Merge pull request #267 from nf-core/fix-263

Fix 263
nf-core · Sep 22, 2023 · da9b375 · da9b375
2 parents 4a8a63f + dad9d8f
commit da9b375
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v2.4.1 - 2023-09-21
 
+- Fix whitelist logic for dropseq ([#267](https://github.com/nf-core/scrnaseq/pull/267))
 - Fix false-positive filename check in cellranger module ([#261](https://github.com/nf-core/scrnaseq/pull/261))
 
 ## v2.4.0 - 2023-08-16 Lime Platinum Crab

diff --git a/modules/local/simpleaf_quant.nf b/modules/local/simpleaf_quant.nf
@@ -34,12 +34,15 @@ process SIMPLEAF_QUANT {
     // check if users are using one of the mutually excludable parameters:
     //    e.g -k,--knee | -e,--expect-cells | -f, --forced-cells
     //
-    if (args_list.any { it in ['-k', '--knee', '-e', '--expect-cells', '-f', '--forced-cells']} || meta.expected_cells) {
-        unfiltered_command = ""
-        save_whitelist     = ""
-    } else {
-        unfiltered_command = "-u whitelist.uncompressed.txt"
-        save_whitelist     = "mv whitelist.uncompressed.txt ${prefix}_alevin_results/"
+    unzip_whitelist = ""
+    unfiltered_command = ""
+    save_whitelist     = ""
+    if (!(args_list.any { it in ['-k', '--knee', '-e', '--expect-cells', '-f', '--forced-cells']} || meta.expected_cells)) {
+        if (whitelist) {
+            unzip_whitelist = "gzip -dcf $whitelist > whitelist.uncompressed.txt"
+            unfiltered_command = "-u whitelist.uncompressed.txt"
+            save_whitelist     = "mv whitelist.uncompressed.txt ${prefix}_alevin_results/"
+        }
     }
 
     // expected cells
@@ -55,7 +58,7 @@ process SIMPLEAF_QUANT {
     simpleaf set-paths
 
     # run simpleaf quant
-    gzip -dcf $whitelist > whitelist.uncompressed.txt
+    $unzip_whitelist
     simpleaf quant \\
         -1 ${forward.join( "," )} \\
         -2 ${reverse.join( "," )} \\