feat(cadd): cd into temp dir

CHANGELOG.md

@@ -5,6 +5,7 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 ## [9.0.4]
 - Increased memory allocation for samtools_subsample_mt
 - Check that vep plugin paths exists prior to executing mip
+- Cd into cadd temp directory before executing cadd in order to escape snakemake lock errors
 
 ## [9.0.3]
 - Changed path and name of slurm job ids file to facilitate analysis monitoring

lib/MIP/Recipes/Analysis/Cadd.pm

@@ -26,7 +26,7 @@ BEGIN {
     use base qw{ Exporter };
 
     # Set the version for version checking
-    our $VERSION = 1.08;
+    our $VERSION = 1.09;
 
     # Functions and variables which can be optionally exported
     our @EXPORT_OK = qw{ analysis_cadd analysis_cadd_panel };
@@ -123,7 +123,7 @@ sub analysis_cadd {
 
     use MIP::Get::File qw{ get_io_files };
     use MIP::Get::Parameter qw{ get_recipe_attributes get_recipe_resources };
-    use MIP::Program::Gnu::Bash qw{ gnu_export gnu_unset };
+    use MIP::Program::Gnu::Bash qw{ gnu_cd gnu_export gnu_unset };
     use MIP::Program::Gnu::Coreutils qw{ gnu_mkdir };
     use MIP::Parse::File qw{ parse_io_outfiles };
     use MIP::Program::Bcftools qw{ bcftools_annotate bcftools_concat bcftools_view };
@@ -326,6 +326,16 @@ sub analysis_cadd {
         );
         print {$xargsfilehandle} $SEMICOLON . $SPACE;
 
+        ## Attempt to escape snakemake lock
+        gnu_cd(
+            {
+                filehandle             => $xargsfilehandle,
+                directory_path         => $temp_outdir_path{$contig},
+                stderrfile_path_append => $stderrfile_path,
+            }
+        );
+        print {$xargsfilehandle} $SEMICOLON . $SPACE;
+
         cadd(
             {
                 filehandle             => $xargsfilehandle,