From ca9c0cf8fdb6e88ca9bfe3ff6cdcd6d3426d71fe Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 4 Apr 2023 15:52:23 +0200
Subject: [PATCH] Further fixes

---
 conf/modules.config | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index 0e7e2ea..32024d9 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -76,7 +76,7 @@ process {
                 path: { "${params.outdir}/analysis_ready_fastqs" },
                 mode: params.publish_dir_mode,
                 pattern: '*.fastq.gz',
-                enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.shortread_complexityfilter_tool && params.perform_shortread_qc && params.save_analysis_ready_fastqs
+                enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs
             ]
         ]
     }
@@ -109,8 +109,8 @@ process {
             [
                 path: { "${params.outdir}/analysis_ready_fastqs" },
                 mode: params.publish_dir_mode,
-                pattern: '*.fastq.gz',
-                enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.shortread_complexityfilter_tool && params.perform_shortread_qc && params.save_analysis_ready_fastqs
+                pattern: params.shortread_qc_mergepairs ? '*merged.fastq.gz' : '*.fastp.fastq.gz',
+                enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs
             ]
         ]
     }
@@ -138,8 +138,8 @@ process {
             [
                 path: { "${params.outdir}/analysis_ready_fastqs" },
                 mode: params.publish_dir_mode,
-                pattern: '*.fastq.gz',
-                enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.shortread_complexityfilter_tool && params.perform_shortread_qc && params.save_analysis_ready_fastqs
+                pattern: '*truncated.fastq.gz',
+                enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs
             ]
         ]
     }
@@ -166,6 +166,12 @@ process {
                 path: { "${params.outdir}/adapterremoval" },
                 mode: params.publish_dir_mode,
                 pattern: '*.settings'
+            ],
+            [
+                path: { "${params.outdir}/analysis_ready_fastqs" },
+                mode: params.publish_dir_mode,
+                pattern: '*{truncated.fastq,singleton.truncated}.gz',
+                enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && !params.shortread_qc_mergepairs && params.save_analysis_ready_fastqs
             ]
         ]
     }
@@ -178,7 +184,7 @@ process {
                 path: { "${params.outdir}/analysis_ready_fastqs" },
                 mode: params.publish_dir_mode,
                 pattern: '*.fastq.gz',
-                enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.shortread_complexityfilter_tool && params.perform_shortread_qc && params.save_analysis_ready_fastqs
+                enabled: !params.perform_runmerging && !params.perform_shortread_hostremoval && !params.perform_shortread_complexityfilter && params.perform_shortread_qc && params.save_analysis_ready_fastqs
             ]
         ]
     }