Chain export_top_loci 1+2+3; fix chr-prefix bug; drop "export" jargon in mnm_postprocessing.ipynb#1323
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Chain export_top_loci 1+2+3; fix chr-prefix bug; drop "export" jargon in mnm_postprocessing.ipynb#1323rfeng2023 wants to merge 2 commits into
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May 13, 2026 15:59
…gon; fix chr-prefix bug
Previously producing per-study top_loci files required two SLURM
array scripts run sequentially (one calling cis_results_export
--step1_only, then one calling export_top_loci per region). This
patch chains both stages plus a final combine into one sos run
invocation, fixes a latent chr-prefix bug surfaced by the chained
flow, and removes "export"/"exported" jargon from output filenames.
Changes:
* Alias export_top_loci_1 onto the cis_results_export_1 step body
so `sos run ... export_top_loci` triggers export (step 1) ->
top_loci extraction (step 2) -> combine (step 3) in one DAG.
* [export_top_loci_2]: glob-based input over step-1 RDS outputs;
parameters renamed to export_prefix/export_suffix to avoid CLI
collision with step-1 --prefix/--suffix. No --region required.
* New [export_top_loci_3]: combines per-region top_loci.bed.gz
into {cwd}/summary/{name}.{qtl_type}[.{variant_tag}].top_loci.bed.gz.
Bash combine tolerates empty per-region outputs. --combine
auto|yes|no controls whether step 3 runs (auto-skips on
--region-name / --region-list; override with yes/no).
* Drop "export"/"exported" jargon from output filenames so legacy
outputs can be purged by pattern (e.g. *.export.*):
*.cis_results_db.export.rds -> *.cis_results_db.rds
*.export_sumstats.rds -> *.cis_results_db.sumstats.rds
*.toploci.bed.gz -> *.top_loci.bed.gz
* Fix chr-prefix handling broken by a pecotmr update. tabix_region
now requires the literal "chr:start-end" format (its parse_region
rejects bare "10:..."). align_to_genoref was stripping the chr
before the call and getting an empty tibble back, which surfaced
as `object 'chr' not found`. Replace gsub("chr","",chr) with
sub("^(chr)?","chr",chr) at three call sites.
* Lower global --job_size default 50 -> 1. With the old default,
one SLURM task bundled 50 substeps x per-substep mem in parallel
(e.g. 50 x 6G = 300G), exceeding typical max_mem caps. Users who
want bundling pass --job_size N explicitly.
* Example Docs: consolidate four cis_results_export variant cells into a
single workflow/modality reference; rewrite the export_top_loci
examples with a placeholder legend explaining the
{prefix}.{region}.{suffix} input filename pattern.
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Summary
sos run ... export_top_locinow does export + top_loci + combine via SOS DAG (was two SLURM array scripts).--combine auto|yes|nocontrols the combine step; auto-skips on--region-name/--region-list..export./.export_sumstats./toplocijargon. Use*.export.*to find legacy files for purging.tabix_regionnow requires literalchr:start-end; three call sites updated.--job_sizedefault 50 → 1 (old default exceeded SLURMmax_mem).--fsusie/--metaQTL/--mnm.Migration
*.cis_results_db.export.rds/*.export_sumstats.rds→ repoint to*.cis_results_db.rds/*.cis_results_db.sumstats.rds.export_top_loci's--prefix/--suffixrenamed to--export_prefix/--export_suffix.Tested codes
--combine yes