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Re-add pairment attachment
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@ -23,6 +23,12 @@ workflow PROFILING {
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// 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]
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ch_input_for_profiling = reads
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.combine(databases)
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meta, reads ->
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def meta_new = meta.clone()
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pairtype = meta_new['single_end'] ? '_se' : '_pe'
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meta_new['id'] = meta_new['id'] + pairtype
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[meta_new, reads]
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}
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.branch {
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malt: it[2]['tool'] == 'malt'
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kraken2: it[2]['tool'] == 'kraken2'
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