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Fix input channels to kraken2

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This commit is contained in:
James Fellows Yates 2022-03-26 06:45:16 +01:00
parent 000f129dab
commit 120382f51d
1 changed files with 6 additions and 6 deletions
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12
workflows/taxprofiler.nf
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@ -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]
}