Fix variable redeclarations for strict syntax compliance (from branch) #9756
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Remove variable redeclarations by renaming closure parameters and local variables that shadow input parameters or previously declared variables. Fixed modules: - bbmap/bbsplit: Renamed 'index' closure parameter to 'idx' in eachWithIndex - bedtools/groupby: Renamed local 'summary_col' to 'summary_col_opt' - mafft/align: Renamed stub section variables with '_stub' suffix - spaceranger/count: Renamed option variables with '_opt' suffix This addresses variable redeclaration errors flagged by nextflow lint in strict syntax mode (NXF_SYNTAX_PARSER=v2). Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Continue fixing variable redeclaration errors for strict syntax mode: - krakentools/extractkrakenreads: Use distinct meta parameter names (meta2, meta3) - mafft/align: Rename local option variables with _opt suffix - blobtk/plot: Add def keyword to script section variables - cellranger/count: Add def keyword to script section variables - diann: Add def keyword to script section variables - flash: Add def keyword to script section variables - scds: Add def keyword to script section variables In strict syntax mode, all variable declarations must use the def keyword explicitly, and variables cannot be redeclared within the same scope. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Continue fixing variable redeclarations: - peka, pureclip: Use distinct meta parameter names for multiple tuple inputs - svtyper/svtyper: Fix duplicate meta2 in inputs, rename vcf shadow variable - svtyper/svtypersso: Rename vcf and fasta shadow variables with _opt suffix - cellrangerarc/mkref: Rename reference_config to reference_config_name - eklipse: Rename ref_gb to ref_gb_path - ichorcna/createpon: Rename exons to exons_opt, add def to prefix - igvreports: Rename fasta to fasta_opt Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Complete fixing all variable redeclaration errors for strict syntax mode: - pureclip: Use distinct meta parameter name (meta3) for third input - jvarkit/sam2tsv, jvarkit/vcf2table: Rename regions_file to regions_opt - hmmer/hmmfetch: Rename index to index_opt - chewbbaca/createschema: Rename prodigal_tf and cds to *_opt - cnvnator/cnvnator: Add def to prefix in script section - crumble: Rename bedout to bedout_opt in both script and stub - gmmdemux: Rename skip and type_report to *_opt - happy/sompy: Rename bams to bams_opt - salsa2: Rename gfa and dup to *_opt - sam2lca/analyze: Rename database to database_path - segemehl/align: Rename reads to reads_opt, add def to prefix - svanalyzer/svbenchmark: Rename bed to bed_opt All 53 variable redeclaration errors have been resolved. Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Addresses review comments from @SPPearce on PR #9684: 1. Remove 'def' from prefix variables used in output blocks: - cnvnator/cnvnator: Remove def from prefix (script & stub) - diann: Remove def from prefix (script & stub) - flash: Remove def from prefix (script & stub) - ichorcna/createpon: Remove def from prefix (script only) - segemehl/align: Remove def from prefix (script only) 2. Remove unnecessary variable declarations: - mafft/align: Remove unused stub variables (args_stub, add_stub, addfragments_stub, addfull_stub, addprofile_stub, addlong_stub) - mafft/align: Remove def from prefix (script) and prefix_stub 3. Improve code formatting: - spaceranger/count: Add backslash continuation between image option variables for better readability All changes verified with: - nextflow lint (all modules pass) - NXF_SYNTAX_PARSER=v2 nextflow inspect (all modules pass) Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
When process inputs use meta2/meta3 to avoid variable redeclaration, the corresponding meta.yml files must document these renamed variables. Updated: - krakentools/extractkrakenreads: meta → meta2, meta3 - peka: meta → meta2 - pureclip: meta → meta2, meta3 - svtyper/svtyper: meta2 → meta3 (for fai input) All modules verified with: - nextflow inspect (standard parser) - NXF_SYNTAX_PARSER=v2 nextflow inspect (strict parser) Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Resolve merge conflicts in: - bbmap/bbsplit: Use _idx for unused loop variable - bedtools/groupby: Use input summary_col with proper syntax - mafft/align: Keep _opt suffix variables to avoid redeclarations Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Remove `def` from prefix variable to make it accessible to the tag directive which is evaluated before the script block. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- hmmer/hmmfetch: Update test data URL from master to 0.9 tag (master branch no longer has the HMM file) - peka: Bump version from 1.0.0 to 1.0.2 (1.0.0 requires numpy 1.17.4 which is no longer available) - crumble: Update test assertions to not use bam() plugin for CRAM (htsjdk doesn't support CRAM 3.1 format) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Update barrnap test data URL from master to 0.9 tag. The master branch no longer has the HMM database files. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- peka: Update versions.yml hash for 1.0.2 - svtyper/svtypersso: Update VCF output hash Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Remove `def` from variables that need to be accessible to templates. Variables defined with `def` are local to the script block and cannot be accessed by template files. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Update to use existing test data from modules branch. The scdownstream branch does not exist. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Update hmmer/hmmrank snapshot with new MD5 hash after barrnap URL fix - Update svtyper/svtypersso snapshot with correct bam test MD5 hash - Fix scds test to use raw_matrix.sce.rds which has required "counts" assay Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
The SCDS test data at scdownstream/samples/SAMN14430801_... doesn't exist. This is a pre-existing issue, not caused by this PR. The module needs proper test data added to nf-core/test-datasets before it can be fixed. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Use existing test data from scdownstream branch (pbmc/SRR28679757_raw_matrix.sce.rds) - Remove def from prefix in both script and stub blocks for template access Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Update svtyper/svtypersso snapshot hashes for bam and bam_vcf_fasta tests - Keep scds prefix fix (remove def) for template access, revert test URL changes as no available test data has required "counts" assay Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
- Use commit-pinned URL for scds test data with counts assay - Update svtyper/svtypersso snapshot hashes for bam and bam_vcf_fasta tests Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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Repeat of #9684 but from a branch, not a fork.