v1 to v2 Migration Guide

This guide maps legacy snpArcher v1-style inputs to the v2 contracts used by the current workflow.

Sample sheet migration

v2 uses a minimal manifest:

• required: sample_id, input_type, input

• optional: library_id, mark_duplicates

Column mapping

v1 column	v2 column	Notes
BioSample	sample_id	Must be alphanumeric plus ._- only.
Run (SRR/ERR/DRR)	input	Use with input_type: srr.
fq1,fq2	input	Join as fq1;fq2 and set input_type: fastq.
LibraryName	library_id	Optional; defaults to sample_id.
mark_duplicates (global or per-row)	mark_duplicates	Optional; defaults to true.
refGenome,refPath	config reference	v2 keeps reference in config, not sample sheet.

Example: v1 fastq row -> v2 row

v1:

BioSample,LibraryName,Run,fq1,fq2
bird_1,bird_1_lib,1,/data/bird_1_R1.fastq.gz,/data/bird_1_R2.fastq.gz

v2:

sample_id,input_type,input,library_id,mark_duplicates
bird_1,fastq,/data/bird_1_R1.fastq.gz;/data/bird_1_R2.fastq.gz,bird_1_lib,true

Example: v1 SRA row -> v2 row

v1:

BioSample,Run
bird_2,SRR12345678

v2:

sample_id,input_type,input
bird_2,srr,SRR12345678

Config migration

v2 uses nested config keys. Core keys are:

• samples

• reference.name

• reference.source

• variant_calling.*

• intervals.*

• callable_sites.*

• modules.*

Common legacy -> v2 config mapping

v1 key	v2 key	Notes
refGenome	reference.name	Required in v2.
refPath	reference.source	Can be local path, URL, or accession.
sentieon	variant_calling.tool	Set to sentieon (else gatk, bcftools, deepvariant, or parabricks as needed).
sentieon_lic	variant_calling.sentieon.license	String path or license value.
minNmer	intervals.min_nmer	Integer.
cov_filter	callable_sites.coverage.enabled	Boolean.
mappability_k	callable_sites.mappability.kmer	Integer.
mappability_min	callable_sites.mappability.min_score	Number in [0,1].
mappability_merge	callable_sites.mappability.merge_distance	Integer.

Notes

• v2 no longer expects per-sample reference columns in the manifest.

• Optional metadata columns from v1 (for example lat, long, SampleType) are not part of the v2 core manifest contract.

• If a sample appears in multiple rows, library_id identifies the library and may repeat across rows for the same library (for example, multiple lanes/runs); it only needs to differ when a sample truly has multiple distinct libraries.