changing name of prepare bam recipe

Clinical-Genomics · Apr 5, 2023 · 1c72a4c · 1c72a4c
1 parent 0b2daa7
commit 1c72a4c
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Showing 5 changed files with 9 additions and 9 deletions.
diff --git a/definitions/rd_dna_initiation_map.yaml b/definitions/rd_dna_initiation_map.yaml
@@ -50,7 +50,7 @@ CHAIN_ALL:
       - sv_reformat
       - vcf2cytosure_ar
     - CHAIN_MOBILE_ELEMENTS:
-      - merge_bam_me
+      - me_merge_bam
       - retroseq
   - CHAIN_MAIN:
     # PARALLEL chains, which inherit from MAIN in initiation, but are merged back to CHAIN_MAIN after execution

diff --git a/definitions/rd_dna_parameters.yaml b/definitions/rd_dna_parameters.yaml
@@ -226,7 +226,7 @@ recipe_core_number:
     gzip_fastq: 0
     manta: 36
     markduplicates: 13
-    merge_bam_me: 5
+    me_merge_bam: 5
     mitodel: 1
     mt_annotation: 1
     multiqc_ar: 1
@@ -358,7 +358,7 @@ recipe_time:
     gzip_fastq: 2
     manta: 30
     markduplicates: 20
-    merge_bam_me: 5
+    me_merge_bam: 5
     mitodel: 2
     mt_annotation: 1
     multiqc_ar: 5
@@ -1256,8 +1256,8 @@ sv_reformat_remove_genes_file:
   mandatory: no
   reference: reference_dir
   type: path
-## Mobile elenment chain
-merge_bam_me:
+## Mobile element chain
+me_merge_bam:
   analysis_mode: sample
   associated_recipe:
     - mip

diff --git a/lib/MIP/Cli/Mip/Analyse/Rd_dna.pm b/lib/MIP/Cli/Mip/Analyse/Rd_dna.pm
@@ -1157,7 +1157,7 @@ q{Default: hgvs, symbol, numbers, sift, polyphen, humdiv, domains, protein, ccds
     );
 
     option(
-        q{merge_bam_me} => (
+        q{me_merge_bam} => (
             cmd_tags      => [q{Analysis recipe switch}],
             documentation => q{Prepare bam files for RetroSeq},
             is            => q{rw},

diff --git a/lib/MIP/Recipes/Analysis/Samtools_merge.pm b/lib/MIP/Recipes/Analysis/Samtools_merge.pm
@@ -480,7 +480,7 @@ sub analysis_samtools_merge_panel {
     ## Special case for mobile elements
     my $stream_for_input      = q{in};
     my $recipe_name_for_input = $recipe_name;
-    if ( $recipe_name eq q{merge_bam_me} ) {
+    if ( $recipe_name eq q{me_merge_bam} ) {
 
         $recipe_name_for_input = $active_parameter_href->{bwa_mem2} ? q{bwa_mem2} : q{bwa_mem};
         $stream_for_input      = q{out};

diff --git a/lib/MIP/Recipes/Pipeline/Analyse_rd_dna.pm b/lib/MIP/Recipes/Pipeline/Analyse_rd_dna.pm
@@ -130,7 +130,7 @@ sub parse_rd_dna {
     Readonly my @ONLY_WGS_VARIANT_CALLER_RECIPES => qw{ cnvnator_ar delly_reformat tiddit };
     Readonly my @ONLY_WGS_RECIPIES =>
       qw{ chromograph_rhoviz cnvnator_ar delly_call delly_reformat expansionhunter
-      gatk_collectreadcounts gatk_denoisereadcounts gens_generatedata merge_bam_me mitodel
+      gatk_collectreadcounts gatk_denoisereadcounts gens_generatedata me_merge_bam mitodel
       retroseq samtools_subsample_mt smncopynumbercaller star_caller telomerecat_ar tiddit };
     Readonly my @REMOVE_CONFIG_KEYS => qw{ associated_recipe };
 
@@ -588,7 +588,7 @@ sub pipeline_analyse_rd_dna {
         gzip_fastq                         => \&analysis_gzip_fastq,
         manta                              => \&analysis_manta,
         markduplicates                     => \&analysis_markduplicates,
-        merge_bam_me                       => \&analysis_samtools_merge_panel,
+        me_merge_bam                       => \&analysis_samtools_merge_panel,
         mitodel                            => \&analysis_mitodel,
         mt_annotation                      => \&analysis_mt_annotation,
         multiqc_ar                         => \&analysis_multiqc,