Release 1.0.0 (dev branch) - #52
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vinisalazar wants to merge 356 commits into
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vinisalazar wants to merge 356 commits into
vinisalazar wants to merge 356 commits into
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Module updates, version topics, snapshots
…for conda and mamba profile
Address review follow-ups from PR #52
vinisalazar
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Aug 5, 2026
The default test disabled FASTQC with ext.when = false, so docs/output.md advertised a fastqc/ directory that the snapshot never contained, which is what jonasscheid flagged on nf-core#52. tests/.nftignore already carried the rule to ignore FastQC report contents, so dropping the gate records the paths without making the snapshot depend on unstable file contents. Runtime goes from ~170s to ~366s. Also add the database versions note jfy133 asked for: the pipeline passes db_path straight through and never checks it against the tool version, plus the tool/database combinations exercised on the pilot cohort.
FastQC was never called, so the citation claimed a tool that never ran. Also carries over the database version table from #76.
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.
Important! Template update for nf-core/tools v4.1.0
jonasscheid
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Well done from my side 👍🏼
jfy133
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Sep 4, 2026
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This can be merged (and released following the release procedure!), once the last two things have been addressed:
- Mifaser activated within
test_full.configand is working - The last input validation moved I mentioned on Slack
The other points on my Slack message are recommended but optional, so I won't block release based on those.
Congratulations on getting the first version (hopefully of many!) pipeline completed! This has not been a trivial set of tools or databases to get together, and it's been great seeing the cross-institutional teamwork forming 💪️
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@nickp60 would you do the honours of merging? 😄 |
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Just working on fixing aws test databases, then yes! |
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Investigating RGI test problem
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).