From 871ef64f3c43199dfa01216ac86db56650c2c8a2 Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Fri, 5 Oct 2018 16:16:20 +1000 Subject: implement types --- lib/types.nix | 64 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 lib/types.nix (limited to 'lib/types.nix') diff --git a/lib/types.nix b/lib/types.nix new file mode 100644 index 0000000..a347046 --- /dev/null +++ b/lib/types.nix @@ -0,0 +1,64 @@ +{bionix, nixpkgs}: + +with nixpkgs; + +let + nix-adt-src = fetchFromGitHub { + owner = "shlevy"; + repo = "nix-adt"; + rev = "dd04b5d08eed65ecd73aafde56a78078e09f1c74"; + sha256 = "0vhk1y7gilgn2pgvj4813bh2ljpw4pvrph8k8b0fsg56dbm8mqxa"; + }; + nix-adt = import "${nix-adt-src}"; + inherit (nix-adt.checked) make-type match any std none; + inherit (std) option; + + idft = sym: ft: _: abort "unhandled filetype (${ft}) for ${sym}"; + idst = sym: st: _: abort "unhandled sorting (${st}) for ${sym}"; + +in +rec { + option-sort = option sorting; + + matchFiletype = sym: y: x: if x ? filetype then match x.filetype ({ + fa = idft sym "fasta"; + fq = idft sym "fastq"; + bam = idft sym "bam"; + sam = idft sym "sam"; + cram = idft sym "cram"; + vcf = idft sym "vcf"; + bed = idft sym "bed"; + gz = idft sym "gz"; + bz2 = idft sym "bz2"; + } // y) else abort "unknown filetype for ${sym}"; + filetype = make-type "filetype" { + fa = {}; + fq = {}; + bam = {ref = any; sorting = option-sort;}; + sam = {ref = any; sorting = option-sort;}; + cram = {ref = any; sorting = option-sort;}; + vcf = {ref = any;}; + bed = {ref = any;}; + gz = filetype; + bz2 = filetype; + }; + + toCram = matchFiletype "bam2cram" { bam = filetype.cram; sam = filetype.cram; cram = filetype.cram; }; + toBam = matchFiletype "bam2cram" { bam = filetype.bam; sam = filetype.bam; cram = filetype.bam; }; + toSam = matchFiletype "bam2cram" { bam = filetype.sam; sam = filetype.sam; cram = filetype.sam; }; + + matchSorting = sym: y: let f = x: match x.sorting { some = z: match z ( { coord = idst sym "coord"; name = idst sym "name"; } // y); none = abort "unknown sort for ${sym}"; }; in matchFiletype sym { bam = f; sam = f; cram = f; }; + sorting = make-type "sorting" { + coord = {}; + name = {}; + }; + coordSort = f: matchFiletype "coordSort" { bam = x: filetype.bam (x // {sorting = option-sort.some (sorting.coord {});}); } {filetype = f;}; + nameSort = f: matchFiletype "nameSort" { bam = x: filetype.bam (x // {sorting = option-sort.some (sorting.name {});}); } {filetype = f;}; + + gunzip = matchFiletype "gunzip" { gz = x: x; }; + bunzip2 = matchFiletype "bunzip2" { bz2 = x: x; }; + + tag = attrs: x: if x ? type && x.type == "derivation" then x // attrs else tagPassthru attrs x; + tagPassthru = attrs: x: if x ? passthru then x // { passthru = x.passthru // attrs; } else x // { passthru = attrs; }; + tagFiletype = ft: tag { filetype = ft; }; +} -- cgit v1.2.3