diff --git a/Snakefile b/Snakefile index 8b6e3d6d8815d2e1b8cf589c382ea7cc5aca1f76..a3f4ad709862d3be2c7d1094553b73c6d9004314 100644 --- a/Snakefile +++ b/Snakefile @@ -67,7 +67,7 @@ BPDENS = [ "selected_j{}_s{}_scedist{}".format(joint, single, scedist) for joint in [0.1] for single in [0.5] for scedist in [5,20] ] -singularity: "docker://smei/mosaicatcher-pipeline:v0.1" +singularity: "docker://smei/mosaicatcher-pipeline:latest" localrules: all, @@ -1083,14 +1083,14 @@ rule aggregate_summary_statistics: shell: "(head -n1 {input.tsv[0]} && (tail -n1 -q {input.tsv} | sort -k1) ) > {output}" -rule evaluate_cell_mixing: - input: - sv_calls = expand('sv_calls/{sample}/{{windows}}.{{bpdens}}/{{method}}.txt', sample=SAMPLES), - truth = '../input-data/ground_truth/RPE-BM510_manual/clonal-events.tsv', - output: - tsv = 'cell-mixing-eval/{windows}.{bpdens}/{method}.tsv' - log: - 'cell-mixing-eval/{windows}.{bpdens}/{method}.log' - run: - names = ','.join(SAMPLES) - shell('utils/evaluate_cell_mixing.py --names {names} {input.truth} {input.sv_calls} > {output.tsv} 2> {log}') +#rule evaluate_cell_mixing: +# input: +# sv_calls = expand('sv_calls/{sample}/{{windows}}.{{bpdens}}/{{method}}.txt', sample=SAMPLES), +# truth = config["ground_truth_clonal"][wildcards.sample], +# output: +# tsv = 'cell-mixing-eval/{sample}/{windows}.{bpdens}/{method}.tsv' +# log: +# 'cell-mixing-eval/{sample}/{windows}.{bpdens}/{method}.log' +# run: +# names = ','.join(SAMPLES) +# shell('utils/evaluate_cell_mixing.py --names {names} {input.truth} {input.sv_calls} > {output.tsv} 2> {log}')