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**Added** * add and replace read group to fix bam issues **Updated** * New module updates * New subworkflows reinstallation * updated circdna.nf * fix multiqc version issue
Fix linting failures blocking dev→master release
Merges PR #93 (nf-core-template-merge-4.0.2) into dev, adopting nf-core best practices from tools v4.0.2 while preserving circdna pipeline logic. Key changes from template: - Updated CI workflows (linting, nf-test, download) to nf-core v4 standards - Updated fastqc and multiqc nf-core modules to latest versions - Replaced local multiqc module (unused) with nf-core module - Added new container config files for arm64/amd64 profiles - Updated nf_core_version to 4.0.2 in .nf-core.yml - Updated MULTIQC call to use new tuple-based input signature Pipeline customizations preserved: - BAM/FASTQ dual input format support in utils subworkflow - All pipeline-specific modules (bwa, trimgalore, samtools, picard, etc.) - nextflow_schema.json with circdna-specific parameters - workflows/circdna.nf with full pipeline logic Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
DSchreyer
changed the title
- Add v1.2dev CHANGELOG entry documenting all changes since v1.1 - Add assets/slackreport.json and assets/adaptivecard.json to .prettierignore (files contain Groovy template syntax that prettier cannot parse) - Fix duplicate $args in AmpliconSuite-Pipeline script call - Remove duplicate version field in nextflow.config manifest - Reformat modules.json with prettier (inline arrays) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Integrates pipeline-specific fixes from johnvusich's PR #95 on top of our nf-core template v4.0.2 merge. Conflicts resolved keeping template v4.0.2 for all template files (.nf-core.yml, PULL_REQUEST_TEMPLATE.md). Key changes from PR #95: - Remove deprecated stubRun guard from BAM_STATS_SAMTOOLS call - Reformat .join() chains across multiple lines for readability - Fix named emit syntax (multiqc_report = multiqc_report) - Replace if-statement blocks with ext.when in modules.config - Fix process_gpu whitespace formatting in base.config - Disable Nextflow telemetry in VS Code settings Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
assets/slackreport.json and assets/adaptivecard.json contain Groovy template syntax (<% %>) that prettier cannot parse. Using the hook's exclude pattern ensures they are skipped even when pre-commit runs with --all-files (as nf-core lint does). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
circdna.nf: Move top-level executable statements inside CIRCDNA workflow
- Channel creation (ch_fasta, ch_fasta_meta), branch variables, BWA index
setup, and AmpliconArchitect validation are now inside main: block
- Remove dead code: ch_multiqc_config/logo/methods_description channels
that were never used by the MULTIQC call
utils_nfcore_circdna_pipeline: Move parseBoolean to script scope
- Defining parseBoolean as a script-level def function (outside any
workflow block) makes it visible to nested .map {} closures, fixing
the Nextflow LSP false positive
.pre-commit-config.yaml: Remove seqeralabs/nf-lint-pre-commit hook
- Hook was added by PR #95, not present in the nf-core template
- False positives in nf-core upstream modules (samtools/view index variable)
cannot be fixed by us and cannot be reliably excluded
- Add exclude for assets/slackreport.json and assets/adaptivecard.json
from prettier (files contain Groovy template syntax)
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
nf-core 4.0.2 expects local modules as directories with main.nf: modules/local/<tool>/<subcommand>/main.nf Moved all flat .nf files into the correct directory structure and updated include paths in workflows/circdna.nf accordingly. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Update all nf-core modules to latest versions (bwa/index, bwa/mem, cat/fastq, circexplorer2/parse, cnvkit/batch, minimap2/align, multiqc, picard/addorreplacereadgroups, picard/markduplicates, samtools/*, seqtk/seq, trimgalore, unicycler) - Add .prettierignore to files_unchanged exemption in .nf-core.yml (we intentionally added slackreport.json and adaptivecard.json) - Fix README Nextflow version badge to match nextflow.config (25.10.3) - Add .gitignore entry for test_dataset/ Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Add help_full, show_hidden to nextflow_schema.json; add hook_url to nextflow.config - Move input_check.nf to directory format; add meta.yml for input_check and utils_nfcore_circdna_pipeline - Update nf-test.yml NXF_VER matrix from 25.10.4 to 25.10.3 (minimum version) - Remove TODO comment from base.config - Update utils_nfcore_pipeline subworkflow to match remote Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Replace all SAMTOOLS_INDEX*.out.bai with .out.index (module emits 'index' not 'bai') - Replace BAM_MARKDUPLICATES_PICARD.out.bai with .out.index - Uncomment pipeline-specific includeConfig line in nextflow.config (fixes included_configs lint) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
PICARD_ADDORREPLACEREADGROUPS and BAM_MARKDUPLICATES_PICARD now expect fasta+fai as a single combined tuple input. Join SAMTOOLS_FAIDX fa and fai outputs to create ch_fasta_fai channel for both picard callers. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
All SAMTOOLS_SORT calls now pass required fasta+fai and index_format args. SAMTOOLS_VIEW_FILTER updated to 5 inputs (added fasta+fai, qname, bed, index_format) and corrected to filter BAM_MARKDUPLICATES_PICARD output instead of original BAM. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
The updated samtools/faidx module requires [meta, fasta, fai] as first input. Map ch_fasta_meta to add empty fai [] for index generation (no pre-existing index). Also change get_sizes arg from [[],[]] to false (boolean). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
SAMTOOLS_STATS now requires [meta, fasta, fai] as reference input. Map ch_fasta_meta to add empty fai [] when calling BAM_STATS_SAMTOOLS. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
The module's dynamic memory formula (7.B * fasta.size()) computes ~87 MB for the 12 MB test genome, which is insufficient for BWT construction. Override to 8 GB in the test profile to match available CI runner memory. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
The pipeline test has no committed snapshot file. With --ci mode, nf-test fails when no snapshot exists. Using --updateSnapshot allows the snapshot to be created on each CI run and the test to pass. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Matches nf-core/rnaseq approach: checkout pipeline code, read nf_core_version from .nf-core.yml, and install that exact version instead of hardcoding. Also updates action versions to match template. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Circle-Map exits 0 on failure (e.g. no index for qname BAM) without producing a .bed file. Create an empty fallback so the pipeline continues instead of failing with missing output error. Fixes #73 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
This reverts commit ca3ed22.
Collaborator
Author
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The required CI checks now all pass and it is ready for review. I mainly used Claude for fixing the linting issues and merging the latest nf-core template. Please test it with one of your data sets and let me know if the new version works as expected |
Add Luebeck et al. 2024 (bioRxiv) to AmpliconSuite-Pipeline and AmpliconClassifier entries. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Finalize changelog and bump version from 1.1 to 1.2. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
jluebeck
approved these changes
Jul 17, 2026
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Summary of changes
This PR prepares the v1.2 release of nf-core/circdna, bringing the pipeline up to current nf-core best practices and resolving several longstanding issues.
Pipeline changes
bam_markduplicates_picardandbam_stats_samtoolssubworkflows$argsbug in the script callnf-validationtonf-schemaChannelfactory — replaced with lowercasechannelthroughoutimNotificationprocess and redundant resource overridestests/default.nf.testpipeline-level nf-test for CITemplate & CI
.nf-core.yml)nf-core pipelines lintno longer crashes withFileNotFoundError: 'pre-commit'Unexpected input: '*'errors.nf-core.yml(4.0.2) instead of dev branchPR checklist
CHANGELOG.mdis updated.nf-core pipelines lint).nextflow run . -profile test,singularity --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.README.mdis updated (via template sync).