From 1071e0a0d32a6f9b7858fce01dded43197a61eea Mon Sep 17 00:00:00 2001
From: Austyn Trull <atrull@uab.edu>
Date: Mon, 2 Oct 2023 11:30:44 -0500
Subject: [PATCH] Correcting processes that show up as 'no matching config
 selector'

---
 conf/modules.config | 53 +++++++++++++++------------------------------
 1 file changed, 18 insertions(+), 35 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 5c67a69..27e9043 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -52,13 +52,15 @@ if (!params.skip_qc && !params.skip_fastqc) {
         ]
         }
 
-        withName: '.*:FASTQC_NANOPLOT_POST_TRIM:FASTQC' {
-            ext.prefix = { "${meta.id}.filtered" }
-            publishDir = [
-                path: { "${params.outdir}/${meta.id}/qc/fastqc/post_trim" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
+        if (!params.skip_trimming) {
+            withName: '.*:FASTQC_NANOPLOT_POST_TRIM:FASTQC' {
+                ext.prefix = { "${meta.id}.filtered" }
+                publishDir = [
+                    path: { "${params.outdir}/${meta.id}/qc/fastqc/post_trim" },
+                    mode: params.publish_dir_mode,
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+            }
         }
 
         withName: '.*:FASTQC_NANOPLOT_POST_EXTRACT:FASTQC' {
@@ -84,12 +86,14 @@ if (!params.skip_qc && !params.skip_nanoplot) {
         ]
         }
 
-        withName: '.*:FASTQC_NANOPLOT_POST_TRIM:NANOPLOT' {
-            publishDir = [
-                path: { "${params.outdir}/${meta.id}/qc/nanoplot/post_trim/" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
+        if (!params.skip_trimming) {
+            withName: '.*:FASTQC_NANOPLOT_POST_TRIM:NANOPLOT' {
+                publishDir = [
+                    path: { "${params.outdir}/${meta.id}/qc/nanoplot/post_trim/" },
+                    mode: params.publish_dir_mode,
+                    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+            ]
+            }
         }
 
         withName: '.*:FASTQC_NANOPLOT_POST_EXTRACT:NANOPLOT' {
@@ -181,7 +185,7 @@ if (!params.skip_qc){
 
 // PREPARE_REFERENCE_FILES
 process {
-    withName: '.*:PREPARE_GTF' {
+    withName: '.*:PREPARE_REFERENCE_FILES:PREPARE_GTF' {
         publishDir = [
             enabled: false
         ]
@@ -321,27 +325,6 @@ process {
     }
 }
 
-// PIGZ
-process {
-    withName: '.*:ZIP_R1' {
-        publishDir = [
-            path: { "${params.outdir}/fastq/pre_extract/${meta.id}" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-}
-
-process {
-    withName: '.*:ZIP_R2' {
-        publishDir = [
-            path: { "${params.outdir}/fastq/pre_extract/${meta.id}" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-}
-
 ///////////////////////
 // BARCODE DETECTION //
 ///////////////////////