Fix for hidden output docs

jpcartailler commented 6 months ago

Issue

There is an open <details markdown="1"> tag in the last working section (### 4.3), but no closing tag.
Then section 5 starts. Then, right after ###6.5 starts, there is dangling closing tag </details>
Then section 7 begins

Fix Move tag to appropriate location

PR checklist

[x] This comment contains a description of changes (with reason).
[x] Output Documentation in docs/output.md is updated.
[x] CHANGELOG.md is updated

github-actions[bot] commented 6 months ago

`nf-core lint` overall result: Failed :x:

Posted for pipeline commit 028f027

+| ✅ 196 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   3 tests had warnings |!
-| ❌   8 tests failed       |-

### :x: Test failures: * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File must be removed: `lib/Utils.groovy` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File must be removed: `lib/WorkflowMain.groovy` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File must be removed: `lib/NfcoreTemplate.groovy` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File must be removed: `lib/WorkflowCutandrun.groovy` * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `.github/workflows/branch.yml` does not match the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `.github/workflows/linting_comment.yml` does not match the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `.github/workflows/linting.yml` does not match the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `pyproject.toml` does not match the template ### :heavy_exclamation_mark: Test warnings: * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config ``manifest.version`` should end in ``dev``: ``3.2.2`` * [pipeline_todos](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/pipeline_todos) - TODO string in `WorkflowCutandrun.groovy`: _Optionally add in-text citation tools to this list._ * [pipeline_todos](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/pipeline_todos) - TODO string in `methods_description_template.yml`: _#Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline_ ### :grey_question: Tests ignored: * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - File ignored due to lint config: `assets/email_template.html` * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - File ignored due to lint config: `assets/email_template.txt` ### :white_check_mark: Tests passed: * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `.gitattributes` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `.gitignore` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `.nf-core.yml` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `.editorconfig` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `.prettierignore` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `.prettierrc.yml` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `CHANGELOG.md` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `CITATIONS.md` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `CODE_OF_CONDUCT.md` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `LICENSE` or `LICENSE.md` or `LICENCE` or `LICENCE.md` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `nextflow_schema.json` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `nextflow.config` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `README.md` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `.github/.dockstore.yml` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `.github/CONTRIBUTING.md` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `.github/ISSUE_TEMPLATE/bug_report.yml` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `.github/ISSUE_TEMPLATE/config.yml` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `.github/ISSUE_TEMPLATE/feature_request.yml` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `.github/PULL_REQUEST_TEMPLATE.md` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `.github/workflows/branch.yml` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `.github/workflows/ci.yml` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `.github/workflows/linting_comment.yml` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `.github/workflows/linting.yml` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `assets/email_template.html` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `assets/email_template.txt` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `assets/sendmail_template.txt` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `assets/nf-core-cutandrun_logo_light.png` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `conf/modules.config` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `conf/test.config` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `conf/test_full.config` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `docs/images/nf-core-cutandrun_logo_light.png` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `docs/images/nf-core-cutandrun_logo_dark.png` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `docs/output.md` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `docs/README.md` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `docs/README.md` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `docs/usage.md` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `main.nf` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `assets/multiqc_config.yml` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `conf/base.config` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `conf/igenomes.config` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `.github/workflows/awstest.yml` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `.github/workflows/awsfulltest.yml` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `modules.json` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File found: `pyproject.toml` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File not found check: `Singularity` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File not found check: `parameters.settings.json` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File not found check: `pipeline_template.yml` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File not found check: `.nf-core.yaml` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File not found check: `bin/markdown_to_html.r` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File not found check: `conf/aws.config` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File not found check: `.github/workflows/push_dockerhub.yml` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File not found check: `.github/ISSUE_TEMPLATE/bug_report.md` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File not found check: `.github/ISSUE_TEMPLATE/feature_request.md` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File not found check: `docs/images/nf-core-cutandrun_logo.png` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File not found check: `.markdownlint.yml` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File not found check: `.yamllint.yml` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File not found check: `lib/Checks.groovy` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File not found check: `lib/Completion.groovy` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File not found check: `lib/Workflow.groovy` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File not found check: `lib/nfcore_external_java_deps.jar` * [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File not found check: `.travis.yml` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.name` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.nextflowVersion` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.description` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.version` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.homePage` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `timeline.enabled` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `trace.enabled` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `report.enabled` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `dag.enabled` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `process.cpus` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `process.memory` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `process.time` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `params.outdir` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `params.input` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `params.validationShowHiddenParams` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `params.validationSchemaIgnoreParams` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.mainScript` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `timeline.file` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `trace.file` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `report.file` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable found: `dag.file` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.nf_required_version` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.container` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.singleEnd` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.igenomesIgnore` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.name` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.enable_conda` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config ``timeline.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config ``report.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config ``trace.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config ``dag.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config ``manifest.name`` began with ``nf-core/`` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable ``manifest.homePage`` began with https://github.com/nf-core/ * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config ``dag.file`` ended with ``.html`` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config variable ``manifest.nextflowVersion`` started with >= or !>= * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config `params.custom_config_version` is set to `master` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config `params.custom_config_base` is set to `https://raw.githubusercontent.com/nf-core/configs/master` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Lines for loading custom profiles found * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - nextflow.config contains configuration profile `test` * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.outdir= ./results * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.spikein_genome= K12-MG1655 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.clip_r1= 0 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.clip_r2= 0 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.three_prime_clip_r1= 0 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.three_prime_clip_r2= 0 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.trim_nextseq= 0 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.aligner= bowtie2 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.normalisation_c= 10000 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.minimum_alignment_q_score= 20 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.end_to_end= true * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.normalisation_mode= Spikein * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.normalisation_binsize= 50 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.peakcaller= seacr * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.use_control= true * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.extend_fragments= true * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.igg_scale_factor= 0.5 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.seacr_peak_threshold= 0.05 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.seacr_norm= non * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.seacr_stringent= stringent * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.macs2_qvalue= 0.01 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.macs_gsize= 2700000000.0 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.macs2_narrow_peak= true * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.macs2_broad_cutoff= 0.1 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.consensus_peak_mode= group * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.replicate_threshold= 1.0 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.igv_show_gene_names= true * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.dt_qc_bam_binsize= 500 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.dt_qc_corr_method= pearson * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.dt_heatmap_gene_beforelen= 3000 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.dt_heatmap_gene_bodylen= 5000 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.dt_heatmap_gene_afterlen= 3000 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.dt_heatmap_peak_beforelen= 3000 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.dt_heatmap_peak_afterlen= 3000 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.dt_calc_all_matrix= true * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.min_frip_overlap= 0.2 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.min_peak_overlap= 0.2 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.igv_sort_by_groups= true * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.custom_config_version= master * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.max_cpus= 16 * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.max_memory= 128.GB * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.max_time= 240.h * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.publish_dir_mode= copy * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.max_multiqc_email_size= 25.MB * [nextflow_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/nextflow_config) - Config default value correct: params.validate_params= true * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `.gitattributes` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `.prettierrc.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `CODE_OF_CONDUCT.md` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `LICENSE` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `.github/.dockstore.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `.github/CONTRIBUTING.md` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `.github/ISSUE_TEMPLATE/bug_report.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `.github/ISSUE_TEMPLATE/config.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `.github/ISSUE_TEMPLATE/feature_request.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `.github/PULL_REQUEST_TEMPLATE.md` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `assets/sendmail_template.txt` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `assets/nf-core-cutandrun_logo_light.png` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `docs/images/nf-core-cutandrun_logo_light.png` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `docs/images/nf-core-cutandrun_logo_dark.png` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `docs/README.md` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `.gitignore` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - `.prettierignore` matches the template * [actions_ci](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/actions_ci) - '.github/workflows/ci.yml' is triggered on expected events * [actions_ci](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/actions_ci) - '.github/workflows/ci.yml' checks minimum NF version * [actions_awstest](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/actions_awstest) - '.github/workflows/awstest.yml' is triggered correctly * [actions_awsfulltest](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/actions_awsfulltest) - `.github/workflows/awsfulltest.yml` is triggered correctly * [actions_awsfulltest](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/actions_awsfulltest) - `.github/workflows/awsfulltest.yml` does not use `-profile test` * [readme](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/readme) - README Nextflow minimum version badge matched config. Badge: `23.04.0`, Config: `23.04.0` * [readme](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/readme) - README Zenodo placeholder was replaced with DOI. * [pipeline_name_conventions](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/pipeline_name_conventions) - Name adheres to nf-core convention * [template_strings](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/template_strings) - Did not find any Jinja template strings (290 files) * [schema_lint](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/schema_lint) - Schema lint passed * [schema_lint](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/schema_lint) - Schema title + description lint passed * [schema_lint](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/schema_lint) - Input mimetype lint passed: 'text/csv' * [schema_params](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/schema_params) - Schema matched params returned from nextflow config * [system_exit](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/system_exit) - No `System.exit` calls found * [actions_schema_validation](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: branch.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: awstest.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: linting.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: ci.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: clean-up.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: fix-linting.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: awsfulltest.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: linting_comment.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: download_pipeline.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: release-announcements.yml * [merge_markers](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/merge_markers) - No merge markers found in pipeline files * [modules_json](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/modules_json) - Only installed modules found in `modules.json` * [multiqc_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/multiqc_config) - 'assets/multiqc_config.yml' contains `report_section_order` * [multiqc_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/multiqc_config) - 'assets/multiqc_config.yml' contains `export_plots` * [multiqc_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/multiqc_config) - 'assets/multiqc_config.yml' contains `report_comment` * [multiqc_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/multiqc_config) - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins. * [multiqc_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/multiqc_config) - 'assets/multiqc_config.yml' contains a matching 'report_comment'. * [multiqc_config](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/multiqc_config) - 'assets/multiqc_config.yml' contains 'export_plots: true'. * [modules_structure](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/modules_structure) - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL' ### Run details * nf-core/tools version 2.13 * Run at `2024-02-28 09:21:03`

chris-cheshire commented 4 months ago

Hi @jpcartailler, sorry for taking so long to get to this, I have been away on Paternity leave. Could you fix the tests and I can merge?

jpcartailler commented 4 months ago

Thanks @chris-cheshire and no worries, being a dad is way more important.

I'm a little puzzled by the errors to be honest. I was just modifying two .md files, but see errors related to the following:

[files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File must be removed: lib/Utils.groovy
    [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File must be removed: lib/WorkflowMain.groovy
    [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File must be removed: lib/NfcoreTemplate.groovy
    [files_exist](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_exist) - File must be removed: lib/WorkflowCutandrun.groovy
    [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - .github/workflows/branch.yml does not match the template
    [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - .github/workflows/linting_comment.yml does not match the template
    [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - .github/workflows/linting.yml does not match the template
    [files_unchanged](https://nf-co.re/tools/docs/2.13/pipeline_lint_tests/files_unchanged) - pyproject.toml does not match the template

Any thoughts or guidance? TY

chris-cheshire commented 4 months ago

Damn i think I need to upgrade the pipeline to pass the new nf-core tools spec. Bear with me, I will update the pipeline and then you will need to pull from dev

jpcartailler commented 4 months ago

Thanks @chris-cheshire - is there anything for me to try yet?

chris-cheshire commented 4 months ago

Not yet no, this needs quite a large update I am afraid. Nf-core have removed all the groovy libs in favour of plugins so its a substantial code change

nf-core / cutandrun