diff --git a/modules/nf-core/modules/motus/profile/main.nf b/modules/nf-core/modules/motus/profile/main.nf index 2747984..bd7a127 100644 --- a/modules/nf-core/modules/motus/profile/main.nf +++ b/modules/nf-core/modules/motus/profile/main.nf @@ -15,6 +15,7 @@ process MOTUS_PROFILE { tuple val(meta), path("*.out"), emit: out tuple val(meta), path("*.bam"), optional: true, emit: bam tuple val(meta), path("*.mgc"), optional: true, emit: mgc + tuple val(meta), path("*.log") , emit: log path "versions.yml" , emit: versions when: @@ -36,7 +37,8 @@ process MOTUS_PROFILE { $refdb \\ -t $task.cpus \\ -n $prefix \\ - -o ${prefix}.out + -o ${prefix}.out \\ + 2> ${prefix}.log ## mOTUs version number is not available from command line. ## mOTUs save the version number in index database folder. diff --git a/modules/nf-core/modules/motus/profile/meta.yml b/modules/nf-core/modules/motus/profile/meta.yml index 19803bd..3c3b660 100644 --- a/modules/nf-core/modules/motus/profile/meta.yml +++ b/modules/nf-core/modules/motus/profile/meta.yml @@ -56,6 +56,10 @@ output: type: file description: Optional intermediate mgc read count table file saved with `-M`. pattern: "*.{mgc}" + - log: + type: file + description: Standard error logging file containing summary statistics + pattern: "*.log" authors: - "@jianhong" diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf index 87a6a98..7c2c90c 100644 --- a/subworkflows/local/profiling.nf +++ b/subworkflows/local/profiling.nf @@ -227,6 +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]} ) } emit: