clindet completeness audit (2026-08-21, pilot)

Upstream: zyllifeworld/clindet @ 582a9131 · Port: oxo-flow-clindet (60 rules, WES default paired path).

This is the pilot for the §15 full-line completeness audit. Coverage tiers: P0 portable gap (must port) · P1 objective blocker (evidence required) · P2 config variant (absorb as [config]).

Upstream run modes vs port

mode	upstream entry	port status
wes	wrapper/wes.smk (incl. the full WGS SV chain)	partial — default caller set ported; gaps below
wgs	wrapper/wgs.smk	absent
rna	wrapper/rna.smk	absent
build_b37	workflow/setup/rules/human_b37.smk (18 rules)	absent (setup tier)
build_hg38	workflow/setup/rules/human_hg38.smk (15 rules)	absent (setup tier)
pull_zenodo	env_setup.smk (container pulls)	absent (setup tier)

Legacy template Snakefiles (template/snake_*.smk) are entry styles, not branches — no porting work. Dead code on disk (bicseq2, octopus, lancet2, ecDNA, virusbreakend, orange, ...) is not part of the executable DAG — excluded from the audit, noted in the upstream inventory.

RNA branch — P0 (first fill campaign)

upstream rule	tool	env pin (upstream)	notes
fastp_trim	fastp	clindet.yaml
STAR_1_pass	STAR	rsem.yaml (star>=2.7.11b)
STAR_arriba_map	STAR	rsem.yaml	arriba-specific params
STAR_mut_map	STAR	rsem.yaml	SplitNCigarReads chain for SNV callers
cal_exp_RSEM, RSEM_sort_genome	RSEM+bowtie2	rsem.yaml
kallisto	kallisto	rsem.yaml
salmon	salmon	rsem.yaml
mutect2_call, M2_filter_unpaired	GATK4	singularity pins
unpaired_freebayes, norm_filter_freebayes	freebayes
call_variants_HaplotypeCaller, norm_filter_HaplotypeCaller	GATK4
unpaired_call_config_strelka, unpaired_call_strelka_manta, unpaired_strelka_filter	strelka+manta	strelka.yaml
lofreq_call_up, lofreq_norm_filter	lofreq
unpaired_vardict_single_mode, unpaired_filter_vardict	vardict-java
varscan2_mpileup_unpaired, varscan2_call_unpaired_snp, varscan2_call_unpaired_indel, varscan2_filter_snp, varscan2_filter_indel, varscan2_merge_unpaired	varscan2	clindet.yaml (varscan=2.4.6)
loop_vcf2maf_rna, merge_rna_maf	vcf2maf	clindet_vep.yaml
arriba_fusion, arriba_draw	arriba 2.4.0	singularity pin	gated genome b37/hg38/hg38_chr21
TRUST4_TBCR	trust4	rsem.yaml (trust4>=1.1.5)	upstream auto-clones repo at runtime → port must pre-pin (conda pin exists)
STAR_isofox_map, isofox_call	isofox 1.7.2	hmftools.yaml	gated genome b37/hg38

Mode notes: redup=False hardcoded (link_bam branch); GATK backend is the default (sentieon backend = P1, see below); RNA stages toggleable (salmon/kallisto/RSEM/TRUST4/arriba/isofox/call_mut) → port as rules + caller-list config (P2 pattern).

WGS branch

• P2 config absorption: WES↔WGS switch is mostly per-rule bed/seqtype differences (seqtype = WXS|WGS, vardict_wgs_bed, sequenza_gc_bins). Absorb as [config] run_type + conditional params where the shared rule shells already exist.
• P0: WGS-only free tools — paired_sage + sage filter/annotation chain (pave), deepvariant_somatic_call (deepsomatic 1.10.0, free), CNA_ASCAT_sc, Battenberg v2/combine/ABSOLUTE_GISTIC (cgpbattenberg, free), sequenza extras.
• P1: call_variants_sentieon / filter_sentieon (commercial license, no OSS fallback in WGS mode).
• P0 (SV chain, shared with WES mode): SV_delly+filter chain, SV_gridss+filter, SV_svaba+anno, SV_brass+bamstat (gated ascat_wgs
• b37/hg38), paired_linx/report_linx, SV_igcaller (needs .sif), jasmine merge chain, delly2bnd/sansa. All tools free; reference-data heavy (P2 data notes).

WES branch extras (already-ported path)

• P0: conpair_* chain (free, gated on conpair refs); SM_check; free CNV callers — freec_* (control-freec 11.6b, free), CNA_exomedepth, facets_* (facets-suite v2.0.8, free), sequenza_* (free). The port's blanket "CNV unbuildable without commercial licenses" claim is wrong for these — only ASCAT is license-gated.
• P1: CNA_ASCAT, ASCAT_EXTRACT_PURITYPLOIDY, ASCAT_GISTIC (academic license/registration; evidence: ASCAT distribution terms).
• P2: unpaired (tumor-only) mode — engine supports control-less pairs; caller selection lists → [config] lists; Mutect2 PoN flavors → config keys; moalmanac_annotation (free MIT, Docker Hub container → container portability convention); run_cancer_report (Rmd report — ported already as the report module? verify during fill).

Setup modes (build_b37 / build_hg38 / pull_zenodo)

Separate tier — reference/container provisioning, not analysis. Recommend: port as a dedicated setup include module (download rules + index builders, free sources: GCS buckets, Zenodo, Sanger/Ensembl/NCBI FTP), after the analysis branches. Not counted in coverage for the analysis line but listed in the fidelity table.

Verdict

• coverage today: default-path (WES default caller set only).
• P0 total: RNA branch (~35 rules) + SV chain (~20) + free CNV (~15) + WGS extras (~8). P1: sentieon (WGS), ASCAT (WES/WGS). P2: unpaired, caller selection, seqtype, PoN, setup tier.
• Fill order: RNA → SV chain → free CNV → WGS absorption → P2 config work → setup module → P1 documentation.

Live evidence — RNA branch (2026-08-22, verdict #21-RNA LIVE-PASS)

26-rule end-to-end exit 0 on tx-ubuntu (4 vCPU/3GB, multi-round resume; final run: 26 succeeded, 0 failed). Coverage: fastp_trim, STAR_1_pass/ arriba_map/mut_map, arriba_fusion (real container uhrigs/arriba:2.4.0 SIF, STAR produced 97-100 cross-chromosome chimeric reads through the full filter chain), link_bam, SplitNCigarReads, mutect2, M2_filter, HaplotypeCaller, lofreq, varscan2 (full chain), strela (config+manta+ filter), freebayes, vardict, all norm_filter.

Fix chain: 12 commits on branch rna-port (6bc051b..f0fd05c) — ln -sf idempotence, lofreq rm -f, {input[0]} positional array, FAI offsets derived in bytes, STAR index invalidation (ref/gtf declared as inputs + unconditional rebuild + pass1-log edge serialization), mini arriba DB, 20kb chrX fusion fixture set. Known fixture limit (documented in the generator docstring, not a port defect): synthetic reads cannot pass arriba's biological filters (end-to-end low support etc.) → 0 fusion rows; upstream parameters kept verbatim.

Engine notes: .oxo-failed move-aside correctly triggered on SplitNCigarReads failure (#118); keep-going exit code is 0 even with required failures — flagged for an engine fix (undocumented contract).

Coverage update

RNA branch: live-verified. Remaining P0: SV chain (~20), free CNV (~15), WGS extras (~8), conpair/SM_check; P1 ASCAT/sentieon; P2 unpaired/selection/seqtype/PoN/setup tier. Coverage stays default-path until the SV+CNV+WGS fills land.

Re-verification (2026-08-23, 9-mini queue 9/9 — campaign closure)

Engine: latest main (post-v0.14.1) · Box: tx-ubuntu (singularity) · Mode: real CLI run, not dry-run (checkpoint cleared, forced real execution).

26 rules really executed / 0 failed, exit 0. Coverage (real): fastp → STAR 1_pass/arriba_map/mut_map → arriba_fusion (planted synthetic BSJ fusion reads detected) → link_bam → SplitNCigarReads → mutect2 → M2_filter → unpaired (strelka/manta/vardict/freebayes) → lofreq call + norm_filter → varscan2 → norm_filter. Box-side only: apptainer depot.galaxyproject.org TLS timeout + /etc/singularity migration residue → sudo cleanup + Mac relay of the freebayes/lofreq sifs into the apptainer cache hash paths. Engine bug candidate recorded (singularity URI→IMG naming, see failure catalog).