diff options
Diffstat (limited to 'tools/gridss.nix')
| -rw-r--r-- | tools/gridss.nix | 72 |
1 files changed, 43 insertions, 29 deletions
diff --git a/tools/gridss.nix b/tools/gridss.nix index 70ba21d..a002e69 100644 --- a/tools/gridss.nix +++ b/tools/gridss.nix @@ -1,81 +1,95 @@ -{bionix}: +{ bionix }: with bionix; with lib; rec { jar = pkgs.fetchurl { - url = "https://github.com/PapenfussLab/gridss/releases/download/v2.12.1/gridss-2.12.1-gridss-jar-with-dependencies.jar"; + url = + "https://github.com/PapenfussLab/gridss/releases/download/v2.12.1/gridss-2.12.1-gridss-jar-with-dependencies.jar"; sha256 = "sha256-wH5O+vYKlWGDJTTnMgKYrSNtzoU7wDHqNraiW8xrxXA="; }; /* Generate configuration file for GRIDSS. Takes attribute sets to GRIDSS ini style format. - Type: genConfig :: attrSet -> ini file + Type: genConfig :: attrSet -> ini file */ - genConfig = callBionix ./gridss-configFile.nix {}; + genConfig = callBionix ./gridss-configFile.nix { }; /* Invoke the callVariants tool - Type: callVariants :: {blacklist :: drv = null, config :: ini = null, heapSize :: String = "31g", ...} -> [bam] -> variants + Type: callVariants :: {blacklist :: drv = null, config :: ini = null, heapSize :: String = "31g", ...} -> [bam] -> variants */ callVariants = callBionixE ./gridss-callVariants.nix; /* Invoke computeSamTags tool - Type: computeSamTags :: {config :: ini = null, heapSize :: String = "1G", ...} -> bam -> bam + Type: computeSamTags :: {config :: ini = null, heapSize :: String = "1G", ...} -> bam -> bam */ computeSamTags = callBionixE ./gridss-computeSamTags.nix; /* Invoke softClipsToSplitReads tool - Type: softClipsToSplitReads :: {alignerStreaming :: Bool = false, config :: ini = null, heapSize :: String = "2G", ...} -> bam -> bam + Type: softClipsToSplitReads :: {alignerStreaming :: Bool = false, config :: ini = null, heapSize :: String = "2G", ...} -> bam -> bam */ softClipsToSplitReads = callBionixE ./gridss-softClipsToSplitReads.nix; /* Invoke collectMetrics tool - Type: collectMetrics :: {thresholdCoverage :: Int = 10000, config :: ini = null, heapSize :: String = "1G", ...} -> bam -> metrics + Type: collectMetrics :: {thresholdCoverage :: Int = 10000, config :: ini = null, heapSize :: String = "1G", ...} -> bam -> metrics */ collectMetrics = callBionixE ./gridss-collectMetrics.nix; /* Invoke extractSVReads tool - Type: extractSVReads :: {unmappedReads :: Bool = false, minClipLength :: Int = 5, config :: ini = null, ...} -> bam -> bam + Type: extractSVReads :: {unmappedReads :: Bool = false, minClipLength :: Int = 5, config :: ini = null, ...} -> bam -> bam */ extractSVReads = callBionixE ./gridss-extractSVReads.nix; /* Invoke assembly tool - Type: assemble :: {config :: ini = null, heapSize :: String = "31g", ...} -> [bam] -> bam + Type: assemble :: {config :: ini = null, heapSize :: String = "31g", ...} -> [bam] -> bam */ assemble = callBionixE ./gridss-assemble.nix; shardedAssemble = n: a: input: - let assemblies = genList (i: bionix.gridss.assemble (a // { jobNodes = n; jobIndex = i;}) input) n; - in if n <= 1 then bionix.gridss.assemble a input else bionix.gridss.assemble (a // {workdirs = map (a: a.work) assemblies;}) input; + let + assemblies = genList (i: + bionix.gridss.assemble (a // { + jobNodes = n; + jobIndex = i; + }) input) n; + in if n <= 1 then + bionix.gridss.assemble a input + else + bionix.gridss.assemble (a // { workdirs = map (a: a.work) assemblies; }) + input; /* Invoke identifyVariants tool - Type: identifyVariants :: {config :: ini = null, heapSize :: String = "4g", ...} -> [bam] -> VCF + Type: identifyVariants :: {config :: ini = null, heapSize :: String = "4g", ...} -> [bam] -> VCF */ - identifyVariants = exec (attrs: input: ((callBionix ./gridss-variants.nix attrs) input).identify); + identifyVariants = exec + (attrs: input: ((callBionix ./gridss-variants.nix attrs) input).identify); /* Invoke annotateVariants tool - Type: annotateVariants :: {config :: ini = null, heapSize :: String = "4g", ...} -> [bam] -> VCF + Type: annotateVariants :: {config :: ini = null, heapSize :: String = "4g", ...} -> [bam] -> VCF */ - annotateVariants = exec (attrs: input: ((callBionix ./gridss-variants.nix attrs) input).annotate); + annotateVariants = exec + (attrs: input: ((callBionix ./gridss-variants.nix attrs) input).annotate); - /* As annotateVariants except include assembly in output */ - annotateAndAssemble = exec (attrs: input: ((callBionix ./gridss-variants.nix attrs) input).annotateAndAssemble); + # As annotateVariants except include assembly in output + annotateAndAssemble = exec (attrs: input: + ((callBionix ./gridss-variants.nix attrs) input).annotateAndAssemble); - /* Preprocess BAM files to extract SV reads and compute required stats - Type: preprocessBam :: bam -> bam + /* Preprocess BAM files to extract SV reads + Type: preprocessBam :: bam -> bam */ preprocessBam = with samtools; flip pipe [ - (gridss.extractSVReads {}) - (sort {nameSort = true;}) - (gridss.computeSamTags {}) - (sort {}) + (gridss.extractSVReads { }) + (sort { nameSort = true; }) + (gridss.computeSamTags { }) + (sort { }) ]; - /* 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 SVs: entire pipeline including preprocessing. It is recommended to use this function rather than the individual above tools. + Type: [bam] -> GRIDSS result */ - call = inputs: gridss.annotateVariants {} (map gridss.preprocessBam inputs); + call = inputs: gridss.annotateVariants { } (map gridss.preprocessBam inputs); - /* As call but include assemblies in output */ - callAndAssemble = inputs: gridss.annotateAndAssemble {} (map gridss.preprocessBam inputs); + # As call but include assemblies in output + callAndAssemble = inputs: + gridss.annotateAndAssemble { } (map gridss.preprocessBam inputs); } |