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symlink specific gridss index files
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genome_gridss_index folder may contain additional files that are staged by nextflow if they are part of the inputs (e.g. someone might have the .dict file in this folder if they created it via gridss.PrepareReference). This causes an error when we try to symlink the entire contents of the folder. Could we change this line to symlink the specific files of interest?
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casslitch authored Jun 4, 2024
1 parent 3dd1e03 commit 3913694
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion modules/local/virusbreakend/main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ process VIRUSBREAKEND {

"""
# Symlink indices next to assembly FASTA
ln -s \$(find -L ${genome_gridss_index} -type f) ./
ln -s \$(find -L ${genome_gridss_index} -type f -name *.gridsscache -o -name *.img) ./
virusbreakend \\
${args} \\
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