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| author | Justin Bedo <cu@cua0.org> | 2019-03-06 13:18:41 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2019-03-06 13:18:41 +1100 |
| commit | 1ff9422ec0ab086a97c4acab5c8f4d15c2026172 (patch) | |
| tree | e30d643b4750e23478ccc7388353e8ca491c4c2f | |
| parent | a86ef4eda927c47791dc0c25852c13ea622f809b (diff) | |
api docs: init bowtie
| -rw-r--r-- | doc/tools-doc.nix | 1 | ||||
| -rw-r--r-- | doc/tools.xml | 1 | ||||
| -rw-r--r-- | tools/bowtie.nix | 7 |
3 files changed, 9 insertions, 0 deletions
diff --git a/doc/tools-doc.nix b/doc/tools-doc.nix index b2cd7ba..e510209 100644 --- a/doc/tools-doc.nix +++ b/doc/tools-doc.nix @@ -24,6 +24,7 @@ stage { nixdoc -c "$1" -d "$2" -f "$1.nix" | sed 's/lib\./bionix./g' |grep -v locations.xml > "$1.xml" } + docgen bowtie 'Bowtie aligner' docgen bwa 'BWA aligner' docgen strelka 'Strelka2 variant caller' diff --git a/doc/tools.xml b/doc/tools.xml index f23dfeb..6b76bf7 100644 --- a/doc/tools.xml +++ b/doc/tools.xml @@ -8,6 +8,7 @@ xmlns:xi="http://www.w3.org/2001/XInclude" xml:id="sec-tools"> <title>Tools</title> + <xi:include href="bowtie.xml" /> <xi:include href="bwa.xml" /> <xi:include href="strelka.xml" /> </section> diff --git a/tools/bowtie.nix b/tools/bowtie.nix index a4439d3..df97d36 100644 --- a/tools/bowtie.nix +++ b/tools/bowtie.nix @@ -3,6 +3,13 @@ with bionix; { + /* Align a sequence against a reference + Type: align :: {ref :: fasta, bamOutput :: bool, ...} -> {input1 :: fastq, input2 :: fastq} -> bam/sam + */ align = callBionixE ./bowtie-align.nix; + + /* Create a Bowtie index + Type: index :: {seed :: int, ...} -> fasta -> index + */ index = callBionixE ./bowtie-index.nix; } |