fix sed

conf/modules.config

@@ -129,7 +129,7 @@ process {
     }
 
     withName: MMSEQS_EASYCLUSTER {
-        ext.args = { "--min-seq-id 0.95 --cov-mode 1 -c 0.9" }
+        ext.args = { "${params.mmseqs_cluster_options}" }
         ext.prefix = { "${params.assemblyid}" }
         publishDir = [
             path: { "${params.outdir}/annotation/clusters/" },
@@ -155,6 +155,7 @@ process {
 
     withName: SED_FASTA_HEADER {
         ext.prefix = { "${meta.assemblyid}" }
+        ext.sed_arg = { "${meta.assemblyid}" }
     }
 
     withName: STROBEALIGN_CREATEINDEX{

modules/sed_fasta_header.nf

@@ -13,7 +13,7 @@ process SED_FASTA_HEADER {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def sed_arg = task.ext.sed_arg ?: "${meta.id}"
     """
-    sed s/^>/>${sed_arg}_/g ${fasta} > ${prefix}.renamed.fasta
+    sed "s/^>/>${sed_arg}_/g" ${fasta} > ${prefix}.renamed.fasta
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

nextflow.config

@@ -32,11 +32,11 @@ params {
     // Annotation options
     enable_annotation               = true
     cluster_genes                   = false
-    mmseqs_cluster_options          = ""
+    mmseqs_cluster_options          = "--min-seq-id 0.95 --cov-mode 1 -c 0.9"
 
     // Coverage options
     enable_coverage                 = true
-    go_list                         = "$baseDir/assets/GOs.csv"
+    go_list                         = "${baseDir}/assets/GOs.csv"
 
     // Boilerplate options
     outdir                     = null

nextflow_schema.json

@@ -119,12 +119,12 @@
         },
         "cluster_genes": {
           "type": "boolean",
-          "default": false,
           "description": "Concatenate all contigs across all assemblies and cluster them prior to annotation."
         },
         "mmseqs_cluster_options": {
           "type": "string",
-          "description": "Mmseqs command-line arguments for the mmseqs cluster call."
+          "description": "Mmseqs command-line arguments for the mmseqs cluster call.",
+          "default": "--min-seq-id 0.95 --cov-mode 1 -c 0.9"
         }
       }
     },