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Remove standardised_tables

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sofstam 2023-02-20 13:48:04 +01:00
parent 599c8d3592
commit 3fa1b0c17d
1 changed files with 0 additions and 13 deletions
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13
subworkflows/local/standardisation_profiles.nf
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@ -18,7 +18,6 @@ workflow STANDARDISATION_PROFILES {
motu_version
main:
ch_standardised_tables = Channel.empty()
ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty()
@ -91,7 +90,6 @@ workflow STANDARDISATION_PROFILES {
KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE ( ch_profiles_for_centrifuge )
ch_standardised_tables = ch_standardised_tables.mix( KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE.out.txt )
ch_multiqc_files = ch_multiqc_files.mix( KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE.out.txt )
ch_versions = ch_versions.mix( KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE.out.versions )
@ -106,7 +104,6 @@ workflow STANDARDISATION_PROFILES {
}
KAIJU_KAIJU2TABLE ( ch_profiles_for_kaiju, ch_input_databases.kaiju.map{it[1]}, params.kaiju_taxon_rank)
ch_standardised_tables = ch_standardised_tables.mix( KAIJU_KAIJU2TABLE.out.summary )
ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary )
ch_versions = ch_versions.mix( KAIJU_KAIJU2TABLE.out.versions )
@ -123,7 +120,6 @@ workflow STANDARDISATION_PROFILES {
}
KRAKENTOOLS_COMBINEKREPORTS_KRAKEN ( ch_profiles_for_kraken2 )
ch_standardised_tables = ch_standardised_tables.mix( KRAKENTOOLS_COMBINEKREPORTS_KRAKEN.out.txt )
ch_multiqc_files = ch_multiqc_files.mix( KRAKENTOOLS_COMBINEKREPORTS_KRAKEN.out.txt )
ch_versions = ch_versions.mix( KRAKENTOOLS_COMBINEKREPORTS_KRAKEN.out.versions )
@ -137,7 +133,6 @@ workflow STANDARDISATION_PROFILES {
}
METAPHLAN3_MERGEMETAPHLANTABLES ( ch_profiles_for_metaphlan3 )
ch_standardised_tables = ch_standardised_tables.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.txt )
ch_multiqc_files = ch_multiqc_files.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.txt )
ch_versions = ch_versions.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.versions )
@ -156,15 +151,7 @@ workflow STANDARDISATION_PROFILES {
MOTUS_MERGE ( ch_profiles_for_motus, ch_input_databases.motus.map{it[1]}, motu_version )
if ( params.generate_biom_output ) {
ch_standardised_tables = ch_standardised_tables.mix ( MOTUS_MERGE.out.biom )
} else {
ch_standardised_tables = ch_standardised_tables.mix ( MOTUS_MERGE.out.txt )
}
ch_versions = ch_versions.mix( MOTUS_MERGE.out.versions )
emit:
tables = ch_standardised_tables
taxpasta = TAXPASTA_MERGE.out.merged_profiles
versions = ch_versions
mqc = ch_multiqc_files