diff --git a/nextflow/modules/autometa.nf b/nextflow/modules/autometa.nf index 25d264388..7aa82cb5c 100644 --- a/nextflow/modules/autometa.nf +++ b/nextflow/modules/autometa.nf @@ -5,7 +5,7 @@ nextflow.enable.dsl = 2 include { LENGTH_FILTER } from './autometa_core/utilities/process/metagenome_length_filter.nf' include { ANALYZE_KMERS } from './autometa_core/utilities/process/analyze_kmers.nf' -include { KMER_COVERAGE } from './autometa_core/utilities/process/kmer_coverage.nf' +include { SPADES_KMER_COVERAGE } from './autometa_core/utilities/process/kmer_coverage.nf' include { PRODIGAL_ORFS } from './autometa_core/utilities/process/orf_calling.nf' include { MARKERS } from './autometa_core/utilities/process/markers.nf' include { TAXON_ASSIGNMENT } from './contig_split_by_taxonomy/taxonomy_workflow.nf' @@ -23,7 +23,7 @@ workflow AUTOMETA { // -------------------------------------------------------------------------------- // contig k-mer coverage vs. contig read coverage // -------------------------------------------------------------------------------- - KMER_COVERAGE(LENGTH_FILTER.out.fasta) + SPADES_KMER_COVERAGE(LENGTH_FILTER.out.fasta) // -------------------------------------------------------------------------------- // Run Prodigal to obtain open reading frames diff --git a/nextflow/modules/autometa_core/utilities/process/kmer_coverage.nf b/nextflow/modules/autometa_core/utilities/process/kmer_coverage.nf index aa54c77eb..53415f983 100644 --- a/nextflow/modules/autometa_core/utilities/process/kmer_coverage.nf +++ b/nextflow/modules/autometa_core/utilities/process/kmer_coverage.nf @@ -1,9 +1,8 @@ #!/usr/bin/env nextflow nextflow.enable.dsl=2 -process KMER_COVERAGE { - tag "Retrieving k-mer coverage from ${metagenome.simpleName} headers" - label "python_cpus" +process SPADES_KMER_COVERAGE { + tag "Calculating k-mer coverage for ${metagenome.simpleName}" publishDir params.interim_dir, pattern: "${metagenome.simpleName}.coverages.tsv" @@ -16,7 +15,6 @@ process KMER_COVERAGE { """ autometa-coverage \ --assembly $metagenome \ - --cpus ${task.cpus} \ --from-spades \ --out ${metagenome.simpleName}.coverages.tsv """