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workflow.py
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workflow.py
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from gwf import Workflow, AnonymousTarget
from os.path import join
from glob import glob
#gwf = Workflow()
gwf = Workflow(
defaults={
'cores': 1,
'memory': '16g',
'walltime': '01:00:00'})
#bam_files=glob('~/genomedk/matov/umiseq_analysis/CRUK5Mb/*/*consensus.sort.bam')
bam_files=glob('*consensus.sort.bam')
#realpath C70A06997D_cfdna_N289-54_consensus.sort.bam
#/home/matov/matovanalysis/umiseq_analysis/CRUK5Mb/C70A06997D_cfdna_N289-54_consensus.sort.bam
print(bam_files)
output_dir = "."
bed_file = "NEW_METHOD_hg38_08feb2016_capture_targets.bed"
for bam in bam_files:
bam_id = bam.split("/")[-1].split(".")[0].replace("-","_")
output = join(output_dir, f"{bam_id}.txt")
gwf.target(
f"UMI_seq_fragment_length_data_{bam_id}",
inputs=[bam, bed_file],
outputs=[output],
walltime="04:00:00",
) << """
python UMI_seq_fragment_length.py {} {} {}
""".format(
bam, bed_file, output
)