Closed verku closed 1 year ago
Testing to simplify file names, removing "reads" (i.e. "{reads}_{mitoref}" instead of "{reads}reads{mitoref}")
Works on Linux, waiting for feedback from the user
The user has been able to run the mitogenomes mapping step on their cluster.
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?