Merge 8ece2e4 into 46a3a2d

containers/hmtnote/Dockerfile

@@ -0,0 +1,23 @@
+################## BASE IMAGE ######################
+
+FROM clinicalgenomics/mip_base:2.1
+
+################## METADATA ######################
+
+LABEL base_image="clinicalgenomics/mip_base:2.1"
+LABEL version="1"
+LABEL software="HmtNote"
+LABEL software.version="0.7.2"
+LABEL extra.binaries="HmtNote"
+LABEL maintainer="Clinical-Genomics/MIP"
+
+RUN conda install pip python=3.7
+
+## Clean up after conda
+RUN /opt/conda/bin/conda clean -tipsy
+
+RUN pip install --no-cache-dir hmtnote==0.7.2
+
+RUN hmtnote dump
+
+WORKDIR /data/

definitions/install_parameters.yaml

@@ -81,6 +81,7 @@ rd_dna:
     - gatk4
     - genmod
     - glnexus
+    - hmtnote
     - htslib
     - manta
     - mip

lib/MIP/Cli/Mip/Install.pm

@@ -132,7 +132,7 @@ sub _build_usage {
                     [
                         qw{ arriba bedtools blobfish bootstrapann bwa bwakit bwa-mem2 cadd chanjo
                           chromograph cnvnator cyrius deeptrio deepvariant delly expansionhunter fastqc gatk
-                          gatk4 genmod gffcompare glnexus htslib manta megafusion mip mip_scripts multiqc
+                          gatk4 genmod gffcompare glnexus hmtnote htslib manta megafusion mip mip_scripts multiqc
                           pdfmerger perl peddy picard plink preseq python rhocall rseqc rtg-tools salmon sambamba
                           smncopynumbercaller star star-fusion stranger stringtie svdb telomerecat tiddit
                           trim-galore ucsc upd utilities varg vcf2cytosure vcfanno vep vts }
@@ -154,7 +154,7 @@ sub _build_usage {
                     [
                         qw{ arriba bedtools blobfish bootstrapann bwa bwakit bwa-mem2 cadd chanjo
                           chromograph cnvnator cyrius deeptrio deepvariant delly expansionhunter fastqc gatk
-                          gatk4 genmod gffcompare glnexus htslib manta megafusion mip mip_scripts multiqc
+                          gatk4 genmod gffcompare glnexus hmtnote htslib manta megafusion mip mip_scripts multiqc
                           pdfmerger perl peddy picard plink preseq python rhocall rseqc rtg-tools salmon sambamba
                           smncopynumbercaller star star-fusion stranger stringtie svdb telomerecat tiddit
                           trim-galore ucsc upd utilities varg vcf2cytosure vcfanno vep vts }

lib/MIP/Program/HmtNote.pm

@@ -0,0 +1,131 @@
+package MIP::Program::HmtNote;
+
+use 5.026;
+use Carp;
+use charnames qw{ :full :short };
+use English qw{ -no_match_vars };
+use open qw{ :encoding(UTF-8) :std };
+use Params::Check qw{ allow check last_error };
+use utf8;
+use warnings;
+use warnings qw{ FATAL utf8 };
+
+## CPANM
+use autodie qw{ :all };
+use Readonly;
+
+## MIPs lib/
+use MIP::Constants qw{ $SPACE };
+use MIP::Environment::Executable qw{ get_executable_base_command };
+use MIP::Unix::Standard_streams qw{ unix_standard_streams };
+use MIP::Unix::Write_to_file qw{ unix_write_to_file };
+
+BEGIN {
+    require Exporter;
+    use base qw{ Exporter };
+
+    # Set the version for version checking
+    # Functions and variables which can be optionally exported
+    our @EXPORT_OK = qw{ hmtnote_annotate };
+}
+
+Readonly my $BASE_COMMAND => q{hmtnote};
+
+sub hmtnote_annotate {
+
+## Function : Perl wrapper for hmtnote version 0.7.2
+## Returns  : @commands
+## Arguments: $filehandle             => Filehandle to write to
+##          : $infile_path            => Input.vcf
+##          : $offline                => An argument if running the command offline
+##          : $outfile_path           => Annotate.vcf
+##          : $stderrfile_path        => Stderrfile path
+##          : $stderrfile_path_append => Append stderr info to file path
+##          : $stdinfile_path         => Stdinfile path
+##          : $stdoutfile_path        => Stdoutfile path
+
+    my ($arg_href) = @_;
+
+    ## Flatten argument(s)
+    my $filehandle;
+    my $infile_path;
+    my $offline;
+    my $outfile_path;
+    my $stderrfile_path;
+    my $stderrfile_path_append;
+    my $stdinfile_path;
+    my $stdoutfile_path;
+
+    ## Default(s)
+
+    my $tmpl = {
+        filehandle => {
+            store => \$filehandle,
+        },
+        infile_path => {
+            defined     => 1,
+            required    => 1,
+            store       => \$infile_path,
+            strict_type => 1,
+        },
+        offline => {
+            allow       => [ undef, 0, 1 ],
+            store       => \$offline,
+            strict_type => 1,
+        },
+        outfile_path => {
+            defined     => 1,
+            required    => 1,
+            store       => \$outfile_path,
+            strict_type => 1,
+        },
+        stderrfile_path => {
+            store       => \$stderrfile_path,
+            strict_type => 1,
+        },
+        stderrfile_path_append => {
+            store       => \$stderrfile_path_append,
+            strict_type => 1,
+        },
+        stdinfile_path  => { store => \$stdinfile_path, strict_type => 1, },
+        stdoutfile_path => {
+            store       => \$stdoutfile_path,
+            strict_type => 1,
+        },
+    };
+
+    check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
+
+    my @commands =
+      ( get_executable_base_command( { base_command => $BASE_COMMAND, } ), qw{ annotate } );
+
+    push @commands, $infile_path;
+    push @commands, $outfile_path;
+
+    if ($offline) {
+
+        push @commands, q{--offline};
+    }
+
+    push @commands,
+      unix_standard_streams(
+        {
+            stderrfile_path        => $stderrfile_path,
+            stderrfile_path_append => $stderrfile_path_append,
+            stdinfile_path         => $stdinfile_path,
+            stdoutfile_path        => $stdoutfile_path,
+        }
+      );
+
+    unix_write_to_file(
+        {
+            commands_ref => \@commands,
+            filehandle   => $filehandle,
+            separator    => $SPACE,
+
+        }
+    );
+    return @commands;
+}
+
+1;

t/hmtnote_annotate.t

@@ -0,0 +1,116 @@
+#!/usr/bin/env perl
+
+use 5.026;
+use Carp;
+use charnames qw{ :full :short };
+use English qw{ -no_match_vars };
+use File::Basename qw{ dirname };
+use File::Spec::Functions qw{ catdir };
+use FindBin qw{ $Bin };
+use open qw{ :encoding(UTF-8) :std };
+use Params::Check qw{ allow check last_error };
+use Test::More;
+use utf8;
+use warnings qw{ FATAL utf8 };
+
+## CPANM
+use autodie qw{ :all };
+use Modern::Perl qw{ 2018 };
+
+## MIPs lib/
+use lib catdir( dirname($Bin), q{lib} );
+use MIP::Constants qw{ $COMMA $SPACE };
+use MIP::Test::Commands qw{ test_function };
+
+BEGIN {
+
+    use MIP::Test::Fixtures qw{ test_import };
+
+### Check all internal dependency modules and imports
+## Modules with import
+    my %perl_module = ( q{MIP::Program::HmtNote} => [qw{ hmtnote_annotate }], );
+
+    test_import( { perl_module_href => \%perl_module, } );
+}
+
+use MIP::Program::HmtNote qw{ hmtnote_annotate };
+
+diag(   q{Test hmtnote_annotate from HmtNote.pm}
+      . $COMMA
+      . $SPACE . q{Perl}
+      . $SPACE
+      . $PERL_VERSION
+      . $SPACE
+      . $EXECUTABLE_NAME );
+
+## Base arguments
+my @function_base_commands = qw{ hmtnote };
+
+my %base_argument = (
+    filehandle => {
+        input           => undef,
+        expected_output => \@function_base_commands,
+    },
+    stderrfile_path => {
+        input           => q{stderrfile.test},
+        expected_output => q{2> stderrfile.test},
+    },
+    stderrfile_path_append => {
+        input           => q{stderrfile.test},
+        expected_output => q{2>> stderrfile.test},
+    },
+    stdoutfile_path => {
+        input           => q{stdoutfile.test},
+        expected_output => q{1> stdoutfile.test},
+    },
+);
+
+## Can be duplicated with %base_argument and/or %specific_argument
+## to enable testing of each individual argument
+my %required_argument = (
+    infile_path => {
+        input           => q{myfile.vcf},
+        expected_output => q{myfile.vcf},
+    },
+    outfile_path => {
+        input           => q{outfile.vcf},
+        expected_output => q{outfile.vcf},
+    },
+);
+
+my %specific_argument = (
+    offline => {
+        input           => 1,
+        expected_output => q{--offline},
+    },
+    infile_path => {
+        input           => q{myfile.vcf},
+        expected_output => q{myfile.vcf},
+    },
+    outfile_path => {
+        input           => q{outfile.vcf},
+        expected_output => q{outfile.vcf},
+    },
+);
+
+## Coderef - enables generalized use of generate call
+my $module_function_cref = \&hmtnote_annotate;
+
+## Test both base and function specific arguments
+my @arguments = ( \%base_argument, \%specific_argument );
+
+ARGUMENT_HASH_REF:
+foreach my $argument_href (@arguments) {
+
+    my @commands = test_function(
+        {
+            argument_href              => $argument_href,
+            do_test_base_command       => 1,
+            function_base_commands_ref => \@function_base_commands,
+            module_function_cref       => $module_function_cref,
+            required_argument_href     => \%required_argument,
+        }
+    );
+}
+
+done_testing();

templates/mip_install_config.yaml

@@ -98,6 +98,10 @@ container:
     executable:
       glnexus_cli:
     uri: quay.io/mlin/glnexus:v1.3.1
+  hmtnote:
+    executable:
+      hmtnote:
+    uri: docker.io/clinicalgenomics/hmtnote:0.7.2
   htslib:
     executable:
       bcftools: