pause R2 trimmed check until file is made

jpsmith5 · jpsmith5 · commit ce3c67884ca7 · 2026-02-19T07:03:42.000-05:00
diff --git a/pipelines/peppro.py b/pipelines/peppro.py
@@ -1413,8 +1413,8 @@ def check_trim(trimmed_fastq, paired_end,
     paired_end = args.paired_end
     if read2:
         pm.run([adapter_command, trim_command], trimmed_fq2,
-               follow=check_trim(processed_fastq, paired_end, trimmed_fq2,
-                                 fastqc_folder=fastqc_folder))
+               follow=lambda: check_trim(processed_fastq, paired_end, trimmed_fq2,
+                                         fastqc_folder=fastqc_folder))
         if args.adapter == "cutadapt":
             output_folder = os.path.join(outfolder, "cutadapt")
         else:
