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refactor: fix inputs of post jabba processes
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,50 @@ | ||
| withAutoprint( | ||
| { | ||
| library(optparse) | ||
| options(bitmapType = "cairo") | ||
|
|
||
| options(error = function() { | ||
| traceback(2) | ||
| quit("no", 1) | ||
| }) | ||
| if (!exists("opt")) { | ||
| option_list <- list( | ||
| make_option(c("-i", "--id"), type = "character", help = "sample id"), | ||
| make_option(c("-g", "--gGraph"), type = "character", help = "an RDS file contains a gGraph or JaBbA graph with cn annotation on nodes and edges"), | ||
| make_option(c("-r", "--gencode"), type = "character", help = "an RDS or GTF file of GENCODE"), | ||
| make_option(c("-o", "--outdir"), type = "character", default = "./", help = "Directory to dump output into"), | ||
| make_option(c("--cores"), type = "integer", default = 1L, help = "Number of cores") | ||
| ) | ||
| parseobj <- OptionParser(option_list = option_list) | ||
| opt <- parse_args(parseobj) | ||
| saveRDS(opt, paste(opt$outdir, "cmd.args.rds", sep = "/")) | ||
| } | ||
|
|
||
| library(gGnome) | ||
| library(gUtils) | ||
| library(parallel) ## needed for mc.cores | ||
|
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| ## setDTthreads(10) | ||
| if (grepl(".rds$", opt$gencode)) { | ||
| gencode <- readRDS(as.character(opt$gencode)) | ||
| } else { | ||
| gencode <- rtracklayer::import(opt$gencode) | ||
| } | ||
|
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||
|
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| ## call complex events | ||
| ## fus = fusions(gG(jab = opt$gGraph), gencode, verbose = TRUE, opt$cores) | ||
| fus <- fusions(gG(jab = opt$gGraph), gencode, verbose = TRUE, mc.cores = opt$cores) | ||
|
|
||
| ## update events with sample id | ||
| if (length(fus)) { | ||
| fus$set(id = opt$id) | ||
| fus$set(mincn = fus$eval(edge = min(cn, na.rm = TRUE))) | ||
| } | ||
|
|
||
| saveRDS(fus, paste0(opt$outdir, "/", "fusions.rds")) | ||
|
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||
| quit("no", 0) | ||
| }, | ||
| echo = FALSE | ||
| ) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,70 @@ | ||
| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Config file for defining DSL2 per module options and publishing paths | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Available keys to override module options: | ||
| ext.args = Additional arguments appended to command in module. | ||
| ext.args2 = Second set of arguments appended to command in module (multi-tool modules). | ||
| ext.args3 = Third set of arguments appended to command in module (multi-tool modules). | ||
| ext.prefix = File name prefix for output files. | ||
| ext.when = When to run the module. | ||
| ---------------------------------------------------------------------------------------- | ||
| */ | ||
| // ALLEIC_CN configs | ||
|
|
||
| process { | ||
|
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||
| withName: 'MSKILABORG_NFJABBA:NFJABBA:ALLEIC_CN:NON_INTEGER_BALANCE' { | ||
| ext.when = { params.tools && params.tools.split(',').contains('alleic_cn') } | ||
| publishDir = [ | ||
| mode: params.publish_dir_mode, | ||
| path: { "${params.outdir}/alleic_cn/non_integer_balance/${meta.id}/" }, | ||
| pattern: "*{.rds*,.command.*}" | ||
| ] | ||
| } | ||
|
|
||
| withName: 'MSKILABORG_NFJABBA:NFJABBA:ALLEIC_CN:NON_INTEGER_BALANCE_WITH_GRIDSS' { | ||
| ext.when = { params.tools && params.tools.split(',').contains('alleic_cn') } | ||
| publishDir = [ | ||
| mode: params.publish_dir_mode, | ||
| path: { "${params.outdir}/alleic_cn/non_integer_balance_with_gridss/${meta.id}/" }, | ||
| pattern: "*{.rds*,.command.*}" | ||
| ] | ||
| } | ||
|
|
||
| withName: 'MSKILABORG_NFJABBA:NFJABBA:ALLEIC_CN:NON_INTEGER_BALANCE_WITH_SVABA' { | ||
| ext.when = { params.tools && params.tools.split(',').contains('alleic_cn') } | ||
| publishDir = [ | ||
| mode: params.publish_dir_mode, | ||
| path: { "${params.outdir}/alleic_cn/non_integer_balance_with_svaba/${meta.id}/" }, | ||
| pattern: "*{.rds*,.command.*}" | ||
| ] | ||
| } | ||
|
|
||
| withName: 'MSKILABORG_NFJABBA:NFJABBA:ALLEIC_CN:LP_PHASED_BALANCE' { | ||
| ext.when = { params.tools && params.tools.split(',').contains('alleic_cn') } | ||
| publishDir = [ | ||
| mode: params.publish_dir_mode, | ||
| path: { "${params.outdir}/alleic_cn/lp_phased_balance/${meta.id}/" }, | ||
| pattern: "*{.rds*,.command.*}" | ||
| ] | ||
| } | ||
|
|
||
| withName: 'MSKILABORG_NFJABBA:NFJABBA:ALLEIC_CN:LP_PHASED_BALANCE_WITH_GRIDSS' { | ||
| ext.when = { params.tools && params.tools.split(',').contains('alleic_cn') } | ||
| publishDir = [ | ||
| mode: params.publish_dir_mode, | ||
| path: { "${params.outdir}/alleic_cn/lp_phased_balance_with_gridss/${meta.id}/" }, | ||
| pattern: "*{.rds*,.command.*}" | ||
| ] | ||
| } | ||
|
|
||
| withName: 'MSKILABORG_NFJABBA:NFJABBA:ALLEIC_CN:LP_PHASED_BALANCE_WITH_SVABA' { | ||
| ext.when = { params.tools && params.tools.split(',').contains('alleic_cn') } | ||
| publishDir = [ | ||
| mode: params.publish_dir_mode, | ||
| path: { "${params.outdir}/alleic_cn/lp_phased_balance_with_svaba/${meta.id}/" }, | ||
| pattern: "*{.rds*,.command.*}" | ||
| ] | ||
| } | ||
| } |
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