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Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2 changed files with 0 additions and 8 deletions
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@ -159,7 +159,6 @@ if (!params.igenomes_ignore) {
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env {
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PYTHONNOUSERSITE = '1'
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// PYTHONUTF8 = '1' // MetaPhlAn3 may fail with a UnicodeDecodeError if the locale is not set appropriately.
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R_PROFILE_USER = "/.Rprofile"
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R_ENVIRON_USER = "/.Renviron"
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JULIA_DEPOT_PATH = "/usr/local/share/julia"
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@ -127,10 +127,3 @@ workflow SHORTREAD_ADAPTERREMOVAL {
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mqc = ch_multiqc_files
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}
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def ensureFastQExtension(row) {
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def (meta, read) = row
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def filename = file(read.parent).resolve("${read.baseName}.fastq.gz")
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read.renameTo(filename.toString())
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return [meta, read]
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}
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