diff options
Diffstat (limited to 'tools/gridss.nix')
| -rw-r--r-- | tools/gridss.nix | 41 |
1 files changed, 23 insertions, 18 deletions
diff --git a/tools/gridss.nix b/tools/gridss.nix index 7372864..db577ad 100644 --- a/tools/gridss.nix +++ b/tools/gridss.nix @@ -10,60 +10,65 @@ rec { }; /* 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 { }; /* 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 + 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; + 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); /* 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); @@ -73,7 +78,7 @@ rec { ((callBionix ./gridss-variants.nix attrs) input).annotateAndAssemble); /* Preprocess BAM files to extract SV reads - Type: preprocessBam :: bam -> bam + Type: preprocessBam :: bam -> bam */ preprocessBam = with samtools; flip pipe [ @@ -84,7 +89,7 @@ rec { ]; /* Call SVs: entire pipeline including preprocessing. It is recommended to use this function rather than the individual above tools. - Type: [bam] -> GRIDSS result + Type: [bam] -> GRIDSS result */ call = inputs: gridss.annotateVariants { } (map gridss.preprocessBam inputs); |