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Only supply single input channel to profiling, as these are merged into single input channel at run_merging

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James Fellows Yates 2022-04-12 10:12:17 +02:00
parent 967b1f7d6e
commit 9f221f84cc
1 changed files with 3 additions and 4 deletions
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7
subworkflows/local/profiling.nf
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@ -9,8 +9,7 @@ include { METAPHLAN3 } from '../../modules/nf-core/modules/meta
workflow PROFILING { workflow PROFILING {
take: take:
shortreads // [ [ meta ], [ reads ] ] reads // [ [ meta ], [ reads ] ]
longreads // [ [ meta ], [ reads ] ]
databases // [ [ meta ], path ] databases // [ [ meta ], path ]
main: main:
@ -22,9 +21,9 @@ workflow PROFILING {
*/ */
// e.g. output [DUMP: reads_plus_db] [['id':'2612', 'run_accession':'combined', 'instrument_platform':'ILLUMINA', 'single_end':1], <reads_path>/2612.merged.fastq.gz, ['tool':'malt', 'db_name':'mal95', 'db_params':'"-id 90"'], <db_path>/malt90] // e.g. output [DUMP: reads_plus_db] [['id':'2612', 'run_accession':'combined', 'instrument_platform':'ILLUMINA', 'single_end':1], <reads_path>/2612.merged.fastq.gz, ['tool':'malt', 'db_name':'mal95', 'db_params':'"-id 90"'], <db_path>/malt90]
ch_input_for_profiling = shortreads ch_input_for_profiling = reads
.mix( longreads )
.combine(databases) .combine(databases)
.dump(tag: "combined_withdbs")
.branch { .branch {
malt: it[2]['tool'] == 'malt' malt: it[2]['tool'] == 'malt'
kraken2: it[2]['tool'] == 'kraken2' kraken2: it[2]['tool'] == 'kraken2'