From 7b925321f4ca7520c6e8a3033c150f519a538271 Mon Sep 17 00:00:00 2001
From: Jim Downie <jimdownie@fastmail.org>
Date: Wed, 27 Mar 2024 19:02:21 +0000
Subject: [PATCH] fix sed

---
 conf/modules.config         | 3 ++-
 modules/sed_fasta_header.nf | 2 +-
 nextflow.config             | 4 ++--
 nextflow_schema.json        | 4 ++--
 4 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index ed0a467..610e8de 100644
--- a/conf/modules.config
+++ b/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{
diff --git a/modules/sed_fasta_header.nf b/modules/sed_fasta_header.nf
index a2e0909..2aa9a32 100644
--- a/modules/sed_fasta_header.nf
+++ b/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}":
diff --git a/nextflow.config b/nextflow.config
index 3109e4d..f40f5be 100644
--- a/nextflow.config
+++ b/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
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 7cc0b99..f133830 100644
--- a/nextflow_schema.json
+++ b/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"
         }
       }
     },