diff options
| -rw-r--r-- | doc/tools-doc.nix | 41 | ||||
| -rw-r--r-- | doc/tools.xml | 14 | ||||
| -rw-r--r-- | tools/bwa.nix | 13 | ||||
| -rw-r--r-- | tools/strelka.nix | 27 |
4 files changed, 90 insertions, 5 deletions
diff --git a/doc/tools-doc.nix b/doc/tools-doc.nix new file mode 100644 index 0000000..b2cd7ba --- /dev/null +++ b/doc/tools-doc.nix @@ -0,0 +1,41 @@ +{ bionix ? import ./.. {} }: + +with bionix; + +stage { + name = "tools-docs"; + src = ../tools; + + xsltFlags = lib.concatStringsSep " " [ + #"--param section.autolabel 1" + #"--param section.label.includes.component.label 1" + #"--stringparam html.stylesheet 'style.css overrides.css highlightjs/mono-blue.css'" + #"--stringparam html.script './highlightjs/highlight.pack.js ./highlightjs/loader.js'" + #"--param xref.with.number.and.title 1" + #"--param toc.section.depth 3" + #"--stringparam admon.style ''" + #"--stringparam callout.graphics.extension .svg" + ]; + + + buildInputs = with pkgs; [ nixdoc libxslt libxml2 ]; + installPhase = '' + function docgen { + nixdoc -c "$1" -d "$2" -f "$1.nix" | sed 's/lib\./bionix./g' |grep -v locations.xml > "$1.xml" + } + + docgen bwa 'BWA aligner' + docgen strelka 'Strelka2 variant caller' + + mkdir $out + cp ${./tools.xml} tools.xml + xmllint --nonet --xinclude --noxincludenode tools.xml --output tools-full.xml + cat tools-full.xml + xsltproc $xsltFlags \ + --nonet \ + --xinclude \ + --output $out/index.html \ + ${pkgs.docbook_xsl_ns}/xml/xsl/docbook/epub/docbook.xsl \ + tools-full.xml + ''; +} diff --git a/doc/tools.xml b/doc/tools.xml new file mode 100644 index 0000000..f23dfeb --- /dev/null +++ b/doc/tools.xml @@ -0,0 +1,14 @@ +<book xmlns="http://docbook.org/ns/docbook" + xmlns:xi="http://www.w3.org/2001/XInclude"> + <info> + <title>Bionix</title> + </info> + <section xmlns="http://docbook.org/ns/docbook" + xmlns:xlink="http://www.w3.org/1999/xlink" + xmlns:xi="http://www.w3.org/2001/XInclude" + xml:id="sec-tools"> + <title>Tools</title> + <xi:include href="bwa.xml" /> + <xi:include href="strelka.xml" /> + </section> +</book> diff --git a/tools/bwa.nix b/tools/bwa.nix index d0ab5ee..03735d1 100644 --- a/tools/bwa.nix +++ b/tools/bwa.nix @@ -2,7 +2,16 @@ with bionix; -{ - align = callBionixE ./bwa-mem.nix; +rec { + /* Align read against a reference: defaults to bwa-mem */ + align = 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; + /* Creates an reference index for BWA + Type: {...} -> fasta -> BWA index + */ index = callBionixE ./bwa-index.nix; } diff --git a/tools/strelka.nix b/tools/strelka.nix index 9a8f1aa..1cf8961 100644 --- a/tools/strelka.nix +++ b/tools/strelka.nix @@ -4,21 +4,42 @@ with bionix; with types; { + /* Calls somatic variants + Type: callSomatic :: {...} -> {tumour, normal} -> somatic results + */ callSomatic = callBionixE ./strelka-callSomatic.nix; + /* Calls variants + Type: call :: {...} -> [input] -> results + */ call = callBionixE ./strelka-call.nix; - variants = drv: stage { + /* Extract VCF file from results + Type: variants :: results -> vcf + */ + variants = + # result of call + drv: stage { name = "strelka-call-variants"; buildCommand = '' ln -s ${drv}/variants/variants.vcf.gz $out ''; passthru.filetype = filetype.gz (filetype.vcf {ref=ref;}); }; - indels = drv: stage { + /* Extract indels from somatic results + Type: indels :: somatic results -> vcf + */ + indels = + # result of callSomatic + drv: stage { name = "strelka-callVariants-indels"; buildCommand = "ln -s ${drv}/variants/somatic.indels.vcf.gz $out"; passthru.filetype = filetype.gz (filetype.vcf {ref = ref;}); }; - snvs = drv: stage { + /* Extract SNVs from somatic results + Type: snvs :: somatic results -> vcf + */ + snvs = + # result of callSomatic + drv: stage { name = "strelka-callVariants-snvs"; buildCommand = "ln -s ${drv}/variants/somatic.snvs.vcf.gz $out"; passthru.filetype = filetype.gz (filetype.vcf {ref = ref;}); |