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Start adding filter for long read and MP3

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This commit is contained in:
James Fellows Yates 2023-01-24 11:50:10 +01:00
parent d3bad1d720
commit 9205831273
1 changed files with 5 additions and 2 deletions
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7
subworkflows/local/profiling.nf
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@ -202,8 +202,11 @@ workflow PROFILING {
ch_input_for_metaphlan3 = ch_input_for_profiling.metaphlan3 ch_input_for_metaphlan3 = ch_input_for_profiling.metaphlan3
.filter{ .filter{
if (it[0].is_fasta) log.warn "[nf-core/taxprofiler] MetaPhlAn3 currently does not accept FASTA files as input. Skipping MetaPhlAn3 for sample ${it[0].id}." meta, report ->
!it[0].is_fasta 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'
} }
.multiMap { .multiMap {
it -> it ->