diff options
author | Justin Bedo <cu@cua0.org> | 2021-07-28 08:07:32 +1000 |
---|---|---|
committer | Justin Bedo <cu@cua0.org> | 2021-07-28 09:17:56 +1000 |
commit | ed98174bbefc85f9895c870fdb7518e2a534a150 (patch) | |
tree | 913c1eb5cb384213d22af6cf4f4e2b8fd2a51276 /tools | |
parent | 134f5e0bfcd5f22e3adee4b707e10693cf71e635 (diff) |
bugfix: use unsorted type for alignment output
Most aligners are only pseudo-name sorted (i.e., pairs adjacant).
Diffstat (limited to 'tools')
-rw-r--r-- | tools/bowtie-align.nix | 2 | ||||
-rw-r--r-- | tools/bwa-mem.nix | 2 | ||||
-rw-r--r-- | tools/bwa-mem2.nix | 2 | ||||
-rw-r--r-- | tools/gridss-assemble.nix | 2 | ||||
-rw-r--r-- | tools/hisat2-align.nix | 2 | ||||
-rw-r--r-- | tools/minimap2-align.nix | 2 | ||||
-rw-r--r-- | tools/snap-align.nix | 2 | ||||
-rw-r--r-- | tools/star-align.nix | 2 | ||||
-rw-r--r-- | tools/whisper-align.nix | 2 |
9 files changed, 9 insertions, 9 deletions
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; } |