From ed98174bbefc85f9895c870fdb7518e2a534a150 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 28 Jul 2021 08:07:32 +1000
Subject: bugfix: use unsorted type for alignment output

Most aligners are only pseudo-name sorted (i.e., pairs adjacant).
---
 tools/bowtie-align.nix    | 2 +-
 tools/bwa-mem.nix         | 2 +-
 tools/bwa-mem2.nix        | 2 +-
 tools/gridss-assemble.nix | 2 +-
 tools/hisat2-align.nix    | 2 +-
 tools/minimap2-align.nix  | 2 +-
 tools/snap-align.nix      | 2 +-
 tools/star-align.nix      | 2 +-
 tools/whisper-align.nix   | 2 +-
 9 files changed, 9 insertions(+), 9 deletions(-)

(limited to 'tools')

diff --git a/tools/bowtie-align.nix b/tools/bowtie-align.nix
index 57b0b01..c83c49c 100644
--- a/tools/bowtie-align.nix
+++ b/tools/bowtie-align.nix
@@ -32,6 +32,6 @@ in stage {
       ${optionalString bamOutput "| samtools view -b"} \
       > $out
   '';
-  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.name {};} else filetype.sam {ref = ref; sorting = sort.name {};};
+  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.none {};} else filetype.sam {ref = ref; sorting = sort.name {};};
   passthru.multicore = true;
 }
diff --git a/tools/bwa-mem.nix b/tools/bwa-mem.nix
index e58ef03..31c9487 100644
--- a/tools/bwa-mem.nix
+++ b/tools/bwa-mem.nix
@@ -35,6 +35,6 @@ in stage {
       ${optionalString bamOutput "| samtools view -b"} \
       > $out
   '';
-  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.name {};} else filetype.sam {ref = ref; sorting = sort.name {};};
+  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.none {};} else filetype.sam {ref = ref; sorting = sort.name {};};
   passthru.multicore = true;
 }
diff --git a/tools/bwa-mem2.nix b/tools/bwa-mem2.nix
index 3de1944..b16b7ea 100644
--- a/tools/bwa-mem2.nix
+++ b/tools/bwa-mem2.nix
@@ -35,6 +35,6 @@ in stage {
       ${optionalString bamOutput "| samtools view -b"} \
       > $out
   '';
-  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.name {};} else filetype.sam {ref = ref; sorting = sort.name {};};
+  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.none {};} else filetype.sam {ref = ref; sorting = sort.name {};};
   passthru.multicore = true;
 }
diff --git a/tools/gridss-assemble.nix b/tools/gridss-assemble.nix
index 9e51cab..1a46eae 100644
--- a/tools/gridss-assemble.nix
+++ b/tools/gridss-assemble.nix
@@ -70,6 +70,6 @@ stage rec {
     touch $out
     cp -r out.gridss.working $work
   '';
-  passthru.filetype = filetype.bam { ref = ref; sorting = sort.name {}; };
+  passthru.filetype = filetype.bam { ref = ref; sorting = sort.none {}; };
   passthru.multicore = true;
 }
diff --git a/tools/hisat2-align.nix b/tools/hisat2-align.nix
index dfd9601..7a216a6 100644
--- a/tools/hisat2-align.nix
+++ b/tools/hisat2-align.nix
@@ -33,6 +33,6 @@ in stage {
       | samtools sort -n \
       > $out
   '';
-  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.name {};} else filetype.sam {ref = ref; sorting = sort.name {};};
+  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.none {};} else filetype.sam {ref = ref; sorting = sort.name {};};
   passthru.multicore = true;
 }
diff --git a/tools/minimap2-align.nix b/tools/minimap2-align.nix
index 7164ace..a6de0b7 100644
--- a/tools/minimap2-align.nix
+++ b/tools/minimap2-align.nix
@@ -32,6 +32,6 @@ in stage {
       ${optionalString bamOutput "| samtools view -b"} \
       > $out
   '';
-  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.name {};} else filetype.sam {ref = ref; sorting = sort.name {};};
+  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.none {};} else filetype.sam {ref = ref; sorting = sort.none {};};
   passthru.multicore = true;
 }
diff --git a/tools/snap-align.nix b/tools/snap-align.nix
index 4647142..279cf20 100644
--- a/tools/snap-align.nix
+++ b/tools/snap-align.nix
@@ -32,6 +32,6 @@ in stage {
       ${optionalString (flags != null) flags} \
       | samtools sort -n > $out
   '';
-  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.name {};} else filetype.sam {ref = ref; sorting = sort.name {};};
+  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.none {};} else filetype.sam {ref = ref; sorting = sort.name {};};
   passthru.multicore = true;
 }
diff --git a/tools/star-align.nix b/tools/star-align.nix
index 0cf9ab9..44dd7f2 100644
--- a/tools/star-align.nix
+++ b/tools/star-align.nix
@@ -33,6 +33,6 @@ in stage {
      --readFilesIn ${fq input1} ${optionalString (input2 != null) (fq input2)}
      ${if bamOutput then "samtools view -b Aligned.out.sam > $out" else "cp Aligned.out.sam $out"}
   '';
-  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.name {};} else filetype.sam {ref = ref; sorting = sort.name {};};
+  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.none {};} else filetype.sam {ref = ref; sorting = sort.name {};};
   passthru.multicore = true;
 }
diff --git a/tools/whisper-align.nix b/tools/whisper-align.nix
index c44205a..1731bfe 100644
--- a/tools/whisper-align.nix
+++ b/tools/whisper-align.nix
@@ -34,6 +34,6 @@ in stage {
       ${optionalString (input2 != null) (fq input2)} \
       > $out
   '';
-  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.name {};} else filetype.sam {ref = ref; sorting = sort.name {};};
+  passthru.filetype = if bamOutput then filetype.bam {ref = ref; sorting = sort.none {};} else filetype.sam {ref = ref; sorting = sort.name {};};
   passthru.multicore = true;
 }
-- 
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