From 4e2b85f3429730667cc4aa1c909848141525bd24 Mon Sep 17 00:00:00 2001 From: LilyAnderssonLee Date: Thu, 5 Sep 2024 13:45:40 +0200 Subject: [PATCH] separate fasta into fasta_shrt and fasta_long --- workflows/taxprofiler.nf | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/workflows/taxprofiler.nf b/workflows/taxprofiler.nf index e500ca0c..93eb55dd 100644 --- a/workflows/taxprofiler.nf +++ b/workflows/taxprofiler.nf @@ -139,9 +139,12 @@ workflow TAXPROFILER { nanopore: instrument_platform == 'OXFORD_NANOPORE' && !meta.is_fasta meta.single_end = true return [ meta + [ type: "long" ], [ fastq_1 ] ] - fasta: meta.is_fasta + fasta_short: meta.is_fasta && instrument_platform == 'ILLUMINA' meta.single_end = true return [ meta + [ type: "short" ], [ fasta ] ] + fasta_long: meta.is_fasta && instrument_platform == 'OXFORD_NANOPORE' + meta.single_end = true + return [ meta + [ type: "long" ], [ fasta ] ] } // Merge ch_input.fastq and ch_input.nanopore into a single channel @@ -289,13 +292,13 @@ workflow TAXPROFILER { meta, reads -> [ meta, [ reads ].flatten() ] } - .mix( ch_input.fasta ) + .mix( ch_input.fasta_short, ch_input.fasta_long) ch_versions = ch_versions.mix(MERGE_RUNS.out.versions) } else { ch_reads_runmerged = ch_shortreads_hostremoved - .mix( ch_longreads_hostremoved, ch_input.fasta ) + .mix( ch_longreads_hostremoved, ch_input.fasta_short, ch_input.fasta_long ) } /*