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QC report2 #1010

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merged 3 commits into from
Sep 15, 2023
Merged

QC report2 #1010

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a53f4b7
qc report colors fix v2
siebrenf Sep 13, 2023
4d899b4
keep spaces between columns ;)
siebrenf Sep 13, 2023
d840a71
Merge branch 'develop' into qc_report2
siebrenf Sep 13, 2023
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -17,6 +17,10 @@ All changed fall under either one of these types: `Added`, `Changed`, `Deprecate

- the init, run, and explain commands display the supported workflows in their --help

### Fixed

- issue when specifying colors in the samples table, causing the QC report not rendering the table correctly anymore.

## [1.0.4] - 2023-09-05

### Changed
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2 changes: 1 addition & 1 deletion seq2science/rules/peak_counts.smk
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Expand Up @@ -337,7 +337,7 @@ rule combine_biological_reps:
benchmark:
expand("{benchmark_dir}/combine_biological_reps/{{peak_caller}}/{{assembly}}_log{{base}}_{{normalisation}}_biological_reps.benchmark.txt", **config)[0]
params:
samples=lambda wildcards: samples[samples["assembly"] == wildcards.assembly].replace(' ', '_', regex=True).to_string(index_names=False),
samples=lambda wildcards: samples[samples["assembly"] == wildcards.assembly].astype(str).replace(" ", "_", regex=True).to_string(index_names=False),
breps=lambda wildcards: breps[breps["assembly"] == wildcards.assembly].index.to_list(),
script:
f"{config['rule_dir']}/../scripts/combine_biological_reps.py"
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2 changes: 1 addition & 1 deletion seq2science/rules/qc.smk
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Expand Up @@ -643,7 +643,7 @@ rule multiqc_samplesconfig:
config_used=len(workflow.overwrite_configfiles) > 0,
configfile=workflow.overwrite_configfiles[-1],
config=config_rerun_parser(config),
samples=lambda wildcards: samples.reset_index().to_string(index_names=False),
samples=lambda wildcards: samples.reset_index().astype(str).replace(" ", "_", regex=True).to_string(index_names=False),
conda:
"../envs/htmltable.yaml"
script:
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