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Snakefile
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Snakefile
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# In R, use snakemake@input[[1]] etc to get the variables
# on harvest:
# create snplist-alltop.txt, snplist-xtop.txt from meta results
# create betas_all.txt with PGS weights from meta
rule all:
"Create all target files."
input:
"/home/julius/Documents/results/tv/table_main.tsv",
"/home/julius/Documents/results/tv/plot_allmain.png",
"/home/julius/Documents/results/tv/plot_pgs5.png",
"/home/julius/Documents/results/tv/plot_explor.png",
"/home/julius/Documents/results/tv/plot_suppcov.png",
"/home/julius/Documents/results/tv/plot_supphaz.png",
"/home/julius/Documents/results/tv/table_diag.tsv",
"/home/julius/Documents/results/tv/plot_coxdiag.png",
"/home/julius/Documents/results/tv/plot_pgs3.png"
rule preliminary:
"Create files for initial analyses. No real need to run this."
input:
expand("/home/julius/Documents/results/tv/report_tvmodels{i}.pdf", i=range(1,23)),
expand("/home/julius/Documents/results/tv/report_tvmodelsX{i}.pdf", i=range(1,3)),
"/home/julius/Documents/results/tv/null-pvals.RData"
rule harvest:
"Things to be produced directly in HARVEST."
input:
"/mnt/work2/jjuod/tmp/ga_cleaned.csv",
"/mnt/work2/jjuod/tmp/ga_cleaned_f.csv",
"/mnt/work2/jjuod/tmp/top1-moba30k-dosage.csv.gz",
"/mnt/work2/jjuod/tmp/top1x-moba30k-dosage.csv.gz",
"/mnt/work2/jjuod/tmp/top1f-moba30k-dosage.csv.gz",
"/mnt/work2/jjuod/tmp/plinktests/res_top_regions.sscore",
"/mnt/work2/jjuod/tmp/plinktests/res_burden_below0.001_rare.sscore",
"/mnt/work2/jjuod/tmp/plinktests/res_burden_below0.001_rec.sscore",
"/mnt/work2/jjuod/tmp/plinktests/pca.eigenvec",
"/mnt/work2/jjuod/tmp/plinktests/chr6-maf1-M.bim"
# -----------------------
# harvest jobs:
rule prep_pheno:
"Clean MFR, create a censoring indicator, export selected columns."
input:
"/mnt/archive2/p1724/v12/PDB1724_MFR_541_v12.csv",
"/mnt/archive2/p1724/v12/parental_ID_to_PREG_ID.csv",
"/mnt/archive2/p1724/v12/linkage_Mother_PDB1724.csv",
"/mnt/archive2/p1724/v12/linkage_Child_PDB1724.csv",
"/mnt/archive/MOBAGENETICS/genotypes-base/aux/flaglist-merged/mobagen-flaglist-n99259.txt",
"/mnt/archive2/p1724/v12/PDB1724_Skjema1_v12.csv" # could pre-cut first 100 columns from this if slow
output:
"/mnt/work2/jjuod/tmp/ga_cleaned.csv",
"/mnt/work2/jjuod/tmp/ga_cleaned_f.csv"
script:
"clean-pheno.R"
# after this, the GWAS and PGS parts can be run.
rule extract_gt:
"Extract the selected SNPs from complete genotyping data."
input:
inauto="snplists/snplist-alltop.txt",
inx="snplists/snplist-xtop.txt",
inf="snplists/snplist-ftop.txt",
chrs=expand("/mnt/archive/MOBAGENETICS/genotypes-base/imputed/all/vcf/{chr}.vcf.gz", chr=range(1,22)),
chrx="/mnt/archive/MOBAGENETICS/genotypes-base/imputed/all/vcf/X.vcf.gz"
output:
"/mnt/work2/jjuod/tmp/top1-moba30k-dosage.csv.gz",
"/mnt/work2/jjuod/tmp/top1x-moba30k-dosage.csv.gz",
"/mnt/work2/jjuod/tmp/top1f-moba30k-dosage.csv.gz"
shell:
"./extract-snps-moba30k.sh {inauto} top1 ; ./extract-snps-moba30k.sh {inx} top1x ; ./extract-snps-moba30k.sh {inf} top1f"
rule explore_pgs_plink:
"Prepare the stats needed for the PGS analysis R script."
input:
expand("/mnt/archive/MOBAGENETICS/genotypes-base/imputed/all/plink/{chr}.bed", chr=range(1,22)),
"/mnt/archive/MOBAGENETICS/genotypes-base/imputed/all/plink/X.bed",
"/mnt/work2/jjuod/tmp/ga_cleaned.csv",
"/mnt/work2/jjuod/tmp/betas_all.txt"
output:
"/mnt/work2/jjuod/tmp/plinktests/res_top_regions.sscore",
"/mnt/work2/jjuod/tmp/plinktests/res_burden_below0.001_rare.sscore",
"/mnt/work2/jjuod/tmp/plinktests/res_burden_below0.001_rec.sscore",
"/mnt/work2/jjuod/tmp/plinktests/pca.eigenvec",
"/mnt/work2/jjuod/tmp/plinktests/chr6-maf1-M.bim"
shell:
"bash pgs-bash.sh"
# -----------------------
rule analyze_all_main:
output:
maintable="/home/julius/Documents/results/tv/table_main.tsv",
mainplot="/home/julius/Documents/results/tv/plot_allmain.png",
suppplot="/home/julius/Documents/results/tv/plot_suppcov.png",
supphaz="/home/julius/Documents/results/tv/plot_supphaz.png"
input:
mfr="/mnt/HARVEST/ga_cleaned.csv",
mfrF="/mnt/HARVEST/ga_cleaned_f.csv",
gt="/mnt/HARVEST/top1-moba30k-dosage.csv.gz",
gtX="/mnt/HARVEST/top1x-moba30k-dosage.csv.gz",
gtF="/mnt/HARVEST/top1f-moba30k-dosage.csv.gz",
pgs="/mnt/HARVEST/PGS.txt",
mobares="snplists/topsnps_meta_summaries.txt"
script:
"run-tvmodels-all.R"
rule analyze_pgs:
output:
mainplotpgs="/home/julius/Documents/results/tv/plot_pgs5.png",
suppplotpgs="/home/julius/Documents/results/tv/plot_pgs3.png",
mainplotpca="/home/julius/Documents/results/tv/plot_explor.png"
input:
mfr="/mnt/HARVEST/ga_cleaned.csv",
pgs="/mnt/HARVEST/PGS.txt",
pgstop="/mnt/HARVEST/plinktests/res_top_regions.sscore",
rarescore="/mnt/HARVEST/plinktests/res_burden_below0.001_rare.sscore",
recscore="/mnt/HARVEST/plinktests/res_burden_below0.001_rec.sscore",
pca="/mnt/HARVEST/plinktests/pca.eigenvec",
chr6pos="/mnt/HARVEST/plinktests/chr6-maf1-M.bim"
script:
"analyse-pgs.R"
rule analyze_diagnostics:
output:
diagtable="/home/julius/Documents/results/tv/table_diag.tsv",
coxdiagplot="/home/julius/Documents/results/tv/plot_coxdiag.png"
input:
mfr="/mnt/HARVEST/ga_cleaned.csv",
mfrF="/mnt/HARVEST/ga_cleaned_f.csv",
gt="/mnt/HARVEST/top1-moba30k-dosage.csv.gz",
gtX="/mnt/HARVEST/top1x-moba30k-dosage.csv.gz",
gtF="/mnt/HARVEST/top1f-moba30k-dosage.csv.gz",
maintable="/home/julius/Documents/results/tv/table_main.tsv"
script:
"run-tvmodels-diag.R"
# ----------------------------S
# unused:
rule prel_analyze_tv:
"Run the preliminary reports for top SNPs in TV models (autosomal SNPs only)."
input:
mfr="/mnt/HARVEST/ga_cleaned.csv",
gt="/mnt/HARVEST/top1-moba30k-dosage.csv.gz",
moba="snplists/topsnps_meta_summaries.txt"
params:
outstem="/home/julius/Documents/results/tv/report_tvmodels"
output:
expand("/home/julius/Documents/results/tv/report_tvmodels{i}.pdf", i=range(1,24))
shell: # This is daft but very important to enforce serial Rmd knitting!!!
""" Rscript -e "for(i in 1:23){{ rmarkdown::render('run-tvmodels.Rmd', params=list(mfrfile='{input.mfr}', gtfile='{input.gt}', mobaresfile='{input.moba}', i=i), output_format='pdf_document', output_file=paste0('{params.outstem}', i, '.pdf')) }}"
"""
rule prel_analyze_tvX:
"Run the preliminary reports for top SNPs in TV models (X chr. SNPs only)."
input:
mfr="/mnt/HARVEST/ga_cleaned.csv",
gt="/mnt/HARVEST/top1x-moba30k-dosage.csv.gz", # note: this uses different sample size
moba="snplists/topsnps_meta_summaries.txt"
params:
outstem="/home/julius/Documents/results/tv/report_tvmodelsX"
output:
expand("/home/julius/Documents/results/tv/report_tvmodelsX{i}.pdf", i=range(1,3))
shell: # This is daft but very important to enforce serial Rmd knitting!!!
""" Rscript -e "for(i in 1:2){{ rmarkdown::render('run-tvmodels.Rmd', params=list(mfrfile='{input.mfr}', gtfile='{input.gt}', mobaresfile='{input.moba}', i=i), output_format='pdf_document', output_file=paste0('{params.outstem}', i, '.pdf')) }}"
"""
rule simulate_null:
"Check if the pam tests maintain alpha by bootstrapping."
input:
mfr="/mnt/HARVEST/ga_cleaned.csv"
output:
"/home/julius/Documents/results/tv/null-pvals.RData"
script:
"simulate-null.R"