Merge pull request #1736 from Clinical-Genomics/release/v9.1.0

Release/v9.1.0
Clinical-Genomics · Dec 7, 2020 · a4fbadf · a4fbadf
2 parents ba2764a + df33665
commit a4fbadf
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,13 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [9.1.0]
+- PNGs generated by chromograph are now uniform in dpi and image size
+- Adds chromograph recipe to generate images of rhocall viz output (regions of autozygosity and fraction of homozygous snps) 
+
+**Tools**  
+chromograph 0.3.3 -> 1.0.0
+
 ## [9.0.6]
 - Use "PAN" key for slurm_jobs_ids file instead of "ALL" as "ALL" has a size constraint
 

diff --git a/containers/chromograph/Dockerfile b/containers/chromograph/Dockerfile
@@ -5,9 +5,9 @@ FROM clinicalgenomics/mip:2.0
 ################## METADATA ######################
 
 LABEL base_image="clinicalgenomics/mip:2.0"
-LABEL version="8"
+LABEL version="9"
 LABEL software="chromograph"
-LABEL software.version="0.3.3"
+LABEL software.version="1.0.0"
 LABEL extra.binaries="chromograph"
 LABEL maintainer="Clinical-Genomics/MIP"
 
@@ -17,14 +17,14 @@ RUN conda install pip python=3.7 matplotlib
 RUN /opt/conda/bin/conda clean -tipsy
 
 ## Download release
-RUN wget --no-verbose https://github.com/mikaell/chromograph/archive/v0.3.3.zip -O /opt/conda/share/chromograph-0.3.3.zip
+RUN wget --no-verbose https://github.com/mikaell/chromograph/archive/v1.0.0.zip -O /opt/conda/share/chromograph-1.0.0.zip
 
 ## Extract
-RUN unzip -o /opt/conda/share/chromograph-0.3.3.zip -d /opt/conda/share/ && \
-    rm /opt/conda/share/chromograph-0.3.3.zip
+RUN unzip -o /opt/conda/share/chromograph-1.0.0.zip -d /opt/conda/share/ && \
+    rm /opt/conda/share/chromograph-1.0.0.zip
 
 ## Move to chromograph directory
-RUN cd /opt/conda/share/chromograph-0.3.3 && \
-    python -m pip install --editable .
+RUN cd /opt/conda/share/chromograph-1.0.0 && \
+    python -m pip install .
 
 WORKDIR /data/
diff --git a/definitions/rd_dna_initiation_map.yaml b/definitions/rd_dna_initiation_map.yaml
@@ -76,8 +76,9 @@ CHAIN_ALL:
     - rhocall_ar
     - vt_ar
     - variant_annotation
-    - CHAIN_RHOCALL_VIZ:
+    - CHAIN_RHOVIZ:
       - rhocall_viz
+      - chromograph_rhoviz
     - CHAIN_UPD:
       - upd_ar
       - chromograph_upd

diff --git a/definitions/rd_dna_parameters.yaml b/definitions/rd_dna_parameters.yaml
@@ -142,6 +142,7 @@ recipe_core_number:
     cadd_ar: 13
     chanjo_sexcheck: 1
     chromograph_cov: 1
+    chromograph_rhoviz: 1
     chromograph_upd: 1
     cnvnator_ar: 13
     delly_call: 36
@@ -209,6 +210,7 @@ recipe_memory:
     cadd_ar: 6
     chanjo_sexcheck: 2
     chromograph_cov: 5
+    chromograph_rhoviz: 5
     chromograph_upd: 5
     delly_reformat: 3
     endvariantannotationblock: 8
@@ -253,6 +255,7 @@ recipe_time:
     cadd_ar: 10
     chanjo_sexcheck: 2
     chromograph_cov: 1
+    chromograph_rhoviz: 1
     chromograph_upd: 1
     cnvnator_ar: 1
     delly_call: 20
@@ -1593,6 +1596,17 @@ chromograph_cov:
   program_executables:
     - chromograph
   type: recipe
+chromograph_rhoviz:
+  analysis_mode: sample
+  associated_recipe:
+    - mip
+  data_type: SCALAR
+  default: 1
+  file_tag: ""
+  outfile_suffix: ".png"
+  program_executables:
+    - chromograph
+  type: recipe
 chromograph_upd:
   analysis_mode: sample
   associated_recipe:

diff --git a/lib/MIP/Cli/Mip/Analyse/Rd_dna.pm b/lib/MIP/Cli/Mip/Analyse/Rd_dna.pm
@@ -17,7 +17,7 @@ use Moose::Util::TypeConstraints;
 ## MIPs lib
 use MIP::Main::Analyse qw{ mip_analyse };
 
-our $VERSION = 1.61;
+our $VERSION = 1.62;
 
 extends(qw{ MIP::Cli::Mip::Analyse });
 
@@ -1565,20 +1565,29 @@ q{Prepare for variant annotation block by copying and splitting files per contig
     );
 
     option(
-        q{chromograph_ar} => (
+        q{chromograph_cov} => (
             cmd_tags      => [q{Analysis recipe switch}],
-            documentation => q{Chromograph},
+            documentation => q{Chromograph coverage},
             is            => q{rw},
             isa           => enum( [ 0, 1, 2 ] ),
         )
     );
 
     option(
-        q{chromograph_cytoband_file} => (
-            cmd_tags      => [q{Default: grch37_cytoband.bed}],
-            documentation => q{Cytoband bed file},
+        q{chromograph_rhoviz} => (
+            cmd_tags      => [q{Analysis recipe switch}],
+            documentation => q{Chromograph on rhocall_viz output},
             is            => q{rw},
-            isa           => Str,
+            isa           => enum( [ 0, 1, 2 ] ),
+        )
+    );
+
+    option(
+        q{chromograph_upd} => (
+            cmd_tags      => [q{Analysis recipe switch}],
+            documentation => q{Chromograph on upd output},
+            is            => q{rw},
+            isa           => enum( [ 0, 1, 2 ] ),
         )
     );
 

diff --git a/lib/MIP/Constants.pm b/lib/MIP/Constants.pm
@@ -20,7 +20,7 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.26;
+    our $VERSION = 1.27;
 
     # Functions and variables which can be optionally exported
 
@@ -80,7 +80,7 @@ Readonly our %ANALYSIS => (
 );
 
 ## Set MIP version
-Readonly our $MIP_VERSION => q{v9.0.6};
+Readonly our $MIP_VERSION => q{v9.1.0};
 
 ## Cli
 Readonly our $MOOSEX_APP_SCEEN_WIDTH => 160;

diff --git a/lib/MIP/Program/Chromograph.pm b/lib/MIP/Program/Chromograph.pm
@@ -25,7 +25,7 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.05;
+    our $VERSION = 1.06;
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ chromograph };
@@ -35,10 +35,12 @@ sub chromograph {
 
 ## Function : Perl wrapper for chromograph.
 ## Returns  : @commands
-## Arguments: $coverage_file_path     => Coverage data infile
+## Arguments: $autozyg_file_path      => Autozygosity data, bed file
+##          : $coverage_file_path     => Coverage data infile
 ##          : $euploid                => Generate png files for all chromosomes
 ##          : $filehandle             => Filehandle to write to
-##          : $ideo_file_path         => Bed file with ideogram data
+##          : $fracsnp_file_path      => Fraction of homozygous SNP, wig file
+##          : $ideogram_file_path     => Bed file with ideogram data
 ##          : $outdir_path            => Outdir path
 ##          : $stderrfile_path        => Stderrfile path
 ##          : $stderrfile_path_append => Append stderr info to file path
@@ -51,10 +53,12 @@ sub chromograph {
     my ($arg_href) = @_;
 
     ## Flatten argument(s)
+    my $autozyg_file_path;
     my $coverage_file_path;
     my $euploid;
     my $filehandle;
-    my $ideo_file_path;
+    my $fracsnp_file_path;
+    my $ideogram_file_path;
     my $outdir_path;
     my $stderrfile_path;
     my $stderrfile_path_append;
@@ -65,7 +69,13 @@ sub chromograph {
     my $upd_sites_file_path;
 
     my $tmpl = {
+        autozyg_file_path => {
+            allow       => qr/ [.] bed \z /xms,
+            store       => \$autozyg_file_path,
+            strict_type => 1,
+        },
         coverage_file_path => {
+            allow       => qr/ [.] wig \z /xms,
             store       => \$coverage_file_path,
             strict_type => 1,
         },
@@ -77,8 +87,14 @@ sub chromograph {
         filehandle => {
             store => \$filehandle,
         },
-        ideo_file_path => {
-            store       => \$ideo_file_path,
+        fracsnp_file_path => {
+            allow       => qr/ [.] wig \z /xms,
+            store       => \$fracsnp_file_path,
+            strict_type => 1,
+        },
+        ideogram_file_path => {
+            allow       => qr/ [.] bed \z /xms,
+            store       => \$ideogram_file_path,
             strict_type => 1,
         },
         outdir_path => {
@@ -106,10 +122,12 @@ sub chromograph {
             strict_type => 1,
         },
         upd_regions_file_path => {
+            allow       => qr/ [.] bed \z /xms,
             store       => \$upd_regions_file_path,
             strict_type => 1,
         },
         upd_sites_file_path => {
+            allow       => qr/ [.] bed \z /xms,
             store       => \$upd_sites_file_path,
             strict_type => 1,
         },
@@ -120,6 +138,11 @@ sub chromograph {
     ## Stores commands depending on input parameters
     my @commands = qw{ chromograph };
 
+    if ($autozyg_file_path) {
+
+        push @commands, q{--autozyg} . $SPACE . $autozyg_file_path;
+    }
+
     if ($coverage_file_path) {
 
         push @commands, q{--coverage} . $SPACE . $coverage_file_path;
@@ -130,9 +153,14 @@ sub chromograph {
         push @commands, q{--euploid};
     }
 
-    if ($ideo_file_path) {
+    if ($fracsnp_file_path) {
+
+        push @commands, q{--fracsnp} . $SPACE . $fracsnp_file_path;
+    }
+
+    if ($ideogram_file_path) {
 
-        push @commands, q{--ideo} . $SPACE . $ideo_file_path;
+        push @commands, q{--ideogram} . $SPACE . $ideogram_file_path;
     }
 
     push @commands, q{--outd} . $SPACE . $outdir_path;