🍏 change kmer_coverage name to spades_kmer_coverage

KwanLab · Jun 3, 2021 · cfa5670 · cfa5670
1 parent 4152096
commit cfa5670
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Showing 2 changed files with 4 additions and 6 deletions.
diff --git 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
@@ -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
   """