hgtseq

Pinned input correction. The bundled schema is an unused FASTQ template. These columns come from the pinned consumer, which reads input1 and optional input2. Paired inputs must have the same extension; BAM/CRAM input cannot have a second mate. Write the sheet explicitly.

--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):

input1,sample

Any of the optional columns above may be appended to the header when your data needs them: input2.

From data files. nfclaw cannot generate this samplesheet: the pinned consumer accepts mixed FASTQ/alignment roles that require an explicit samplesheet.

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 hgtseq --input samplesheet.csv --outdir results --taxonomy-id <taxonomy_id> -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 = '!>=22.10.1'.

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

nfclaw run hgtseq ... --nxf-ver 22.10.1

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

Nextflow 22.10.1 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.

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

This pinned consumer requires input1/input2, but its moving demo sheet now uses newer columns. For a bare bundled demo, nfclaw stages a three-sample historical CSV with immutable read/GFF URLs from test-datasets commit 800330ec8f47c93caabe8157e20dd23e243de4e1 and matched immutable FASTA/Kraken/Krona inputs from 56591d0269db196203af3b0cb2191da22384d24a. The CSV is bundled in provenance and rebased for replay; no remote sheet is rescanned. Explicit input, reference/database/data-base selectors, extra profiles or --config disable this entire recipe so reference choices are not mixed. Other releases retain their own defaults.