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"""
A test case for this bug
"""
n_files = 4
rule all:
input:
faa='all.faa',
fasta='all.fasta'
checkpoint make_files:
output:
files=directory('files')
run:
os.makedirs(output.files)
for i in range(n_files):
filename = f'{output.files}/f{i}.fasta'
with open(filename, 'wt') as fasta_out:
fasta_out.write('>blank\nACTGACTG\n')
def get_report_files(wildcards):
" get the names of the faa files to be created "
files_dir = checkpoints.make_files.get().output.files
files, = glob_wildcards(f'{files_dir}/{{file}}.fasta')
return expand(f'{files_dir}/{{file}}.txt', file=files)
rule pattern:
input: "{any_file}.fasta"
output: "{any_file}.faa"
shell: "cp {input} {output}"
rule multiple:
""" in my original example, compiled a bunch of sets of report, fasta and faa files
into a master file of each type.
only the reports were the actual inputs. Neitheer the fasta or faa were listed
"""
input:
reports=get_report_files
output:
fasta='all.fasta',
faa='all.faa'
shell:
"touch {output}"
rule report:
input:
"f{n}.faa"
output:
"f{n}.txt"
shell: "wc {input} > {output}"
rule make_fasta:
" just create a placehlder"
output: "f{n}.fasta"
shell: "echo {wildcards.n} > {output}"
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