fq/lint: constrain reads input to arity 1..2#11227
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pinin4fjords merged 1 commit intomasterfrom Apr 20, 2026
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`fq lint` only accepts `<R1>` or `<R1> <R2>`. Downstream pipelines that
inadvertently forward more than two FASTQs (e.g. from a loose
`path(...)` collection upstream) currently fail with a cryptic
`fq lint: unexpected argument` error inside the container. Declaring
`arity: '1..2'` on the input surfaces the cardinality problem as a
clear Nextflow-level error at channel bind, e.g.:
Incorrect number of input files for process `FQ_LINT (1)`
-- expected 1..2, found 3
Reported by @edmundmiller in nf-core/rnaseq#1807.
Also adds a test case that supplies three FASTQs and asserts the
process fails, locking the constraint in place.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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This was referenced Apr 20, 2026
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Apr 22, 2026
…ntegration Bump to the latest upstream of: - fq/lint (nf-core/modules#11227): constrain reads arity to 1..2 - ribodetector (nf-core/modules#11258): unpin GPU container from pytorch-gpu=1.11.0; emit cuda version on the topic - tximeta/tximport (nf-core/modules#11141): fix gene-level crash on mismatched transcript FASTA/GTF - fastq_fastqc_umitools_trimgalore (nf-core/modules#11228): handle null trim_log in the read-count map - custom/catadditionalfasta (nf-core/modules#11256): topic-based versions, explicit out/\${prefix}.{fasta,gtf} paths, task.ext.prefix ?: meta.id prefix handling The custom/catadditionalfasta interface change needs pipeline-side follow-up in conf/modules/prepare_genome.config: - Fix the stale CAT_ADDITIONAL_FASTA selector (now CUSTOM_CATADDITIONALFASTA) and split PREPROCESS_TRANSCRIPTS_FASTA_GENCODE into its own block. - Set ext.prefix = "\${params.genome ?: fasta.baseName}_\${add_fasta.baseName}" so output filenames follow the previous {genome}_{add_name} pattern; the new module default (meta.id) would otherwise rename outputs to genome_transcriptome.{fasta,gtf}. Behaviour note: fixing the withName selector also exposes a pre-existing intent that was masked. CUSTOM_CATADDITIONALFASTA outputs now only publish when --save_reference is set; the stale selector previously let them fall through to the default publishDir and land in <outdir>/custom/out/ regardless of --save_reference. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Summary
fq lintonly accepts<R1>or<R1> <R2>. Downstream pipelines that accidentally forward more than two FASTQs into this module currently fail inside the container with a cryptic message like:Declaring
arity: '1..2'on the input surfaces the cardinality mismatch as a clear Nextflow-level error at channel bind:Makes accidental over-forwarding (e.g. a
path(...)glob that picks up more files than the user realised) fail fast and obvious, rather than requiring someone to read the container stderr.Reported by @edmundmiller in nf-core/rnaseq#1807.
Changes
modules/nf-core/fq/lint/main.nf: addarity: '1..2'to thefastqinput.modules/nf-core/fq/lint/tests/main.nf.test: addtest_fq_lint_rejects_more_than_two_fastqsto lock the constraint in place.Test
PR checklist
CHANGELOG.mdis updated.nf-core modules test <MODULE> --profile docker).meta.ymlis up to date (no changes needed here).🤖 Generated with Claude Code