From 3fa1b0c17d8a023184edad1325e1c42518f189ce Mon Sep 17 00:00:00 2001 From: sofstam Date: Mon, 20 Feb 2023 13:48:04 +0100 Subject: [PATCH 1/2] Remove standardised_tables --- subworkflows/local/standardisation_profiles.nf | 13 ------------- 1 file changed, 13 deletions(-) diff --git a/subworkflows/local/standardisation_profiles.nf b/subworkflows/local/standardisation_profiles.nf index de58622..2506680 100644 --- a/subworkflows/local/standardisation_profiles.nf +++ b/subworkflows/local/standardisation_profiles.nf @@ -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 From 90aa7551a9b56040eb04cb4cc1f9f0d5cbac2bd9 Mon Sep 17 00:00:00 2001 From: sofstam Date: Mon, 20 Feb 2023 14:27:57 +0100 Subject: [PATCH 2/2] Fix the motus_versions --- subworkflows/local/standardisation_profiles.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/subworkflows/local/standardisation_profiles.nf b/subworkflows/local/standardisation_profiles.nf index 2506680..2c6a591 100644 --- a/subworkflows/local/standardisation_profiles.nf +++ b/subworkflows/local/standardisation_profiles.nf @@ -150,7 +150,8 @@ workflow STANDARDISATION_PROFILES { } MOTUS_MERGE ( ch_profiles_for_motus, ch_input_databases.motus.map{it[1]}, motu_version ) - + ch_versions = ch_versions.mix( MOTUS_MERGE.out.versions ) + emit: taxpasta = TAXPASTA_MERGE.out.merged_profiles versions = ch_versions