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Snakefile
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Snakefile
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rule wrangle:
input:
"metadata/kallistosamples.txt",
"results/kallistocounts.txt"
output:
"metadata/00_colData.csv",
"results/00_countData.csv"
shell:
"Rscript analysis/00_wrangle.R"
rule fig1:
input:
"metadata/00_colData.csv",
"results/00_countData.csv"
output:
"figures/fig1-1.pdf"
shell:
"Rscript analysis/01_fig1.R"
rule deseq2:
input:
"metadata/00_colData.csv",
"results/00_countData.csv"
output:
"results/DESeq2/treatment/hypothalamus_vsd.csv",
"results/DESeq2/sex/hypothalamus_DEGs.csv"
threads: 6
shell:
"Rscript analysis/02_DESeq2.R"
rule vsd:
input:
"results/DESeq2/treatment/female_hypothalamus_vsd.csv",
"R/genelists.R"
output:
"results/03_hypvsdf.csv",
"results/03_candidatevsd.csv",
"results/03_shinyvsd.csv"
shell:
"Rscript analysis/03_vsd.R"
rule degs:
input:
"results/DESeq2/treatment/female_gonads_control_early_DEGs.csv"
output:
"results/04_allDEG.csv",
"results/table1a.csv",
"results/tableS1.csv"
shell:
"Rscript analysis/04_DEGs.R"
rule figs23:
input:
"results/03_hypvsdf.csv",
"results/04_allDEG.csv"
output:
"figures/fig2-1.pdf",
"figures/fig3-1.pdf"
shell:
"Rscript analysis/05_figs23.R"
rule figsup1:
input:
"figures/images/fig_supfig1a.png"
output:
"figures/figsup1-1.pdf"
shell:
"Rscript analysis/06_figsup1.R"