From 9ccf39bace12a83a1043609e401c04832972fa3d Mon Sep 17 00:00:00 2001
From: AmstlerStephan <stephan.amstler@student.uibk.ac.at>
Date: Thu, 20 Jun 2024 16:10:10 +0200
Subject: [PATCH] Update merge_input process for deterministic behaviour

---
 lib/processes/merge_input.nf                 |  2 +-
 tests/lib/processes/merge_input.nf.test      |  4 ++--
 tests/lib/processes/merge_input.nf.test.snap | 10 +++++-----
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/lib/processes/merge_input.nf b/lib/processes/merge_input.nf
index 59c17ea..f05bb22 100644
--- a/lib/processes/merge_input.nf
+++ b/lib/processes/merge_input.nf
@@ -12,6 +12,6 @@ process MERGE_FASTQ {
         catfishq \
             --min-length ${params.min_read_length} \
             --min-qscore ${params.min_qscore} \
-            ${sample} > ${merged_fastq}
+            ${sample}/* > ${merged_fastq}
     """
 }
\ No newline at end of file
diff --git a/tests/lib/processes/merge_input.nf.test b/tests/lib/processes/merge_input.nf.test
index ab2b1f9..dcc9106 100644
--- a/tests/lib/processes/merge_input.nf.test
+++ b/tests/lib/processes/merge_input.nf.test
@@ -13,7 +13,7 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = Channel.from("$baseDir/tests/input/merge_fastq/").collect(sort: true)
+                input[0] = Channel.from("$baseDir/tests/input/merge_fastq/")
                 """
             }
         }
@@ -35,7 +35,7 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = Channel.from("$baseDir/tests/input/merge_fastq/").collect(sort: true)
+                input[0] = Channel.from("$baseDir/tests/input/merge_fastq/").view()
                 """
             }
         }
diff --git a/tests/lib/processes/merge_input.nf.test.snap b/tests/lib/processes/merge_input.nf.test.snap
index d643c67..5169041 100644
--- a/tests/lib/processes/merge_input.nf.test.snap
+++ b/tests/lib/processes/merge_input.nf.test.snap
@@ -31,22 +31,22 @@
                     [
                         "merge_fastq",
                         "target",
-                        "merged.fastq:md5,226ecd48aa7c4b401dcbb0a3fe771365"
+                        "merged.fastq:md5,1a65a32bc2d389105716ebebf13a3d40"
                     ]
                 ],
                 "merged_fastq": [
                     [
                         "merge_fastq",
                         "target",
-                        "merged.fastq:md5,226ecd48aa7c4b401dcbb0a3fe771365"
+                        "merged.fastq:md5,1a65a32bc2d389105716ebebf13a3d40"
                     ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.0"
+            "nf-test": "0.9.0-rc2",
+            "nextflow": "24.05.0"
         },
-        "timestamp": "2024-03-12T11:17:41.974206"
+        "timestamp": "2024-06-20T16:09:39.595045"
     }
 }
\ No newline at end of file