remove test mode for analysis (#1741)

* remove test mode for analysis * update analyse test
Clinical-Genomics · Dec 3, 2020 · f18b023 · f18b023
1 parent 08d6151
commit f18b023
Show file tree

Hide file tree

Showing 8 changed files with 1 addition and 22 deletions.
diff --git a/definitions/analyse_parameters.yaml b/definitions/analyse_parameters.yaml
@@ -279,12 +279,6 @@ temp_directory:
     - mip
   data_type: SCALAR
   type: path
-test_mode:
-  associated_recipe:
-    - mip
-  data_type: SCALAR
-  mandatory: no
-  type: mip
 ## Version collecting
 version_collect_ar:
   analysis_mode: case

diff --git a/lib/MIP/Cli/Mip/Analyse.pm b/lib/MIP/Cli/Mip/Analyse.pm
@@ -361,16 +361,6 @@ q{Default: jobid, jobname%50, account, partition, alloccpus, TotalCPU, elapsed,
         )
     );
 
-    option(
-        q{test_mode} => (
-            documentation =>
-              q{Run MIP in test mode, i.e. not launching any child processes},
-            is       => q{rw},
-            isa      => Bool,
-            required => 0,
-        ),
-    );
-
     option(
         q{version_collect} => (
             cmd_tags      => [q{Analysis recipe switch}],

diff --git a/mip_install_perl.sh b/mip_install_perl.sh
@@ -71,7 +71,7 @@ else
   conda create --name "$ENV_NAME" --yes  -c conda-forge libgcc-ng gxx_linux-64=7.3.0 python=3.7.7
 fi
 
-conda install --name "$ENV_NAME" --yes -c bioconda -c conda-forge perl=5.26.2=h516909a_1006 perl-app-cpanminus perl-log-log4perl perl-moosex-app perl-file-copy-recursive perl-timedate perl-set-intervaltree perl-params-validate
+conda install --name "$ENV_NAME" --yes -c bioconda -c conda-forge perl=5.26.2=h516909a_1006 perl-app-cpanminus perl-log-log4perl perl-moosex-app perl-file-copy-recursive perl-timedate perl-set-intervaltree perl-params-validate bcftools=1.9=ha228f0b_4
 
 conda activate "$ENV_NAME"
 

diff --git a/t/mip_analyse_dragen_rd_dna.test b/t/mip_analyse_dragen_rd_dna.test
@@ -121,7 +121,6 @@ my $cmds_ref = [
     qw{ --dra --vb },
     q{--vcfanno_config},
     $toml_config_path,
-    q{--test_mode},
 ];
 
 my %process_return = child_process(

diff --git a/t/mip_analyse_rd_dna.test b/t/mip_analyse_rd_dna.test
@@ -145,7 +145,6 @@ my @cmds = (
         $cluster_constant_path,
         qw{ test_data 643594-miptest_sorted_md_brecal_comb_BOTH.bcf }
     ),
-    q{--test_mode},
 );
 
 PEDIGREE:

diff --git a/t/mip_analyse_rd_dna_panel.test b/t/mip_analyse_rd_dna_panel.test
@@ -118,7 +118,6 @@ my $cmds_ref = [
     $toml_config_path,
     q{--pedigree},
     catfile( $cluster_constant_path, qw{ 643594-miptest 643594-panel_pedigree.yaml } ),
-    q{--test_mode},
 ];
 
 my %process_return = child_process(

diff --git a/t/mip_analyse_rd_dna_vcf_rerun.test b/t/mip_analyse_rd_dna_vcf_rerun.test
@@ -119,7 +119,6 @@ my $cmds_ref = [
     qw{ --dra --vb },
     q{--vcfanno_config},
     $toml_config_path,
-    q{--test},
 ];
 
 my %process_return = child_process(

diff --git a/t/mip_analyse_rd_rna.test b/t/mip_analyse_rd_rna.test
@@ -101,7 +101,6 @@ my @base_cmds = (
         $cluster_constant_path, qw{ 118-rnatest test_data 118-2-2U fastq=118-2-2U }
     ),
     qw{--dra --vb },
-    q{--test_mode},
 );
 
 my %process_return = child_process(