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Fix input to profiling

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This commit is contained in:
James Fellows Yates 2022-04-12 10:14:05 +02:00
parent 9f221f84cc
commit 2ef21c6ef3
2 changed files with 1 additions and 2 deletions
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1
subworkflows/local/profiling.nf
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@ -23,7 +23,6 @@ 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 = reads ch_input_for_profiling = reads
.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'

2
workflows/taxprofiler.nf
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@ -167,7 +167,7 @@ workflow TAXPROFILER {
SUBWORKFLOW: PROFILING SUBWORKFLOW: PROFILING
*/ */
PROFILING ( ch_reads_runmerged, ch_longreads_preprocessed, DB_CHECK.out.dbs ) PROFILING ( ch_reads_runmerged, DB_CHECK.out.dbs )
ch_versions = ch_versions.mix( PROFILING.out.versions ) ch_versions = ch_versions.mix( PROFILING.out.versions )
/* /*