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methylarray_lint.md

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Nextflow lint results

  • Generated: 2026-02-18T00:22:28.714109033Z
  • Nextflow version: 26.01.1-edge
  • Summary: 4 errors, 19 warnings

❌ Errors

  • Error: conf/test_full.config:22:29: Unexpected character: '#'

        remove_xreactive = true # TODO: removes too many probes
                            ^

  • Error: modules/local/remove_confounding_probes/main.nf:10:15: samplesheet_name is already declared

        tuple val(samplesheet_name), path(bVals)
              ^^^^^^^^^^^^^^^^

  • Error: modules/local/remove_confounding_probes/main.nf:11:15: samplesheet_name is already declared

        tuple val(samplesheet_name), path(RData_REMOVESNP)
              ^^^^^^^^^^^^^^^^

  • Error: modules/local/remove_sex_chromosomes/main.nf:10:15: samplesheet_name is already declared

        tuple val(samplesheet_name), path(RData_rgSet)
              ^^^^^^^^^^^^^^^^

⚠️ Warnings

  • Warning: modules/local/remove_confounding_probes/main.nf:9:15: Variable was declared but not used

        tuple val(samplesheet_name), path(mVals)
              ^^^^^^^^^^^^^^^^

  • Warning: modules/local/remove_confounding_probes/main.nf:10:15: Variable was declared but not used

        tuple val(samplesheet_name), path(bVals)
              ^^^^^^^^^^^^^^^^

  • Warning: modules/local/remove_sex_chromosomes/main.nf:9:15: Variable was declared but not used

        tuple val(samplesheet_name), path(RData_SNPPROBES)
              ^^^^^^^^^^^^^^^^

  • Warning: modules/local/xreactive_probes_find_remove/main.nf:25:5: Variable was declared but not used

        chrom_number = params.xreactive_chr_targets ? params.xreactive_chr_targets : 'all'
    ^^^^^^^^^^^^

  • Warning: subworkflows/local/utils_nfcore_methylarray_pipeline/main.nf:32:5: Parameter was not used -- prefix with _ to suppress warning

        monochrome_logs   // boolean: Do not use coloured log outputs
    ^^^^^^^^^^^^^^^

  • Warning: subworkflows/local/utils_nfcore_methylarray_pipeline/main.nf:35:5: Parameter was not used -- prefix with _ to suppress warning

        input             //  string: Path to input samplesheet
    ^^^^^

  • Warning: subworkflows/local/utils_nfcore_methylarray_pipeline/main.nf:105:11: The use of Channel to access channel factories is deprecated -- use channel instead

            ? Channel.fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) : Channel.empty()
          ^^^^^^^

  • Warning: subworkflows/local/utils_nfcore_methylarray_pipeline/main.nf:105:105: The use of Channel to access channel factories is deprecated -- use channel instead

            ? Channel.fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json")) : Channel.empty()
                                                                                                        ^^^^^^^

  • Warning: workflows/methylarray.nf:42:5: Variable was declared but not used

        ch_preprocessed_files = channel.empty()
    ^^^^^^^^^^^^^^^^^^^^^

  • Warning: workflows/methylarray.nf:49:26: Parameter was not used -- prefix with _ to suppress warning

            .map{ meta, red, green -> red.getName().replaceFirst(/_Red\.idat(?:\.gz)?$/,"") + "," + meta.id }
                         ^^^^^

  • Warning: workflows/methylarray.nf:54:22: Parameter was not used -- prefix with _ to suppress warning

            ch_input.map{meta, red, green -> [red, green]}.collect(),
                     ^^^^

  • Warning: workflows/methylarray.nf:90:22: The use of Channel to access channel factories is deprecated -- use channel instead

        final_bVals_ch = Channel.empty()
                     ^^^^^^^

  • Warning: workflows/methylarray.nf:91:24: The use of Channel to access channel factories is deprecated -- use channel instead

        current_bVals_ch = Channel.empty()
                       ^^^^^^^

  • Warning: workflows/methylarray.nf:95:135: Implicit closure parameter is deprecated, declare an explicit parameter instead

            current_bVals_ch = params.remove_snp_probes ? REMOVE_SNP_PROBES.out.csv_bVals : XREACTIVE_PROBES_FIND_REMOVE.out.csv.filter { it == "bVals_noXprob.csv" }
                                                                                                                                      ^^

  • Warning: workflows/methylarray.nf:96:135: Implicit closure parameter is deprecated, declare an explicit parameter instead

            current_mVals_ch = params.remove_snp_probes ? REMOVE_SNP_PROBES.out.csv_mVals : XREACTIVE_PROBES_FIND_REMOVE.out.csv.filter { it == "mVals_noXprob.csv" }
                                                                                                                                      ^^

  • Warning: workflows/methylarray.nf:97:137: Implicit closure parameter is deprecated, declare an explicit parameter instead

            current_mSetSqFlt_ch = params.remove_snp_probes ? REMOVE_SNP_PROBES.out.rdata : XREACTIVE_PROBES_FIND_REMOVE.out.rdata.filter { it == "mSetSqFlt_noXprob.RData" }
                                                                                                                                        ^^

  • Warning: workflows/methylarray.nf:161:30: Parameter was not used -- prefix with _ to suppress warning

            ch_input.map { meta, red, green -> "${meta.id},${meta.group}" }
                             ^^^

  • Warning: workflows/methylarray.nf:161:35: Parameter was not used -- prefix with _ to suppress warning

            ch_input.map { meta, red, green -> "${meta.id},${meta.group}" }
                                  ^^^^^

  • Warning: workflows/methylarray.nf:204:26: The use of Channel to access channel factories is deprecated -- use channel instead

        def topic_versions = Channel.topic("versions")
                         ^^^^^^^