From 8e804e07e6329bb97112e2dbfdb4c9e8a2dfd2b9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Gordon=20J=2E=20K=C3=B6hn?= Date: Thu, 12 Sep 2024 14:59:24 +0200 Subject: [PATCH] fixing relative_amplicon_coverage rule --- workflows/amplicon_cov.smk | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/workflows/amplicon_cov.smk b/workflows/amplicon_cov.smk index eee61ae..33c447e 100644 --- a/workflows/amplicon_cov.smk +++ b/workflows/amplicon_cov.smk @@ -12,14 +12,14 @@ primers_fp = "../resources/amplicon_cov/articV3primers.bed" rule relative_amplicon_coverage: input: sample_list = "/cluster/project/pangolin/work-amplicon-coverage/test_data/samples.tsv", - samples = "/cluster/project/pangolin/work-amplicon-coverage/test_data/samples", + samples = "/cluster/project/pangolin/work-amplicon-coverage/test_data/samples" output: - output_dir = output_dir+ "/cov_heatmap.pdf" + output_dir = output_dir + "/cov_heatmap.pdf" shell: - f""" - python ../scripts/amplicon_covs.py -pv / - -s {{input.sample_list}} / - -f {{input.samples}} / - -r articV3primers.bed / - -o {{output.output_dir}} / + """ + python ../scripts/amplicon_covs.py \ + -s {input.sample_list} \ + -f {input.samples} \ + -r articV3primers.bed \ + -o {output.output_dir} """ \ No newline at end of file