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Remove standardised_tables
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599c8d3592
commit
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1 changed files with 0 additions and 13 deletions
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@ -18,7 +18,6 @@ workflow STANDARDISATION_PROFILES {
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motu_version
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main:
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ch_standardised_tables = Channel.empty()
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ch_versions = Channel.empty()
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ch_multiqc_files = Channel.empty()
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@ -91,7 +90,6 @@ workflow STANDARDISATION_PROFILES {
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KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE ( ch_profiles_for_centrifuge )
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ch_standardised_tables = ch_standardised_tables.mix( KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE.out.txt )
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ch_multiqc_files = ch_multiqc_files.mix( KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE.out.txt )
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ch_versions = ch_versions.mix( KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE.out.versions )
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@ -106,7 +104,6 @@ workflow STANDARDISATION_PROFILES {
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}
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KAIJU_KAIJU2TABLE ( ch_profiles_for_kaiju, ch_input_databases.kaiju.map{it[1]}, params.kaiju_taxon_rank)
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ch_standardised_tables = ch_standardised_tables.mix( KAIJU_KAIJU2TABLE.out.summary )
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ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary )
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ch_versions = ch_versions.mix( KAIJU_KAIJU2TABLE.out.versions )
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@ -123,7 +120,6 @@ workflow STANDARDISATION_PROFILES {
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}
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KRAKENTOOLS_COMBINEKREPORTS_KRAKEN ( ch_profiles_for_kraken2 )
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ch_standardised_tables = ch_standardised_tables.mix( KRAKENTOOLS_COMBINEKREPORTS_KRAKEN.out.txt )
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ch_multiqc_files = ch_multiqc_files.mix( KRAKENTOOLS_COMBINEKREPORTS_KRAKEN.out.txt )
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ch_versions = ch_versions.mix( KRAKENTOOLS_COMBINEKREPORTS_KRAKEN.out.versions )
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@ -137,7 +133,6 @@ workflow STANDARDISATION_PROFILES {
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}
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METAPHLAN3_MERGEMETAPHLANTABLES ( ch_profiles_for_metaphlan3 )
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ch_standardised_tables = ch_standardised_tables.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.txt )
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ch_multiqc_files = ch_multiqc_files.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.txt )
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ch_versions = ch_versions.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.versions )
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@ -156,15 +151,7 @@ workflow STANDARDISATION_PROFILES {
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MOTUS_MERGE ( ch_profiles_for_motus, ch_input_databases.motus.map{it[1]}, motu_version )
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if ( params.generate_biom_output ) {
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ch_standardised_tables = ch_standardised_tables.mix ( MOTUS_MERGE.out.biom )
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} else {
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ch_standardised_tables = ch_standardised_tables.mix ( MOTUS_MERGE.out.txt )
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}
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ch_versions = ch_versions.mix( MOTUS_MERGE.out.versions )
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emit:
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tables = ch_standardised_tables
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taxpasta = TAXPASTA_MERGE.out.merged_profiles
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versions = ch_versions
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mqc = ch_multiqc_files
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