32601072006
91%
master: 91%

Ran 22 Aug 2026 09:59PM UTC

Jobs 2

Files 3

Run time 1min

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Committed 22 Aug 2026 09:57PM UTC coverage: 91.228%. Remained the same

Build # 32601072006

Build Type

push

github

Committed by

cokelaer

Commit Message

Add a multiqc report and containerize the trimming

MultiQC aggregates the FastQC and cutadapt results in multiqc/multiqc_report.html
and each sample report links it. The rule uses the multiqc container and the
sequana_wrappers shell, as in the other pipelines.

The trimming used to build its command line inside a python 'run' directive,
which cannot be executed in a container. It is now a plain shell rule using
the cutadapt container (cutadapt 4.6). The atropos variant is kept as a
separate rule; atropos has no container so it must be available locally. Its
own report is no longer overwritten by the standard output.

The rules that remain in python (the fastq statistics and the extraction of
the mapped reads) now have a log file, which they write as they go: the
pipeline monitor follows the modification times to report the elapsed time.
Those rules use the sequana library directly, which the report generation
requires on the host anyway, hence no container for them.

Also require sequana >=0.24.1, declare multiqc in tools.txt and in the conda
environment, and run the summary rule locally.

Coverage Stats

52 of 57 relevant lines covered (91.23%)

1.82 hits per line

Jobs

ID	Job ID	Ran	Files	Coverage
1	32601072006.1	22 Aug 2026 09:59PM UTC	3	91.23	GitHub Action Run
2	32601072006.2	22 Aug 2026 10:00PM UTC	3	91.23	GitHub Action Run

cokelaer / quality_control / 32601072006
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master: 91%

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