Fix sample discovery when tumor-only run without pairs file; minor issue with pairs.tsv in test dataset

[samarth8392]

Changes

XAVIER could fail at Snakefile parse time with:
Fatal: Either a valid pairs file or sample names must be provided.
Sample names provided: set()

even when valid *.fastq.gz inputs were provided and tumor-only mode should have proceeded.

Root cause

Sample discovery depends on name_symlinks, which is normally created by sym_safe() symlinking discovered inputs into:
input_files/fastq/ (FASTQ mode) or
input_files/bam/ (BAM mode)

However, the Snakefile logic previously did this:
If input_files/fastq existed, it only globbed input_files/fastq/*.fastq.gz and did not run sym_safe() again.
If the directory existed but was empty (e.g., from a partial init/failed run/manual mkdir), then name_symlinks=[] → samples=set() → read_pairsfile() raised the fatal error before any rules executed.

Issues

Harden sample discovery to repopulate symlinks when the input directory exists but contains no files:
Always os.makedirs(input_fqdir, exist_ok=True) / os.makedirs(input_bamdir, exist_ok=True)
Prefer existing symlinks when present
If globbing the directory returns empty, call sym_safe(...) to (re)populate it
Add an early, actionable error message if samples still cannot be inferred

This makes tumor-only runs robust to stale/empty input_files/* directories and prevents parse-time failure.

Fixes #172
Fixes #173

PR Checklist

(Strikethrough any points that are not applicable.)

• This comment contains a description of changes with justifications, with any relevant issues linked.
• [ ] Update docs if there are any API changes.
• Update CHANGELOG.md with a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/

[kelly-sovacool]

Looks good @samarth8392! Can you just confirm that you tested this branch on biowulf and it works as expected now?

[samarth8392]

Yes, I ran the test run on the test dataset

./bin/xavier run \
	--input ./tests/data/*R?*.fastq.gz \
	--output $MAINDIR/runs/xavier_hg38 \
	--genome hg38 \
	--mode slurm \
	--runmode run

and I can confirm that the bam_check ran without issues

 $ grep "bam_check" snakemake.log.jobby.short.tsv | less

bam_check.samples=WES_NC_N_1_sub        COMPLETED       
bam_check.samples=WES_NC_T_1_sub        COMPLETED

[samarth8392]

This PR also fixed #173 as I have updated the names in the test data pairs.tsv file

[kelly-sovacool]

excellent, thanks for these fixes Samarth!