out_dir / --out-dir broken

% hostile dehost --fastq1 tests/data/h37rv_10.r1.fastq.gz --fastq2 tests/data/h37rv_10.r2.fastq.gz --out-dir test
INFO: Using Bowtie2
INFO: Using cached human index (/Users/bede/Library/Application Support/hostile/human-bowtie2)
Dehosting:   0%|                                                                                                                | 0/1 [00:00<?, ?it/s]Exception occurred during executing command bowtie2 -x '/Users/bede/Library/Application Support/hostile/human-bowtie2' -1 'tests/data/h37rv_10.r1.fastq.gz' -2 'tests/data/h37rv_10.r2.fastq.gz' -k 1 --mm -p 10| tee >(samtools view -F 256 -c - > test/h37rv_10.r1.reads_in.txt)| samtools view --threads 5 -f 12 - | tee >(samtools view -F 256 -c - > test/h37rv_10.r1.reads_out.txt) | awk 'BEGIN{FS=OFS="\t"} {$1=int((NR+1)/2)" "; print $0}' | samtools fastq --threads 5 -c 6 -N -1 'test/h37rv_10.r1.dehosted_1.fastq.gz' -2 'test/h37rv_10.r2.dehosted_2.fastq.gz': Command '['/bin/bash', '-c', 'bowtie2 -x \'/Users/bede/Library/Application Support/hostile/human-bowtie2\' -1 \'tests/data/h37rv_10.r1.fastq.gz\' -2 \'tests/data/h37rv_10.r2.fastq.gz\' -k 1 --mm -p 10| tee >(samtools view -F 256 -c - > test/h37rv_10.r1.reads_in.txt)| samtools view --threads 5 -f 12 - | tee >(samtools view -F 256 -c - > test/h37rv_10.r1.reads_out.txt) | awk \'BEGIN{FS=OFS="\\t"} {$1=int((NR+1)/2)" "; print $0}\' | samtools fastq --threads 5 -c 6 -N -1 \'test/h37rv_10.r1.dehosted_1.fastq.gz\' -2 \'test/h37rv_10.r2.dehosted_2.fastq.gz\'']' returned non-zero exit status 1.
Dehosting: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████| 1/1 [00:00<00:00, 11.09it/s]
Traceback (most recent call last):
  File "/Users/bede/miniconda3/envs/hostile/bin/hostile", line 8, in <module>
    sys.exit(main())
  File "/Users/bede/Research/Git/hostile/src/hostile/cli.py", line 68, in main
    defopt.run(
  File "/Users/bede/miniconda3/envs/hostile/lib/python3.10/site-packages/defopt.py", line 356, in run
    return call()
  File "/Users/bede/Research/Git/hostile/src/hostile/cli.py", line 28, in dehost
    stats = lib.dehost_paired_fastqs(
  File "/Users/bede/Research/Git/hostile/src/hostile/lib.py", line 140, in dehost_paired_fastqs
    stats = gather_stats(fastqs, out_dir=out_dir)
  File "/Users/bede/Research/Git/hostile/src/hostile/lib.py", line 89, in gather_stats
    n_reads_in = util.parse_count_file(n_reads_in_path)
  File "/Users/bede/Research/Git/hostile/src/hostile/util.py", line 55, in parse_count_file
    with open(path, "r") as fh:
FileNotFoundError: [Errno 2] No such file or directory: 'test/h37rv_10.r1.reads_in.txt'
bede / hostile

out_dir / --out-dir broken #4
