Fix: use VCF as input in glimpse2

[atrigila]

Error reported via Slack:

Hi I am able to run bam files with glimpse, but when I give it a vcf.gz file it gives the following
[ee/c06ee5] PIP…sis_set_plus_decoy_hla.fa) | 1 of 1 ✔
[b8/4af64f] NFC…CF_CHR_EXTRACT (Sample_46) | 1 of 1 ✔
[- ] NFC…HECK_INPUT:BAM_CHR_EXTRACT -
[- ] NFC…HECK_TRUTH:VCF_CHR_EXTRACT -
[- ] NFC…HECK_TRUTH:BAM_CHR_EXTRACT -
[fa/7cbe0a] NFC…F_CHR_EXTRACT (1000G chr4) | 23 of 23 ✔
[- ] NFC…HECK_PANEL:BAM_CHR_EXTRACT -
[- ] NFC…E:PHASEIMPUTE:LIST_TO_FILE -
[- ] NFC…TE_GLIMPSE2:GLIMPSE2_PHASE -
[- ] NFC…_GLIMPSE2:BCFTOOLS_INDEX_1 -
[- ] NFC…E_GLIMPSE2:GLIMPSE2_LIGATE -
[- ] NFC…_GLIMPSE2:BCFTOOLS_INDEX_2 -
[- ] NFC…T_GLIMPSE2:BCFTOOLS_CONCAT -
[- ] NFC…UTE:BCFTOOLS_QUERY_IMPUTED -
[- ] NFC…E:PHASEIMPUTE:GAWK_IMPUTED -
[- ] NFC…PUTED:BCFTOOLS_PLUGINSPLIT -
[- ] NFC…MPUTE:BCFTOOLS_STATS_TOOLS -
[- ] NFC…IMPUTE:PHASEIMPUTE:MULTIQC -
02:06
-[nf-core/phaseimpute] Pipeline completed successfully-
Completed at: 04-Feb-2025 21:06:12
Duration : 4m 23s
CPU hours : 0.4
Succeeded : 26
02:07
I ran this with:
nextflow run nf-core/phaseimpute -r 1.0.0
--input ./samplesheet_VCF.csv
--tools glimpse2
--steps "impute"
--panel /carter/users/pschofield/projects/GLIMPSE_2_3_25/g38results/prep_panel/csv/panel.csv
--chunks /carter/users/pschofield/projects/GLIMPSE_2_3_25/g38results/prep_panel/csv/chunks.csv
--outdir "VCF_results"
--fasta /carter/users/pschofield/references/GRCh38_full_analysis_set_plus_decoy_hla.fa
-profile "apptainer"
(editado)
Why is it not running imputation and finishing pipeline without errors?

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
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• Output Documentation in docs/output.md is updated.
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[LouisLeNezet]

Thanks for finding that !!