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This commit is contained in:
James Fellows Yates 2022-12-03 21:38:25 +01:00
parent cf8ad96771
commit 0dccfddc24
1 changed files with 1 additions and 5 deletions
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6
subworkflows/local/profiling.nf
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@ -147,14 +147,10 @@ workflow PROFILING {
def ch_kraken2_output = KRAKEN2_KRAKEN2.out.report
.filter {
meta, report ->
meta['tool'] == 'bracken' && meta['instrument_platform'] != 'OXFORD_NANOPORE'
if ( meta['instrument_platform'] == 'OXFORD_NANOPORE' ) log.warn "[nf-core/taxprofiler] Bracken has not been evaluated for Nanopore data. Skipping Bracken for sample ${meta.id}."
meta['tool'] == 'bracken' && meta['instrument_platform'] != 'OXFORD_NANOPORE'
}
// If necessary, convert the eight column output to six column output.
if (params.kraken2_save_minimizers) {
ch_kraken2_output = KRAKEN2_STANDARD_REPORT(ch_kraken2_output).report