Add blobtk depth for read coverage

[sainsachiko]

• Add blobtk depth for read coverage

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• Make sure your code lints (nf-core lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[sanger-tolsoft]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.2.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

[muffato]

Can you update the CHANGELOG too ?

I can reproduce the issue with -resume you were saying this morning. Did you find out why ? If you run Nextflow with -dump-hashes you can find out what changes between runs, cf https://www.nextflow.io/docs/latest/cache-and-resume.html#comparing-the-hashes-of-two-runs

[muffato]

I've just found there's an issue with the BAM output !
When running this branch with the --outfmt bam option, the output (BAM) files only contain the header, not any read alignment.

[muffato]

And another issue is that pacbio samples (i.e. mMelMel3_T3 and mMelMel3_T4) go through CONVERT_STATS twice. They may be going twice earlier than that but I'm not sure. I may be confused by the chunking.

$ grep CONVERT_STATS:SAMTOOLS_FLAGSTAT results/pipeline_info/execution_trace_2025-07-15_10-54-16.txt | cut -f4 | awk '{print $2}' | sort | uniq -c
      1 (mMelMel1_T1)
      1 (mMelMel2_T1)
      1 (mMelMel3_T1)
      1 (mMelMel3_T2)
      2 (mMelMel3_T3)
      2 (mMelMel3_T4)

[muffato]

I've run some tests (CRAM/BAT/both, and with/without header). No issue about empty BAM file like this morning.

In BAM + no-header mode, the BAM files are not published (but the BAI are)

results_coverage8_noh_bam/read_mapping/hic
results_coverage8_noh_bam/read_mapping/hic/GCA_922984935.2.subset.unmasked.hic.mMelMel3_T1.flagstat
results_coverage8_noh_bam/read_mapping/hic/GCA_922984935.2.subset.unmasked.hic.mMelMel3_T1.coverage.bedGraph.gz
results_coverage8_noh_bam/read_mapping/hic/GCA_922984935.2.subset.unmasked.hic.mMelMel3_T1.stats
results_coverage8_noh_bam/read_mapping/hic/GCA_922984935.2.subset.unmasked.hic.mMelMel3_T1.idxstats
results_coverage8_noh_bam/read_mapping/hic/GCA_922984935.2.subset.unmasked.hic.mMelMel3_T1.bam.bai

(to enable the no-header mode, I edit conf/test.config and comment out the line)