diff options
| -rw-r--r-- | test-tnpair.nix | 2 | ||||
| -rw-r--r-- | tools/bwa-index2.nix | 23 | ||||
| -rw-r--r-- | tools/bwa-mem2-app.nix | 15 | ||||
| -rw-r--r-- | tools/bwa-mem2.nix | 40 | ||||
| -rw-r--r-- | tools/bwa.nix | 8 |
5 files changed, 86 insertions, 2 deletions
diff --git a/test-tnpair.nix b/test-tnpair.nix index 0e13338..76fcfab 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -62,6 +62,8 @@ let (ln tnpairResult.variants.snvs "strelka.snvs.vcf") (ln tnpairResult.glvariants.variants "strelka.gl.vcf") (ln (bowtie.align {inherit ref;} tnpair.normal.files) "alignments/bowtie-normal.bam") + (ln (bwa.mem {inherit ref;} tnpair.normal.files) "alignments/bwa-mem.bam") + (ln (bwa.mem2 {inherit ref;} tnpair.normal.files) "alignments/bwa-mem2.bam") (ln (minimap2.align {inherit ref; preset = "sr"; } tnpair.normal.files) "alignments/minimap2-normal.bam") (ln (snap.align {inherit ref; } tnpair.normal.files) "alignments/snap-normal.bam") (ln (gridss.callVariants {} (with tnpairResult.alignments; [normal tumour])) "gridss") diff --git a/tools/bwa-index2.nix b/tools/bwa-index2.nix new file mode 100644 index 0000000..f5cc69b --- /dev/null +++ b/tools/bwa-index2.nix @@ -0,0 +1,23 @@ +{ bionix +, flags ? null +}: + +ref: + +with bionix; +with lib; +with types; + +assert (matchFiletype "bwa-index" { fa = _: true; } ref); + +stage { + name = "bwa-index2"; + buildInputs = with pkgs; [ bionix.bwa.app2 ]; + buildCommand = '' + ln -s ${ref} ref.fa + bwa-mem2 index ${optionalString (flags != null) flags} ref.fa + mkdir $out + mv ref.fa.* $out + grep '^>[^ \t]*_alt$' ref.fa | tr -d '^>' > $out/idxbase.alt || true + ''; +} diff --git a/tools/bwa-mem2-app.nix b/tools/bwa-mem2-app.nix new file mode 100644 index 0000000..8cca5a5 --- /dev/null +++ b/tools/bwa-mem2-app.nix @@ -0,0 +1,15 @@ +{ bwa, fetchFromGitHub }: + bwa.overrideAttrs (_: + { + name = "bwa-mem2"; + src = fetchFromGitHub { + owner = "bwa-mem2"; + repo = "bwa-mem2"; + rev = "f882015f7f46845f72c10094a621264f78d206d8"; + sha256 = "1wfx8j9mwbb29jw4zxp28lajmj774jy1l5x229nf065cqr2dgyqg"; + }; + installPhase = '' + mkdir -p $out/bin + cp bwa-mem2 $out/bin + ''; + }) diff --git a/tools/bwa-mem2.nix b/tools/bwa-mem2.nix new file mode 100644 index 0000000..3de1944 --- /dev/null +++ b/tools/bwa-mem2.nix @@ -0,0 +1,40 @@ +{ bionix +, ref +, bamOutput ? true +, flags ? null +, indexAttrs ? {} +}: + +{ input1 +, input2 ? null +}: + +with bionix; +with lib; +with types; +with compression; + +let + fa = f: matchFiletype "bwa-ref" { fa = _: f; } f; + fq = f: matchFiletype "bwa-input" { fq = _: f; gz = matchFiletype' "bwa-input" { fq = _: f; }; } f; + +in stage { + name = "bwa-mem2"; + buildInputs = with pkgs; [ bionix.bwa.app2 bc ] ++ optional bamOutput samtools; + buildCommand = '' + ln -s ${fa ref} ref.fa + for f in ${bionix.bwa.index2 indexAttrs ref}/* ; do + ln -s $f + done + cores=$(echo $NIX_BUILD_CORES ${optionalString bamOutput "- 1"} | bc) + if [[ $cores -lt 1 ]] ; then + cores=1 + fi + bwa-mem2 mem ${optionalString (flags != null) flags} -t $cores ref.fa ${fq input1} \ + ${optionalString (input2 != null) (fq input2)} \ + ${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.multicore = true; +} diff --git a/tools/bwa.nix b/tools/bwa.nix index 58f9651..90a8bd3 100644 --- a/tools/bwa.nix +++ b/tools/bwa.nix @@ -3,15 +3,19 @@ with bionix; rec { + app2 = pkgs.callPackage ./bwa-mem2-app.nix {}; + /* Align read against a reference: defaults to bwa-mem */ - align = bwa-mem; + align = bionix.bwa.mem; /* Align reads against a reference using bwa-mem Type: bwa-mem :: {ref :: fasta, bamOutput :: bool, ...} -> {input1, input2} -> bam/sam */ - bwa-mem = callBionixE ./bwa-mem.nix; + mem = callBionixE ./bwa-mem.nix; + mem2 = callBionixE ./bwa-mem2.nix; /* Creates an reference index for BWA Type: index :: {...} -> fasta -> BWA index */ index = callBionixE ./bwa-index.nix; + index2 = callBionixE ./bwa-index2.nix; } |