fix: same gene prefix issue in prediction module

The prediction module failed with the default input of the homology and the transcriptome module due having the same gene prefix. this fixes this issue adding an specific prefix in each module.
EI-CoreBioinformatics · Jan 25, 2024 · 7483ca4 · 7483ca4
1 parent 1654b81
commit 7483ca4
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/annotation/homology_module/main.wdl b/annotation/homology_module/main.wdl
@@ -275,7 +275,7 @@ task MikadoPick {
     --start-method=spawn --json-conf=pick_config.yaml \
     --loci-out ~{output_prefix}.loci.gff3 -lv INFO ~{"-db " + mikado_db} \
     --subloci-out ~{output_prefix}.subloci.gff3 --monoloci-out ~{output_prefix}.monoloci.gff3 \
-    ~{transcripts}
+    --prefix Mikado_homology ~{transcripts}
     mikado compare -r ~{output_prefix}.loci.gff3 -l ~{output_prefix}-index_loci.log --index
     mikado util stats  ~{output_prefix}.loci.gff3 ~{output_prefix}.loci.gff3.stats
     >>>

diff --git a/annotation/prediction_module/main.wdl b/annotation/prediction_module/main.wdl
@@ -1681,7 +1681,7 @@ task MikadoPick {
 		--start-method=spawn --json-conf=pick_config.yaml \
 		--loci-out ~{output_prefix}.loci.gff3 -lv INFO ~{"-db " + mikado_db} \
 		--subloci-out ~{output_prefix}.subloci.gff3 --monoloci-out ~{output_prefix}.monoloci.gff3 \
-		~{transcripts}
+		--prefix Mikado_prediction ~{transcripts}
 		mikado compare -r ~{output_prefix}.loci.gff3 -l ~{output_prefix}-index_loci.log --index
 		mikado util stats  ~{output_prefix}.loci.gff3 ~{output_prefix}.loci.gff3.stats
 	>>>

diff --git a/annotation/transcriptome_module/subworkflows/mikado/wf_mikado.wdl b/annotation/transcriptome_module/subworkflows/mikado/wf_mikado.wdl
@@ -235,7 +235,7 @@ task MikadoPick {
     ~{"--flank " + flank} --start-method=spawn --json-conf=pick_config.yaml \
     --loci-out ~{output_prefix}.loci.gff3 -lv INFO ~{"-db " + mikado_db} \
     --subloci-out ~{output_prefix}.subloci.gff3 --monoloci-out ~{output_prefix}.monoloci.gff3 \
-    ~{transcripts}
+    --prefix Mikado_transcriptome ~{transcripts}
     mikado compare -r ~{output_prefix}.loci.gff3 -l ~{output_prefix}-index_loci.log --index
     mikado util stats  ~{output_prefix}.loci.gff3 ~{output_prefix}.loci.gff3.stats
     >>>