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NBISweden / GenErode

GitHub repository for GenErode, a Snakemake pipeline for the analysis of whole-genome sequencing data from historical and modern samples to study patterns of genome erosion.
GNU General Public License v3.0
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Wrong input file in rule index_realigned_bams in workflow 3.1_bam_rmdup_realign_indels.smk? #44

Closed johannanvs closed 1 year ago

johannanvs commented 1 year ago

Hi,

On line 545 in '3.1_bam_rmdup_realign_indels.smk' you find the rule 'index_realigned_bams', which is designed to index the output bam file from the previous rule 'indel_realigner', as I understood it.

The output bam file from rule 'indel_realigner' is: {sample}.merged.rmdup.merged.realn.bam

The input bam file for rule 'index_realigned_bams' is: {sample}.merged.rmdup.merged.bam The output bai file from rule 'index_realigned_bams' is: {sample}.merged.rmdup.merged.realn.bam.bai

Am I missing something, or should not the input bam file for rule index_realigned_bams' then be: {sample}.merged.rmdup.merged.realn.bam?

Sincerely, Johanna

verku commented 1 year ago

Yes, you are right! I'll correct it in the upcoming version. Thanks for letting me know!