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Module updates, version topics, snapshots
…for conda and mamba profile
Removes three things that were documented or declared but never wired up: the `profileUsesContainers` variable left behind when its guard was deleted, the commented-out igenomes params, and `save_runmerged_reads`, which was in the schema and advertised FASTQ output the pipeline never publishes. Also moves the profile subworkflow helpers below the workflow bodies, trims the eggNOG-mapper publishDir comment, and converts the remaining GitHub-style admonitions in usage.md and output.md to the nf-core website syntax, fixing an unclosed `::` block in the process. Co-authored-by: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com>
Address review follow-ups from PR #52
FastQC was never called, so the citation claimed a tool that never ran. Also carries over the database version table from #76.
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jfy133
commented
Aug 19, 2026
Samplesheet rows are validated and turned into their final [meta, [reads]] form in PIPELINE_INITIALISATION, so a bad sheet aborts before any task is submitted; DATAPREP now only merges runs and concatenates. The platform, fastq_1 and long-read checks move into assets/schema_input.json, which no longer offers OXFORD_NANOPORE or PACBIO_SMRT. validateProfilerDatabases() does the same for the database sheet, replacing the lazy checks inside getDbPath() and the fmhfunprofiler db_params check inside PROFILE. Drops the unread db_type column from the database schema.
Drops leftover debug output and a duplicated ${args} from HUMANN4, adds a
header comment saying why the humann4 modules are local, and credits the
authors who modified them.
tests/nextflow.config goes back to the template shape so -profile test can be run without nf-test, and test_full says why some profilers are off.
One sentence per line, GitHub admonitions instead of Astro, output file lists in collapsible blocks, a database-preparation section per tool, and the db_name/db_entity distinction spelled out before the examples.
Drops the preprocessing node, which 1.0.0 does not have, and collapses the per-profiler lines into reads, databases, profiles and logs.
Replaces the map with the version drawn for the ISME20 poster, which was laid out against nf-core/taxprofiler's tube map and answers the review comments asking for fewer lanes. Six lines instead of eleven: short reads, concatenated reads, summary statistics, and a three-strand database bundle collapsed into one legend row. Blue stops at run merging and green carries every profiler, RGI included; that is a simplification, since RGI is fed the unconcatenated reads. MetaPhlAn is drawn as the HUMAnN prescreen, the seven profiler outputs converge on an unnamed junction that splits once to the tables and to MultiQC, and hollow versus filled markers separate the opt-in profilers from what runs by default. The section holding MERGE_RUNS is called "Run merging", not "Preprocessing": 1.0.0 does no read QC.
Collaborator
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Thanks @jfy133, I believe I addressed most of the comments, point by point below: Applied commits:
Schemas and inputs
Docs
Modules
Subworkflows
Tests
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Important! Template update for nf-core/tools v4.1.0
Collaborator
vinisalazar
marked this pull request as ready for review
September 4, 2026 04:51
vinisalazar
marked this pull request as draft
September 4, 2026 04:51
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This PR SHOULD NOT BE MERGED, and is only used for a 'clean' reviewing experience of
devagainst the latest template (vs. main, which will have an older version of the template).