Fix contig2bin processing

sanger-tol · Dec 6, 2024 · 8cef726 · 8cef726
1 parent 629cdd2
commit 8cef726
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Showing 3 changed files with 5 additions and 5 deletions.
diff --git 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
@@ -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
@@ -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