From 600d44169946f9e3c58de239fde0991066292892 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Gordon=20J=2E=20K=C3=B6hn?= Date: Fri, 11 Oct 2024 13:33:16 +0200 Subject: [PATCH 1/2] Enable Parallel Deconvolution --- workflow/rules/signatures.smk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/rules/signatures.smk b/workflow/rules/signatures.smk index 7ae9fa01..316edd1e 100644 --- a/workflow/rules/signatures.smk +++ b/workflow/rules/signatures.smk @@ -362,7 +362,7 @@ rule deconvolution: threads: config.deconvolution["threads"] shell: """ - {params.LOLLIPOP} deconvolute "--output={output.deconvoluted}" "--out-json={output.deconv_json}" "--var={input.var_conf}" "--vd={input.var_dates}" "--dec={input.deconv_conf}" "--filters={input.filters}" {params.out_format} {params.seed} "{input.tallymut}" 2> >(tee -a {log.errfile} >&2) > >(tee -a {log.outfile}) + {params.LOLLIPOP} deconvolute "--output={output.deconvoluted}" "--out-json={output.deconv_json}" "--var={input.var_conf}" "--vd={input.var_dates}" "--dec={input.deconv_conf}" "--filters={input.filters}" {params.out_format} --seed={params.seed} --n-cores={threads} "{input.tallymut}" 2> >(tee -a {log.errfile} >&2) > >(tee -a {log.outfile}) """ From dedb2875b97416f563364591baf0f87c31f9d97b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Gordon=20J=2E=20K=C3=B6hn?= Date: Fri, 11 Oct 2024 13:38:34 +0200 Subject: [PATCH 2/2] bump lollipop version --- workflow/envs/lollipop.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/envs/lollipop.yaml b/workflow/envs/lollipop.yaml index a42daa39..979ef34f 100644 --- a/workflow/envs/lollipop.yaml +++ b/workflow/envs/lollipop.yaml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - lollipop =0.4.1 + - lollipop =0.4.2