From 96c9a8880a690d2d8058663a805c3b363e416a8d Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 9 Feb 2022 12:13:59 +1100
Subject: don't strip store paths from bams

Due to BAM compression attempting to strip store
paths is a waste of time.
---
 tools/bowtie-align.nix                 | 1 +
 tools/bwa-mem.nix                      | 1 +
 tools/bwa-mem2.nix                     | 1 +
 tools/gridss-assemble.nix              | 1 +
 tools/gridss-softClipsToSplitReads.nix | 1 +
 tools/hisat2-align.nix                 | 1 +
 tools/minimap2-align.nix               | 1 +
 tools/snap-align.nix                   | 1 +
 tools/star-align.nix                   | 1 +
 tools/subread-align.nix                | 1 +
 tools/whisper-align.nix                | 1 +
 11 files changed, 11 insertions(+)

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;
 }
-- 
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