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scaffolds sample_name #9

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Merged
merged 2 commits into from
Jan 31, 2025
Merged

scaffolds sample_name #9

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d1a5d88
scaffolds sample_name
antgonza Jan 30, 2025
b12d2cb
fix test
antgonza Jan 30, 2025
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2 changes: 1 addition & 1 deletion qp_spades/qp_spades.py
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Original file line number Diff line number Diff line change
Expand Up @@ -167,7 +167,7 @@ def spades(qclient, job_id, parameters, out_dir):
outfiles = []
for run_prefix, sname in prep_info.items():
scaffold = join(out_dir, run_prefix, 'scaffolds.fasta')
new_scaffold = join(out_dir, run_prefix, f'{run_prefix}.fasta')
new_scaffold = join(out_dir, run_prefix, f'{sname}.fasta')
if exists(scaffold):
run(['mv', scaffold, new_scaffold], stdout=PIPE)
else:
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4 changes: 2 additions & 2 deletions qp_spades/tests/test_spades.py
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Expand Up @@ -176,9 +176,9 @@ def test_spades(self):
self.assertTrue(success)
self.assertEqual(1, len(ainfo))
self.assertEqual(ainfo[0].files,
[(f'{out_dir}/S22205_S104/S22205_S104.fasta',
[(f'{out_dir}/S22205_S104/1.SKB8.640193.fasta',
'preprocessed_fasta'),
(f'{out_dir}/S22282_S102/S22282_S102.fasta',
(f'{out_dir}/S22282_S102/1.SKD8.640184.fasta',
'preprocessed_fasta')])


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