removing s argument in msmeqs cluster

Author: Joon-Klaps

nextflow.config

@@ -209,8 +209,8 @@ params {
     arguments_extract_precluster = "--keep-unclassified ${params.keep_unclassified} --merge-strategy lca"
     arguments_cdhit              = "-c ${params.identity_threshold} -mask rRyYkKsSwWmMbBdDhHvVnN"
     arguments_vsearch            = "--maxseqlength ${params.max_contig_size} --id ${params.identity_threshold} --strand both --iddef 0 --no_progress --qmask none"
-    arguments_mmseqs_linclust    = "--min-seq-id ${params.identity_threshold} -c 0.700 --cov-mode 2 -s 7 --cluster-mode 0"
-    arguments_mmseqs_cluster     = "--min-seq-id ${params.identity_threshold} -c 0.700 --cov-mode 2 -s 7 --cluster-mode 0"
+    arguments_mmseqs_linclust    = "--min-seq-id ${params.identity_threshold} -c 0.700 --cov-mode 2 --cluster-mode 0"
+    arguments_mmseqs_cluster     = "--min-seq-id ${params.identity_threshold} -c 0.700 --cov-mode 2 --cluster-mode 0"
     arguments_vrhyme             = '--mems 50'
     arguments_mash_dist          = '-s 4000 -k 15'
     arguments_network_cluster    = "--score ${params.identity_threshold}"
@@ -263,7 +263,7 @@ params {
     arguments_checkv            = '--remove_tmp'
     arguments_mafft_iterations  = '--auto --adjustdirection'
     arguments_mafft_qc          = '--auto --adjustdirection'
-    params.arguments_blastn_qc = '-max_target_seqs 5'
+    params.arguments_blastn_qc  = '-max_target_seqs 5'
     arguments_prokka            = '--centre X --compliant --force --kingdom Viruses'
     arguments_mmseqs_search     = '--search-type 4 --rescore-mode 3'
     arguments_quast_qc          = null