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Remove metaphlan profiling for nanopore as it appears to always result in 100% unclassified

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James Fellows Yates 2023-01-24 13:05:52 +01:00
parent 9205831273
commit 0358489be0
1 changed files with 2 additions and 5 deletions
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7
subworkflows/local/profiling.nf
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@ -202,11 +202,8 @@ workflow PROFILING {
ch_input_for_metaphlan3 = ch_input_for_profiling.metaphlan3
.filter{
meta, report ->
if (meta.is_fasta) log.warn "[nf-core/taxprofiler] MetaPhlAn3 currently does not accept FASTA files as input. Skipping MetaPhlAn3 for sample ${meta.id}."
!meta.is_fasta
if ( meta['instrument_platform'] == 'OXFORD_NANOPORE' ) log.warn "[nf-core/taxprofiler] MetaPhlAn3 has not been evaluated for Nanopore data. Skipping MetaPhlAn3 for sample ${meta.id}."
meta['tool'] == 'metaphlan3' && meta['instrument_platform'] != 'OXFORD_NANOPORE'
if (it[0].is_fasta || it[0].instrument_platform == 'OXFORD_NANOPORE' ) log.warn "[nf-core/taxprofiler] MetaPhlAn3 currently does not accept FASTA files as input and/or has not been evaluated for Nanopore data. Skipping MetaPhlAn3 for sample ${it[0].id}."
!(it[0].is_fasta || it[0].instrument_platform == 'OXFORD_NANOPORE')
}
.multiMap {
it ->