From 49a0849c5c61b34aaf1f9f32c1b1fa9784cdced1 Mon Sep 17 00:00:00 2001
From: Jorrit Boekel <jorrit.boekel@scilifelab.se>
Date: Wed, 30 Aug 2023 11:28:19 +0200
Subject: [PATCH] Fix phospho algo for luciphor to also play nicely with new
 openms activation type spec (auto==hcd/hcid), default to HCD when any
 activation type are present

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

diff --git a/main.nf b/main.nf
index c818a5b..f472f7f 100644
--- a/main.nf
+++ b/main.nf
@@ -1122,7 +1122,7 @@ process luciphorPTMLocalizationScoring {
   msstitch split -i "${allpsms}" --splitcol \$(head -n1 "${allpsms}" | tr '\t' '\n' | grep -n ^TD\$ | cut -f 1 -d':')
   export MZML_PATH=\$(pwd)
   export MINPSMS=${params.minpsms_luciphor}
-  export ALGO=${params.activation == 'hcd' ? '1' : '0'}
+  export ALGO=${['hcd', 'auto'].any { it == params.activation } ? '1' : '0'}
   export MAXPEPLEN=${params.maxpeplen}
   export MAXCHARGE=${params.maxcharge}
   export THREAD=${task.cpus * params.threadspercore}