Merge 745f473 into ce1c9b5

.travis.yml

@@ -7,11 +7,6 @@ sudo: required
 before_install:
 ## Install SSL
   - sudo apt-get update
-#  - sudo apt-get install libssl1.0.0 libssl-dev libcrypto++9 libcrypto++-dev
-#  - cd /lib/x86_64-linux-gnu
-#  - sudo ln -s libssl.so.1.0.0 libssl.so.10
-#  - sudo ln -s libcrypto.so.1.0.0 libcrypto.so.10
-#  - cd -
 
 ## Install conda
 ##  - wget https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
@@ -46,9 +41,6 @@ install:
 script:
 ## Test MIP rd_dna
   - conda activate mip_travis
-#  - cd /lib/x86_64-linux-gnu
-#  - sudo ln -s "$ROOTSYS"/lib/*so .
-#  - cd -
 ## Set-up test coverage for test directory "t"
   - PERL5OPT=-MDevel::Cover=-ignore,"^t/",+ignore,"prove",-coverage,statement,branch,condition,path,subroutine prove -lrs -j 9 t
 ### Download
@@ -63,6 +55,8 @@ script:
   - PERL5OPT=-MDevel::Cover=-ignore,"^t/",-coverage,statement,branch,condition,path,subroutine perl t/mip_analyse_rd_dna_vcf_rerun.test
 ## Set-up test coverage for mip qccollect
   - PERL5OPT=-MDevel::Cover=-ignore,"^t/",-coverage,statement,branch,condition,path,subroutine perl mip qccollect --log_file qc_metrics_qccollect.log --regexp_file t/data/references/qc_regexp_-v1.22-.yaml --sample_info_file t/data/test_data/643594-miptest_qc_sample_info_travis.yaml --evaluate_plink_gender --outfile qc_metrics.yaml
+## Set-up test coverage for mip_analyse_vcf_rerun.test
+  - PERL5OPT=-MDevel::Cover=-ignore,"^t/",-coverage,statement,branch,condition,path,subroutine perl t/mip_analyse_dragen_rd_dna.test
 ## Set-up test coverage for mip_analyse_rna.test
   - conda activate MIP_rd_rna
   - PERL5OPT=-MDevel::Cover=-ignore,"^t/",-coverage,statement,branch,condition,path,subroutine perl t/mip_analyse_rd_rna.test 

definitions/dragen_rd_dna_initiation_map.yaml

@@ -0,0 +1,23 @@
+CHAIN_ALL:
+   - CHAIN_MAIN:
+      - dragen_dna
+      - CHAIN_SV:
+         - sv_annotate
+         - sv_varianteffectpredictor
+         - sv_vcfparser
+         - sv_rankvariant
+         - sv_reformat
+         - vcf2cytosure_ar
+   - CHAIN_MAIN:
+      - prepareforvariantannotationblock
+      - rhocall_ar
+      - vt_ar
+      - frequency_filter
+      - cadd_ar
+      - varianteffectpredictor
+      - vcfparser_ar
+      - snpeff
+      - rankvariant
+      - endvariantannotationblock
+   - analysisrunstatus
+   - sacct 

definitions/rd_dna_dragen_parameters.yaml → definitions/dragen_rd_dna_parameters.yaml

@@ -7,7 +7,6 @@ decompose_normalize_references:
   default:
    - fqf_vcfanno_config
    - snpsift_annotation_files
-   - sv_vcfanno_config
   element_separator: ,
   type: mip
 gatk_logging_level:
@@ -44,6 +43,21 @@ human_genome_reference_file_endings:
   mandatory: no
   reference: reference_dir
   type: path
+infile_dirs:
+  associated_recipe:
+   - mip
+  exists_check: directory
+  data_type: HASH
+  type: path
+  update_path: absolute_path
+picardtools_path:
+  associated_recipe:
+#   - dragen_dna
+   - prepareforvariantannotationblock
+  data_type: SCALAR
+  exists_check: directory
+  type: path
+  update_path: absolute_path
 ####Bash
 recipe_core_number:
   associated_recipe:
@@ -77,8 +91,8 @@ recipe_memory:
     snpeff: 8
     sv_reformat: 24
     sv_varianteffectpredictor: 7
-    varianteffectpredictor: 3
-    vcf2cytosure_ar: 2
+    varianteffectpredictor: 7
+    vcf2cytosure_ar: 6
   type: mip
 recipe_time:
   associated_recipe:
@@ -99,7 +113,6 @@ recipe_time:
     sv_rankvariant: 3
     sv_reformat: 1
     sv_varianteffectpredictor: 10
-    sv_vcf_rerun_reformat: 1
     sv_vcfparser: 2
     varianteffectpredictor: 10
     vcfparser_ar: 5
@@ -119,9 +132,24 @@ dragen_dna:
    - mip
   data_type: SCALAR
   default: 1
-  file_tag: _dragen
+  file_tag: _drg
   outfile_suffix: ".vcf"
+#  program_executables:
+ #  - dragen
   type: recipe
+dragen_fastq_list_file_path:
+  associated_recipe:
+   - dragen_dna
+  data_type: SCALAR
+  type: path
+dragen_hash_ref_dir_path:
+  associated_recipe:
+   - dragen_dna
+#  build_file: 1
+  data_type: SCALAR
+  exists_check: directory
+  reference: reference_dir
+  type: path
 sv_annotate:
   analysis_mode: case
   associated_recipe:
@@ -159,33 +187,6 @@ sv_svdb_query_db_files:
   exists_check: file
   reference: reference_dir
   type: path
-sv_vcfanno:
-  associated_recipe:
-   - sv_annotate
-  data_type: SCALAR
-  default: 0
-  type: recipe_argument
-sv_vcfannotation_header_lines_file:
-  associated_recipe:
-   - sv_annotate
-  data_type: SCALAR
-  exists_check: file
-  reference: reference_dir
-  type: path
-sv_vcfanno_config:
-  associated_recipe:
-   - sv_annotate
-  data_type: SCALAR
-  exists_check: file
-  reference: reference_dir
-  type: path
-sv_vcfanno_lua:
-  associated_recipe:
-   - sv_annotate
-  data_type: SCALAR
-  exists_check: file
-  reference: reference_dir
-  type: path
 sv_varianteffectpredictor:
   analysis_mode: case
   associated_recipe:

lib/MIP/Check/Pedigree.pm

@@ -199,7 +199,7 @@ sub check_pedigree_sample_allowed_values {
     check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
 
     my %allowed_values = (
-        analysis_type => [qw{ wes wgs vrn wts }],
+        analysis_type => [qw{ dragen_rd_dna vrn wes wgs wts }],
         phenotype     => [qw{ affected unaffected unknown }],
         sex           => [qw{ female male other unknown }],
     );