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Append pairment to ID at profiling to prevent multiqc-level filename crash
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parent
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commit
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1 changed files with 8 additions and 5 deletions
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@ -147,8 +147,6 @@ workflow TAXPROFILER {
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skip: true
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}
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ch_reads_for_cat_branch.cat.dump(tag: "for_catting")
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ch_reads_runmerged = CAT_FASTQ ( ch_reads_for_cat_branch.cat ).reads
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.mix( ch_reads_for_cat_branch.skip )
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.map {
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@ -157,8 +155,6 @@ workflow TAXPROFILER {
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[ meta, [ reads ].flatten() ]
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}
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ch_reads_runmerged.dump(tag: "ch_reads_runmerged" )
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} else {
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ch_reads_runmerged = ch_shortreads_filtered
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.mix( ch_longreads_preprocessed )
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@ -168,8 +164,15 @@ workflow TAXPROFILER {
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COMBINE READS WITH POSSIBLE DATABASES
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*/
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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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// 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 = ch_reads_runmerged
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.map {
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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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.combine(DB_CHECK.out.dbs)
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.branch {
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malt: it[2]['tool'] == 'malt'
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