From 3e74b7be028a1e53724adb375dd65a3affb1568c Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Tue, 15 Oct 2024 18:15:48 +0100
Subject: [PATCH] Don't skip whole trimming workflows

---
 .../nf-core/fastq_qc_trim_filter_setstrandedness/main.nf      | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf
index 05078d23dcb..c655af41588 100644
--- a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf
+++ b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf
@@ -139,7 +139,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS {
     //
     // SUBWORKFLOW: Read QC, extract UMI and trim adapters with TrimGalore!
     //
-    if (trimmer == 'trimgalore' && !skip_trimming) {
+    if (trimmer == 'trimgalore') {
         FASTQ_FASTQC_UMITOOLS_TRIMGALORE (
             ch_filtered_reads,
             skip_fastqc,
@@ -162,7 +162,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS {
     //
     // SUBWORKFLOW: Read QC, extract UMI and trim adapters with fastp
     //
-    if (trimmer == 'fastp' && !skip_trimming) {
+    if (trimmer == 'fastp') {
         FASTQ_FASTQC_UMITOOLS_FASTP (
             ch_filtered_reads,
             skip_fastqc,