Explicitly define all gridss index files to be symlinked

Accomodates users using externally created GRIDSS indexes that may contain clashing file names.
nf-core · Jun 5, 2024 · 6a26bee · 6a26bee
1 parent 3913694
commit 6a26bee
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Showing 4 changed files with 4 additions and 4 deletions.
diff --git a/modules/local/svprep/assemble/main.nf b/modules/local/svprep/assemble/main.nf
@@ -69,7 +69,7 @@ process GRIDSS_ASSEMBLE {
     done
 
     # Symlink indices next to assembly FASTA
-    ln -s \$(find -L ${genome_gridss_index} -type f) ./
+    ln -s \$(find -L ${genome_gridss_index} -regex '.*\.\(amb\|ann\|pac\|gridsscache\|sa\|bwa\|img\|alt\)') ./
 
     # Run
     gridss_svprep \\

diff --git a/modules/local/svprep/call/main.nf b/modules/local/svprep/call/main.nf
@@ -67,7 +67,7 @@ process GRIDSS_CALL {
     shadow_input_directory ${assemble_dir}
 
     # Symlink indices next to assembly FASTA
-    ln -s \$(find -L ${genome_gridss_index} -type f) ./
+    ln -s \$(find -L ${genome_gridss_index} -regex '.*\.\(amb\|ann\|pac\|gridsscache\|sa\|bwa\|img\|alt\)') ./
 
     # Run
     gridss_svprep \\

diff --git a/modules/local/svprep/preprocess/main.nf b/modules/local/svprep/preprocess/main.nf
@@ -29,7 +29,7 @@ process GRIDSS_PREPROCESS {
 
     """
     # Symlink indices next to assembly FASTA
-    ln -s \$(find -L ${genome_gridss_index} -type f) ./
+    ln -s \$(find -L ${genome_gridss_index} -regex '.*\.\(amb\|ann\|pac\|gridsscache\|sa\|bwa\|img\|alt\)') ./
 
     gridss_svprep \\
         ${args} \\

diff --git a/modules/local/virusbreakend/main.nf b/modules/local/virusbreakend/main.nf
@@ -29,7 +29,7 @@ process VIRUSBREAKEND {
 
     """
     # Symlink indices next to assembly FASTA
-    ln -s \$(find -L ${genome_gridss_index} -type f -name *.gridsscache -o -name *.img) ./
+    ln -s \$(find -L ${genome_gridss_index} -regex '.*\.\(amb\|ann\|pac\|gridsscache\|sa\|bwa\|img\|alt\)') ./
 
     virusbreakend \\
         ${args} \\