diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf index ac48d77..c74c583 100644 --- a/subworkflows/local/profiling.nf +++ b/subworkflows/local/profiling.nf @@ -70,7 +70,6 @@ workflow PROFILING { } ch_input_for_centrifuge = ch_input_for_profiling.centrifuge - .dump(tag: "input for centrifuge") .multiMap { it -> reads: [ it[0] + it[2], it[1] ] diff --git a/subworkflows/local/shortread_fastp.nf b/subworkflows/local/shortread_fastp.nf index 18baf17..9fb9425 100644 --- a/subworkflows/local/shortread_fastp.nf +++ b/subworkflows/local/shortread_fastp.nf @@ -10,7 +10,7 @@ workflow SHORTREAD_FASTP { reads // [[meta], [reads]] main: - ch_versions = Channel.empty() + ch_versions = Channel.empty() ch_multiqc_files = Channel.empty() ch_input_for_fastp = reads diff --git a/workflows/taxprofiler.nf b/workflows/taxprofiler.nf index 237f1ea..4b9f927 100644 --- a/workflows/taxprofiler.nf +++ b/workflows/taxprofiler.nf @@ -85,6 +85,7 @@ workflow TAXPROFILER { DB_CHECK ( ch_databases ) + ch_versions = ch_versions.mix(DB_CHECK.out.versions) /* MODULE: Run FastQC @@ -101,6 +102,7 @@ workflow TAXPROFILER { SUBWORKFLOW: PERFORM PREPROCESSING */ if ( params.shortread_clipmerge ) { + ch_shortreads_preprocessed = SHORTREAD_PREPROCESSING ( INPUT_CHECK.out.fastq ).reads } else { ch_shortreads_preprocessed = INPUT_CHECK.out.fastq