fix cascadia search

Author: mriffle

main.nf

@@ -148,7 +148,6 @@ workflow {
         replicate_metadata = get_input_files.out.replicate_metadata
     }
     fasta = get_input_files.out.fasta
-    skyline_fasta = get_input_files.out.skyline_fasta
     skyline_template_zipfile = get_input_files.out.skyline_template_zipfile
     skyr_file_ch = get_input_files.out.skyr_files
 
@@ -161,7 +160,13 @@ workflow {
     )
     search_engine_version = dia_search.out.search_engine_version
     final_speclib = dia_search.out.final_speclib
-    fasta = dia_search.out.search_fasta
+
+    if (params.search_engine.toLowerCase() == 'cascadia') {
+        // Always use fasta generated by Cascadia search for Skyline
+        skyline_fasta = dia_search.out.search_fasta
+    } else {
+        skyline_fasta = get_input_files.out.skyline_fasta
+    }
 
     skyline (
         wide_mzml_ch,
@@ -179,7 +184,7 @@ workflow {
                 dia_qc_version).splitText()
 
     input_files = fasta.map{ it -> ['Fasta file', it.name] }.concat(
-        fasta.map{ it -> ['Skyline fasta file', it.name] },
+        skyline_fasta.map{ it -> ['Skyline fasta file', it.name] },
         spectral_library.map{ it -> ['Spectra library', it.baseName] },
         all_mzml_ch.map{ it -> ['Spectra file', it.baseName] })
 
@@ -205,7 +210,7 @@ workflow {
             search_engine,
             skyline.out.final_skyline_file,
             all_mzml_ch,
-            fasta,
+            dia_search.out.search_fasta,
             spectral_library,
             config_file,
             run_details_file,