Review on #2088 Abotyper Review comment by Copilot on fmobegi's pull request Pull request overview Note Copilot was unable to run its full agentic suite in this review. Updates the abotyper pipeline's test dataset, regenerating reference index files and per-sample processing outputs (haplotype scans, polymorphism reports, phenotype reports, alignment stats, and logs) for two test samples. The phenotype report also adds new A2-subtype diagnostic positions and revises the interpretive descriptions for several existing positions. Changes: • Refresh reference

.fai

indices and add new per-sample exon6/exon7 haploscan outputs, alignment stats, and logs for

ABO_AA_barcode01

and

ABO_AB_barcode02

. • Update

ABOPhenotype.txt

outputs with new A2 diagnostic positions (e.g., 33, 152, 153, 283, 329, 348, 368, 397, 404, 455, 533, 635, 658, 685) and revised interpretation labels. • Bump samtools version reference from 1.21 to 1.23.1 in

.stats

files and refresh log timestamps to 2026-06-02. Reviewed changes Copilot reviewed 27 out of 43 changed files in this pull request and generated 4 comments. Show a summary per file | File | Description | | ------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------- | | abotyper/refs/REF.README.txt | No content change; line-number annotation refresh. | | abotyper/refs/ABO_Database.fasta.fai | No content change; line-number annotation refresh. | | abotyper/refs/A1_01_01_1_reference_Exon7.fasta(.fai) | No content change; line-number annotation refresh. | | abotyper/refs/A1_01_01_1_reference_Exon6.fasta(.fai) | No content change; line-number annotation refresh. | | abotyper/per_sample_processing/ABO_AB_barcode02/exon7/* | New haploscan outputs, polymorphism report, updated stats, log, and revised phenotype output. | | abotyper/per_sample_processing/ABO_AB_barcode02/exon6/* | New haploscan outputs, alignment statistics TSV, polymorphism report, updated stats, log, and revised phenotype output. | | abotyper/per_sample_processing/ABO_AA_barcode01/exon7/* | New haploscan outputs, polymorphism report, updated stats, log, and revised phenotype output. | | abotyper/per_sample_processing/ABO_AA_barcode01/exon6/* | New haploscan outputs, alignment statistics TSV, polymorphism report, updated stats, log, and revised phenotype output. | Comments suppressed due to low confidence (1) abotyper/per_sample_processing/ABO_AB_barcode02/exon7/haploscan/ABOReadPolymorphisms.txt:1 • Same inconsistency as in the AA sample: Mat+Mis+Ins+Del = 98 (not 100), while A+G+C+T = 57. Other positions in this same file sum cleanly to 100 across Mat+Mis. Please verify how rows containing deletions are normalized so the report is self-consistent. --- 💡 </nf-core/test-datasets/new/abotyper?filename=.github/instructions/*.instructions.md|Add Copilot custom instructions> for smarter, more guided reviews. Learn how to get started. nf-core/test-datasets

Review on #2088 Abotyper Review approved by maxulysse on fmobegi's pull request nf-core/test-datasets

#2088 Abotyper Pull request merged by fmobegi nf-core/test-datasets