From 0dbceb1b4682f915584435821580542aadcaaaf6 Mon Sep 17 00:00:00 2001
From: matrulda <matilda.aslin@medsci.uu.se>
Date: Fri, 20 Feb 2026 11:24:15 +0100
Subject: [PATCH 1/2] Adjust for the fact that zipped empty files have file
 size > 0

---
 main.nf                                            |   2 +-
 .../AB-1234/EmptyFastq_S1_L001_R1_001.fastq.gz     | Bin 0 -> 52 bytes
 .../AB-1234/EmptyFastq_S1_L001_R2_001.fastq.gz     | Bin 0 -> 52 bytes
 3 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index 9ba5a19..22eac55 100644
--- a/main.nf
+++ b/main.nf
@@ -89,7 +89,7 @@ def get_project_and_reads(run_folder) {
     Channel
         .fromPath("${run_folder}/${params.demultiplexer_outdir}/**.fastq.gz")
         .filter { file -> file.name =~ /.*_[^I]\d_001\.fastq\.gz$/ }
-        .filter { file -> file.size() > 0 }
+        .filter { file -> file.size() > 100 }
         .ifEmpty { error "Error: No fastq files found under ${run_folder}/!" }
         .map { file ->
             file.toString().indexOf('Undetermined') > 0 ?
diff --git a/test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/AB-1234/EmptyFastq_S1_L001_R1_001.fastq.gz b/test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/AB-1234/EmptyFastq_S1_L001_R1_001.fastq.gz
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..5c253f8b33775167919b0424b107fa577075608d 100644
GIT binary patch
literal 52
xcmb2|=HOVlYHB6}vukcaNu^t2aY<o(uwlH9fq`LskYPNK(n|vgGB7j1006Fx4PF2M

literal 0
HcmV?d00001

diff --git a/test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/AB-1234/EmptyFastq_S1_L001_R2_001.fastq.gz b/test_data/230825_M04034_0043_000000000-L6NVV/Unaligned/AB-1234/EmptyFastq_S1_L001_R2_001.fastq.gz
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..338bb83d2fbbe1102f976ae15b0f17061496f7e7 100644
GIT binary patch
literal 52
xcmb2|=HS@6YHB6}vukcaNu^t2aY<o(uwlH9fq`LskWoC4(n|vgGB7j1006M!4Ql`Z

literal 0
HcmV?d00001


From 0c9f0a5396736acfb3ad88793a2e8d3f9ffa2cad Mon Sep 17 00:00:00 2001
From: matrulda <matilda.aslin@medsci.uu.se>
Date: Fri, 20 Feb 2026 12:56:06 +0100
Subject: [PATCH 2/2] Add comment about empty gzip file size

---
 main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index 22eac55..5b5f7ae 100644
--- a/main.nf
+++ b/main.nf
@@ -89,7 +89,7 @@ def get_project_and_reads(run_folder) {
     Channel
         .fromPath("${run_folder}/${params.demultiplexer_outdir}/**.fastq.gz")
         .filter { file -> file.name =~ /.*_[^I]\d_001\.fastq\.gz$/ }
-        .filter { file -> file.size() > 100 }
+        .filter { file -> file.size() > 100 } // An empty gzip file is ~ 50 bytes in size
         .ifEmpty { error "Error: No fastq files found under ${run_folder}/!" }
         .map { file ->
             file.toString().indexOf('Undetermined') > 0 ?