diff options
| -rw-r--r-- | default.nix | 1 | ||||
| -rw-r--r-- | test-tnpair.nix | 1 | ||||
| -rw-r--r-- | tools/last-align.nix | 39 | ||||
| -rw-r--r-- | tools/last-index.nix | 21 | ||||
| -rw-r--r-- | tools/last.nix | 8 |
5 files changed, 70 insertions, 0 deletions
diff --git a/default.nix b/default.nix index 41ad190..12ca5b3 100644 --- a/default.nix +++ b/default.nix @@ -44,6 +44,7 @@ let manta = callBionix ./tools/manta.nix {}; delly = callBionix ./tools/delly.nix {}; lumpy = callBionix ./tools/lumpy.nix {}; + lastal = callBionix ./tools/last.nix {}; slurm = attrs: bionix.extend (self: super: with self; rec { slurmDefs = { ppn = 1; mem = 1; walltime = "24:00:00"; partition = null; slurmFlags = null; salloc = "/usr/bin/salloc"; srun = "/usr/bin/srun"; } // attrs; diff --git a/test-tnpair.nix b/test-tnpair.nix index 38eb509..38e3333 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -53,6 +53,7 @@ let alignments = { "bowtie-normal.bam" = bowtie.align {inherit ref;} tnpair.normal.files; + "last.maf" = lastal.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; "minimap2-normal.bam" = minimap2.align {inherit ref; preset = "sr"; } tnpair.normal.files; diff --git a/tools/last-align.nix b/tools/last-align.nix new file mode 100644 index 0000000..b2c8460 --- /dev/null +++ b/tools/last-align.nix @@ -0,0 +1,39 @@ +{ bionix +, ref +, flags ? null +, indexAttrs ? {} +}: + +{ input1 +, input2 ? null +}: + +with bionix; +with lib; +with types; + +let + fa = f: matchFiletype "last-ref" { fa = _: f; } f; + fq = f: matchFiletype "last-input" { fq = _: f; } f; + fqfa = f: matchFiletype "last-input" { fq = _: f; fa = _: f; } f; + Q = f: matchFiletype "last-input" { fq = _: 1; fa = _: 0; } f; + parallel = f: matchFiletype "last-input" { fq = _: "parallel-fastq"; fa = _: "parallel-fasta"; } f; + +in stage { + name = "last-align"; + buildInputs = with pkgs; [ last ]; + buildCommand = '' + ${if (input2 != null) then "fastq-interleave ${fq input1} ${fq input2}" else "cat ${fa input1}"} | \ + ${parallel input1} -j $NIX_BUILD_CORES \ + lastal -Q${toString (Q input1)} \ + ${optionalString (input2 != null) "-i1"} \ + ${optionalString (flags != null) flags} \ + ${bionix.lastal.index indexAttrs ref}/index \ + > tmp + '' + (if input2 == null then '' + cp tmp $out + '' else '' + last-pair-probs tmp > $out + ''); + passthru.multicore = true; +} diff --git a/tools/last-index.nix b/tools/last-index.nix new file mode 100644 index 0000000..af74f65 --- /dev/null +++ b/tools/last-index.nix @@ -0,0 +1,21 @@ +{ bionix +, flags ? null +}: + +ref: + +with bionix; +with lib; +with types; + +assert (matchFiletype "last-index" { fa = _: true; } ref); + +stage { + name = "last-index"; + buildInputs = with pkgs; [ last ]; + buildCommand = '' + ln -s ${ref} ref.fa + mkdir $out + lastdb ${optionalString (flags != null) flags} $out/index ref.fa + ''; +} diff --git a/tools/last.nix b/tools/last.nix new file mode 100644 index 0000000..4e40a65 --- /dev/null +++ b/tools/last.nix @@ -0,0 +1,8 @@ +{ bionix }: + +with bionix; + +rec { + align = callBionixE ./last-align.nix; + index = callBionixE ./last-index.nix; +} |