From 81ba00167925a5606fe3e7222d63b17a1e687e07 Mon Sep 17 00:00:00 2001
From: "Edward S. Rice" <edsrice@gmail.com>
Date: Fri, 11 Oct 2024 14:54:11 +0200
Subject: [PATCH 1/3] Fix #380

---
 modules/local/star_align.nf | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/modules/local/star_align.nf b/modules/local/star_align.nf
index 4b3df1e1..b7e2bf58 100644
--- 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.txt
+    else
+        cp $whitelist whitelist.txt
+    fi
+
     STAR \\
         --genomeDir $index \\
         --readFilesIn ${reverse.join( "," )} ${forward.join( "," )} \\
         --runThreadN $task.cpus \\
         --outFileNamePrefix $prefix. \\
-        --soloCBwhitelist <(gzip -cdf $whitelist) \\
+        --soloCBwhitelist whitelist.txt \\
         --soloType $protocol \\
         --soloFeatures $star_feature \\
         $other_10x_parameters \\

From 017e0d3ef954b0e6b4b347a76d217f291ae5f1af Mon Sep 17 00:00:00 2001
From: "Edward S. Rice" <edsrice@gmail.com>
Date: Fri, 11 Oct 2024 15:26:40 +0200
Subject: [PATCH 2/3] Fix same error as last commit, but for alevin

The alevin-fry workflow for this pipeline has the same issue as the STAR
workflow: it assumes the whitelist is gzipped, and crashes if it is not.
This commit fixes that by only trying to unzip the whitelist if it is in
fact gzipped.
---
 modules/local/simpleaf_quant.nf | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/modules/local/simpleaf_quant.nf b/modules/local/simpleaf_quant.nf
index abb58404..53e0ccb2 100644
--- 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/"
         }

From 9d13a7e1e113c51428db41a9d912d531f8ccaa09 Mon Sep 17 00:00:00 2001
From: "Edward S. Rice" <edsrice@gmail.com>
Date: Mon, 28 Oct 2024 11:41:36 +0100
Subject: [PATCH 3/3] Fix potential filename conflict

Call the uncompressed whitelist whitelist.uncompressed.txt instead of
whitelist.txt.
---
 modules/local/star_align.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/local/star_align.nf b/modules/local/star_align.nf
index b7e2bf58..0b26e037 100644
--- a/modules/local/star_align.nf
+++ b/modules/local/star_align.nf
@@ -55,9 +55,9 @@ process STAR_ALIGN {
     def (forward, reverse) = reads.collate(2).transpose()
     """
     if [[ $whitelist == *.gz ]]; then
-        gzip -cdf $whitelist > whitelist.txt
+        gzip -cdf $whitelist > whitelist.uncompressed.txt
     else
-        cp $whitelist whitelist.txt
+        cp $whitelist whitelist.uncompressed.txt
     fi
 
     STAR \\
@@ -65,7 +65,7 @@ process STAR_ALIGN {
         --readFilesIn ${reverse.join( "," )} ${forward.join( "," )} \\
         --runThreadN $task.cpus \\
         --outFileNamePrefix $prefix. \\
-        --soloCBwhitelist whitelist.txt \\
+        --soloCBwhitelist whitelist.uncompressed.txt \\
         --soloType $protocol \\
         --soloFeatures $star_feature \\
         $other_10x_parameters \\