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INPUT_FILE = 'Snakefile'
OUTPUT_ROOT = 'checkpoint-test'
BINS_DIR = Path(OUTPUT_ROOT) / 'bins'
BIN_DIR_TEMPLATE = BINS_DIR / '{bin_id}'
BIN_FILE_TEMPLATE = BINS_DIR / '{bin_id}' / 'read_list.txt'
BIN_FILE2_TEMPLATE = OUTPUT_ROOT + '.bin.{bin_id}.clust.info.csv'
rule all:
input: OUTPUT_ROOT + '.final_file'
rule rule1:
input: INPUT_FILE
output: OUTPUT_ROOT + '.file1'
shell:
'touch {output}'
checkpoint checkpoint1:
" defines some bins "
input: OUTPUT_ROOT + '.file1'
output:
bins_dir=directory(BINS_DIR)
run:
# 20 bins
for bin_id in range(1,20):
# create bin specific subdir of BINS_DIR
bin_dir = str(BIN_DIR_TEMPLATE).format(bin_id=bin_id)
os.makedirs(bin_dir, exist_ok=True)
# create a bin specific output file
rlist_fn = str(BIN_FILE_TEMPLATE).format(bin_id=bin_id)
with open(rlist_fn, 'w') as fh:
fh.write(str(bin_id) + '\n')
def expand_template_from_bins(wildcards, template):
# get dir through checkpoints to throw Exception if checkpoint is pending
checkpoint_dir = checkpoints.checkpoint1.get(**wildcards).output
# get bins from files
bins, = glob_wildcards(BIN_FILE_TEMPLATE)
# expand template
return expand(str(template), bin_id=bins)
# the second input is key here
rule rule2:
input:
bin_file=BIN_FILE_TEMPLATE,
other=OUTPUT_ROOT + '.file1'
output: BIN_FILE2_TEMPLATE
shell:
'touch {output}'
rule final_rule:
""" access all bin files """
input: lambda w: expand_template_from_bins(w, BIN_FILE2_TEMPLATE)
output: OUTPUT_ROOT + '.final_file'
shell: 'touch {output}'
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