From 8cef72617d43cb3c668d06a775f1d6c832530a3f Mon Sep 17 00:00:00 2001
From: Jim Downie <jd42@sanger.ac.uk>
Date: Fri, 6 Dec 2024 11:40:49 +0000
Subject: [PATCH] Fix contig2bin processing

---
 conf/modules.config                    | 6 +++---
 modules/local/contig2bin2fasta/main.nf | 2 +-
 modules/local/magscot/magscot/main.nf  | 2 +-
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index ad382a3..9188bdb 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -212,10 +212,10 @@ process {
     }
 
     withName: 'RENAME_DASTOOL_BINS' {
+        ext.prefix = { "${meta.id}_${meta.assembler}_dastool_contig2bin" }
         ext.args   = { "" }
-        ext.args2  = { "'{if(\$2 != prev) { count++ }; print \$1,"${prefix}_"count; prev = \$2}'" }
-        ext.prefix = { "${meta.id}_${meta.assembler}_${meta.binner}_contig2bin" }
-        tag        = { "${meta.id}_${meta.assembler}_${meta.binner}" }
+        ext.args2  = { "'{if(\$2 != prev) { count++ }; print \$1,\"${meta.id}_${meta.assembler}_dastool_\"count; prev = \$2}'" }
+        tag        = { "${meta.id}_${meta.assembler}_dastool" }
     }
 
     withName: 'SEQKIT_STATS' {
diff --git a/modules/local/contig2bin2fasta/main.nf b/modules/local/contig2bin2fasta/main.nf
index c6fba1b..21c6730 100644
--- a/modules/local/contig2bin2fasta/main.nf
+++ b/modules/local/contig2bin2fasta/main.nf
@@ -17,7 +17,7 @@ process CONTIG2BIN2FASTA {
 
     script:
     def args      = task.ext.args   ?: ''
-    def prefix    = task.ext.prefix ?: ""
+    def prefix    = task.ext.prefix ?: "${meta.id}"
     def extension = input_is_prodigal_aa ? "faa" : "fa"
     def input_aa  = input_is_prodigal_aa ? "_.*" : ""
     """
diff --git a/modules/local/magscot/magscot/main.nf b/modules/local/magscot/magscot/main.nf
index 65ac04f..1865b03 100644
--- a/modules/local/magscot/magscot/main.nf
+++ b/modules/local/magscot/magscot/main.nf
@@ -28,7 +28,7 @@ process MAGSCOT_MAGSCOT {
     mv MAGScoT.refined.out ${prefix}.MAGScoT.refined.out
 
     ## magscot puts out contig2bin file in wrong format
-    awk 'NR > 1 {print \$2 \$1}' MAGScoT.refined.contig_to_bin.out > ${prefix}.MAGScoT.refined.contig_to_bin.out
+    awk 'BEGIN{OFS="\t"} NR > 1 {print \$2,\$1}' MAGScoT.refined.contig_to_bin.out > ${prefix}.MAGScoT.refined.contig_to_bin.out
     rm MAGScoT.refined.contig_to_bin.out
 
     cat <<-END_VERSIONS > versions.yml