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start updating json schema#281

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abartlett004 wants to merge 1 commit intonf-core:devfrom
abartlett004:json-schema-improvements
Draft

start updating json schema#281
abartlett004 wants to merge 1 commit intonf-core:devfrom
abartlett004:json-schema-improvements

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@abartlett004 abartlett004 commented Mar 26, 2025

As part of the hackathon, I started updating the json schemas but didn't get to finish. It seems many parameters and their specifications may need to be added, which is maybe better done by someone more familiar with the pipeline.

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github-actions bot commented Mar 26, 2025 •
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nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit e29152a

+| ✅ 259 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗  30 tests had warnings |!
-| ❌  43 tests failed       |-
Details

❌ Test failures:

  • files_exist - File must be removed: lib/NfcoreTemplate.groovy
  • files_exist - File must be removed: lib/Utils.groovy
  • files_exist - File must be removed: lib/WorkflowMain.groovy
  • files_exist - File must be removed: lib/WorkflowCutandrun.groovy
  • nextflow_config - Config variable (incorrectly) found: params.max_cpus
  • nextflow_config - Config variable (incorrectly) found: params.max_memory
  • nextflow_config - Config variable (incorrectly) found: params.max_time
  • nextflow_config - Config variable (incorrectly) found: params.validationFailUnrecognisedParams
  • nextflow_config - Config variable (incorrectly) found: params.validationLenientMode
  • nextflow_config - Config variable (incorrectly) found: params.validationSchemaIgnoreParams
  • nextflow_config - Config variable (incorrectly) found: params.validationShowHiddenParams
  • nextflow_config - Old lines for loading custom profiles found. File should contain: ```groovy
    // Load nf-core custom profiles from different Institutions
    includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml does not match the template
  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/branch.yml does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - .gitignore does not match the template
  • files_unchanged - .prettierignore does not match the template
  • actions_awsfulltest - .github/workflows/awsfulltest.yml is not triggered correctly
  • schema_params - Param fragment_size from nextflow config not found in nextflow_schema.json
  • schema_params - Param igenomes_base from nextflow config not found in nextflow_schema.json
  • schema_params - Param validationSchemaIgnoreParams from nextflow config not found in nextflow_schema.json
  • schema_params - Param run_genome_prep from nextflow config not found in nextflow_schema.json
  • schema_params - Param run_alignment from nextflow config not found in nextflow_schema.json
  • schema_params - Param run_reporting from nextflow config not found in nextflow_schema.json
  • schema_params - Param run_input_check from nextflow config not found in nextflow_schema.json
  • schema_params - Param run_cat_fastq from nextflow config not found in nextflow_schema.json
  • schema_params - Param run_trim_galore_fastqc from nextflow config not found in nextflow_schema.json
  • schema_params - Param run_read_filter from nextflow config not found in nextflow_schema.json
  • schema_params - Param run_preseq from nextflow config not found in nextflow_schema.json
  • schema_params - Param run_mark_dups from nextflow config not found in nextflow_schema.json
  • schema_params - Param run_remove_dups from nextflow config not found in nextflow_schema.json
  • schema_params - Param run_remove_linear_dups from nextflow config not found in nextflow_schema.json
  • schema_params - Param run_peak_calling from nextflow config not found in nextflow_schema.json
  • schema_params - Param run_consensus_all from nextflow config not found in nextflow_schema.json
  • schema_params - Param run_deeptools_heatmaps from nextflow config not found in nextflow_schema.json
  • schema_params - Param run_deeptools_qc from nextflow config not found in nextflow_schema.json
  • schema_params - Param run_peak_qc from nextflow config not found in nextflow_schema.json
  • schema_params - Param run_multiqc from nextflow config not found in nextflow_schema.json
  • schema_params - Param run_igv from nextflow config not found in nextflow_schema.json
  • schema_params - Param callers from nextflow config not found in nextflow_schema.json

❗ Test warnings:

  • files_exist - File not found: conf/igenomes_ignored.config
  • files_exist - File not found: ro-crate-metadata.json
  • nextflow_config - Config variable not found: validation.help.beforeText
  • nextflow_config - Config variable not found: validation.help.afterText
  • nextflow_config - Config variable not found: validation.summary.beforeText
  • nextflow_config - Config variable not found: validation.summary.afterText
  • nextflow_config - Config manifest.version should end in dev: 3.2.2
  • files_unchanged - LICENSE does not match the template
  • 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
  • pipeline_todos - TODO string in WorkflowCutandrun.groovy: Optionally add in-text citation tools to this list.
  • local_component_structure - peak_frip.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - multiqc.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - gtf2bed.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - samtools_custom_view.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - custom_dumpsoftwareversions.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - peak_counts.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
  • local_component_structure - extract_metadata_awk.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - consensus_peaks.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - extract_fragments.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - align_bowtie2.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - mark_duplicates_picard.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - deeptools_qc.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - deduplicate_linear.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - fastqc_trimgalore.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_genome.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - samtools_view_sort_stats.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - prepare_peakcalling.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - input_check.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • local_component_structure - peak_qc.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
  • nfcore_yml - nf-core version not set in .nf-core.yml

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt

✅ Tests passed:

Run details

  • nf-core/tools version 3.2.0
  • Run at 2025-03-26 18:15:39

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@abartlett004