From 139cf0d6aa9fb93ed3596f5106a4ddf214287927 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Tue, 26 Jul 2022 10:12:33 +0200 Subject: [PATCH] Fix --- subworkflows/local/profiling.nf | 8 ++++---- workflows/taxprofiler.nf | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf index 7c2c90c..1099155 100644 --- a/subworkflows/local/profiling.nf +++ b/subworkflows/local/profiling.nf @@ -110,7 +110,7 @@ workflow PROFILING { } MEGAN_RMA2INFO (ch_maltrun_for_megan, params.malt_generate_megansummary ) - ch_multiqc_files = ch_multiqc_files.mix( MALT_RUN.out.log.collect{it[1]}.ifEmpty([]) ) + ch_multiqc_files = ch_multiqc_files.mix( MALT_RUN.out.log ) ch_versions = ch_versions.mix( MALT_RUN.out.versions.first(), MEGAN_RMA2INFO.out.versions.first() ) ch_raw_classifications = ch_raw_classifications.mix( ch_maltrun_for_megan ) ch_raw_profiles = ch_raw_profiles.mix( MEGAN_RMA2INFO.out.txt ) @@ -127,7 +127,7 @@ workflow PROFILING { } KRAKEN2_KRAKEN2 ( ch_input_for_kraken2.reads, ch_input_for_kraken2.db, params.kraken2_save_reads, params.kraken2_save_readclassification ) - ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.report.collect{it[1]}.ifEmpty([]) ) + ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.report ) ch_versions = ch_versions.mix( KRAKEN2_KRAKEN2.out.versions.first() ) ch_raw_classifications = ch_raw_classifications.mix( KRAKEN2_KRAKEN2.out.classified_reads_assignment ) ch_raw_profiles = ch_raw_profiles.mix( KRAKEN2_KRAKEN2.out.report ) @@ -185,7 +185,7 @@ workflow PROFILING { KAIJU_KAIJU ( ch_input_for_kaiju.reads, ch_input_for_kaiju.db) KAIJU_KAIJU2TABLE (KAIJU_KAIJU.out.results, ch_input_for_kaiju.db, params.kaiju_taxon_name) - ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary.collect{it[1]}.ifEmpty([]) ) + ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary ) ch_versions = ch_versions.mix( KAIJU_KAIJU.out.versions.first() ) ch_raw_classifications = ch_raw_classifications.mix( KAIJU_KAIJU.out.results ) ch_raw_profiles = ch_raw_profiles.mix( KAIJU_KAIJU2TABLE.out.summary ) @@ -227,7 +227,7 @@ workflow PROFILING { MOTUS_PROFILE ( ch_input_for_motus.reads, ch_input_for_motus.db ) ch_versions = ch_versions.mix( MOTUS_PROFILE.out.versions.first() ) ch_raw_profiles = ch_raw_profiles.mix( MOTUS_PROFILE.out.out ) - ch_multiqc_files = ch_multiqc_files.mix( MOTUS_PROFILE.out.log.map{it[1]} ) + ch_multiqc_files = ch_multiqc_files.mix( MOTUS_PROFILE.out.log ) } emit: diff --git a/workflows/taxprofiler.nf b/workflows/taxprofiler.nf index 85a3a51..b6f3a37 100644 --- a/workflows/taxprofiler.nf +++ b/workflows/taxprofiler.nf @@ -266,7 +266,7 @@ workflow TAXPROFILER { ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_HOSTREMOVAL.out.mqc.collect{it[1]}.ifEmpty([])) } - ch_multiqc_files = ch_multiqc_files.mix( PROFILING.out.mqc ) + ch_multiqc_files = ch_multiqc_files.mix( PROFILING.out.mqc.collect{it[1]}.ifEmpty([]) ) // TODO create multiQC module for metaphlan MULTIQC (