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authorJustin Bedo <cu@cua0.org>2022-08-23 18:36:40 +1000
committerJustin Bedo <cu@cua0.org>2022-09-26 11:51:52 +1000
commit81cfa50e6b345942951b68eac0e184ea025f2ae4 (patch)
tree65064330cded2a7aa448ef5dce0bcdab36f37211
parent5107449eeb29963b98cb5b6ded6418d930590c23 (diff)
last: align only a single fastq file
-rw-r--r--test-tnpair.nix2
-rw-r--r--tools/last-align.nix8
2 files changed, 4 insertions, 6 deletions
diff --git a/test-tnpair.nix b/test-tnpair.nix
index 169d531..195ac27 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -60,7 +60,7 @@ let
alignments = {
"bowtie-normal.bam" = bowtie.align { inherit ref; } tnpair.normal.files;
"subread.bam" = subread.align { inherit ref; } tnpair.normal.files;
- "last.maf" = lastal.align { inherit ref; } tnpair.normal.files;
+ "last.maf" = lastal.align { inherit ref; } tnpair.normal.files.input1;
"whisper.bam" = whisper.align { inherit ref; } tnpair.normal.files;
"bwa-mem.bam" = bwa.mem { inherit ref; } tnpair.normal.files;
"bwa-mem2.bam" = bwa.mem2 { inherit ref; } tnpair.normal.files;
diff --git a/tools/last-align.nix b/tools/last-align.nix
index fbc0914..0643419 100644
--- a/tools/last-align.nix
+++ b/tools/last-align.nix
@@ -5,9 +5,7 @@
, indexAttrs ? { }
}:
-{ input1
-, input2 ? null
-}:
+input:
with bionix;
with lib;
@@ -23,13 +21,13 @@ stage {
last-train -P $NIX_BUILD_CORES \
${optionalString (trainFlags != null) flags} \
${bionix.lastal.index indexAttrs ref}/index \
- ${fq input1} ${optionalString (input2 != null) (fq input2)}\
+ ${fq input} -Q 1\
> train
lastal -P $NIX_BUILD_CORES \
${optionalString (flags != null) flags} \
${bionix.lastal.index indexAttrs ref}/index \
-p train \
- ${fq input1} ${optionalString (input2 != null) (fq input2)}\
+ ${fq input} -Q 1 \
> tmp
cp tmp $out
'';