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change parameters
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@jeantristanb
jeantristanb committed Mar 20, 2024
1 parent a7f9d9d commit 7e0507a
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3 changes: 2 additions & 1 deletion assoc/README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,7 @@ The key options are:
* you can used `sample_snps_rel` (default 0), will used plink to sample snps :
* `sample_snps_rel_paramplkl` : parameter for plink to obtained independnat pairwise ([default : 100 20 0.1 --maf 0.01 ])
* `snps_include_rel` : bed file (chro begin end rs) to include on plink command to defined independant snps [default : ""]
* `snp_rel_param_plk` : [default --maf 0.01 --mac 10]
* `file_rs_buildrelat` : file with rs list (one by lines) to build genetics models (relatdness), for gemma `-snps`, boltlmm `--modelSnps`, regenie to build step 1

### other option
Expand Down Expand Up @@ -185,7 +186,7 @@ and then for all the tests except _gemma_, _boltlmm_ and _fastlmm_, do you want
* `regenie_bin` : binary of regenie [default: regenie]
* `regenie` : perform a regenie analyse yes : 1, no : 0 [default : 0]
* maf :
* `regenie_mafstep1` : maf for step 1
* for step1 see : `snp_rel_param_plk`
* bsize (size of the genotype blocks) :
* `regenie_bsize` : bsize used for step 1 and 2 if `regenie_bsize_step1` and `regenie_bsize_step2` are 0 [default 100]
* `regenie_bsize_step1`: bsize for step 1 [default 0]
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32 changes: 18 additions & 14 deletions assoc/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -92,7 +92,7 @@ def checkmultiparam(params, listparams, type, min=null, max=null, possibleval=nu

def helps = [ 'help' : 'help' ]

allowed_params_input = ["input_dir","input_pat","output","output_dir","data","plink_mem_req","covariates", "work_dir", "scripts", "high_ld_regions_fname", "accessKey", "access-key", "secretKey", "secret-key", "region", "pheno","big_time", "gemma_mat_rel", "file_rs_buildrelat","genetic_map_file", "rs_list", "gemma_bin", "bgen", "bgen_sample", "list_bgen", "exclude_snps", "bolt_impute2filelist", "bolt_impute2fidiid", "bolt_otheropt","bolt_bin", "bolt_ld_scores_col" , "bolt_ld_scores_col", "bolt_impute2filelist", "bolt_impute2fidiid", "bolt_otheropt","bolt_bin", 'gxe','fastlmmc_bin','list_vcf', 'vcf_field', "regenie_otheropt_step1","regenie_otheropt_step2", "gcta_bin", "AMI", "instance-type", "boot-storage-size", "sharedStorageMount", "instanceType", "bolt_ld_score_file" , "saige_impute_method", "gcta_grmfile","fastgwa_type", "snps_include_rel", "sample_snps_rel_paramplkl", "shared-storage-mount", "queue", 'output_testing', "chrom","regenie_bin" , "saige_bin_fitmodel", "saige_bin_spatest"]
allowed_params_input = ["input_dir","input_pat","output","output_dir","data","plink_mem_req","covariates", "work_dir", "scripts", "high_ld_regions_fname", "accessKey", "access-key", "secretKey", "secret-key", "region", "pheno","big_time", "gemma_mat_rel", "file_rs_buildrelat","genetic_map_file", "rs_list", "gemma_bin", "bgen", "bgen_sample", "list_bgen", "exclude_snps", "bolt_impute2filelist", "bolt_impute2fidiid", "bolt_otheropt","bolt_bin", "bolt_ld_scores_col" , "bolt_ld_scores_col", "bolt_impute2filelist", "bolt_impute2fidiid", "bolt_otheropt","bolt_bin", 'gxe','fastlmmc_bin','list_vcf', 'vcf_field', "regenie_otheropt_step1","regenie_otheropt_step2", "gcta_bin", "AMI", "instance-type", "boot-storage-size", "sharedStorageMount", "instanceType", "bolt_ld_score_file" , "saige_impute_method", "gcta_grmfile","fastgwa_type", "snps_include_rel", "sample_snps_rel_paramplkl", "shared-storage-mount", "queue", 'output_testing', "chrom","regenie_bin" , "saige_bin_fitmodel", "saige_bin_spatest", "snp_rel_param_plk"]

allowed_params_input_mp = ["bolt_covariates_type", 'covariates_type']
allowed_params=allowed_params_input
Expand All @@ -103,7 +103,7 @@ allowed_params_intother=["max_forks", "mperm", "regenie_bsize_step1", "regenie_b
allowed_params+=allowed_params_intother
allowed_params_bolother=["adjust", "mperm", "sample_snps_rel","bolt_use_missing_cov", 'gemma_multi', 'pheno_bin', 'fastlmm_multi', "regenie_loco", "sexinfo_available", "print_pca", "saige_loco","saige_imputed_data"]
allowed_params+=allowed_params_bolother
allowed_params_float=["cut_maf", "bgen_mininfo", "regenie_mafstep1", "grm_cutoff", "grm_maf","vcf_minmac"]
allowed_params_float=["cut_maf", "bgen_mininfo", "grm_cutoff", "grm_maf","vcf_minmac"]
allowed_params+=allowed_params_float
allowed_params_memory=["gemma_mem_req" , "plink_mem_req", "other_mem_req", "bolt_mem_req", 'fastlmm_mem_req', 'saige_mem_req', "regenie_mem_req", "fastgwa_mem_req", "bootStorageSize", "bootStorageSize", "boot-storage-size", "sharedStorageMount", "other_process_mem_req"]
allowed_params+=allowed_params_memory
Expand Down Expand Up @@ -143,6 +143,7 @@ params.bgen=""
params.bgen_sample=""
params.bgen_mininfo=0.6
params.list_bgen=""
params.snp_rel_param_plk=" --maf 0.01 --mac 10 "


params.regenie_bin="regenie"
Expand All @@ -154,7 +155,7 @@ params.regenie_otheropt_step2=""
params.regenie_loco=1
params.regenie_num_cores=6
params.regenie_mem_req="10GB"
params.regenie_mafstep1=0.01
//params.regenie_mafstep1=0.01
params.regenie=0
params.saige_imputed_data=1
params.saige_impute_method="best_guess" //best_guess, mean or minor
Expand Down Expand Up @@ -246,7 +247,7 @@ params.grm_cutoff = 0.05
params.covariates_type=""
params.gcta_grmfile=""
params.sample_snps_rel=0
params.sample_snps_rel_paramplkl="100 20 0.1 --maf 0.01"
params.sample_snps_rel_paramplkl="100 20 0.1"
params.pheno_bin=0
params.snps_include_rel=""

Expand Down Expand Up @@ -284,6 +285,7 @@ checkmultiparam(params,allowed_params_float, [java.lang.Float, java.lang.Integer
data_ch_pheno = Channel.fromPath(params.data, checkIfExists:true)
data_ch_show = Channel.fromPath(params.data, checkIfExists:true)
data_ch_gemma = Channel.fromPath(params.data, checkIfExists:true)
data_ch_rsselect= Channel.fromPath(params.data, checkIfExists:true)

if (params.help) {
params.each {
Expand Down Expand Up @@ -522,6 +524,7 @@ if(params.boltlmm+params.gemma+params.fastlmm+params.fastgwa+params.saige+params
time params.big_time
input :
tuple path(bed),path(bim), path(fam) from ch_select_rs_format
path(data) from data_ch_rsselect
path(snp_inclrel) from snpinclrel
output:
file("${prune}.prune.in") into filers_matrel_mat_fast, filers_matrel_mat_GWA, filers_matrel_mat_gem, filers_matrel_bolt, filers_count_line, filers_her_saige,filers_matrel_regenie
Expand All @@ -530,7 +533,7 @@ if(params.boltlmm+params.gemma+params.fastlmm+params.fastgwa+params.saige+params
prune= "${base}-prune"
extract=(params.snps_include_rel=='')? "" : " -extract range $snp_inclrel "
"""
plink --bfile ${base} --indep-pairwise ${params.sample_snps_rel_paramplkl} --out $prune --threads ${params.max_plink_cores} $extract --autosome
plink --bfile ${base} --indep-pairwise ${params.sample_snps_rel_paramplkl} --out $prune --threads ${params.max_plink_cores} $extract --autosome --keep $data ${params.snp_rel_param_plk}
"""
}
//BoltNbMaxSnps=filers_count_line.countLines()
Expand Down Expand Up @@ -1796,7 +1799,7 @@ if(params.saige==1){
bfile=plk[1].baseName
out=bfile+'_subrs'
"""
plink -bfile $bfile --extract $rs --make-bed -out $out --keep-allele-order
plink -bfile $bfile --extract $rs --make-bed -out $out --keep-allele-order ${params.snp_rel_param_plk}
"""
}
}else{
Expand Down Expand Up @@ -2196,15 +2199,14 @@ if(params.regenie==1){
path(rsrel) from filers_matrel_regenie
tuple path(bed), path(bim), path(fam) from ch_regenie_assoc
each pheno from pheno_cols_ch_regenie
errorStrategy { task.exitStatus == 1 ; return 'ignore' }
publishDir "${params.output_dir}/regenie/step1", overwrite:true, mode:'copy', pattern: "*.cmd"
publishDir "${params.output_dir}/regenie/step1", overwrite:true, mode:'copy', pattern: "*.list"
//errorStrategy { task.exitStatus == 1 ; return 'ignore' }
publishDir "${params.output_dir}/regenie/step1", overwrite:true, mode:'copy', pattern: "*.loco"
publishDir "${params.output_dir}/regenie/step1", overwrite:true, mode:'copy', pattern: "*.log"
publishDir "${params.output_dir}/regenie/step1", overwrite:true, mode:'copy', pattern: "*.list"
publishDir "${params.output_dir}/regenie/step1", overwrite:true, mode:'copy', pattern: "*regenie_step1.err*"
output :
tuple val(our_pheno), path("$phef"),path("${out}_pred.list"), path("${out}_1.loco"),path(bed), path(bim), path(fam), optional :true into ch_regenie_pheno
path("${out}.log")
path("*regenie_step1.cmd")
path("${out}.report")
path("*_regenie_step1*")
script :
our_pheno = pheno.replaceAll(/\/np.\w+/,"").replaceAll(/[0-9]+@@@/,"")
phef=pheno+".pheno"
Expand All @@ -2223,13 +2225,15 @@ if(params.regenie==1){
"""
all_covariate.py --data $data --inp_fam $fam $covoption \
--pheno $pheno --phe_out ${phef} --form_out 2 --nona 1 $gxe
plink -bfile $bfile $keeppos --make-bed -out $bfilesub -maf ${params.regenie_mafstep1} --keep $phef
plink -bfile $bfile $keeppos --make-bed -out $bfilesub --keep $phef ${params.snp_rel_param_plk}
${params.regenie_bin} --step 1 --bed $bfilesub --phenoFile $phef --phenoCol ${our_pheno} --bsize $bsize $regenie_loco --out $out --threads ${params.regenie_num_cores} ${params.regenie_otheropt_step1} $covoption_regenie
if [ ! -f $out"_1.loco" ]
then
touch $out"_1.loco"
fi
cp .command.sh "${our_pheno}"_regenie_step1.cmd
cp .command.sh "${our_pheno}"_regenie_step1.cmd.report
cp .command.log "${our_pheno}"_regenie_step1.log.report
cp .command.err "${our_pheno}"_regenie_step1.err.report
"""
}
ch_regenie_pheno_2=ch_regenie_pheno.combine(bgen_ch_regenie).combine(bgensample_ch_regenie)
Expand Down

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