plasmodiumdrugres_lint.md

Nextflow lint results

• Generated: 2026-10-22T00:19:36.117766280Z
• Nextflow version: 26.10.3
• Summary: 21 warnings

⚠️ Warnings

• Warning: modules/local/add_ref_seqs_with_full_genome_ref_fasta/main.nf:23:5: The when section is deprecated -- use conditional logic in the calling workflow, or the process.when config option to disable a process at runtime

      when:
      ^^^^

• Warning: modules/local/add_ref_seqs_with_targeted_ref_fasta/main.nf:23:5: The when section is deprecated -- use conditional logic in the calling workflow, or the process.when config option to disable a process at runtime

      when:
      ^^^^

• Warning: modules/local/concat_tables/main.nf:26:5: The when section is deprecated -- use conditional logic in the calling workflow, or the process.when config option to disable a process at runtime

      when:
      ^^^^

• Warning: modules/local/dcifer_slaf_wrapper/main.nf:22:5: The when section is deprecated -- use conditional logic in the calling workflow, or the process.when config option to disable a process at runtime

      when:
      ^^^^

• Warning: modules/local/estimate_allele_frequency_naive/main.nf:23:5: The when section is deprecated -- use conditional logic in the calling workflow, or the process.when config option to disable a process at runtime

      when:
      ^^^^

• Warning: modules/local/estimate_allele_prevalence_naive/main.nf:22:5: The when section is deprecated -- use conditional logic in the calling workflow, or the process.when config option to disable a process at runtime

      when:
      ^^^^

• Warning: modules/local/estimate_multilocus_prevfreq_naive/main.nf:25:5: The when section is deprecated -- use conditional logic in the calling workflow, or the process.when config option to disable a process at runtime

      when:
      ^^^^

• Warning: modules/local/extract_allele_table/main.nf:23:5: The when section is deprecated -- use conditional logic in the calling workflow, or the process.when config option to disable a process at runtime

      when:
      ^^^^

• Warning: modules/local/extract_allele_table/main.nf:35:15: The use of projectDir in a process is discouraged -- input files should be provided as process inputs

      python3 ${projectDir}/bin/pmo_allele_table_to_specimens.py \
                ^^^^^^^^^^

• Warning: modules/local/extract_panel_info_to_bed/main.nf:23:5: The when section is deprecated -- use conditional logic in the calling workflow, or the process.when config option to disable a process at runtime

      when:
      ^^^^

• Warning: modules/local/extract_population_map_from_pmo/main.nf:24:5: The when section is deprecated -- use conditional logic in the calling workflow, or the process.when config option to disable a process at runtime

      when:
      ^^^^

• Warning: modules/local/fem_wrapper/main.nf:23:5: The when section is deprecated -- use conditional logic in the calling workflow, or the process.when config option to disable a process at runtime

      when:
      ^^^^

• Warning: modules/local/idm_wrapper/main.nf:22:5: The when section is deprecated -- use conditional logic in the calling workflow, or the process.when config option to disable a process at runtime

      when:
      ^^^^

• Warning: modules/local/index_population_assignment/main.nf:23:5: The when section is deprecated -- use conditional logic in the calling workflow, or the process.when config option to disable a process at runtime

      when:
      ^^^^

• Warning: modules/local/merge_tables/main.nf:25:5: The when section is deprecated -- use conditional logic in the calling workflow, or the process.when config option to disable a process at runtime

      when:
      ^^^^

• Warning: modules/local/mlbm_wrapper/main.nf:23:5: The when section is deprecated -- use conditional logic in the calling workflow, or the process.when config option to disable a process at runtime

      when:
      ^^^^

• Warning: modules/local/slaf_from_mhaps_freqs/main.nf:23:5: The when section is deprecated -- use conditional logic in the calling workflow, or the process.when config option to disable a process at runtime

      when:
      ^^^^

• Warning: modules/local/slaf_from_stave_mlaf/main.nf:22:5: The when section is deprecated -- use conditional logic in the calling workflow, or the process.when config option to disable a process at runtime

      when:
      ^^^^

• Warning: modules/local/split_aa_table_by_population/main.nf:24:5: The when section is deprecated -- use conditional logic in the calling workflow, or the process.when config option to disable a process at runtime

      when:
      ^^^^

• Warning: modules/local/split_allele_table_by_population/main.nf:24:5: The when section is deprecated -- use conditional logic in the calling workflow, or the process.when config option to disable a process at runtime

      when:
      ^^^^

• Warning: modules/local/translate_loci_of_interest/main.nf:27:5: The when section is deprecated -- use conditional logic in the calling workflow, or the process.when config option to disable a process at runtime

      when:
      ^^^^