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Merge pull request #242 from genomic-medicine-sweden/minor_fixes

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Remove standardised_tables
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James A. Fellows Yates 2023-02-20 20:43:09 +01:00 committed by GitHub
commit 3d1659dac7
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1 changed files with 1 additions and 13 deletions
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12
subworkflows/local/standardisation_profiles.nf
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@ -18,7 +18,6 @@ workflow STANDARDISATION_PROFILES {
motu_version motu_version
main: main:
ch_standardised_tables = Channel.empty()
ch_versions = Channel.empty() ch_versions = Channel.empty()
ch_multiqc_files = Channel.empty() ch_multiqc_files = Channel.empty()
@ -91,7 +90,6 @@ workflow STANDARDISATION_PROFILES {
KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE ( ch_profiles_for_centrifuge ) 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_multiqc_files = ch_multiqc_files.mix( KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE.out.txt )
ch_versions = ch_versions.mix( KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE.out.versions ) 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) 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_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary )
ch_versions = ch_versions.mix( KAIJU_KAIJU2TABLE.out.versions ) ch_versions = ch_versions.mix( KAIJU_KAIJU2TABLE.out.versions )
@ -123,7 +120,6 @@ workflow STANDARDISATION_PROFILES {
} }
KRAKENTOOLS_COMBINEKREPORTS_KRAKEN ( ch_profiles_for_kraken2 ) 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_multiqc_files = ch_multiqc_files.mix( KRAKENTOOLS_COMBINEKREPORTS_KRAKEN.out.txt )
ch_versions = ch_versions.mix( KRAKENTOOLS_COMBINEKREPORTS_KRAKEN.out.versions ) ch_versions = ch_versions.mix( KRAKENTOOLS_COMBINEKREPORTS_KRAKEN.out.versions )
@ -137,7 +133,6 @@ workflow STANDARDISATION_PROFILES {
} }
METAPHLAN3_MERGEMETAPHLANTABLES ( ch_profiles_for_metaphlan3 ) 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_multiqc_files = ch_multiqc_files.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.txt )
ch_versions = ch_versions.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.versions ) ch_versions = ch_versions.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.versions )
@ -155,16 +150,9 @@ workflow STANDARDISATION_PROFILES {
} }
MOTUS_MERGE ( ch_profiles_for_motus, ch_input_databases.motus.map{it[1]}, motu_version ) 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 ) ch_versions = ch_versions.mix( MOTUS_MERGE.out.versions )
emit: emit:
tables = ch_standardised_tables
taxpasta = TAXPASTA_MERGE.out.merged_profiles taxpasta = TAXPASTA_MERGE.out.merged_profiles
versions = ch_versions versions = ch_versions
mqc = ch_multiqc_files mqc = ch_multiqc_files