Fix the kraken anchor and add the missing log files - #6
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The key was written "anchor'" with a stray quote, so the section had no anchor and its sidebar entry pointed to nothing.
Up to standards ✅🟢 Issues
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Thirteen shell rules had no log directive, so the pipeline monitor could not follow their progress and reported a couple of seconds instead of the real duration. This matters for the slow ones (laa, bam2ccs, raxml, mafft). Each rule now redirects to its log, following the shape of the command: the tools writing their result on the standard output (samtools stats, bamtools stats, samtools fastq, mafft, cat) only redirect the standard error, the piped command of split_multiallelic is wrapped in a subshell, and the laa rule, which changes directory, is wrapped as well so that the log path stays relative to the working directory. dot2svg is left as it is: its wrapper writes no message and it is now a local rule, together with rulegraph.
cokelaer
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Pull request overview
Updates the LAA pipeline to fix the Kraken report anchor and add runtime logging for previously unlogged rules.
Changes:
- Corrects the Kraken summary anchor.
- Adds log directives and appropriate redirection.
- Marks
rulegraphanddot2svgas local rules.
Suppressed comments (1)
sequana_pipelines/laa/laa.rules:1107
- The PR description says the same anchor typo was fixed in the
quality_controlandrnaseqpipelines, but this PR contains onlysequana_pipelines/laa/laa.rulesand no changes for those pipelines. Please either include those fixes or narrow the description to the change actually delivered here.
"anchor": "kraken",
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Two commits.
Anchor of the kraken section
The kraken section of the summary report declared its anchor with a stray quote in the key name (
"anchor'"instead of"anchor"), so the section had no anchor and did not show up in the report sidebar. The same typo was fixed in the quality_control and rnaseq pipelines.Missing log files
Thirteen shell rules had no
log:directive. The pipeline monitor follows the modification time of the log files to report progress, so those rules showed a couple of seconds instead of their real duration:copy_genbank,laa,bam2ccs,ccs2fastq,copy_reference,samtools_stats,bamtools_stats,mapping_index,split_multiallelic,mafft,raxml_mltree,raxml_bipartitionsandbuild_fasta.The redirection follows the shape of each command:
samtools stats,bamtools stats,samtools fastq,mafft,cat) only redirect the standard errorsplit_multiallelicis wrapped in a subshelllaarule changes directory, so it is wrapped as well and the log path stays relative to the working directoryrulegraphanddot2svgare now declared as local rules.dot2svgkeeps no log: its wrapper prints nothing and it runs in a second.Validation
Full run on the test data with
--apptainer-prefix: 52 of 52 steps done,summary.htmlandmultiqc/multiqc_report.htmlcreated, and the new log files are written (mafft.log1158 bytes,raxml_bipartitions.log1864 bytes; the silent commands such ascpandcatleave an empty file, created when the job starts, which is what the monitor needs).🤖 Generated with Claude Code