bactmap

For this exact commit, nfclaw run applies bactmap-demo-order-preview-v2 in a separate verified working copy. The test profile preserves module defaults and overrides only its intended leaves, with explicit IQ-TREE and RAxML seeds. Pseudogenomes are aligned in sample-name order. Preview skips the unbound MultiQC wait; real execution still waits for its report. The original pinned checkout stays unchanged. The direct Nextflow command omits this correction. The actual corrected bytes, recipe, source archive and executable modes are recorded for replay; resume refuses missing or changed source identity. Use NFCLAW_SOURCE_CACHE to select another writable user cache. Recorded source corrections explains the exact scope and validation.

This release publishes no samplesheet schema for --input, so nfclaw does not pre-check its contents. The parameter reads: Path to a sample sheet describing paths to input fastq files. Configure the other inputs via parameters (see reference.md).

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 bactmap --input <input> --outdir results --reference <reference> -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 = '!>=21.04.0'.

That minimum predates Nextflow's Java 17 support (21.10.0): on the Java 17+ nf-claw requires it fails to compile the configuration (Unsupported class file major version 61), and nfclaw run refuses it. Run this release on a later engine — the one nf-claw's acceptance gate checks such releases on:

nfclaw run bactmap ... --nxf-ver 24.10.5

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

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

This pinned bundled test uses missing moving data URLs. For a bare demo, nfclaw stages the three original paired samples and matched NCTC13799 reference from immutable test-datasets commit 02195cfa96ca496173e9d63dd58e34bf02fcf55a. The generated sheet and data commit are recorded and rebased for replay. Explicit input or reference, custom profiles or --config disable the entire fixture. Other releases retain their defaults. Bare demos default to max_cpus=1: native two-CPU runs reordered identical reads and changed downstream alignments and pseudogenome masking; the single-CPU control matched. Explicit --max-cpus or params-file values win. Resource limits are ceilings and do not raise this default. Tree branch lengths and bootstrap support still need separate comparison. A source-bound working copy preserves module defaults, orders the pseudogenome alignment by sample name, seeds IQ-TREE and RAxML under the test profile, and skips the unbound MultiQC report wait only during preview; real runs still wait for the report.