paired-end reads from coverage and base count computations
@@ -867,6 +860,7 @@ sub samtools_stats {
     ## Flatten argument(s)
     my $filehandle;
     my $infile_path;
+    my $insert_size;
     my $outfile_path;
     my $regions_ref;
     my $stderrfile_path;
@@ -891,18 +885,22 @@ sub samtools_stats {
             store       => \$infile_path,
             strict_type => 1,
         },
+        insert_size => {
+            allow       => qr/ ^\d+$ /sxm,
+            store       => \$insert_size,
+            strict_type => 1,
+        },
         outfile_path   => { store => \$outfile_path, strict_type => 1, },
         remove_overlap => {
             allow       => [ undef, 0, 1 ],
             default     => 1,
             store       => \$remove_overlap,
             strict_type => 1,
         },
-        regions_ref => { default => [], store => \$regions_ref, strict_type => 1, },
-        stderrfile_path => { store => \$stderrfile_path, strict_type => 1, },
-        stderrfile_path_append =>
-          { store => \$stderrfile_path_append, strict_type => 1, },
-        stdoutfile_path => {
+        regions_ref            => { default => [], store => \$regions_ref, strict_type => 1, },
+        stderrfile_path        => { store   => \$stderrfile_path,        strict_type => 1, },
+        stderrfile_path_append => { store   => \$stderrfile_path_append, strict_type => 1, },
+        stdoutfile_path        => {
             strict_type => 1,
             store       => \$stdoutfile_path,
         },
@@ -918,6 +916,11 @@ sub samtools_stats {
         push @commands, q{-s};
     }
 
+    if ($insert_size) {
+
+        push @commands, q{--insert-size} . $SPACE . $insert_size;
+    }
+
     if ($remove_overlap) {
 
         push @commands, q{--remove-overlaps};