From 4d7afc9cb1b4e50b98c632b5c28f03978d463327 Mon Sep 17 00:00:00 2001 From: Daniel Lundin Date: Tue, 3 Oct 2023 15:09:04 +0200 Subject: [PATCH 1/2] Typo --- subworkflows/local/eggnog.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/eggnog.nf b/subworkflows/local/eggnog.nf index 83cf3485..b9aa6ff6 100644 --- a/subworkflows/local/eggnog.nf +++ b/subworkflows/local/eggnog.nf @@ -26,7 +26,7 @@ workflow EGGNOG { if ( ! eggnogfile.exists() ) { EGGNOG_DOWNLOAD() - ch_dpath = EGGNOG_DOWNLOAD.out.db + ch_dbpath = EGGNOG_DOWNLOAD.out.db ch_versions = ch_versions.mix ( EGGNOG_DOWNLOAD.out.versions ) } else { From 73dcd9c214749b20efc8033929fac86c673d2bf8 Mon Sep 17 00:00:00 2001 From: Daniel Lundin Date: Tue, 24 Oct 2023 12:39:31 +0200 Subject: [PATCH 2/2] One can't interleave single end reads --- workflows/metatdenovo.nf | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/workflows/metatdenovo.nf b/workflows/metatdenovo.nf index 96d59bee..5e92beff 100644 --- a/workflows/metatdenovo.nf +++ b/workflows/metatdenovo.nf @@ -264,9 +264,7 @@ workflow METATDENOVO { ch_interleaved = Channel.empty() if ( ! params.assembly ) { if ( params.se_reads) { - SEQTK_MERGEPE(ch_clean_reads) - ch_interleaved_se = SEQTK_MERGEPE.out.reads - ch_versions = ch_versions.mix(SEQTK_MERGEPE.out.versions) + ch_single_end = ch_clean_reads } else { SEQTK_MERGEPE(ch_clean_reads) ch_interleaved = SEQTK_MERGEPE.out.reads @@ -280,11 +278,11 @@ workflow METATDENOVO { if ( ! params.assembly ) { if ( params.se_reads ) { if ( params.bbnorm ) { - BBMAP_BBNORM(ch_interleaved_se.collect { meta, fastq -> fastq }.map {[ [id:'all_samples', single_end:true], it ] } ) + BBMAP_BBNORM(ch_single_end.collect { meta, fastq -> fastq }.map {[ [id:'all_samples', single_end:true], it ] } ) ch_se_reads_to_assembly = BBMAP_BBNORM.out.fastq.map { it[1] } ch_pe_reads_to_assembly = Channel.empty() } else { - ch_se_reads_to_assembly = ch_interleaved_se.map { meta, fastq -> fastq } + ch_se_reads_to_assembly = ch_single_end.map { meta, fastq -> fastq } ch_pe_reads_to_assembly = Channel.empty() } }