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-rw-r--r--README.md3
-rw-r--r--tools/delly.nix3
-rw-r--r--tools/fastp.nix4
-rw-r--r--tools/gridss.nix4
-rw-r--r--tools/kallisto.nix4
-rw-r--r--tools/last.nix3
-rw-r--r--tools/lumpy.nix3
-rw-r--r--tools/manta.nix3
-rw-r--r--tools/mosdepth.nix7
-rw-r--r--tools/mutect.nix4
-rw-r--r--tools/octopus.nix7
-rw-r--r--tools/picard.nix3
-rw-r--r--tools/platypus.nix3
-rw-r--r--tools/sambamba.nix23
-rw-r--r--tools/snpeff.nix7
-rw-r--r--tools/snver.nix3
-rw-r--r--tools/star.nix3
-rw-r--r--tools/whisper.nix4
-rw-r--r--tools/xenomapper.nix3
19 files changed, 90 insertions, 4 deletions
diff --git a/README.md b/README.md
index 1310b02..6ae6eb6 100644
--- a/README.md
+++ b/README.md
@@ -114,5 +114,4 @@ distributed machines. See the
For general questions, issues, and
[contributing](https://git-send-email.io), please
[email](mailto:bionix@cua0.org) or [subscribe
-to](mailto:bionix+subscribe@cua0.org) our mailing list. You may also
-chat with us at [#bionix:cua0.org](http://matrix.to/#/#bionix:cua0.org).
+to](mailto:bionix+subscribe@cua0.org) our mailing list.
diff --git a/tools/delly.nix b/tools/delly.nix
index 9bac4c6..d94457c 100644
--- a/tools/delly.nix
+++ b/tools/delly.nix
@@ -3,5 +3,8 @@
with bionix;
{
+ /* Call structural variants
+ Type: call { ... } -> [bam] -> vcf
+ */
call = callBionixE ./delly-call.nix;
}
diff --git a/tools/fastp.nix b/tools/fastp.nix
index 90f6c1d..551d270 100644
--- a/tools/fastp.nix
+++ b/tools/fastp.nix
@@ -4,6 +4,10 @@ with bionix;
rec {
app = pkgs.callPackage ./fastp-app.nix {};
+
+ /* Check and filter fastqs
+ Type: { ... } -> { input1, input2 ? null } -> { out :: html, fastq1 :: fastq, fastq2 :: fastq, json :: JSON }
+ */
check = callBionixE ./fastp-check.nix;
}
diff --git a/tools/gridss.nix b/tools/gridss.nix
index 28af089..9e30dea 100644
--- a/tools/gridss.nix
+++ b/tools/gridss.nix
@@ -72,8 +72,8 @@ rec {
(sort {})
];
- /* Call SVs: entire pipeline including preprocessing. It is recommended to use this function rather than the individual above tools.
- Type: [bam] -> GRIDSS result
+ /* Call SVs: entire pipeline including preprocessing. It is recommended to use this function rather than the individual tools above.
+ Type: call :: [bam] -> GRIDSS result
*/
call = inputs: gridss.annotateVariants {} (map gridss.preprocessBam inputs);
diff --git a/tools/kallisto.nix b/tools/kallisto.nix
index 31e15d9..13de61e 100644
--- a/tools/kallisto.nix
+++ b/tools/kallisto.nix
@@ -4,5 +4,9 @@ with bionix;
{
index = callBionixE ./kallisto-index.nix;
+
+ /* Quantify reads against a transcriptome
+ Type: { bias :: bool, bootstrapSamples :: int, seed :: int, plaintext :: bool, fusion :: bool, single :: bool, frStranded :: bool, rfStranded :: bool, fragmentLength :: Int, fragmentSD :: real } -> [fastq] -> kallisto
+ */
quant = callBionixE ./kallisto-quant.nix;
}
diff --git a/tools/last.nix b/tools/last.nix
index 4e40a65..3755bde 100644
--- a/tools/last.nix
+++ b/tools/last.nix
@@ -3,6 +3,9 @@
with bionix;
rec {
+ /* Align reads against a reference genome
+ Type: { ref :: fastq, ... } -> { input1, input2} -> last
+ */
align = callBionixE ./last-align.nix;
index = callBionixE ./last-index.nix;
}
diff --git a/tools/lumpy.nix b/tools/lumpy.nix
index 0894054..f82134e 100644
--- a/tools/lumpy.nix
+++ b/tools/lumpy.nix
@@ -3,5 +3,8 @@
with bionix;
{
+ /* Call structural variants
+ Type: { ... } -> [bam] -> vcf
+ */
call = callBionixE ./lumpy-call.nix;
}
diff --git a/tools/manta.nix b/tools/manta.nix
index 8136fa7..b34753f 100644
--- a/tools/manta.nix
+++ b/tools/manta.nix
@@ -3,5 +3,8 @@
with bionix;
{
+ /* Call structural variants
+ Type: { ... } -> { normals :: [bam], tumour :: bam } -> manta
+ */
call = callBionixE ./manta-call.nix;
}
diff --git a/tools/mosdepth.nix b/tools/mosdepth.nix
index a5083a7..cbebdfb 100644
--- a/tools/mosdepth.nix
+++ b/tools/mosdepth.nix
@@ -3,6 +3,13 @@
with bionix;
{
+ /* Compute coverage of a reference given an alignemnt
+ Type: { ... } -> bam -> mosdepth
+ */
depth = callBionixE ./mosdepth-depth.nix;
+
+ /* Plot sample coverages. Names are optional.
+ Type: { ... } -> { inputs :: [mosdepth], names :: [string] } -> html
+ */
plot = callBionixE ./mosdepth-plot.nix;
}
diff --git a/tools/mutect.nix b/tools/mutect.nix
index 54a9fac..addea77 100644
--- a/tools/mutect.nix
+++ b/tools/mutect.nix
@@ -4,5 +4,9 @@ with bionix;
{
app = pkgs.callPackage ./mutect-app.nix {};
+
+ /* Call somatic variants with mutect
+ Type: { cosmic, dbsnp, ... } -> { normal :: bam, tumour :: bam } -> vcf
+ */
call = callBionixE ./mutect-call.nix;
}
diff --git a/tools/octopus.nix b/tools/octopus.nix
index 4d0c7f6..858d133 100644
--- a/tools/octopus.nix
+++ b/tools/octopus.nix
@@ -3,6 +3,13 @@
with bionix;
{
+ /* Call variants for a population
+ Type: { fast :: bool, very-fast :: bool, max-genotypes :: int, targets :: FilePath + [string], ... } -> [bam] -> vcf
+ */
call = callBionixE ./octopus-call.nix;
+
+ /* Call somatic variants
+ Type: { fast :: bool, very-fast :: bool, max-genotypes :: int, targets :: FilePath + [string], ... } -> { normal :: bam, tumours :: [bam] } -> vcf
+ */
callSomatic = callBionixE ./octopus-callSomatic.nix;
}
diff --git a/tools/picard.nix b/tools/picard.nix
index 551995f..4246afe 100644
--- a/tools/picard.nix
+++ b/tools/picard.nix
@@ -3,5 +3,8 @@
with bionix;
{
+ /* Mark duplicates
+ Type: { ... } -> bam -> bam
+ */
markDuplicates = callBionixE ./picard-markDuplicates.nix;
} \ No newline at end of file
diff --git a/tools/platypus.nix b/tools/platypus.nix
index 4379675..c93a2d8 100644
--- a/tools/platypus.nix
+++ b/tools/platypus.nix
@@ -3,5 +3,8 @@
with bionix;
{
+ /* Call variants
+ Type: { ... } -> [bam] -> vcf
+ */
call = callBionixE ./platypus-callVariants.nix;
}
diff --git a/tools/sambamba.nix b/tools/sambamba.nix
index 552e6e3..3c1d1fd 100644
--- a/tools/sambamba.nix
+++ b/tools/sambamba.nix
@@ -6,10 +6,33 @@ let
gen = callBionixE ./sambamba-generic.nix;
in {
+ /* Sort aligned reads
+ Type: { nameSort :: bool, ... } -> bam -> bam
+ */
sort = callBionixE ./sambamba-sort.nix;
+
+ /* Build an index
+ Type: { ... } -> bam -> index
+ */
index = def gen {tool = "index"; };
+
+ /* Merge bam files
+ Type: { ... } -> [bam] -> bam
+ */
merge = def gen {tool = "merge"; };
+
+ /* Slice a region out of a bam file
+ Type: { region, ... } -> bam -> bam
+ */
slice = def gen {tool = "slice"; };
+
+ /* Compute flag statistics
+ Type: { ... } -> bam -> flagstat
+ */
flagstat = def gen {tool = "flagstat"; };
+
+ /* Mark duplicates
+ Type: { ... } -> bam -> bam
+ */
markdup = def gen {tool = "markdup"; };
}
diff --git a/tools/snpeff.nix b/tools/snpeff.nix
index c5ef04d..fb3f4a9 100644
--- a/tools/snpeff.nix
+++ b/tools/snpeff.nix
@@ -3,6 +3,13 @@
with bionix;
{
+ /* Annotate variants with SNPEff database. Some annotation DBs available in bionix.ref (e.g., bionix.ref.grch38.snpeff.db).
+ Type: { db, ... } -> vcf -> vcf
+ */
annotate = callBionixE ./snpeff-annotate.nix;
+
+ /* Annotate variants with dbNSFP database. Some dbNSFP annotation DBs available in bionix.ref (e.g., bionix.ref.grch38.snpeff.dbNSFP).
+ Type: { dbnsfp, ... } -> vcf -> vcf
+ */
dbnsfp = callBionixE ./snpeff-dbnsfp.nix;
}
diff --git a/tools/snver.nix b/tools/snver.nix
index 7c84777..6f95e1b 100644
--- a/tools/snver.nix
+++ b/tools/snver.nix
@@ -6,5 +6,8 @@ with pkgs;
{
app = callPackage ./snver-app.nix {};
+ /* Call variants
+ Type: { ploidy, ... } -> [bam] -> vcf
+ */
call = callBionix ./snver-call.nix;
}
diff --git a/tools/star.nix b/tools/star.nix
index a0a2d58..744c4e0 100644
--- a/tools/star.nix
+++ b/tools/star.nix
@@ -3,6 +3,9 @@
with bionix;
{
+ /* Align RNA against a reference genome
+ Type: { ref, ... } -> { input1, input2 } -> bam
+ */
align = callBionixE ./star-align.nix;
index = callBionixE ./star-index.nix;
}
diff --git a/tools/whisper.nix b/tools/whisper.nix
index b729675..ff56f8a 100644
--- a/tools/whisper.nix
+++ b/tools/whisper.nix
@@ -4,5 +4,9 @@ with bionix;
rec {
index = callBionixE ./whisper-index.nix;
+
+ /* Align reads against a reference
+ Type: { ref, ... } -> { input1, input2 } -> bam
+ */
align = callBionixE ./whisper-align.nix;
}
diff --git a/tools/xenomapper.nix b/tools/xenomapper.nix
index 8247e25..d22f84b 100644
--- a/tools/xenomapper.nix
+++ b/tools/xenomapper.nix
@@ -3,5 +3,8 @@
with bionix;
{
+ /* Split aligned reads based on primary and secondary alignments
+ Type: { ... } -> { primary :: bam, secondary :: bam } -> { primary_specific :: bam, primary_multi :: bam, secondary_specific :: bam, secondary_multi :: bam, unassigned :: bam, unresolved :: bam }
+ */
allocate = callBionixE ./xenomapper-allocate.nix;
} \ No newline at end of file
generated by cgit v1.2.3 (git 2.25.1) at 2024-12-26 04:37:55 +0000