diff options
| -rw-r--r-- | default.nix | 1 | ||||
| -rw-r--r-- | test-tnpair.nix | 4 | ||||
| -rw-r--r-- | tools/octopus-call.nix | 37 | ||||
| -rw-r--r-- | tools/octopus-callSomatic.nix | 53 | ||||
| -rw-r--r-- | tools/octopus.nix | 8 |
5 files changed, 103 insertions, 0 deletions
diff --git a/default.nix b/default.nix index 9bc7b6c..3077470 100644 --- a/default.nix +++ b/default.nix @@ -36,6 +36,7 @@ let strelka = callBionix ./tools/strelka.nix {}; ascat = callBionix ./tools/ascat.nix {}; fastp = callBionix ./tools/fastp.nix {}; + octopus = callBionix ./tools/octopus.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 76fcfab..f90e3a9 100644 --- a/test-tnpair.nix +++ b/test-tnpair.nix @@ -37,8 +37,10 @@ let processPair = { tumour, normal }: rec { alignments = mapAttrs (_: x: markdup (sort (fixmate (alignWithRG x.name x.files)))) { inherit normal tumour; }; variants = callVariants alignments; + octopusSomatic = octopus.callSomatic {} {inherit (alignments) normal; tumours = [ alignments.tumour ];}; glvariants = strelka.call {} (builtins.attrValues alignments); platypusVars = platypus.call {} (builtins.attrValues alignments); + octopusVars = octopus.call {} (builtins.attrValues alignments); shards = pipe [ (shard.fastQPair 2) (map (bwa.align {inherit ref;})) @@ -56,6 +58,8 @@ let (ln (facets.callCNV {} {vcf = tnpairResult.platypusVars; bams = with tnpairResult.alignments; [ normal tumour ];}) "facets") (ln cnvkitResults.cnvs "cnvkit") (ln cnvkitResults.plot "cnvkit.pdf") + (ln tnpairResult.octopusVars "octopus.vcf") + (ln tnpairResult.octopusSomatic "octopus-somatic.vcf") (ln tnpairResult.variants "strelka") (ln tnpairResult.glvariants "strelka-gl") (ln tnpairResult.variants.indels "strelka.indels.vcf") diff --git a/tools/octopus-call.nix b/tools/octopus-call.nix new file mode 100644 index 0000000..f88960c --- /dev/null +++ b/tools/octopus-call.nix @@ -0,0 +1,37 @@ +{ bionix +, faidxAttrs ? {} +, indexAttrs ? {} +, flags ? ""}: + +with bionix; +with lib; +with types; + +inputs: + +let + getref = f: matchFiletype "octopus-callSomatic" { bam = {ref, ...}: ref; cram = {ref, ...}: ref;} f; + refs = map getref inputs; + ref = head refs; + +in + +assert (length (unique refs) == 1); + +stage { + name = "octopus-call"; + buildInputs = with pkgs; [ octopus-caller ]; + buildCommand = '' + ln -s ${ref} ref.fa + ln -s ${samtools.faidx faidxAttrs ref} ref.fai + ${concatMapStringsSep "\n" (i: '' + ln -s ${i} $(basename ${i}).bam + ln -s ${samtools.index indexAttrs i} $(basename ${i}).bai + '') inputs} + octopus -R ref.fa -I *.bam -o $out \ + --threads=$NIX_BUILD_CORES \ + ${flags} + ''; + passthru.filtype = filetype.vcf {ref = ref;}; + passthru.multicore = true; +} diff --git a/tools/octopus-callSomatic.nix b/tools/octopus-callSomatic.nix new file mode 100644 index 0000000..e1c7ce6 --- /dev/null +++ b/tools/octopus-callSomatic.nix @@ -0,0 +1,53 @@ +{ bionix +, faidxAttrs ? {} +, indexAttrs ? {} +, flags ? ""}: + +with bionix; +with lib; +with types; + +{normal, tumours}: + +let + smScript = pkgs.writeText "smScript.awk" '' + /^@RG/{ + for(i = 1; i <= NF; i++) { + n=split($i, fields, ":") + if(n == 2 && fields[1] == "SM"){ + print fields[2] + exit + } + } + } + ''; + + inputs = [normal] ++ tumours; + getref = f: matchFiletype "octopus-callSomatic" { bam = {ref, ...}: ref; cram = {ref, ...}: ref;} f; + refs = map getref inputs; + ref = head refs; + +in + +assert (length (unique refs) == 1); + + +stage { + name = "octopus-callSomatic"; + buildInputs = with pkgs; [ octopus-caller samtools ]; + buildCommand = '' + ln -s ${ref} ref.fa + ln -s ${samtools.faidx faidxAttrs ref} ref.fai + ${concatMapStringsSep "\n" (i: '' + ln -s ${i} $(basename ${i}).bam + ln -s ${samtools.index indexAttrs i} $(basename ${i}).bai + '') inputs} + normal=$(samtools view -H ${normal} | awk -f ${smScript}) + octopus -R ref.fa -I *.bam -o $out \ + --threads=$NIX_BUILD_CORES \ + -N $normal \ + ${flags} + ''; + passthru.filetype = filetype.vcf {ref = ref;}; + passthru.multicore = true; +} diff --git a/tools/octopus.nix b/tools/octopus.nix new file mode 100644 index 0000000..4d0c7f6 --- /dev/null +++ b/tools/octopus.nix @@ -0,0 +1,8 @@ +{ bionix }: + +with bionix; + +{ + call = callBionixE ./octopus-call.nix; + callSomatic = callBionixE ./octopus-callSomatic.nix; +} |