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| author | Justin Bedo <cu@cua0.org> | 2022-08-23 18:36:40 +1000 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2022-09-26 11:51:52 +1000 |
| commit | 81cfa50e6b345942951b68eac0e184ea025f2ae4 (patch) | |
| tree | 65064330cded2a7aa448ef5dce0bcdab36f37211 | |
| parent | 5107449eeb29963b98cb5b6ded6418d930590c23 (diff) | |
last: align only a single fastq file
| -rw-r--r-- | test-tnpair.nix | 2 | ||||
| -rw-r--r-- | tools/last-align.nix | 8 |
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 ''; |