Merge ea36613 into 0e268ce

Clinical-Genomics · Sep 14, 2021 · 617ec9b · 617ec9b
2 parents 0e268ce + ea36613
commit 617ec9b
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Showing 38 changed files with 1,058 additions and 96 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,6 +9,7 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 - Updating to latest and greatest versions
 - Mitochondrial deletion analysis
 - GATK Haplotypecaller has been turned off in favour of Deepvariant
+- Introduces possibility to store singularity images locally as a .sif file
 
 ### Tools
 

diff --git a/definitions/analyse_parameters.yaml b/definitions/analyse_parameters.yaml
@@ -84,7 +84,7 @@ case_id:
     - mip
   data_type: SCALAR
   type: mip
-install_config_file:
+container_config_file:
   associated_recipe:
     - mip
   data_type: SCALAR

diff --git a/definitions/download_parameters.yaml b/definitions/download_parameters.yaml
@@ -124,7 +124,7 @@ custom_default_parameters:
     - mip
   data_type: ARRAY
   default:
-    - install_config_file
+    - container_config_file
     - reference_dir
     - temp_directory
   type: mip
@@ -281,7 +281,7 @@ human_reference:
   program_executables:
     - samtools
   type: recipe
-install_config_file:
+container_config_file:
   associated_recipe:
     - mip
   data_type: SCALAR

diff --git a/definitions/dragen_rd_dna_parameters.yaml b/definitions/dragen_rd_dna_parameters.yaml
@@ -8,7 +8,7 @@ custom_default_parameters:
     - conda_path
     - exome_target_bed
     - infile_dirs
-    - install_config_file
+    - container_config_file
     - pedigree_fam_file
     - picardtools_path
     - reference_dir

diff --git a/definitions/install_parameters.yaml b/definitions/install_parameters.yaml
@@ -147,12 +147,25 @@ container:
   data_type: HASH
   mandatory: no
   type: mip
+container_directory_path:
+  associated_recipe:
+    - mip
+  data_type: SCALAR
+  mandatory: no
+  type: path
+  update_path: absolute_path
 select_programs:
   associated_recipe:
     - mip
   data_type: ARRAY
   mandatory: no
   type: mip
+singularity_local_install:
+  associated_recipe:
+    - mip
+  data_type: SCALAR
+  mandatory: no
+  type: mip
 skip_programs:
   associated_recipe:
     - mip

diff --git a/definitions/rd_dna_panel_parameters.yaml b/definitions/rd_dna_panel_parameters.yaml
@@ -10,7 +10,7 @@ custom_default_parameters:
     - bwa_mem2_build_reference
     - exome_target_bed
     - infile_dirs
-    - install_config_file
+    - container_config_file
     - pedigree_fam_file
     - picardtools_path
     - qccollect_store_metrics_outfile

diff --git a/definitions/rd_dna_parameters.yaml b/definitions/rd_dna_parameters.yaml
@@ -10,7 +10,7 @@ custom_default_parameters:
     - bwa_mem2_build_reference
     - exome_target_bed
     - infile_dirs
-    - install_config_file
+    - container_config_file
     - pedigree_fam_file
     - picardtools_path
     - qccollect_store_metrics_outfile

diff --git a/definitions/rd_dna_vcf_rerun_parameters.yaml b/definitions/rd_dna_vcf_rerun_parameters.yaml
@@ -8,7 +8,7 @@ custom_default_parameters:
     - conda_path
     - exome_target_bed
     - infile_dirs
-    - install_config_file
+    - container_config_file
     - pedigree_fam_file
     - picardtools_path
     - reference_dir

diff --git a/definitions/rd_rna_parameters.yaml b/definitions/rd_rna_parameters.yaml
@@ -8,7 +8,7 @@ custom_default_parameters:
     - conda_path
     - fusion_select_file
     - infile_dirs
-    - install_config_file
+    - container_config_file
     - pedigree_fam_file
     - picardtools_path
     - qccollect_store_metrics_outfile

diff --git a/lib/MIP/Active_parameter.pm b/lib/MIP/Active_parameter.pm
@@ -50,9 +50,9 @@ BEGIN {
       remove_sample_id_from_gender
       set_conda_paths
       set_default_analysis_type
+      set_default_container_config_file
       set_default_human_genome
       set_default_infile_dirs
-      set_default_install_config_file
       set_default_parameter
       set_default_pedigree_fam_file
       set_default_program_test_file
@@ -2215,7 +2215,7 @@ sub set_include_y {
     return;
 }
 
-sub set_default_install_config_file {
+sub set_default_container_config_file {
 
 ## Function : Set default install config file to active parameters
 ## Returns  :
@@ -2242,7 +2242,7 @@ sub set_default_install_config_file {
     check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
 
     ## Build default for mip install config
-    my $path = catfile( $Bin, qw{ templates mip_install_config.yaml } );
+    my $path = catfile( $Bin, qw{ templates mip_container_config.yaml } );
 
     $active_parameter_href->{$parameter_name} = $path;
     return;

diff --git a/lib/MIP/Cli/Mip/Analyse.pm b/lib/MIP/Cli/Mip/Analyse.pm
@@ -155,7 +155,7 @@ q{Check analysis output and sets the analysis run status flag to finished in sam
     );
 
     option(
-        q{install_config_file} => (
+        q{container_config_file} => (
             documentation => q{File with install configuration parameters in YAML format},
             is            => q{rw},
             isa           => Str,

diff --git a/lib/MIP/Cli/Mip/Download.pm b/lib/MIP/Cli/Mip/Download.pm
@@ -101,6 +101,14 @@ sub _build_usage {
         )
     );
 
+    option(
+        q{container_config_file} => (
+            documentation => q{File with install configuration parameters in YAML format},
+            is            => q{rw},
+            isa           => Str,
+        )
+    );
+
     option(
         q{core_ram_memory} => (
             cmd_tags      => [q{Default: 5}],
@@ -148,7 +156,7 @@ sub _build_usage {
     );
 
     option(
-        q{install_config_file} => (
+        q{container_config_file} => (
             documentation => q{File with install configuration parameters in YAML format},
             is            => q{rw},
             isa           => Str,

diff --git a/lib/MIP/Cli/Mip/Install.pm b/lib/MIP/Cli/Mip/Install.pm
@@ -78,6 +78,16 @@ sub _build_usage {
         )
     );
 
+    option(
+        q{container_directory_path} => (
+            cmd_tags      => [q{Default: "<conda_path>/<env>/bin"}],
+            documentation =>
+              q{Save singularity images to directory. Requires singularity_local_install option},
+            is  => q{rw},
+            isa => Str,
+        )
+    );
+
     option(
         q{environment_name} => (
             cmd_aliases   => [qw{ envn }],
@@ -143,6 +153,17 @@ sub _build_usage {
         ),
     );
 
+    option(
+        q{singularity_local_install} => (
+            cmd_tags      => [q{Default: off}],
+            documentation =>
+q{Save singularity images to sif and update run instructions for offline mip execution},
+            is       => q{rw},
+            isa      => Bool,
+            required => 0,
+        ),
+    );
+
     option(
         q{skip_programs} => (
             cmd_aliases   => [qw{ skip }],

diff --git a/lib/MIP/Config.pm b/lib/MIP/Config.pm
@@ -94,32 +94,32 @@ sub check_cmd_config_vs_definition_file {
 sub get_install_containers {
 
 ## Function : Get install containers from install config file
-## Returns  : $install_config{container}
-## Arguments: $install_config_file => File with containers from install config
+## Returns  : $container_config
+## Arguments: $container_config_file => File with containers from install config
 
     my ($arg_href) = @_;
 
     ## Flatten argument(s)
-    my $install_config_file;
+    my $container_config_file;
 
     my $tmpl = {
-        install_config_file => {
+        container_config_file => {
             defined     => 1,
             required    => 1,
-            store       => \$install_config_file,
+            store       => \$container_config_file,
             strict_type => 1,
         },
     };
 
     check( $tmpl, $arg_href, 1 ) or croak q{Could not parse arguments!};
 
-    my %install_config = read_from_file(
+    my %container_config = read_from_file(
         {
             format => q{yaml},
-            path   => $install_config_file,
+            path   => $container_config_file,
         }
     );
-    return %{ $install_config{container} };
+    return %container_config;
 }
 
 sub parse_config {