Bumping bcftools to 1.18 in bcftools.yml?

[scunnac]

Hi,
First of all, thank you all so much for the amazing work and the fantastic tools you are creating in the metagenomics area. It is just great to be able to use them for my research!

Second, I have been having errors in the samtools_mpileup_wc rule:

[W::bgzf_read_block] EOF marker is absent. The input may be truncated
Error: could not parse the input VCF
[Wed Oct 18 10:20:52 2023]
Error in rule samtools_mpileup_wc:
jobid: 25
input: output/genomes/GCF_001746675.1_genomic.fna.gz, output/mapping/enriched_mix_1.x.GCF_001746675.1.bam
output: output/mapping/enriched_mix_1.x.GCF_001746675.1.bcf, output/mapping/enriched_mix_1.x.GCF_001746675.1.vcf.gz, output/mapping/enriched_mix_1.x.GCF_001746675.1.vcf.gz.csi
conda-env: /home/cunnac/TEMP/sourmashTests/girst/condaEnvs/87360d332bd28e925ae853bbc5fb0681_
shell:

    genomefile=$(mktemp -t grist.genome.XXXXXXX)
    gunzip -c output/genomes/GCF_001746675.1_genomic.fna.gz > $genomefile
    bcftools mpileup -Ou -f $genomefile output/mapping/enriched_mix_1.x.GCF_001746675.1.bam | bcftools call -mv -Ob -o output/mapping/enriched_mix_1.x.GCF_001746675.1.bcf
    rm $genomefile
    bcftools view output/mapping/enriched_mix_1.x.GCF_001746675.1.bcf | bgzip > output/mapping/enriched_mix_1.x.GCF_001746675.1.vcf.gz
    bcftools index output/mapping/enriched_mix_1.x.GCF_001746675.1.vcf.gz

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job samtools_mpileup_wc since they might be corrupted:
output/mapping/enriched_mix_1.x.GCF_001746675.1.bcf

I looked around for the potential origin of this EOF marker is absent error and it appeared that updating bcftools could solve the issue.

I updated the genome_grist/conf/env/bcftools.yml on my install with this:

dependencies:
  - bcftools=1.18
  - samtools=1.18

And genome-grist worked just fine.