Update biobase to 0.1.16

[claude]

Summary

Checked all bulker/biobase container images for newer registry tags (quay.io/biocontainers, quay.io/xujishu, Docker Hub broadinstitute/bioconductor). One genuine update found.

Updated images

tool	old tag	new tag
salmon	2.3.4--hfa8f182_0	2.4.1--hfa8f182_0

Checked, no update needed

All other ~60 images (bcftools, bedtools, bismark, bowtie2, bwa, cellranger, cutadapt, deeptools, gatk, hisat2, htseq, homer, htslib, kallisto, macs2, minimap2, multiqc, picard, R/Rscript (bioconductor_docker), rsem, samtools, seqtk, STAR, trim_galore, ucsc-* tools, vep, etc.) are already at their latest available tag.

Note: cutadapt, sra-tools, and htseq each had newer-looking tags on quay.io (e.g. sra-tools:3.4.1--2_linux_64, htseq:2.1.2--py311h483b626_2), but these are same-version rebuilds for a different Python ABI/architecture, not newer tool versions — left unchanged per the "be conservative" rule.

Skipped (per skill rules)

• nsheff/pigz — custom image, no registry API
• databio/refgenie — custom image, uses latest

🤖 Generated with the update-biobase skill

[claude]

Refreshed with additional updates found in a follow-up check (all images re-verified via registry API, timestamps confirmed for genuine version/build bumps vs. simultaneous multi-variant re-publishes):

Tool	Old	New
bcftools	1.24--h487d631_1	1.24--h118bc1c_2
gatk	4.6.2.0	4.7.0.0
hisat2	2.2.2--h503566f_0	2.2.3--h8471819_0
htseq	2.1.2--py313h420c3f6_2	2.1.2--py313h9d32f87_3
picard	3.4.0	3.5.0
salmon	2.4.1--hfa8f182_0 (this PR's original)	2.5.1--hfa8f182_0
ensembl-vep	116.0--pl5321h2a3209d_0	116.1--pl5321h2a3209d_0

Checked and confirmed no update needed for all other images, including cellranger (6.0.1 already latest ≥6.0.0), bioconductor_docker (RELEASE_3_23 already latest), and several biocontainers entries that looked like ties (cufflinks, cutadapt, sra-tools, genometools-genometools, macs2) but turned out to be simultaneous multi-variant republishes rather than real newer versions, verified via last_modified timestamps. pigz, refgenie skipped as pinned/custom per skill instructions.

python validate_manifests.py --check-tags passes with 0 errors for bulker/biobase_0.1.16.yaml.