diff options
author | Justin Bedo <cu@cua0.org> | 2021-02-03 11:49:23 +1100 |
---|---|---|
committer | Justin Bedo <cu@cua0.org> | 2021-02-03 11:49:23 +1100 |
commit | c7756678c8a543f216654d518eeee3c4bd6a4b8f (patch) | |
tree | 098183330e8d7f5505570e7769a985eef83ecc51 /tools | |
parent | cac21d3ab1fd96724b568f675794c83273a27aee (diff) |
add inline documentation
Diffstat (limited to 'tools')
-rw-r--r-- | tools/delly.nix | 3 | ||||
-rw-r--r-- | tools/fastp.nix | 4 | ||||
-rw-r--r-- | tools/gridss.nix | 4 | ||||
-rw-r--r-- | tools/kallisto.nix | 4 | ||||
-rw-r--r-- | tools/last.nix | 3 | ||||
-rw-r--r-- | tools/lumpy.nix | 3 | ||||
-rw-r--r-- | tools/manta.nix | 3 | ||||
-rw-r--r-- | tools/mosdepth.nix | 7 | ||||
-rw-r--r-- | tools/mutect.nix | 4 | ||||
-rw-r--r-- | tools/octopus.nix | 7 | ||||
-rw-r--r-- | tools/picard.nix | 3 | ||||
-rw-r--r-- | tools/platypus.nix | 3 | ||||
-rw-r--r-- | tools/sambamba.nix | 23 | ||||
-rw-r--r-- | tools/snpeff.nix | 7 | ||||
-rw-r--r-- | tools/snver.nix | 3 | ||||
-rw-r--r-- | tools/star.nix | 3 | ||||
-rw-r--r-- | tools/whisper.nix | 4 | ||||
-rw-r--r-- | tools/xenomapper.nix | 3 |
18 files changed, 89 insertions, 2 deletions
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 |