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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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Moritz E. Beber 2022-04-03 00:21:09 +02:00 committed by GitHub
parent be93eae640
commit f5baf910be
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2 changed files with 0 additions and 8 deletions
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1
nextflow.config
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@ -159,7 +159,6 @@ if (!params.igenomes_ignore) {
env { env {
PYTHONNOUSERSITE = '1' PYTHONNOUSERSITE = '1'
// PYTHONUTF8 = '1' // MetaPhlAn3 may fail with a UnicodeDecodeError if the locale is not set appropriately.
R_PROFILE_USER = "/.Rprofile" R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron" R_ENVIRON_USER = "/.Renviron"
JULIA_DEPOT_PATH = "/usr/local/share/julia" JULIA_DEPOT_PATH = "/usr/local/share/julia"

7
subworkflows/local/shortread_adapterremoval.nf
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@ -127,10 +127,3 @@ workflow SHORTREAD_ADAPTERREMOVAL {
mqc = ch_multiqc_files mqc = ch_multiqc_files
} }
def ensureFastQExtension(row) {
def (meta, read) = row
def filename = file(read.parent).resolve("${read.baseName}.fastq.gz")
read.renameTo(filename.toString())
return [meta, read]
}