QC report2 (#1010)

* qc report colors fix v2 * keep spaces between columns ;)
vanheeringen-lab · Sep 15, 2023 · 7f37602 · 7f37602
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -25,6 +25,10 @@ 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

diff --git a/seq2science/rules/peak_counts.smk b/seq2science/rules/peak_counts.smk
@@ -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"

diff --git a/seq2science/rules/qc.smk b/seq2science/rules/qc.smk
@@ -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: