Nextflow lint results

Generated: 2026-03-24T10:44:51.643175222Z
Nextflow version: 26.03.0-edge
Summary: 52 warnings

⚠️ Warnings

Warning: modules/local/btk/input/main.nf:27:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    ].findAll { it.value } // filter out falsy values (null, false, "", [], etc)
                ^^
```
Warning: modules/local/cpretext/input/main.nf:22:17: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    ].findAll { it.value } // filter out falsy values (null, false, "", [], etc)
                ^^
```
Warning: modules/nf-core/cat/cat/main.nf:23:40: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def file_list = files_in.collect { it.toString() }
                                       ^^
```
Warning: modules/nf-core/cat/cat/main.nf:58:42: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def file_list   = files_in.collect { it.toString() }
                                         ^^
```
Warning: modules/nf-core/gunzip/main.nf:43:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/merquryfk/merquryfk/main.nf:42:9: Variable was declared but not used

    def mat_ktab = matktab ? "${matktab.find{ it.toString().endsWith(".ktab") }}" : ''
        ^^^^^^^^

Warning: modules/nf-core/merquryfk/merquryfk/main.nf:42:47: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def mat_ktab = matktab ? "${matktab.find{ it.toString().endsWith(".ktab") }}" : ''
                                              ^^

Warning: modules/nf-core/merquryfk/merquryfk/main.nf:43:9: Variable was declared but not used

    def pat_ktab = patktab ? "${patktab.find{ it.toString().endsWith(".ktab") }}" : ''
        ^^^^^^^^

Warning: modules/nf-core/merquryfk/merquryfk/main.nf:43:47: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def pat_ktab = patktab ? "${patktab.find{ it.toString().endsWith(".ktab") }}" : ''
                                              ^^

Warning: subworkflows/local/utils_nfcore_ear_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_ear_pipeline/main.nf:39:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/yaml_input/main.nf:10:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/yaml_input/main.nf:17:15: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_hap1 = Channel.fromPath(inputs.reference_hap1, checkIfExists: true)
              ^^^^^^^
```

Warning: subworkflows/local/yaml_input/main.nf:21:11: The use of Channel to access channel factories is deprecated -- use channel instead

        ? Channel.fromPath(inputs.reference_hap2, checkIfExists: true).map { fasta -> tuple([id: inputs.assembly_id, file: 'hap2'], fasta) }
          ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:22:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        : Channel.empty()
          ^^^^^^^
```

Warning: subworkflows/local/yaml_input/main.nf:25:11: The use of Channel to access channel factories is deprecated -- use channel instead

        ? Channel.fromPath(inputs.reference_haplotigs, checkIfExists: true).map { fasta -> tuple([id: inputs.assembly_id, file: 'haplotigs'], fasta) }
          ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:26:11: The use of Channel to access channel factories is deprecated -- use channel instead
```
        : Channel.empty()
          ^^^^^^^
```
Warning: subworkflows/local/yaml_input/main.nf:51:31: The use of Channel to access channel factories is deprecated -- use channel instead
```
    sample_id               = Channel.of([id: inputs.assembly_id])
                              ^^^^^^^
```

Warning: subworkflows/local/yaml_input/main.nf:52:54: The use of Channel to access channel factories is deprecated -- use channel instead

    longread_type           = inputs.longread.type ? Channel.of(inputs.longread.type): Channel.empty()
                                                     ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:52:88: The use of Channel to access channel factories is deprecated -- use channel instead

    longread_type           = inputs.longread.type ? Channel.of(inputs.longread.type): Channel.empty()
                                                                                       ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:53:53: The use of Channel to access channel factories is deprecated -- use channel instead

    longread_dir            = inputs.longread.dir ? Channel.fromPath(inputs.longread.dir, checkIfExists: true, type: 'dir') : Channel.empty()
                                                    ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:53:127: The use of Channel to access channel factories is deprecated -- use channel instead

    longread_dir            = inputs.longread.dir ? Channel.fromPath(inputs.longread.dir, checkIfExists: true, type: 'dir') : Channel.empty()
                                                                                                                              ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:58:64: The use of Channel to access channel factories is deprecated -- use channel instead

    cpretext_aligner        = inputs.curationpretext.aligner ? Channel.of(inputs.curationpretext.aligner) : Channel.empty()
                                                               ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:58:109: The use of Channel to access channel factories is deprecated -- use channel instead

    cpretext_aligner        = inputs.curationpretext.aligner ? Channel.of(inputs.curationpretext.aligner) : Channel.empty()
                                                                                                            ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:59:71: The use of Channel to access channel factories is deprecated -- use channel instead

    cpretext_telomere_motif = inputs.curationpretext.telomere_motif ? Channel.of([id: inputs.assembly_id], inputs.curationpretext.telomere_motif) : Channel.empty()
                                                                      ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:59:149: The use of Channel to access channel factories is deprecated -- use channel instead

    cpretext_telomere_motif = inputs.curationpretext.telomere_motif ? Channel.of([id: inputs.assembly_id], inputs.curationpretext.telomere_motif) : Channel.empty()
                                                                                                                                                    ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:60:64: The use of Channel to access channel factories is deprecated -- use channel instead

    cpretext_hic_dir        = inputs.curationpretext.hic_dir ? Channel.fromPath(inputs.curationpretext.hic_dir, checkIfExists: true, type: 'dir') : Channel.empty()
                                                               ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:60:149: The use of Channel to access channel factories is deprecated -- use channel instead

    cpretext_hic_dir        = inputs.curationpretext.hic_dir ? Channel.fromPath(inputs.curationpretext.hic_dir, checkIfExists: true, type: 'dir') : Channel.empty()
                                                                                                                                                    ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:62:61: The use of Channel to access channel factories is deprecated -- use channel instead

    fastk_hist              = inputs.merquryfk.fastk_hist ? Channel.fromPath(inputs.merquryfk.fastk_hist, checkIfExists: true) : Channel.empty()
                                                            ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:62:130: The use of Channel to access channel factories is deprecated -- use channel instead

    fastk_hist              = inputs.merquryfk.fastk_hist ? Channel.fromPath(inputs.merquryfk.fastk_hist, checkIfExists: true) : Channel.empty()
                                                                                                                                 ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:63:61: The use of Channel to access channel factories is deprecated -- use channel instead

    fastk_ktab              = inputs.merquryfk.fastk_ktab ? Channel.fromPath(inputs.merquryfk.fastk_ktab, hidden: true).collect()  : Channel.empty() // Collect as a list
                                                            ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:63:134: The use of Channel to access channel factories is deprecated -- use channel instead

    fastk_ktab              = inputs.merquryfk.fastk_ktab ? Channel.fromPath(inputs.merquryfk.fastk_ktab, hidden: true).collect()  : Channel.empty() // Collect as a list
                                                                                                                                     ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:65:56: The use of Channel to access channel factories is deprecated -- use channel instead

    btk_nt_database         = inputs.btk.nt_database ? Channel.fromPath(inputs.btk.nt_database, checkIfExists: true) : Channel.empty()
                                                       ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:65:120: The use of Channel to access channel factories is deprecated -- use channel instead

    btk_nt_database         = inputs.btk.nt_database ? Channel.fromPath(inputs.btk.nt_database, checkIfExists: true) : Channel.empty()
                                                                                                                       ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:66:63: The use of Channel to access channel factories is deprecated -- use channel instead

    btk_nt_database_prefix  = inputs.btk.nt_database_prefix ? Channel.of(inputs.btk.nt_database_prefix) : Channel.empty()
                                                              ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:66:107: The use of Channel to access channel factories is deprecated -- use channel instead

    btk_nt_database_prefix  = inputs.btk.nt_database_prefix ? Channel.of(inputs.btk.nt_database_prefix) : Channel.empty()
                                                                                                          ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:67:69: The use of Channel to access channel factories is deprecated -- use channel instead

    btk_nr_diamond_database = inputs.btk.diamond_nr_database_path ? Channel.fromPath(inputs.btk.diamond_nr_database_path, checkIfExists: true) : Channel.empty()
                                                                    ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:67:146: The use of Channel to access channel factories is deprecated -- use channel instead

    btk_nr_diamond_database = inputs.btk.diamond_nr_database_path ? Channel.fromPath(inputs.btk.diamond_nr_database_path, checkIfExists: true) : Channel.empty()
                                                                                                                                                 ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:68:74: The use of Channel to access channel factories is deprecated -- use channel instead

    btk_un_diamond_database = inputs.btk.diamond_uniprot_database_path ? Channel.fromPath(inputs.btk.diamond_uniprot_database_path, checkIfExists: true) : Channel.empty()
                                                                         ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:68:156: The use of Channel to access channel factories is deprecated -- use channel instead

    btk_un_diamond_database = inputs.btk.diamond_uniprot_database_path ? Channel.fromPath(inputs.btk.diamond_uniprot_database_path, checkIfExists: true) : Channel.empty()
                                                                                                                                                           ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:69:63: The use of Channel to access channel factories is deprecated -- use channel instead

    btk_ncbi_taxonomy_path  = inputs.btk.ncbi_taxonomy_path ? Channel.fromPath(inputs.btk.ncbi_taxonomy_path, checkIfExists: true) : Channel.empty()
                                                              ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:69:134: The use of Channel to access channel factories is deprecated -- use channel instead

    btk_ncbi_taxonomy_path  = inputs.btk.ncbi_taxonomy_path ? Channel.fromPath(inputs.btk.ncbi_taxonomy_path, checkIfExists: true) : Channel.empty()
                                                                                                                                     ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:70:50: The use of Channel to access channel factories is deprecated -- use channel instead

    btk_taxid               = inputs.btk.taxid ? Channel.of(inputs.btk.taxid) : Channel.empty()
                                                 ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:70:81: The use of Channel to access channel factories is deprecated -- use channel instead

    btk_taxid               = inputs.btk.taxid ? Channel.of(inputs.btk.taxid) : Channel.empty()
                                                                                ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:71:58: The use of Channel to access channel factories is deprecated -- use channel instead

    btk_gca_accession       = inputs.btk.gca_accession ? Channel.of(inputs.btk.gca_accession) : Channel.empty()
                                                         ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:71:97: The use of Channel to access channel factories is deprecated -- use channel instead

    btk_gca_accession       = inputs.btk.gca_accession ? Channel.of(inputs.btk.gca_accession) : Channel.empty()
                                                                                                ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:72:53: The use of Channel to access channel factories is deprecated -- use channel instead

    busco_lineages          = inputs.btk.lineages ? Channel.of(inputs.btk.lineages) : Channel.empty()
                                                    ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:72:87: The use of Channel to access channel factories is deprecated -- use channel instead

    busco_lineages          = inputs.btk.lineages ? Channel.of(inputs.btk.lineages) : Channel.empty()
                                                                                      ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:73:51: The use of Channel to access channel factories is deprecated -- use channel instead

    busco_config            = inputs.btk.config ? Channel.fromPath(inputs.btk.config, checkIfExists: true) : Channel.empty()
                                                  ^^^^^^^

Warning: subworkflows/local/yaml_input/main.nf:73:110: The use of Channel to access channel factories is deprecated -- use channel instead

    busco_config            = inputs.btk.config ? Channel.fromPath(inputs.btk.config, checkIfExists: true) : Channel.empty()
                                                                                                             ^^^^^^^

Warning: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:101:98: The use of Channel to access channel factories is deprecated -- use channel instead

    return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML()))
                                                                                                 ^^^^^^^

Warning: workflows/ear.nf:51:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

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