From 06b38f3699edd49d1d4a25e02196e012d9221dba Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Sat, 23 Apr 2022 08:36:01 +0200 Subject: [PATCH] Fix crash, add missing versions --- subworkflows/local/db_check.nf | 2 +- subworkflows/local/profiling.nf | 2 +- workflows/taxprofiler.nf | 5 ++--- 3 files changed, 4 insertions(+), 5 deletions(-) diff --git a/subworkflows/local/db_check.nf b/subworkflows/local/db_check.nf index a718fa9..f3464d5 100644 --- a/subworkflows/local/db_check.nf +++ b/subworkflows/local/db_check.nf @@ -34,7 +34,7 @@ workflow DB_CHECK { emit: dbs = ch_final_dbs // channel: [ val(meta), [ db ] ] - versions = DATABASE_CHECK.out.versions // channel: [ versions.yml ] + versions = DATABASE_CHECK.out.versions.mix(UNTAR.out.versions.first()) // channel: [ versions.yml ] } def create_db_channels(LinkedHashMap row) { diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf index 8d19bfe..a5afaaf 100644 --- a/subworkflows/local/profiling.nf +++ b/subworkflows/local/profiling.nf @@ -129,7 +129,7 @@ workflow PROFILING { MEGAN_RMA2INFO (ch_maltrun_for_megan, params.malt_generatemegansummary ) ch_multiqc_files = ch_multiqc_files.mix( MALT_RUN.out.log.collect{it[1]}.ifEmpty([]) ) - ch_versions = ch_versions.mix( MALT_RUN.out.versions.first() ) + ch_versions = ch_versions.mix( MALT_RUN.out.versions.first(), MEGAN_RMA2INFO.out.versions.first() ) ch_raw_profiles = ch_raw_profiles.mix( MEGAN_RMA2INFO.out.txt ) } diff --git a/workflows/taxprofiler.nf b/workflows/taxprofiler.nf index 9981ca4..a0046b2 100644 --- a/workflows/taxprofiler.nf +++ b/workflows/taxprofiler.nf @@ -196,10 +196,8 @@ workflow TAXPROFILER { MODULE: MultiQC */ - ch_versions = ch_versions.mix(MULTIQC.out.versions) - CUSTOM_DUMPSOFTWAREVERSIONS ( - ch_versions.dump(tag: "software_versions_beforeuniqe").unique().dump(tag: "software_versions").collectFile(name: 'collated_versions.yml') + ch_versions.unique().collectFile(name: 'collated_versions.yml') ) @@ -236,6 +234,7 @@ workflow TAXPROFILER { ch_multiqc_files.collect() ) multiqc_report = MULTIQC.out.report.toList() + ch_versions = ch_versions.mix(MULTIQC.out.versions) } /*