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initial ncRNA annotation pipeline implementation using Infernal/cmsearch against Rfam#1

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pmb59 merged 30 commits intomasterfrom
dev
Mar 10, 2026
Merged

initial ncRNA annotation pipeline implementation using Infernal/cmsearch against Rfam#1
pmb59 merged 30 commits intomasterfrom
dev

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@pmb59 pmb59 commented Mar 1, 2026 •
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Add first version of the pipeline

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github-actions bot commented Mar 1, 2026 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit c13c3ca

+| ✅ 197 tests passed       |+
#| ❔   4 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   2 tests had warnings |!
-| ❌  13 tests failed       |-
Details

❌ Test failures:

  • nextflow_config - Config manifest.version should not contain dev for a release: 1.0dev
  • files_unchanged - .gitignore does not match the template
  • template_strings - Found a Jinja template string in /home/runner/work/ncrnannotator/ncrnannotator/tests/data/rfam_test.seed L1521: .{{{{.{{{))))..........}}
  • template_strings - Found a Jinja template string in /home/runner/work/ncrnannotator/ncrnannotator/tests/data/rfam_test.seed L1522: .{{{{.{{)))))...........}}
  • template_strings - Found a Jinja template string in /home/runner/work/ncrnannotator/ncrnannotator/tests/data/rfam_test.seed L1523: .{{{{.{{)))))...........}}
  • template_strings - Found a Jinja template string in /home/runner/work/ncrnannotator/ncrnannotator/tests/data/rfam_test.seed L2994: :{{{-.{{{{{{{,{{{{{{{{{-----{{.{-{{{,,<<---<<<..............................----<<.................>>.---.>>>>>,,,,,,[[[,,,,.,,((((--((--.((.----((((,,.......................................................................,,,,,,,,,,<<<<--.--<<<<<.<<>>>>>>>----->>>>,,,,,,....<<<<<--<<................................................................>>--..>.>>>>,,,,<<<<<<--------..<<<<--.............................................................................--<<<____....>>>---............-->>>>------..>>>>>>,,,,,,.........,,,<<<<...-<<<<.......................>>>>...>>>>.,,,)))).---).)))--))))<<<--<-.<<<.-..---<<<<.<<.<<..__.......>>.>>>>>>.>>>----->>>>,,,<<<<<<<<..........................>>>>---.>.>>>]]..],<<<<<<__>>>>>>,<<<<>>>>,,,}}
  • template_strings - Found a Jinja template string in /home/runner/work/ncrnannotator/ncrnannotator/tests/data/rfam_test.seed L2994: :{{{{{-.{{{{{{{.-.-{{,,.{{{.{{{{{{.{{{{.{{{{.,,,,<<<<>>>>,,,,.,,,,.{{{{{{{,,.,......,<<<<<.--------<<.<<.<<.........>>>>.>>-.-----.>>>>>,,.,[[-[[[[--[[[[[[[[.[,,,((.(((.(<<<...>>>,,<<<<...>>>>.,,)))).)),,,,,((((,<.<<-<<<<-.-.<<<<......................................................................................................................................................................___________________>>>>.-->>>>>>.>,,.<.<<<<<.<<...........................................................>>>>>>>>,,,,,)))),,,,].]]]-]]].-.--]-]]]]]]].,,,,,}}
  • template_strings - Found a Jinja template string in /home/runner/work/ncrnannotator/ncrnannotator/tests/data/rfam_test.seed L3214: >{{{{{{,,,,(((.((((((((((,,<<<--<<<<<<.......................................>>>>>>...-->>>,,,<<>>,,,...............................................................................................,,,,<<<<<--<<<........................................................>>>--->>>>>,<<<.<<.<<<...---<<.....................................................................................................................>>---..>>>->>>->>..,,,,))))))))))))),,[[-[---[[[[[[,,,((((((((((((,<<<<---<<<<<<<>>>>>>>---->>>>,,,<<<<-<<-<<___>>>.>>>>>,,)-))))))))))),<<<.>>>.,,,,,,]]]]]]------].-]],,[[[[[[,,,,<<<<<>>>>>,,(((((((..,....,,,,...................,,,,<<<<<<<<----<<<----<<<<<<<<<<--<<<<<<.-<..>-.>>>>>>>>>>>>>>>>-->>->---->>>>>>.>>.,.<<<.<.<<.<<<.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................>>>>>.>.>>>,,,..,,,,,,,,......))))))),,,,,<<<.<.<<<<<<>>>>>>>>>>,,,,<<<>>>,,,(((((-(---(((------(-(..--(((----.-.-------------(((-((((((((((-------(((((,<<<--<<<.>>>-->>><><---<<...>>->,))))).---)))))))).)))))-----------.-----.--.-)))--.....)).)))---)-)))))<<<<<<..<<<.__..........................................>>>>>>>.>>,,,,]]].......]].]..<-<<<<<<<<..<.<..........----.--<<-...---<<<.>>>--->>---...>>.>>.>>>>>>-->,,,,,}}
  • template_strings - Found a Jinja template string in /home/runner/work/ncrnannotator/ncrnannotator/tests/data/rfam_test.seed L3214: >{{{{,,.,,,{{{{,,{{,,,<<<<<..<---<<>>->>>>>>,,,,,,{{{,((---((<.<<-.<<.<._>>.>..>>>,,,..,,,...<<<...................................................................................................................................._>>>......,,,,,))----)),,,<<<<<.>>>>>,,[[[[.....................................-[[[[[[[.......,,,...<<<<.................................................>>>>...,,.,,,,((((((---((((.-(((((((-(((<<.<<<<>>>>>>,,,.<<<.<<......----......-<<...<<<<<<<<<<<.__>>>>>>>..>>>.>...>>.-----............>.>.>>>,,,,,,<<<<<<<...._____..............................................................................>>>>>.>>,,)).).---))))).))-.))))---------)))))),,,,,,,,,,,............................................................................................................................................]]...-]]]]].........]]]],}}
  • template_strings - Found a Jinja template string in /home/runner/work/ncrnannotator/ncrnannotator/tests/data/rfam_test.seed L3214: .{{.{{.----{{{{{{{{.-{{{,,,,,,,,,,,,,,<<<<<.---<<.....>>---->>>>><<<<<<<<<<<<<<-<<<.<..<.<<<<.<<<..-<<.<<-----<<<<.....<<<.<.<<<.<.<<<<.<<<<<<<<<.<<<<<<<........................................................................>>>>>>>>.>>>>>>>.>>>..>>>...>>>>>>>-..>>>>----...>>>>->>>---..--------.............................................................................................................................................................................................................................................................................----..-->>>>>>>>>.---..---...>>.>>>-->>>>>>>>><._>,,,,,,,[[[[[[[[[,,<<<.>>>,,<<<<<<<<.-.<-<<<<_____>>>>-..>.--->>>>>>>>,,((((,<<<--<<<<<<-<--<<<----<<<<<..>>>>>----..>>>>>>>>-->>>>><<<<<<_>>>>>><.................................................................................................................................................................................................................................................................................................................................................................>,,,...,,,,,,,,,,,,<<.<<<<_____>>>>>>,,,,,,,,,,)))),,,]]-]]]]]]],,,,}}
  • template_strings - Found a Jinja template string in /home/runner/work/ncrnannotator/ncrnannotator/tests/data/rfam_test.seed L3214: :{{{{{{.{{-.{{{.-{{,,,,,,{{{{-{{{{{{{.,[[[[---[[[[[[[...,,<<<<<<<<<<<<<<<<<<---------<<<<<...--..<<.......................................>>------------>>>>>>>>>>>>>->>>>>>>>.>>,,,.(((((.-----((((.,,,,<.<<<<...................................................>>>>>,,,,,,,,,,,.,,,..,,<<<<<................................................................................................................................................................................................................................................................................................................................................................................................>>.>>>,,.))))--....))))).,,,,,]]]]]]]----]]]],,<<<<>>>-><<<<<<______>>>>>>,,[[,,,,((((((.<<-<<<<<.<.>>>>>>--->><<.._____>>,,,,)))))),,,,<<<<<<<<<>>>>>>>>...>,<<<>>>,]],,,,,,,,,,<<<<<<-........-<<<<____.....................................................................................................................................................................................................................................................................................................................................................................................................................................................................>>>>>>>>>>,,,,,,,,,.}}
  • version_consistency - manifest.version was not numeric: 1.0dev!
  • version_consistency - nfcore_yml.version was not numeric: 1.0dev!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • schema_lint - Parameter input is not defined in the correct subschema (input_output_options)

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-ncrnannotator_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-ncrnannotator_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-ncrnannotator_logo_dark.png
  • included_configs - included_configs

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.2
  • Run at 2026-03-10 23:24:19

pmb59 and others added 15 commits March 1, 2026 01:23
@pmb59 @claude
Rename all ncrnatools references to ncrnaflow and regenerate pipeline…
ff23cb1 
… logos

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
@pmb59
Update workflow for ncrnaflow repository
751ce05
@pmb59
Update AWS test workflow for ncrnaflow repository
7ff8077
@pmb59
Update repository check in branch workflow
d74955d
@pmb59
Update repository reference in linting workflow
fd6d819
@pmb59
Fix syntax for self-hosted runner configuration
9c75d67
@pmb59
fix linting issues
58ee5be
@pmb59
Merge branch 'dev' of https://github.com/Rfam/ncrnaflow into dev
edbd79a
@pmb59
Fix pipeline config, Infernal version, CM W field parsing, and add lo…
281f8f2 
…cal resource config
@pmb59
modified propoerties in nextflow_schema.json, and addition to assets …
b2f40e5 
…in .nf-core.yml
@pmb59
Add GITHUB_TOKEN to download_pipeline.yml
46c8184
@pmb59
Add mgnify-assembly mode and rewrite pipeline documentation
e2caea2 
  Implement a new mgnify-assembly annotation mode for metagenomic assemblies:
  - Skip FILTER_RFAM_CM (full Rfam.cm used directly)
  - Use 50 Mbp genome chunks by default
  - Pass --noali --hmmonly -Z 1000 --cut_ga flags to cmsearch
  - Add --include_prokaryotic_rrna flag to parse_rfam_results.py to retain
    bacterial and archaeal rRNA hits (SSU/LSU) filtered out in Ensembl modes
  - Wire mode-specific ext.args in conf/modules.config
  - Add mgnify-assembly to nextflow_schema.json mode enum

  Also rewrite docs/usage.md and docs/output.md with real ncrnaflow content
  (all three modes, HPC/SLURM examples, params file usage, output column
  descriptions, biotype reference table) and add assets/params_example.yaml.
@pmb59
Fix mgnify-assembly validation, clean up template TODOs, and update c…
af68705 
…itations
@pmb59
no message
cf2682d
@pmb59
Add --full annotation mode using complete Rfam without clade filterin…
ae044cf 
…g. add ncrnaflow.svg generated with nf-metro
@pmb59 pmb59 requested a review from Vicbeg March 3, 2026 10:26
Vicbeg
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tests/default.nf.test
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@Vicbeg Vicbeg Mar 5, 2026

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Current coverage is mostly an end-to-end snapshot test in tests/default.nf.test, with no direct unit tests for bin/parse_rfam_results.py, bin/filter_rfam_cm.py, or bin/rfam_to_formats.py. This leaves parsing/filtering edge-case regressions under-protected unless they visibly alter final snapshots.

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Generally looks well written, but I have added a few comments to consider/address. I haven't yet run the pipeline myself as I wanted to run the test profile but was unable to since currently I would have to provide some files myself. I think it is necessary to add some small test files for nf-core standards.

@pmb59 pmb59 merged commit 355770d into master Mar 10, 2026
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