First version by Vicbeg · Pull Request #2 · RNAcentral/nf-core-rnastructurome

Vicbeg · 2026-03-19T15:12:30Z

Prepared a first version of this analysis pipeline using nf-core/modules and RNA framework.
Some output types may still be missing before it is complete.

PR checklist

…pliance issues

…ample_id param, and format docs

Add RNAFramework analysis modules (rf-count, rf-norm, rf-fold)

…urome into dev

…m metadata

…rity

…urce requirements.

…ed processing

github-actions · 2026-03-19T15:14:49Z

`nf-core pipelines lint` overall result: Failed ❌

Posted for pipeline commit 8ee2cf8

+| ✅ 271 tests passed       |+
#| ❔   4 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   4 tests had warnings |!
-| ❌  12 tests failed       |-

Details

❌ Test failures:

nextflow_config - Config manifest.version should not contain dev for a release: 1.0.0dev
nextflow_config - Lines for loading custom profiles not found. File should contain:

// Load nf-core custom profiles from different institutions
includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"

nextflow_config - Config default value incorrect: params.rffold_vienna_rnaplot is set as RNAplot in nextflow_schema.json but is /usr/local/bin/RNAplot in nextflow.config.
nextflow_config - Config default value incorrect: params.rnaframework_container is set as docker.io/rnastructurome/rnaframework:2.9.6-r1 in nextflow_schema.json but is ghcr.io/vicbeg/rnaframework:2.9.6-r2-runtime in nextflow.config.
nf_test_content - 'tests/main.nf.test' does not snapshot a 'versions.yml' file
files_unchanged - .gitignore does not match the template
schema_params - Param rfnorm_norm_method from nextflow config not found in nextflow_schema.json
schema_params - Default value for param genomes invalid: Not in pipeline parameters. Check nextflow.config.
multiqc_config - assets/multiqc_config.yml does not meet requirements: Section software_versions 'order' must be < 0
version_consistency - manifest.version was not numeric: 1.0.0dev!
version_consistency - nfcore_yml.version was not numeric: 1.0.0dev!
included_configs - Pipeline config does not include custom configs. Please uncomment the includeConfig line.

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
files_exist - File not found: conf/igenomes_ignored.config
readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
schema_params - Schema param genomes not found from nextflow config

❔ Tests ignored:

files_unchanged - File ignored due to lint config: assets/email_template.html
files_unchanged - File ignored due to lint config: assets/nf-core-rnastructurome_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-rnastructurome_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-rnastructurome_logo_dark.png

❔ Tests fixed:

rocrate_readme_sync - Mismatch fixed: RO-Crate description updated from README.md.

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/nf-test.yml
files_exist - File found: .github/actions/get-shards/action.yml
files_exist - File found: .github/actions/nf-test/action.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-rnastructurome_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-rnastructurome_logo_light.png
files_exist - File found: docs/images/nf-core-rnastructurome_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: nf-test.config
files_exist - File found: tests/default.nf.test
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
files_exist - File found: ro-crate-metadata.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-rnastructurome_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowRnastructurome.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Found nf-schema plugin
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.ensembl_base_url= https://ftp.ensembl.org/pub
nextflow_config - Config default value correct: params.ensembl_release= current
nextflow_config - Config default value correct: params.cutadapt_quality_only= false
nextflow_config - Config default value correct: params.cutadapt_5quality= 20
nextflow_config - Config default value correct: params.cutadapt_3quality= 20
nextflow_config - Config default value correct: params.cutadapt_len= 25
nextflow_config - Config default value correct: params.cutadapt_min_align= 1
nextflow_config - Config default value correct: params.cutadapt_trim_n= true
nextflow_config - Config default value correct: params.bowtie_manual_only= false
nextflow_config - Config default value correct: params.bowtie_all= false
nextflow_config - Config default value correct: params.bowtie_norc= false
nextflow_config - Config default value correct: params.bowtie_trim5= 0
nextflow_config - Config default value correct: params.bowtie_trim3= 0
nextflow_config - Config default value correct: params.bowtie_n= 2
nextflow_config - Config default value correct: params.bowtie_max= 1
nextflow_config - Config default value correct: params.bowtie_chunkmbs= 128
nextflow_config - Config default value correct: params.bowtie2_N= 0
nextflow_config - Config default value correct: params.bowtie2_D= 15
nextflow_config - Config default value correct: params.bowtie2_R= 2
nextflow_config - Config default value correct: params.bowtie2_mp= 6,2
nextflow_config - Config default value correct: params.bowtie2_dpad= 15
nextflow_config - Config default value correct: params.bowtie2_rdg= 5,3
nextflow_config - Config default value correct: params.bowtie2_rfg= 5,3
nextflow_config - Config default value correct: params.bowtie2_softclip= false
nextflow_config - Config default value correct: params.bowtie2_ma= 2
nextflow_config - Config default value correct: params.bowtie2_dovetail= false
nextflow_config - Config default value correct: params.rfcount_img= true
nextflow_config - Config default value correct: params.rfcount_trim_5prime= 0
nextflow_config - Config default value correct: params.rfcount_primary_only= false
nextflow_config - Config default value correct: params.rfcount_paired_only= false
nextflow_config - Config default value correct: params.rfcount_properly_paired= false
nextflow_config - Config default value correct: params.rfcount_map_sort_by_read_name= false
nextflow_config - Config default value correct: params.rfcount_map_discard_shorter= 1
nextflow_config - Config default value correct: params.rfcount_map_min_quality= 20
nextflow_config - Config default value correct: params.rfcount_map_collapse_consecutive= true
nextflow_config - Config default value correct: params.rfcount_map_max_collapse_distance= 2
nextflow_config - Config default value correct: params.rfnorm_remap_reactivities= false
nextflow_config - Config default value correct: params.rfnorm_norm_independent= false
nextflow_config - Config default value correct: params.rfnorm_raw= false
nextflow_config - Config default value correct: params.rfnorm_ignore_lower_than_untreated= false
nextflow_config - Config default value correct: params.rfnorm_mean_coverage= 0.0
nextflow_config - Config default value correct: params.rfnorm_median_coverage= 0.0
nextflow_config - Config default value correct: params.rfnorm_nan= 10
nextflow_config - Config default value correct: params.rfnorm_img= true
nextflow_config - Config default value correct: params.rffold_img= true
nextflow_config - Config default value correct: params.rffold_ct= false
nextflow_config - Config default value correct: params.rffold_window= true
nextflow_config - Config default value correct: params.rffold_unconstrained= false
nextflow_config - Config default value correct: params.rffold_vienna_no_lonely_pairs= false
nextflow_config - Config default value correct: params.rffold_vienna_constrained= false
nextflow_config - Config default value correct: params.rffold_dotplot= true
nextflow_config - Config default value correct: params.rffold_shannon_entropy= false
nextflow_config - Config default value correct: params.rnaframework_r_path= /usr/bin/R
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
nf_test_content - 'tests/main.nf.test' contains outdir parameter
nf_test_content - 'tests/rnastructurome.workflow.nf.test' contains outdir parameter
nf_test_content - 'tests/rnastructurome.workflow.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/rnastructurome.workflow.nf.test' contains outdir parameter
nf_test_content - 'tests/rnastructurome.workflow.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/rnastructurome.workflow.nf.test' contains outdir parameter
nf_test_content - 'tests/rnastructurome.workflow.nf.test' contains outdir parameter
nf_test_content - 'tests/rnastructurome.workflow.nf.test' contains outdir parameter
nf_test_content - 'tests/rnastructurome.workflow.nf.test' contains outdir parameter
nf_test_content - 'tests/rnastructurome.workflow.nf.test' contains outdir parameter
nf_test_content - 'tests/rnastructurome.workflow.nf.test' contains outdir parameter
nf_test_content - 'tests/rnastructurome.workflow.nf.test' contains outdir parameter
nf_test_content - 'tests/rnastructurome.workflow.nf.test' contains outdir parameter
nf_test_content - 'tests/rnastructurome.workflow.nf.test' contains outdir parameter
nf_test_content - 'tests/rnastructurome.workflow.nf.test' contains outdir parameter
nf_test_content - 'tests/rnastructurome.workflow.nf.test' contains outdir parameter
nf_test_content - 'tests/rnastructurome.workflow.nf.test' contains outdir parameter
nf_test_content - 'tests/default.nf.test' contains outdir parameter
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'nf-test.config' sets a testsDir
nf_test_content - 'nf-test.config' sets a workDir
nf_test_content - 'nf-test.config' sets a configFile
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .prettierignore matches the template
actions_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
actions_nf_test - '.github/workflows/nf-test.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 25.04.0, Config: 25.04.0
readme - README nf-core template version badge found.
pipeline_todos - No TODO strings found
pipeline_if_empty_null - No ifEmpty(null) strings found
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - assets/multiqc_config.yml found and not ignored.
multiqc_config - assets/multiqc_config.yml contains report_section_order
multiqc_config - assets/multiqc_config.yml contains export_plots
multiqc_config - assets/multiqc_config.yml contains report_comment
multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - CUTADAPT_RTSTOP found in conf/modules.config and Nextflow scripts.
modules_config - CUTADAPT_MAP found in conf/modules.config and Nextflow scripts.
modules_config - UMITOOLS_EXTRACT found in conf/modules.config and Nextflow scripts.
modules_config - BOWTIE_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - BOWTIE2_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_SORT found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_MARKDUP found in conf/modules.config and Nextflow scripts.
modules_config - RNAFRAMEWORK_RFCOUNT found in conf/modules.config and Nextflow scripts.
modules_config - RNAFRAMEWORK_RFNORM found in conf/modules.config and Nextflow scripts.
modules_config - ENSEMBL_TRANSCRIPTOME found in conf/modules.config and Nextflow scripts.
modules_config - ENSEMBL_GTF found in conf/modules.config and Nextflow scripts.
modules_config - RNAFRAMEWORK_RFFOLD found in conf/modules.config and Nextflow scripts.
modules_config - RNAFRAMEWORK_DOTPLOT2BP found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.5.2
rocrate_readme_sync - RO-Crate description matches the README.md.
version_consistency - Version tags are consistent: manifest.version = 1.0.0dev, nfcore_yml.version = 1.0.0dev

Run details

nf-core/tools version 3.5.2
Run at 2026-03-19 15:14:32

Vicbeg and others added 30 commits February 19, 2026 13:25

Download modules

47da8ce

Add samplesheet parsing

6fd8023

Implement cutadapt and bowtie

b24db42

Add umitools and update

8c9b639

Add samtools and umitools implementation

503c3da

Add RNAFramework rf-count/norm/fold local modules and fix nf-core com…

0743ede

…pliance issues

Fix linting and pre-commit CI failures: restore template files, add s…

f169bdc

…ample_id param, and format docs

fix remaining lint failures and fill in README introduction

8409659

docs: add missing tool citations and editorconfig

8494486

Merge pull request #1 from RNAcentral/dev-pm

3a190de

Add RNAFramework analysis modules (rf-count, rf-norm, rf-fold)

Check if fasta is provided before downloading

b341839

Merge branch 'dev' of https://github.com/RNAcentral/nf-core-rnastruct…

beb5084

…urome into dev

Add nextflow and testfiles to .gitignore

866b063

Add bowtie mapping options and defaults

1589d3d

Fixes and add nf-core/samtools/faidx module

c86ff6f

Add options for RFNORM and tests

da30138

Add options for rf-norm and run MultiQC before

dd18321

Added cat fastq to handle resequencing of samples

744386f

Remove duplicates properly

1893f7d

wired in rf-fold, tests and update docs

aec65c9

Switched to using transcriptome and fixed tests

309b9fe

Fixed remaining issues with transcript fasta use

297e6ac

Add test for Ensembl transcriptome module and remove genome_build fro…

5bc2f26

…m metadata

Added fasta sorting to match rf-index

3dfe0b3

Update config for cutadapt, add public rnaframework image for singula…

2c671cf

…rity

Exposed log files for RNAFramework and changed config for FASTQC reso…

d549158

…urce requirements.

updated docker, singularity config

a9c274d

Fix path issues for singularity

bade7e5

configurating multiQC

bad1b4a

fix for MultiQC

70985b6

Vicbeg added 25 commits March 11, 2026 14:31

New image with just RNAframework modules and multiqc config updates.

eb35364

Image changes for RNAframework modules only.

51b94a4

Addind metadata and fix multiqc config

6d6954c

Fix Cutadapt MultiQC helper

d2edaa0

Fix to RNAFramework paths

0f5599a

Increase threading for RNAframework modules

3059260

Add script to create test fastq files

adf64f7

use samtools on singularity

b9b3590

fix subseting script for test data

0dd2304

Added module to convert .dp to .bp for IGV viewing

5e6014d

Improved joining of samples for normalisation

b393ace

fixed issues with processing both treated and untreated samples

6ceda40

Fix for RFNORM where log was being written to folder before it finish…

9a93ff3

…ed processing

added nf-metro svg (static and animated)

33a2697

Add tests to make 100% test coverage

546eca4

Fixing linting issues

f598037

Added test data for test profile

48eebf5

default to windowed folding

57cacc8

make nf-schema compatible with nextflow on the cluster

3cbdcbd

Add colours to .bp output and fixed docker profile

d99ed80

Fixing configs and refactoring some code

a095190

Fixing tests and test data

91ab596

fix test linting issues

41f6add

Add testdata

5ba8a31

remove some unnecessary files

8ee2cf8

Vicbeg assigned Vicbeg, afg1 and pmb59 and unassigned Vicbeg Mar 19, 2026

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Vicbeg wants to merge 56 commits intomasterfrom
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Vicbeg commented Mar 19, 2026

Uh oh!

github-actions bot commented Mar 19, 2026

❌ Test failures:

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Vicbeg commented Mar 19, 2026

PR checklist

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github-actions bot commented Mar 19, 2026

nf-core pipelines lint overall result: Failed ❌

❌ Test failures:

❗ Test warnings:

❔ Tests ignored:

❔ Tests fixed:

✅ Tests passed:

Run details

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`nf-core pipelines lint` overall result: Failed ❌