marsseq

--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):

batch,fastq_1,fastq_2,amp_batches,seq_batches,well_cells

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: fastq_1/fastq_2 from FastQ files (mates paired by _R1/_R2, or by _1/_2 when their read names show they are mates). Set the required columns no file determines with --sheet-set COLUMN=VALUE (a constant or a {sample}/{lane} template): batch (matching ^\S+$); amp_batches (matching ^\S+.xlsx$); seq_batches (matching ^\S+.xlsx$); well_cells (matching ^\S+.xlsx$). Preview it with --check; a run records it in <outdir>/provenance/ for replay.

--genome defaults to mm10. The pinned configuration gives --genome mm10 the FASTA ${params.genomes_base}/mm10/GRCm39.fa; a genome key's name need not be the assembly it selects, so confirm it is the one you intend. A genome name alone does not specify where reference files come from. Confirm the selected reference's paths and source in the pinned upstream/nextflow.config and upstream/conf/ before running. To supply your own reference, use e.g. --fasta; the reference_genome_options group in reference.md lists every reference option.

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 marsseq --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 = '!>=23.04.0'.

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

nfclaw run marsseq ... --nxf-ver 23.04.0

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

Nextflow 23.04.0 predates process.resourceLimits (24.04.0), so --limit-* cannot be combined with this pin — nfclaw refuses it rather than run without the ceiling; cap resources with the release's own --max-cpus, --max-memory, --max-time instead.