11 files changed, 11 insertions, 0 deletions
diff --git a/tools/bowtie-align.nix b/tools/bowtie-align.nix
index cca12a2..d8c0dc5 100644
--- a/tools/bowtie-align.nix
+++ b/tools/bowtie-align.nix
@@ -38,4 +38,5 @@ stage {
   '';
   passthru.filetype = if bamOutput then filetype.bam { inherit ref; sorting = sort.none { }; } else filetype.sam { inherit ref; sorting = sort.name { }; };
   passthru.multicore = true;
+  stripStorePaths = !bamOutput;
 }
diff --git a/tools/bwa-mem.nix b/tools/bwa-mem.nix
index 84038d9..6cefc57 100644
--- a/tools/bwa-mem.nix
+++ b/tools/bwa-mem.nix
@@ -39,4 +39,5 @@ stage {
   '';
   passthru.filetype = if bamOutput then filetype.bam { inherit ref; sorting = sort.none { }; } else filetype.sam { inherit ref; sorting = sort.name { }; };
   passthru.multicore = true;
+  stripStorePaths = !bamOutput;
 }
diff --git a/tools/bwa-mem2.nix b/tools/bwa-mem2.nix
index e6237f0..1c98167 100644
--- a/tools/bwa-mem2.nix
+++ b/tools/bwa-mem2.nix
@@ -40,4 +40,5 @@ stage {
   '';
   passthru.filetype = if bamOutput then filetype.bam { inherit ref; sorting = sort.none { }; } else filetype.sam { inherit ref; sorting = sort.name { }; };
   passthru.multicore = true;
+  stripStorePaths = !bamOutput;
 }
diff --git a/tools/gridss-assemble.nix b/tools/gridss-assemble.nix
index 15e5ca6..56c318f 100644
--- a/tools/gridss-assemble.nix
+++ b/tools/gridss-assemble.nix
@@ -72,4 +72,5 @@ stage rec {
   '';
   passthru.filetype = filetype.bam { inherit ref; sorting = sort.none { }; };
   passthru.multicore = true;
+  stripStorePaths = false;
 }
diff --git a/tools/gridss-softClipsToSplitReads.nix b/tools/gridss-softClipsToSplitReads.nix
index ef53322..ac87178 100644
--- a/tools/gridss-softClipsToSplitReads.nix
+++ b/tools/gridss-softClipsToSplitReads.nix
@@ -40,4 +40,5 @@ stage rec {
   '';
   passthru.filetype = filetype.bam { inherit ref; sorting = sort.none { }; };
   passthru.multicore = true;
+  stripStorePaths = false;
 }
diff --git a/tools/hisat2-align.nix b/tools/hisat2-align.nix
index 0a1eb25..736d848 100644
--- a/tools/hisat2-align.nix
+++ b/tools/hisat2-align.nix
@@ -36,4 +36,5 @@ stage {
   '';
   passthru.filetype = if bamOutput then filetype.bam { inherit ref; sorting = sort.none { }; } else filetype.sam { inherit ref; sorting = sort.name { }; };
   passthru.multicore = true;
+  stripStorePaths = !bamOutput;
 }
diff --git a/tools/minimap2-align.nix b/tools/minimap2-align.nix
index e7e71c6..fdb62cf 100644
--- a/tools/minimap2-align.nix
+++ b/tools/minimap2-align.nix
@@ -37,4 +37,5 @@ stage {
   '';
   passthru.filetype = if bamOutput then filetype.bam { inherit ref; sorting = sort.none { }; } else filetype.sam { inherit ref; sorting = sort.none { }; };
   passthru.multicore = true;
+  stripStorePaths = false;
 }
diff --git a/tools/snap-align.nix b/tools/snap-align.nix
index f0bcb21..dca3e9f 100644
--- a/tools/snap-align.nix
+++ b/tools/snap-align.nix
@@ -35,4 +35,5 @@ stage {
   '';
   passthru.filetype = if bamOutput then filetype.bam { inherit ref; sorting = sort.none { }; } else filetype.sam { inherit ref; sorting = sort.name { }; };
   passthru.multicore = true;
+  stripStorePaths = false;
 }
diff --git a/tools/star-align.nix b/tools/star-align.nix
index 670c6bf..160b65e 100644
--- a/tools/star-align.nix
+++ b/tools/star-align.nix
@@ -36,4 +36,5 @@ stage {
   '';
   passthru.filetype = if bamOutput then filetype.bam { inherit ref; sorting = sort.none { }; } else filetype.sam { inherit ref; sorting = sort.name { }; };
   passthru.multicore = true;
+  stripStorePaths = false;
 }
diff --git a/tools/subread-align.nix b/tools/subread-align.nix
index 0b0f4c1..ede2d6d 100644
--- a/tools/subread-align.nix
+++ b/tools/subread-align.nix
@@ -35,4 +35,5 @@ stage {
   '';
   passthru.filetype = filetype.bam { inherit ref; sorting = sort.none { }; };
   passthru.multicore = true;
+  stripStorePaths = false;
 }
diff --git a/tools/whisper-align.nix b/tools/whisper-align.nix
index 19eef0d..e76e921 100644
--- a/tools/whisper-align.nix
+++ b/tools/whisper-align.nix
@@ -37,4 +37,5 @@ stage {
   '';
   passthru.filetype = if bamOutput then filetype.bam { inherit ref; sorting = sort.none { }; } else filetype.sam { inherit ref; sorting = sort.name { }; };
   passthru.multicore = true;
+  stripStorePaths = false;
 }