Retire three non-functional scripts: master-script.sh, invoke-bcl2fastq.sh, shock-push-fastq.sh

[wilke]

Summary

Three scripts in bin/ cannot run as written and appear not to have run
successfully in about two years. Recommending deletion, not repair —
bin/bcl2fastq.sh already does the job.

1. bin/master-script.sh — never executes anything

CLAUDE.md describes this as the "main BCL to FASTQ conversion orchestrator".
It does not convert anything.

• Line 81 echos the bcl2fastq command instead of running it.
• Lines 56-68 assign BM_OPTION eight times consecutively, so only the
  last (--use-bases-mask y151,y12,y151) survives; the other seven are dead.
• Line 49: WE STILL NEED TO WORK OUT THE ADAPTER STORY
• Line 54: BM_OPTION NEEDS TO BE SET BY THE INVOKING SCRIPT
• Line 70: TALK TO SARAH ABOUT THIS

The comments read as notes-to-self, not as a shipped tool.

2. bin/invoke-bcl2fastq.sh — two hard errors

Near-identical copy with the same 8x BM_OPTION clobber, plus:

• Line 54 ECHO "..." (uppercase) — command not found.
• Line 81 references ${OPTION} while getopts sets ${OPTIONS}.

It also calls bcl2fastq2, a binary not present in any container here.

3. bin/shock-push-fastq.sh — wrong three ways

• Line 223 is exit 1 placed before the cleanup rm, so the script
  always exits non-zero and leaks /var/tmp/<RUN>.sav.tar.gz on every run.
• Line 181 tars runParameters.xml and SampleSheet.csv. Neither exists on
  these NextSeq runs — the real names are RunParameters.xml and
  <date>_COVID_WW.csv. The SAV archive is therefore missing its contents.
• Lines 135-153 derive node attributes by positional awk -F/, assuming
  RUN/unaligned/Project_X/Sample_Y/file.fastq.gz. The current layout is
  RUN/<date>_fastq/<batch>/file.fastq.gz, which matches neither branch, so
  group/project/sample are wrong and name is empty for every modern
  run already in SHOCK.

Recommendation

Delete all three. bin/bcl2fastq.sh — a thin Apptainer wrapper around
bcl2fastq_2.20.0.sif — is the only conversion script that works, and option
assembly belongs in whatever calls it.

If SHOCK pushes are still required, shock-push-fastq.sh needs a rewrite rather
than a patch, and the existing node attributes for modern runs need correcting.
If they are not required, delete it too. That needs an explicit decision.

Provenance

reports/work-260730.seqtrack.md.