`align_file` flag in align_target_bowtie not working as expected

[susheelbhanu]

Hi @aubreyodom,

I'm running the following:

target_map <-
        align_target_bowtie(
    read1 = read1,
    read2 = read2,
    lib_dir = target_ref,
    libs = snakemake@params[["index"]],,
    align_dir = out_dir,
    align_file = snakemake@wildcards["sid"],
    overwrite = TRUE,
    threads = snakemake@threads[[1]],
    quiet = FALSE
  )

The expected output for align_file is the sample name, i.e. BT24.bam. However, the command is outputting the following: BT24_F_filt.fastq.target.bam.

Note that it's generating the filename based on the input file itself. Is this expected behaviour?

Thanks!

[susheelbhanu]

This is resolved at the end of the run. Snakemake creates some latency in file generation. Sorry ;)