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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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Missing input files error for group job in mitogenome mapping step #15

Closed verku closed 1 year ago

verku commented 2 years ago

On a different HPC than Uppmax, input file names are scrambled for some rules in the mitogenome mapping step, throwing an error in the group job historical_mito_bams_group:

Missing input files for rule mitogenome_bam_stats: results/historical/mitogenomes_mapping/CC022_02_L4_merged_cow_NC_reads_006853.sorted.bam

Try out constraining the wildcard mitoref?

verku commented 2 years ago

Testing to simplify file names, removing "reads" (i.e. "{reads}_{mitoref}" instead of "{reads}reads{mitoref}")

verku commented 2 years ago

Works on Linux, waiting for feedback from the user

verku commented 1 year ago

The user has been able to run the mitogenomes mapping step on their cluster.