22 lines (19 with data), 633 Bytes

shell.prefix('set -x;')
include: 'common.snakemake'

with open(data_dir + '/bam_files.txt', 'r') as f:
    bam_files = dict(line.strip().split('\t') for line in f)

rule all:
    input:
        fasta=expand('{output_dir}/unmapped/{sample_id}/clean.fa.gz',
            output_dir=output_dir, sample_id=sample_ids)

rule bam_to_fasta:
    input:
        bam=lambda wildcards: bam_files[wildcards.sample_id]
    output:
        fasta='{output_dir}/unmapped/{sample_id}/clean.fa.gz'
    params:
        flags=2816
    shell:
        '''samtools fastq -F {params.flags} {input.bam} \
        | fastq_to_fasta -r -z -o {output}
        '''