feat(rna_recipes): removing seperate markduplicates recipe for rna

Clinical-Genomics · Jan 20, 2021 · 1966e5f · 1966e5f
1 parent 3b2149d
commit 1966e5f
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Showing 6 changed files with 68 additions and 612 deletions.
diff --git a/definitions/rd_dna_parameters.yaml b/definitions/rd_dna_parameters.yaml
@@ -502,6 +502,7 @@ markduplicates:
   outfile_suffix: ".bam"
   program_executables:
     - picard
+    - samtools
   type: recipe
 markduplicates_picardtools_opt_dup_dist:
   associated_recipe:

diff --git a/definitions/rd_rna_parameters.yaml b/definitions/rd_rna_parameters.yaml
@@ -198,7 +198,7 @@ recipe_core_number:
     gffcompare_ar: 1
     gzip_fastq: 0
     multiqc_ar: 1
-    markduplicates: 16
+    markduplicates: 13
     picardtools_collectrnaseqmetrics: 1
     picardtools_mergesamfiles: 13
     preseq_ar: 1
@@ -524,7 +524,7 @@ markduplicates:
   outfile_suffix: ".bam"
   program_executables:
     - picard
-    - sambamba
+    - samtools
   type: recipe
 markduplicates_picardtools_opt_dup_dist:
   associated_recipe:

diff --git a/lib/MIP/Recipes/Analysis/Gatk_baserecalibration.pm b/lib/MIP/Recipes/Analysis/Gatk_baserecalibration.pm
@@ -149,7 +149,6 @@ sub analysis_gatk_baserecalibration {
     use MIP::Parse::File qw{ parse_io_outfiles };
     use MIP::Processmanagement::Processes qw{ submit_recipe };
     use MIP::Program::Gatk qw{ gatk_applybqsr gatk_baserecalibrator gatk_gatherbqsrreports };
-    use MIP::Program::Picardtools qw{ picardtools_gatherbamfiles };
     use MIP::Program::Samtools qw{ samtools_index samtools_view };
     use MIP::Recipe qw{ parse_recipe_prerequisites };
     use MIP::Recipes::Analysis::Xargs qw{ xargs_command };
@@ -384,68 +383,6 @@ sub analysis_gatk_baserecalibration {
         say {$xargsfilehandle} $NEWLINE;
     }
 
-    ## Gather BAM files
-    say {$filehandle} q{## Gather BAM files};
-
-    ## Assemble infile paths in contig order and not per size
-    my @gather_infile_paths =
-      map { $outfile_path{$_} } @{ $file_info_href->{bam_contigs} };
-    my $store_outfile_path = $outfile_path_prefix . $outfile_suffix;
-
-    picardtools_gatherbamfiles(
-        {
-            create_index     => q{true},
-            filehandle       => $filehandle,
-            infile_paths_ref => \@gather_infile_paths,
-            java_jar => catfile( $active_parameter_href->{picardtools_path}, q{picard.jar} ),
-            java_use_large_pages => $active_parameter_href->{java_use_large_pages},
-            memory_allocation    => q{Xmx4g},
-            outfile_path         => $outfile_path_prefix . $outfile_suffix,
-            referencefile_path   => $referencefile_path,
-            temp_directory       => $temp_directory,
-        }
-    );
-    say {$filehandle} $NEWLINE;
-
-    ## Rename the bam file index file so that Expansion Hunter can find it
-    say {$filehandle}
-      q{## Copy index file to ".bam.bai" so that Expansionhunter can find it downstream};
-
-    gnu_cp(
-        {
-            filehandle   => $filehandle,
-            force        => 1,
-            infile_path  => $outfile_path_prefix . q{.bai},
-            outfile_path => $outfile_path_prefix . $outfile_suffix . q{.bai},
-        }
-    );
-    say {$filehandle} $NEWLINE;
-
-    ## Create BAM to CRAM for long term storage
-
-    $store_outfile_path = $outfile_path_prefix . $DOT . q{cram};
-
-    say {$filehandle} q{## Convert BAM to CRAM for long term storage};
-    samtools_view(
-        {
-            filehandle         => $filehandle,
-            infile_path        => $outfile_path_prefix . $outfile_suffix,
-            outfile_path       => $store_outfile_path,
-            output_format      => q{cram},
-            referencefile_path => $referencefile_path,
-            thread_number      => $parallel_processes,
-        }
-    );
-    say {$filehandle} $NEWLINE;
-
-    ## Index CRAM
-    samtools_index(
-        {
-            filehandle  => $filehandle,
-            infile_path => $store_outfile_path,
-        }
-    );
-
     close $xargsfilehandle;
     close $filehandle;
 
@@ -455,24 +392,13 @@ sub analysis_gatk_baserecalibration {
         set_recipe_outfile_in_sample_info(
             {
                 infile           => $outfile_name_prefix,
-                path             => $store_outfile_path,
+                path             => $outfile_paths[0],
                 recipe_name      => $recipe_name,
                 sample_id        => $sample_id,
                 sample_info_href => $sample_info_href,
             }
         );
 
-        set_file_path_to_store(
-            {
-                format           => q{cram},
-                id               => $sample_id,
-                path             => $store_outfile_path,
-                path_index       => $store_outfile_path . $DOT . q{crai},
-                recipe_name      => $recipe_name,
-                sample_info_href => $sample_info_href,
-            }
-        );
-
         submit_recipe(
             {
                 base_command                      => $profile_base_command,
@@ -589,9 +515,8 @@ sub analysis_gatk_baserecalibration_panel {
     use MIP::Parse::File qw{ parse_io_outfiles };
     use MIP::Processmanagement::Processes qw{ submit_recipe };
     use MIP::Program::Gatk qw{ gatk_applybqsr gatk_baserecalibrator };
-    use MIP::Program::Samtools qw{ samtools_index samtools_view };
     use MIP::Recipe qw{ parse_recipe_prerequisites };
-    use MIP::Sample_info qw{ set_file_path_to_store set_recipe_outfile_in_sample_info };
+    use MIP::Sample_info qw{ set_recipe_outfile_in_sample_info };
     use MIP::Script::Setup_script qw{ setup_script };
 
     ### PREPROCESSING:
@@ -730,30 +655,6 @@ sub analysis_gatk_baserecalibration_panel {
     );
     say {$filehandle} $NEWLINE;
 
-    ## Create BAM to CRAM for long term storage
-    my $store_outfile_path = $outfile_path_prefix . $DOT . q{cram};
-
-    say {$filehandle} q{## Convert BAM to CRAM for long term storage};
-    samtools_view(
-        {
-            filehandle         => $filehandle,
-            infile_path        => $outfile_path,
-            outfile_path       => $store_outfile_path,
-            output_format      => q{cram},
-            referencefile_path => $referencefile_path,
-            thread_number      => $parallel_processes,
-        }
-    );
-    say {$filehandle} $NEWLINE;
-
-    ## Index CRAM
-    samtools_index(
-        {
-            filehandle  => $filehandle,
-            infile_path => $store_outfile_path,
-        }
-    );
-
     close $filehandle;
 
     if ( $recipe{mode} == 1 ) {
@@ -762,24 +663,13 @@ sub analysis_gatk_baserecalibration_panel {
         set_recipe_outfile_in_sample_info(
             {
                 infile           => $outfile_name_prefix,
-                path             => $store_outfile_path,
+                path             => $outfile_path,
                 recipe_name      => $recipe_name,
                 sample_id        => $sample_id,
                 sample_info_href => $sample_info_href,
             }
         );
 
-        set_file_path_to_store(
-            {
-                format           => q{cram},
-                id               => $sample_id,
-                path             => $store_outfile_path,
-                path_index       => $store_outfile_path . $DOT . q{crai},
-                recipe_name      => $recipe_name,
-                sample_info_href => $sample_info_href,
-            }
-        );
-
         submit_recipe(
             {
                 base_command                      => $profile_base_command,