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Fix variable typo in amrfinderplus/run #3892

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merged 2 commits into from
Sep 28, 2023
Merged

Fix variable typo in amrfinderplus/run #3892

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4b7584d
Fix variable typo in amrfinderplus
jasmezz Sep 28, 2023
1f2bed4
Merge branch 'master' into fix_amrfinderplus
jasmezz Sep 28, 2023
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2 changes: 1 addition & 1 deletion modules/nf-core/amrfinderplus/run/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ process AMRFINDERPLUS_RUN {
script:
def args = task.ext.args ?: ''
def is_compressed_fasta = fasta.getName().endsWith(".gz") ? true : false
def is_compressed_db = fasta.getName().endsWith(".gz") ? true : false
def is_compressed_db = db.getName().endsWith(".gz") ? true : false
prefix = task.ext.prefix ?: "${meta.id}"
organism_param = meta.containsKey("organism") ? "--organism ${meta.organism} --mutation_all ${prefix}-mutations.tsv" : ""
fasta_name = fasta.getName().replace(".gz", "")
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