bamtofastq

--input must match ^\S+\.csv$.

The samplesheet is a CSV with this header (the columns the schema requires); fill each value per the table above and reference.md (no example value is invented here):

sample_id,mapped,file_type

Any of the optional columns above may be appended to the header when your data needs them: index.

From data files. --input may also be the data files — a directory (searched recursively), a quoted glob, or files (--input once per file) — from which nfclaw writes this samplesheet: sample_id from file names; mapped, index from files matching their patterns, by sample name. Set the required columns no file determines with --sheet-set COLUMN=VALUE (a constant or a {sample}/{lane} template): file_type (one of bam, cram). Preview it with --check; a run records it in <outdir>/provenance/ for replay.

No reference genome is set by default: supply your own reference. The schema declares AWS iGenomes at s3://ngi-igenomes/igenomes/; selecting --genome <id> uses the paths in the pipeline's reference configuration. Access to that remote source is required. To supply your own reference, use e.g. --fasta; the reference_genome_options group in reference.md lists every reference option. Set --igenomes-ignore true to disable the lookup entirely. Confirm the selected reference's paths and source in the pinned upstream/nextflow.config and upstream/conf/ before running.

Resource requests follow the pipeline's configs and selected profiles. nf-core's resource labels often assume a server — a single step can request far more memory than a workstation has, and retry rules can increase requests. If a run fails with Process requirement exceeds available memory (or CPUs), cap every request, and every retry, at what this machine actually has:

nfclaw run bamtofastq --input samplesheet.csv --outdir results -profile docker \
  --limit-cpus 4 --limit-memory 15.GB

nfclaw turns those into Nextflow's process.resourceLimits and passes them as a -c config — the mechanism nf-core prescribes for exactly this (docs). Set them to the machine's real capacity. --limit-time DURATION also caps how long any one task may run: a task that needs longer is stopped, and so is every retry, so set it only as a deliberate ceiling, never as a guess at how long the analysis takes. The generated config is kept in <outdir>/provenance/, so commands.sh replays the run under the same ceiling.

This release declares nextflowVersion = '!>=25.10.4'.

To pin this release's declared minimum engine — useful when a newer Nextflow has incompatible config parsing:

nfclaw run bamtofastq ... --nxf-ver 25.10.4

--nxf-ver is recorded in <outdir>/provenance/, so the replay uses the same engine. See known-issues.

nfclaw run bamtofastq --demo --outdir results   # adds the upstream test profile (-profile test,docker)

This pinned test profile omits its required reference. For the bundled demo input, nfclaw supplies the matched chr22:1-40001 test FASTA from immutable test-datasets commit 618f1541382c4ad49eff566dadf13d5ccbd0ebb4 and records it in params/provenance. Explicit --fasta or params-file values override it. Your own input, genome, test-data base, extra profiles or --config disable this demo default; choose a reference matched to your data. The correction applies only to the bundled test plus engine profiles. Its two-sample demo sheet is staged from immutable test-datasets commit e228f0e5412ed0bed20e7a99e1588cbf95f65102 (the same bytes as the moving branch it names) and bundled in provenance, so a replay reads the recorded sheet. Other releases retain their own defaults.