From 120382f51d184bed0375ab8c642f6bdab77a617f Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Sat, 26 Mar 2022 06:45:16 +0100 Subject: [PATCH] Fix input channels to kraken2 --- workflows/taxprofiler.nf | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/workflows/taxprofiler.nf b/workflows/taxprofiler.nf index 0a907bf..c1d7f34 100644 --- a/workflows/taxprofiler.nf +++ b/workflows/taxprofiler.nf @@ -37,11 +37,11 @@ ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multi // // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules // -include { INPUT_CHECK } from '../subworkflows/local/input_check' +include { INPUT_CHECK } from '../subworkflows/local/input_check' -include { DB_CHECK } from '../subworkflows/local/db_check' +include { DB_CHECK } from '../subworkflows/local/db_check' include { SHORTREAD_PREPROCESSING } from '../subworkflows/local/shortread_preprocessing' -include { LONGREAD_PREPROCESSING } from '../subworkflows/local/longread_preprocessing' +include { LONGREAD_PREPROCESSING } from '../subworkflows/local/longread_preprocessing' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -171,7 +171,7 @@ workflow TAXPROFILER { [ temp_meta, it[1], db ] } .groupTuple(by: [0,2]) - .dump(tag: "input for malt") + .dump(tag: "input_for_malt") .multiMap { it -> reads: [ it[0], it[1].flatten() ] @@ -180,10 +180,10 @@ workflow TAXPROFILER { // We can run Kraken2 one-by-one sample-wise ch_input_for_kraken2 = ch_input_for_profiling.kraken2 - .dump(tag: "input for kraken") + .dump(tag: "input_for_kraken") .multiMap { it -> - reads: [ it[0] + it[2], it[1] ] + reads: [ it[0] + it[2], it[1].flatten() ] db: it[3] }