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WIP: incorporates the latest changes from production testing. #83

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WIP: incorporates the latest changes from production testing. #83

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7 changes: 3 additions & 4 deletions qp_klp/Step.py
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Original file line number Diff line number Diff line change
Expand Up @@ -797,17 +797,16 @@ def _overwrite_prep_files(self, prep_file_paths):

# prep files are named in the form:
# 20220423_FS10001773_12_BRB11603-0615.Matrix_Tube_LBM_14332.1.tsv
# search on project_name vs qiita_id since it's slightly more
# unique.
fqp_name = "%s_%s" % (project_name, qiita_id)
matching_files = [prep_file for prep_file in prep_file_paths if
project_name in prep_file]
fqp_name in prep_file]

if len(matching_files) == 0:
continue

if len(matching_files) > 1:
raise ValueError("More than one match found for project "
f"'{project_name}': {str(matching_files)}")
f"'{fqp_name}': {str(matching_files)}")

Step._replace_with_tube_ids(matching_files[0],
self.tube_id_map[qiita_id])
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3 changes: 2 additions & 1 deletion qp_klp/tests/data/process_all_fastq_files.sh
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Expand Up @@ -9,6 +9,8 @@
### as well as sbatch -c. demux threads remains fixed at 1.
### Note -c set to 4 and thread counts set to 7 during testing.
#SBATCH -c 2
#SBATCH --gres=node_jobs:4


echo "---------------"
echo "Run details:"
Expand Down Expand Up @@ -253,4 +255,3 @@ echo "$(date) :: demux start"
demux-runner
echo "$(date) :: demux stop"

touch ${OUTPUT}/${SLURM_JOB_NAME}.${SLURM_JOB_ID}.completed
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