Merge 2dbd369 into b3ebb15

Clinical-Genomics · Jan 22, 2021 · fbe2c8e · fbe2c8e
2 parents b3ebb15 + 2dbd369
commit fbe2c8e
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Showing 7 changed files with 71 additions and 79 deletions.
diff --git a/definitions/rd_rna_initiation_map.yaml b/definitions/rd_rna_initiation_map.yaml
@@ -2,7 +2,6 @@
 CHAIN_ALL:
   - CHAIN_MAIN:
     - gzip_fastq
-  # Parallel chains (branch)
   - CHAIN_FASTQC:
     - fastqc_ar
   - CHAIN_MAIN:
@@ -17,27 +16,26 @@ CHAIN_ALL:
   - CHAIN_MAIN:
     - star_aln
     - picardtools_mergesamfiles
-    - CHAIN_PTCRM:
-      - picardtools_collectrnaseqmetrics
     - CHAIN_STRINGTIE:
       - stringtie_ar
       - gffcompare_ar
     - CHAIN_QC:
       - PARALLEL:
+        - picardtools_collectrnaseqmetrics
         - preseq_ar
         - rseqc
         - genebody_coverage
-  - CHAIN_ASE:
-    - markduplicates
-    - gatk_splitncigarreads
-    - gatk_baserecalibration
-    - gatk_haplotypecaller
-    - gatk_variantfiltration
-    - dna_vcf_reformat
-    - gatk_asereadcounter
-    - bootstrapann
-    - bcftools_merge
-    - varianteffectpredictor
+    - CHAIN_ASE:
+      - markduplicates
+      - gatk_splitncigarreads
+      - gatk_baserecalibration
+      - gatk_haplotypecaller
+      - gatk_variantfiltration
+      - dna_vcf_reformat
+      - gatk_asereadcounter
+      - bootstrapann
+      - bcftools_merge
+      - varianteffectpredictor
   - qccollect_ar
   - version_collect_ar
   - multiqc_ar

diff --git a/definitions/rd_rna_parameters.yaml b/definitions/rd_rna_parameters.yaml
@@ -131,15 +131,15 @@ recipe_time:
     fastqc_ar: 1
     gatk_asereadcounter: 2
     gatk_baserecalibration: 5
-    gatk_haplotypecaller: 4
+    gatk_haplotypecaller: 6
     gatk_splitncigarreads: 8
     gatk_variantfiltration: 1
     genebody_coverage: 3
     gffcompare_ar: 1
     gzip_fastq: 2
     markduplicates: 8
     multiqc_ar: 1
-    picardtools_collectrnaseqmetrics: 1
+    picardtools_collectrnaseqmetrics: 2
     picardtools_mergesamfiles: 2
     preseq_ar: 2
     qccollect_ar: 1
@@ -163,12 +163,12 @@ recipe_memory:
     dna_vcf_reformat: 2
     gatk_asereadcounter: 25
     gatk_variantfiltration: 8
-    genebody_coverage: 8
+    genebody_coverage: 12
     multiqc_ar: 10
     picardtools_collectrnaseqmetrics: 5
     picardtools_mergesamfiles: 5
     preseq_ar: 8
-    rseqc: 25
+    rseqc: 30
     salmon_quant: 2
     star_aln: 3
     star_fusion: 3
@@ -277,6 +277,7 @@ salmon_quant:
   file_tag: quant
   outfile_suffix: ".sf"
   program_executables:
+    - pigz
     - salmon
   type: recipe
 salmon_quant_reference_genome:

diff --git a/lib/MIP/Program/Pigz.pm b/lib/MIP/Program/Pigz.pm
@@ -60,31 +60,29 @@ sub pigz {
     my $verbose;
 
     my $tmpl = {
+        decompress  => { store => \$decompress, strict_type => 1, },
+        filehandle  => { store => \$filehandle, },
         infile_path => {
             defined     => 1,
-            required    => 1,
             store       => \$infile_path,
             strict_type => 1,
         },
-        stdout       => { store => \$stdout,       strict_type => 1, },
-        decompress   => { store => \$decompress,   strict_type => 1, },
         outfile_path => { store => \$outfile_path, strict_type => 1, },
         processes    => {
             allow       => qr{ \A\d+\z }sxm,
             store       => \$processes,
             strict_type => 1,
         },
-        filehandle      => { store => \$filehandle, },
-        stderrfile_path => { store => \$stderrfile_path, strict_type => 1, },
-        stderrfile_path_append =>
-          { store => \$stderrfile_path_append, strict_type => 1, },
         quiet => {
             allow       => [ 0, 1 ],
             default     => 0,
             store       => \$quiet,
             strict_type => 1,
         },
-        verbose => {
+        stderrfile_path        => { store => \$stderrfile_path,        strict_type => 1, },
+        stderrfile_path_append => { store => \$stderrfile_path_append, strict_type => 1, },
+        stdout                 => { store => \$stdout,                 strict_type => 1, },
+        verbose                => {
             allow       => [ 0, 1 ],
             default     => 0,
             store       => \$verbose,
@@ -96,6 +94,11 @@ sub pigz {
 
     my @commands = ( get_executable_base_command( { base_command => q{pigz} } ), );
 
+    if ($decompress) {
+
+        push @commands, q{--decompress};
+    }
+
     if ($processes) {
 
         push @commands, q{--processes} . $SPACE . $processes;
@@ -106,23 +109,21 @@ sub pigz {
         push @commands, q{--quiet};
     }
 
-    if ($verbose) {
+    if ($stdout) {
 
-        push @commands, q{--verbose};
+        push @commands, q{--stdout};
     }
 
-    if ($decompress) {
+    if ($verbose) {
 
-        push @commands, q{--decompress};
+        push @commands, q{--verbose};
     }
 
-    if ($stdout) {
+    if ($infile_path) {
 
-        push @commands, q{--stdout};
+        push @commands, $infile_path;
     }
 
-    push @commands, $infile_path;
-
     if ($outfile_path) {
 
         push @commands, q{>} . $SPACE . $outfile_path;

diff --git a/lib/MIP/Program/Salmon.pm b/lib/MIP/Program/Salmon.pm
@@ -136,13 +136,13 @@ sub salmon_quant {
     my $outdir_path;
     my $read_1_fastq_paths_ref;
     my $read_2_fastq_paths_ref;
+    my $read_files_command;
     my $stderrfile_path;
     my $stderrfile_path_append;
     my $stdoutfile_path;
 
     ## Default(s)
     my $lib_type;
-    my $read_files_command;
     my $validate_mappings;
 
     my $tmpl = {
@@ -185,7 +185,8 @@ sub salmon_quant {
             strict_type => 1,
         },
         read_files_command => {
-            default     => q{pigz -dc},
+            required    => 1,
+            defined     => 1,
             store       => \$read_files_command,
             strict_type => 1,
         },

diff --git a/lib/MIP/Recipes/Analysis/Salmon_quant.pm b/lib/MIP/Recipes/Analysis/Salmon_quant.pm
@@ -17,7 +17,7 @@ use List::MoreUtils qw{ uniq };
 use Readonly;
 
 ## MIPs lib/
-use MIP::Constants qw{ $LOG_NAME $NEWLINE };
+use MIP::Constants qw{ $LOG_NAME $NEWLINE $SPACE };
 
 BEGIN {
 
@@ -129,6 +129,7 @@ sub analysis_salmon_quant {
 
     use MIP::File_info qw{ get_sample_file_attribute };
     use MIP::File_info qw{ get_io_files parse_io_outfiles };
+    use MIP::Program::Pigz qw{ pigz };
     use MIP::Program::Salmon qw{ salmon_quant };
     use MIP::Processmanagement::Processes qw{ submit_recipe };
     use MIP::Recipe qw{ parse_recipe_prerequisites };
@@ -230,6 +231,13 @@ sub analysis_salmon_quant {
         }
     );
 
+    my @read_file_commands = pigz(
+        {
+            decompress => 1,
+            stdout     => 1,
+        }
+    );
+
     ## For paired end
     if ( $sequence_run_type eq q{paired-end} ) {
 
@@ -249,6 +257,8 @@ sub analysis_salmon_quant {
                 outdir_path            => $outdir_path,
                 read_1_fastq_paths_ref => \@read_1_fastq_paths,
                 read_2_fastq_paths_ref => \@read_2_fastq_paths,
+                read_files_command     => join $SPACE,
+                @read_file_commands,
             }
         );
         say {$filehandle} $NEWLINE;
@@ -263,6 +273,8 @@ sub analysis_salmon_quant {
                 index_path             => $referencefile_dir_path,
                 outdir_path            => $outdir_path,
                 read_1_fastq_paths_ref => \@infile_paths,
+                read_files_command     => join $SPACE,
+                @read_file_commands,
             }
         );
         say {$filehandle} $NEWLINE;

diff --git a/t/pigz.t b/t/pigz.t
@@ -23,16 +23,13 @@ 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::Pigz}  => [qw{ pigz }],
-);
+    my %perl_module = ( q{MIP::Program::Pigz} => [qw{ pigz }], );
 
     test_import( { perl_module_href => \%perl_module, } );
 }
@@ -57,24 +54,15 @@ my %base_argument = (
     },
 );
 
-## Can be duplicated with %base_argument and/or %specific_argument
-## to enable testing of each individual argument
-my %required_argument = (
-    filehandle => {
-        input           => undef,
-        expected_output => \@function_base_commands,
-    },
-    infile_path => {
-        input           => q{infile_path},
-        expected_output => q{infile_path},
-    },
-);
-
 my %specific_argument = (
     decompress => {
         input           => q{decompress},
         expected_output => q{--decompress},
     },
+    infile_path => {
+        input           => q{infile_path},
+        expected_output => q{infile_path},
+    },
     outfile_path => {
         input           => q{outfile_path},
         expected_output => q{> outfile_path},
@@ -109,20 +97,13 @@ my %specific_argument = (
 ## Coderef - enables generalized use of generate call
 my $module_function_cref = \&pigz;
 
-## Test both base and function specific arguments
-my @arguments = ( \%required_argument, \%specific_argument );
-
-HASHES_OF_ARGUMENTS:
-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,
-        }
-    );
-}
+my @commands = test_function(
+    {
+        argument_href              => \%specific_argument,
+        do_test_base_command       => 1,
+        function_base_commands_ref => \@function_base_commands,
+        module_function_cref       => $module_function_cref,
+    }
+);
 
 done_testing();
diff --git a/t/salmon_quant.t b/t/salmon_quant.t
@@ -23,16 +23,13 @@ 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::Salmon} => [qw{ salmon_quant }],
-);
+    my %perl_module = ( q{MIP::Program::Salmon} => [qw{ salmon_quant }], );
 
     test_import( { perl_module_href => \%perl_module, } );
 }
@@ -81,8 +78,7 @@ my %required_argument = (
         expected_output => q{--output} . $SPACE . catdir(qw{ dir output_dir }),
     },
     read_1_fastq_paths_ref => {
-        inputs_ref =>
-          [ catfile(qw{ dir hi_r1.fastq.gz }), catfile(qw{ dir hello_r1.fastq.gz }) ],
+        inputs_ref => [ catfile(qw{ dir hi_r1.fastq.gz }), catfile(qw{ dir hello_r1.fastq.gz }) ],
         expected_output => q{-1}
           . $SPACE . q{<(}
           . $READ_FILES_COMMAND
@@ -92,6 +88,10 @@ my %required_argument = (
           . catfile(qw{ dir hello_r1.fastq.gz })
           . $SPACE . q{)}
     },
+    read_files_command => {
+        input           => $READ_FILES_COMMAND,
+        expected_output => $READ_FILES_COMMAND,
+    },
 );
 
 my %specific_argument = (
@@ -108,8 +108,7 @@ my %specific_argument = (
         expected_output => q{--output} . $SPACE . catdir(qw{ dir output_dir }),
     },
     read_1_fastq_paths_ref => {
-        inputs_ref =>
-          [ catfile(qw{ dir hi_r1.fastq.gz }), catfile(qw{ dir hello_r1.fastq.gz }) ],
+        inputs_ref => [ catfile(qw{ dir hi_r1.fastq.gz }), catfile(qw{ dir hello_r1.fastq.gz }) ],
         expected_output => q{-1}
           . $SPACE . q{<(}
           . $READ_FILES_COMMAND
@@ -120,8 +119,7 @@ my %specific_argument = (
           . $SPACE . q{)}
     },
     read_2_fastq_paths_ref => {
-        inputs_ref =>
-          [ catfile(qw{ dir hi_r2.fastq.gz }), catfile(qw{ dir hello_r2.fastq.gz }) ],
+        inputs_ref => [ catfile(qw{ dir hi_r2.fastq.gz }), catfile(qw{ dir hello_r2.fastq.gz }) ],
         expected_output => q{-2}
           . $SPACE . q{<(}
           . $READ_FILES_COMMAND