Merge pull request #382 from esrice/fix-star-gzip-error

Fix gzip error
nf-core · Oct 28, 2024 · eaa74dd · eaa74dd
2 parents 44c9360 + 9d13a7e
commit eaa74dd
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Showing 2 changed files with 12 additions and 2 deletions.
diff --git a/modules/local/simpleaf_quant.nf b/modules/local/simpleaf_quant.nf
@@ -39,7 +39,11 @@ process SIMPLEAF_QUANT {
     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"
+            if (whitelist.name.endsWith('.gz')) {
+                unzip_whitelist = "gzip -dcf $whitelist > whitelist.uncompressed.txt"
+            } else {
+                unzip_whitelist = "cp $whitelist whitelist.uncompressed.txt"
+            }
             unfiltered_command = "-u whitelist.uncompressed.txt"
             save_whitelist     = "mv whitelist.uncompressed.txt ${prefix}_alevin_results/"
         }

diff --git a/modules/local/star_align.nf b/modules/local/star_align.nf
@@ -54,12 +54,18 @@ process STAR_ALIGN {
     // separate forward from reverse pairs
     def (forward, reverse) = reads.collate(2).transpose()
     """
+    if [[ $whitelist == *.gz ]]; then
+        gzip -cdf $whitelist > whitelist.uncompressed.txt
+    else
+        cp $whitelist whitelist.uncompressed.txt
+    fi
+
     STAR \\
         --genomeDir $index \\
         --readFilesIn ${reverse.join( "," )} ${forward.join( "," )} \\
         --runThreadN $task.cpus \\
         --outFileNamePrefix $prefix. \\
-        --soloCBwhitelist <(gzip -cdf $whitelist) \\
+        --soloCBwhitelist whitelist.uncompressed.txt \\
         --soloType $protocol \\
         --soloFeatures $star_feature \\
         $other_10x_parameters \\