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Fix language server errors in arriba/arriba #7845

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Merged
nvnieuwk merged 1 commit into from
Mar 18, 2025
Merged

Fix language server errors in arriba/arriba #7845

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16 changes: 8 additions & 8 deletions modules/nf-core/arriba/arriba/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -27,10 +27,10 @@ process ARRIBA_ARRIBA {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def blacklist = blacklist ? "-b $blacklist" : "-f blacklist"
def known_fusions = known_fusions ? "-k $known_fusions" : ""
def cytobands = cytobands ? "-d $cytobands" : ""
def protein_domains = protein_domains ? "-p $protein_domains" : ""
def blacklist_arg = blacklist ? "-b $blacklist" : "-f blacklist"
def known_fusions_arg = known_fusions ? "-k $known_fusions" : ""
def cytobands_arg = cytobands ? "-d $cytobands" : ""
def protein_domains_arg = protein_domains ? "-p $protein_domains" : ""

"""
arriba \\
Expand All @@ -39,10 +39,10 @@ process ARRIBA_ARRIBA {
-g $gtf \\
-o ${prefix}.fusions.tsv \\
-O ${prefix}.fusions.discarded.tsv \\
$blacklist \\
$known_fusions \\
$cytobands \\
$protein_domains \\
$blacklist_arg \\
$known_fusions_arg \\
$cytobands_arg \\
$protein_domains_arg \\
$args

cat <<-END_VERSIONS > versions.yml
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