From 5044819ae8bab4fb342de97be62270f6e2404b52 Mon Sep 17 00:00:00 2001
From: skchronicles <kuhnsa3@gmail.com>
Date: Tue, 22 Mar 2022 13:30:10 -0400
Subject: [PATCH] Updating the output structure for rules prep_metaquast and
 metaquast

---
 workflow/Snakefile            |  4 ++--
 workflow/rules/paired-end.smk | 13 +++++++------
 2 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/workflow/Snakefile b/workflow/Snakefile
index c1151c7..cf3bb4b 100644
--- a/workflow/Snakefile
+++ b/workflow/Snakefile
@@ -116,10 +116,10 @@ rule all:
         ),
         # Metaquast, quality report of assembly
         expand(
-            join(workpath,"temp","{name}","{name}.metaquast.fa"),
+            join(workpath,"{name}","temp","{name}.metaquast.fa"),
             name=samples
         ),
         expand(
-            join(workpath,"output","{name}","{name}_metaquast","report.html"),
+            join(workpath,"{name}","output","{name}_metaquast","report.html"),
             name=samples
         )
diff --git a/workflow/rules/paired-end.smk b/workflow/rules/paired-end.smk
index 983f142..df9ec95 100644
--- a/workflow/rules/paired-end.smk
+++ b/workflow/rules/paired-end.smk
@@ -528,12 +528,12 @@ rule prep_metaquast:
     input:
         report=join(workpath,"{name}","info","{name}.reads_kraken2_report.txt"),
     output:
-        txt=join(workpath,"temp","{name}","{name}_reads_class_names.txt"),
-        fa=join(workpath,"temp","{name}","{name}.metaquast.fa"),
+        txt=join(workpath,"{name}","temp","{name}_reads_class_names.txt"),
+        fa=join(workpath,"{name}","temp","{name}.metaquast.fa"),
     params:
         rname='prepmetaq',
         ncbi_viral=config['references']['ncbi_viral_fasta'],
-        outdir=join(workpath,"temp","{name}","metaquastref"),
+        outdir=join(workpath,"{name}","temp","metaquastref"),
     threads: int(allocated("threads", "prep_metaquast", cluster))
     envmodules:
         config['tools']['ucsc']
@@ -570,12 +570,13 @@ rule metaquast:
     input:
         metaspades=join(workpath,"{name}","output","{name}.metaspades.contigs.fa"),
         megahit=join(workpath,"{name}","output","{name}.megahit.contigs.fa"),
+        dep=join(workpath,"{name}","temp","{name}.metaquast.fa"),
     output:
-        report=join(workpath,"output","{name}","{name}_metaquast","report.html")
+        report=join(workpath,"{name}","output","{name}_metaquast","report.html")
     params:
         rname='metaq',
-        ref=join(workpath,"temp","{name}","metaquastref"),
-        outdir=join(workpath,"output","{name}","{name}_metaquast"),
+        ref=join(workpath,"{name}","temp","metaquastref"),
+        outdir=join(workpath,"{name}","output","{name}_metaquast"),
     threads: int(allocated("threads", "metaquast", cluster))
     container:
         config['images']['metaquast']