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Add support for single-end samples in python runner. #47

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Add support for single-end samples in python runner. #47

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dbc85c0
Add support for single-end samples to run_phanta.py script.
njohner Oct 2, 2024
30d6f7b
Update runner readme with how to use it for single-end data.
njohner Oct 22, 2024
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2 changes: 2 additions & 0 deletions RUNNER.md
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Original file line number Diff line number Diff line change
Expand Up @@ -65,6 +65,8 @@ you can specify the suffixes with `--fwd` and `--rev`:
* `--fwd`: forward read suffix [default: `_R1`]
* `--rev`: reverse read suffix [default: `_R2`]

Samples will be treated as single-end if a file is found for the forward reads but not for the reverse reads.

## Environment variables

To avoid having to pass the database path as an argument, you can set:
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7 changes: 5 additions & 2 deletions run_phanta.py
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Expand Up @@ -70,9 +70,12 @@ def make_mapping(input_dir, output_file, for_tag, rev_tag):
found = 0
with open(output_file, "w") as fh:
for basename, paths in files.items():
if "forward" in paths and "reverse" in paths:
if "forward" in paths:
found += 1
print(basename, paths["forward"], paths["reverse"], sep="\t", file=fh)
if "reverse" in paths:
print(basename, paths["forward"], paths["reverse"], sep="\t", file=fh)
else:
print(basename, paths["forward"], sep="\t", file=fh)
logger.debug("Adding sample: %s" % basename)
logger.info("Found %d samples" % found)

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