From 8f3f23ee2bf854030f8e2945d0907c7504761d9b Mon Sep 17 00:00:00 2001
From: Alexander <alexander.berger@jax.org>
Date: Tue, 30 Sep 2025 06:57:12 -0400
Subject: [PATCH] Switch from readLines to splitText in
 single-mouse-corrected-corners

---
 nextflow/workflows/io.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/nextflow/workflows/io.nf b/nextflow/workflows/io.nf
index 127ed24..0ec46b9 100644
--- a/nextflow/workflows/io.nf
+++ b/nextflow/workflows/io.nf
@@ -54,9 +54,9 @@ workflow PREPARE_DATA {
 
     // Files should be appropriately URLified to avoid collisions within the pipeline
     if (skip_urlify) {
-        file_processing_channel = file_batch.readLines().flatMap { line -> file(line) }
+        file_processing_channel = file_batch.splitText().map { line -> file(line.trim()) }
     } else {
-        file_processing_channel = URLIFY_FILE(file_batch.readLines().flatMap(), params.path_depth).file
+        file_processing_channel = URLIFY_FILE(file_batch.splitText().map { it.trim() }, params.path_depth).file
     }
 
     emit: