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chore: remove fixme comments
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4 changed files with 0 additions and 6 deletions
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@ -45,8 +45,6 @@ workflow LONGREAD_HOSTREMOVAL {
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SAMTOOLS_INDEX ( MINIMAP2_ALIGN.out.bam )
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ch_versions = ch_versions.mix( SAMTOOLS_INDEX.out.versions.first() )
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// FIXME: This join is performed using entire maps as keys.
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// Please replace with joining on specific keys instead.
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bam_bai = MINIMAP2_ALIGN.out.bam
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.join(SAMTOOLS_INDEX.out.bai)
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@ -87,7 +87,6 @@ workflow PROFILING {
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[ new_meta, reads, db ]
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}
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// FIXME: Groups elements in the channel using the meta map as key. Replace with grouping on specific keys.
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.groupTuple(by: [0,2])
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.multiMap {
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meta, reads, db ->
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@ -321,7 +320,6 @@ workflow PROFILING {
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meta, reads, db_meta, db ->
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[[id: db_meta.db_name, single_end: meta.single_end], reads, db_meta, db]
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}
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// FIXME: Groups elements in the channel using the meta map as key. Replace with grouping on specific keys.
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.groupTuple(by: [0,2,3])
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.multiMap {
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single_meta, reads, db_meta, db ->
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@ -30,7 +30,6 @@ workflow STANDARDISATION_PROFILES {
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meta_new.tool = meta.tool == 'metaphlan3' ? 'metaphlan' : meta.tool == 'malt' ? 'megan6' : meta.tool
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[meta_new, profile]
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}
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// FIXME: Groups elements in the channel using the meta map as key. Replace with grouping on specific keys.
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.groupTuple ()
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.map { [ it[0], it[1].flatten() ] }
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@ -197,7 +197,6 @@ workflow TAXPROFILER {
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meta_new.remove('run_accession')
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[ meta_new, reads ]
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}
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// FIXME: Groups elements in the channel using the meta map as key. Replace with grouping on specific keys.
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.groupTuple()
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.map {
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meta, reads ->
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