def run(self):
# Gather input filepaths and labels
tgt_dict = self.input()
sample_ids = list(tgt_dict.keys())
fpaths = [tgt_dict[sample_id]['abundance'].path for sample_id in sample_ids]
# Merge columns
annotations, est_counts = merge_column(fpaths, sample_ids, data_col='est_counts', annot=False)
annotations, tpm = merge_column(fpaths, sample_ids, data_col='tpm', annot=False)
csv_to_s3(est_counts, self.output()['est_counts'].path)
csv_to_s3(tpm, self.output()['tpm'].path)
def run(self):
# Gather input filepaths and labels
tgt_dict = self.input()
sample_ids = list(tgt_dict.keys())
fpaths = [
tgt_dict[sample_id]['abundance'].path for sample_id in sample_ids
]
# Merge columns
annotations, est_counts = merge_column(fpaths,
sample_ids,
data_col='est_counts',
annot=False)
annotations, tpm = merge_column(fpaths,
sample_ids,
data_col='tpm',
annot=False)
csv_to_s3(est_counts, self.output()['est_counts'].path)
csv_to_s3(tpm, self.output()['tpm'].path)