feat(sample_id): disable sample_id in filename check

Clinical-Genomics · Jan 15, 2021 · 8b49948 · 8b49948
1 parent d8e54ec
commit 8b49948
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Showing 5 changed files with 43 additions and 6 deletions.
diff --git a/definitions/analyse_parameters.yaml b/definitions/analyse_parameters.yaml
@@ -79,6 +79,12 @@ exclude_contigs:
   data_type: ARRAY
   mandatory: no
   type: mip
+external_data:
+  associated_recipe:
+    - mip
+  data_type: SCALAR
+  mandatory: no
+  type: mip
 case_id:
   associated_recipe:
     - mip

diff --git a/lib/MIP/Active_parameter.pm b/lib/MIP/Active_parameter.pm
@@ -1273,6 +1273,7 @@ sub parse_infiles {
         ## Check infiles found and that they contain sample_id
         check_infiles(
             {
+                external_data    => $active_parameter_href->{external_data},
                 infiles_ref      => \@infiles,
                 infile_directory => $infile_directory,
                 sample_id        => $sample_id,

diff --git a/lib/MIP/Cli/Mip/Analyse.pm b/lib/MIP/Cli/Mip/Analyse.pm
@@ -66,6 +66,15 @@ q{Check analysis output and sets the analysis run status flag to finished in sam
         )
     );
 
+    parameter(
+        q{case_id} => (
+            documentation => q{Group id of samples to be compared},
+            is            => q{rw},
+            isa           => Str,
+            required      => 1,
+        )
+    );
+
     option(
         q{cluster_constant_path} => (
             documentation => q{Set the cluster constant path},
@@ -136,12 +145,11 @@ q{Check analysis output and sets the analysis run status flag to finished in sam
         )
     );
 
-    parameter(
-        q{case_id} => (
-            documentation => q{Group id of samples to be compared},
+    option(
+        q{external_data} => (
+            documentation => q{Disable checks of fastq filename},
             is            => q{rw},
-            isa           => Str,
-            required      => 1,
+            isa           => Bool,
         )
     );
 

diff --git a/lib/MIP/Validate/Case.pm b/lib/MIP/Validate/Case.pm
@@ -29,18 +29,25 @@ sub check_infiles {
 
 ## Function : Check infiles found and that they contain sample_id
 ## Returns  :
-## Arguments: $infiles_ref      => Infiles to check {REF}
+## Arguments: $external data    => Skip check on external data
+##          : $infiles_ref      => Infiles to check {REF}
 ##          : $infile_directory => Infile directory
 ##          : $sample_id        => Sample id
 
     my ($arg_href) = @_;
 
     ## Flatten argument(s)
+    my $external_data;
     my $infiles_ref;
     my $infile_directory;
     my $sample_id;
 
     my $tmpl = {
+        external_data => {
+            allow       => [ undef, 0, 1 ],
+            store       => \$external_data,
+            strict_type => 1,
+        },
         infile_directory => {
             defined     => 1,
             required    => 1,
@@ -74,6 +81,8 @@ sub check_infiles {
         exit 1;
     }
 
+    return 1 if ($external_data);
+
     ## Check that infiledirs/infile contains sample_id in filename
   INFILE:
     foreach my $infile ( @{$infiles_ref} ) {

diff --git a/t/check_infiles.t b/t/check_infiles.t
@@ -130,4 +130,17 @@ my $is_ok = check_infiles(
 ## Then return true
 ok( $is_ok, q{Passed check} );
 
+## Given external indata
+$is_ok = check_infiles(
+    {
+        external_data    => 1,
+        infiles_ref      => \@wrong_infiles,
+        infile_directory => $infile_directory,
+        sample_id        => $sample_id,
+    }
+);
+
+## Then return true
+ok( $is_ok, q{Passed check for external data} );
+
 done_testing();