From f9f7e5f0bc4c930f3520f1d366165245ddee5f93 Mon Sep 17 00:00:00 2001
From: Chris Fields <cjfields@illinois.edu>
Date: Tue, 26 Mar 2024 14:41:58 -0500
Subject: [PATCH] updates for trimming

---
 conf/modules.config | 22 ++++++++++++++++++++++
 nextflow.config     |  8 ++++----
 2 files changed, 26 insertions(+), 4 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index e3ea8fa..2ae6a0b 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -22,6 +22,28 @@ process {
         ext.args = '--quiet'
     }
 
+    withName: PLOTQUALITYPROFILE {
+        publishDir = [
+                [
+                    path: { "${params.outdir}/Plots/" },
+                    mode: params.publish_dir_mode,
+                    pattern: "*.pdf"
+                ],
+                [
+                    path: { "${params.outdir}/R/Plots/" },
+                    mode: params.publish_dir_mode,
+                    pattern: "*.RDS"
+                ]
+                ]
+    }
+
+    withName: FILTERANDTRIM {
+        publishDir = [
+            path: { "${params.outdir}/TrimmedReads/" },
+            mode: params.publish_dir_mode
+        ]
+    }
+
     withName: CUSTOM_DUMPSOFTWAREVERSIONS {
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },
diff --git a/nextflow.config b/nextflow.config
index 1db288e..47f2cbd 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -53,14 +53,14 @@ params {
     trim_rev = 0
     trunc_for = 0
     trunc_rev = 0
-    maxEE_for = 0
-    maxEE_rev = 0
+    maxEE_for = 2
+    maxEE_rev = 2
     truncQ = 2 //default
     maxN = 0 //default
-    max_read_len = null // default, this can be coersed in R using as.numeric
+    max_read_len = "Inf" // default, this can be coersed in R using as.numeric
     min_read_len = 50 // default
     // I think we can make these bool 'false' as above with R coersion (either through as.logical or using optparse in a Rscript)
-    rmPhiX = false  // TODO: test using false instead of string
+    rmPhiX = false  
 
     // Error model
     qualityBinning = false  // false, set to true if using binned qualities (NovaSeq)