23 lines (19 with data), 628 Bytes

include: 'common.snakemake'

rule all:
    input:
        expand('{output_dir}/count_matrix/mirna_and_domains_rna.txt', output_dir=output_dir)


rule combine_mirna_and_domains_rna:
    '''Count matrix of miRNA and domains
    Remove genomic regions
    '''
    input:
        mirna='{output_dir}/count_matrix/transcript_mirna.txt',
        domains_long='{output_dir}/count_matrix/domains_long.txt'
    output:
        '{output_dir}/count_matrix/mirna_and_domains_rna.txt'
    shell:
        '''{{
            cat {input.mirna}
            awk '(NR>1)&&(!($0 ~ /genomic/))' {input.domains_long}
        }} > {output}
        '''