Nextflow lint results

Generated: 2026-01-16T10:27:25.499886172Z
Nextflow version: 25.12.0-edge
Summary: 2 errors, 90 warnings

❌ Errors

Error: conf/test.config:26:14: pipelines_testdata_base_path is not defined

    input  = pipelines_testdata_base_path + 'reportho/testdata/samplesheet/samplesheet.csv'
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_fasta.config:27:14: pipelines_testdata_base_path is not defined

    input  = pipelines_testdata_base_path + 'reportho/testdata/samplesheet/samplesheet_fasta.csv'
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

⚠️ Warnings

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/diamond/cluster/main.nf:41:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/gawk/main.nf:25:51: Implicit closure parameter is deprecated, declare an explicit parameter instead

    suffix = task.ext.suffix ?: "${input.collect{ it.getExtension()}.get(0)}" // use the first extension of the input files
                                                  ^^

Warning: modules/nf-core/gawk/main.nf:28:32: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    lst_gz    = input.collect{ it.getExtension().endsWith("gz") }
                               ^^
```
Warning: subworkflows/local/get_orthologs.nf:27:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions     = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/local/get_orthologs.nf:28:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_orthogroups  = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/local/get_orthologs.nf:34:16: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        return it
               ^^
```
Warning: subworkflows/local/get_orthologs.nf:160:34: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    id          = ch_query.map { it[1] }
                                 ^^
```
Warning: subworkflows/local/get_orthologs.nf:161:34: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    taxid       = ch_query.map { it[2] }
                                 ^^
```
Warning: subworkflows/local/get_orthologs.nf:162:34: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    exact       = ch_query.map { it[3] }
                                 ^^
```
Warning: subworkflows/local/get_sequences.nf:17:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/get_sequences.nf:31:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_fasta  = Channel.empty()
                ^^^^^^^
```
Warning: subworkflows/local/get_sequences.nf:32:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_hits   = Channel.empty()
                ^^^^^^^
```
Warning: subworkflows/local/get_sequences.nf:33:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_misses = Channel.empty()
                ^^^^^^^
```
Warning: subworkflows/local/merge_ids.nf:15:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/merge_ids.nf:16:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_id_clusters = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/local/merge_ids.nf:32:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            single_entry: it[2] == 1
                          ^^
```
Warning: subworkflows/local/merge_ids.nf:33:31: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            multiple_entries: it[2] > 1
                              ^^
```

Warning: subworkflows/local/merge_ids.nf:40:32: Parameter was not used -- prefix with _ to suppress warning

            .map { meta, file, count -> [ meta, file ] }
                               ^^^^^

Warning: subworkflows/local/merge_ids.nf:50:32: Parameter was not used -- prefix with _ to suppress warning

            .map { meta, file, count -> [ meta, file ] }
                               ^^^^^

Warning: subworkflows/local/report.nf:7:5: Parameter was not used -- prefix with _ to suppress warning
```
    use_centroid
    ^^^^^^^^^^^^
```
Warning: subworkflows/local/report.nf:8:5: Parameter was not used -- prefix with _ to suppress warning
```
    min_score
    ^^^^^^^^^
```
Warning: subworkflows/local/report.nf:22:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions  = Channel.empty()
                   ^^^^^^^
```
Warning: subworkflows/local/report.nf:23:5: Variable was declared but not used
```
    ch_fasta     = ch_seqinfo.map { [it[0], []] }
    ^^^^^^^^
```
Warning: subworkflows/local/report.nf:23:38: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    ch_fasta     = ch_seqinfo.map { [it[0], []] }
                                     ^^
```
Warning: subworkflows/local/report.nf:26:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_seqinfo.map { [it[0], it[3]] },
                          ^^
```
Warning: subworkflows/local/report.nf:26:34: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_seqinfo.map { [it[0], it[3]] },
                                 ^^
```
Warning: subworkflows/local/score_orthologs.nf:23:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

Warning: subworkflows/local/score_orthologs.nf:33:34: Parameter was not used -- prefix with _ to suppress warning

        .map { id, score, query, taxid, exact -> [id, score, query] }
                                 ^^^^^

Warning: subworkflows/local/score_orthologs.nf:33:41: Parameter was not used -- prefix with _ to suppress warning

        .map { id, score, query, taxid, exact -> [id, score, query] }
                                        ^^^^^

Warning: subworkflows/local/score_orthologs.nf:45:39: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    ch_supportsplot = ch_query.map { [it[0], []]}
                                      ^^
```
Warning: subworkflows/local/score_orthologs.nf:46:39: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    ch_vennplot     = ch_query.map { [it[0], []]}
                                      ^^
```
Warning: subworkflows/local/score_orthologs.nf:47:39: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    ch_jaccardplot  = ch_query.map { [it[0], []]}
                                      ^^
```
Warning: subworkflows/local/score_orthologs.nf:70:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .collect { it[1] }
                   ^^
```
Warning: subworkflows/local/score_orthologs.nf:71:30: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [[id: "all"], it] }
                             ^^
```
Warning: subworkflows/local/score_orthologs.nf:81:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_merge_table      = Channel.empty()
                          ^^^^^^^
```
Warning: subworkflows/local/score_orthologs.nf:82:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_aggregated_merge = Channel.empty()
                          ^^^^^^^
```
Warning: subworkflows/local/score_orthologs.nf:94:24: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .collect { it[1] }
                       ^^
```
Warning: subworkflows/local/score_orthologs.nf:95:34: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .map { [[id: "all"], it] }
                                 ^^
```
Warning: subworkflows/local/score_orthologs.nf:123:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .collect { it[1] }
                   ^^
```
Warning: subworkflows/local/score_orthologs.nf:124:30: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [[id: "all"], it] }
                             ^^
```
Warning: subworkflows/local/utils_nfcore_reportho_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_reportho_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_reportho_pipeline/main.nf:42:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

Warning: subworkflows/local/utils_nfcore_reportho_pipeline/main.nf:67:144: Implicit closure parameter is deprecated, declare an explicit parameter instead

    after_text = """${workflow.manifest.doi ? "\n* The pipeline\n" : ""}${workflow.manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${workflow.manifest.doi ? "\n" : ""}
                                                                                                                                               ^^

Warning: subworkflows/local/utils_nfcore_reportho_pipeline/main.nf:104:5: The use of Channel to access channel factories is deprecated -- use channel instead
```
    Channel
    ^^^^^^^
```

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/reportho.nf:32:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions      = Channel.empty()
                       ^^^^^^^
```
Warning: workflows/reportho.nf:33:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_files = Channel.empty()
                       ^^^^^^^
```

Warning: workflows/reportho.nf:34:52: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_fasta_query   = ch_samplesheet_query.map { [it[0], []] }.mix(ch_samplesheet_fasta.map { [it[0], file(it[1])] })
                                                   ^^

Warning: workflows/reportho.nf:34:97: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_fasta_query   = ch_samplesheet_query.map { [it[0], []] }.mix(ch_samplesheet_fasta.map { [it[0], file(it[1])] })
                                                                                                ^^

Warning: workflows/reportho.nf:34:109: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_fasta_query   = ch_samplesheet_query.map { [it[0], []] }.mix(ch_samplesheet_fasta.map { [it[0], file(it[1])] })
                                                                                                            ^^

Warning: workflows/reportho.nf:36:42: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_oma_groups    = params.oma_path ? Channel.value(file(params.oma_path)) : Channel.empty()
                                         ^^^^^^^

Warning: workflows/reportho.nf:36:81: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_oma_groups    = params.oma_path ? Channel.value(file(params.oma_path)) : Channel.empty()
                                                                                ^^^^^^^

Warning: workflows/reportho.nf:37:50: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_oma_uniprot   = params.oma_uniprot_path ? Channel.value(file(params.oma_uniprot_path)) : Channel.empty()
                                                 ^^^^^^^

Warning: workflows/reportho.nf:37:97: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_oma_uniprot   = params.oma_uniprot_path ? Channel.value(file(params.oma_uniprot_path)) : Channel.empty()
                                                                                                ^^^^^^^

Warning: workflows/reportho.nf:38:50: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_oma_ensembl   = params.oma_ensembl_path ? Channel.value(file(params.oma_ensembl_path)) : Channel.empty()
                                                 ^^^^^^^

Warning: workflows/reportho.nf:38:97: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_oma_ensembl   = params.oma_ensembl_path ? Channel.value(file(params.oma_ensembl_path)) : Channel.empty()
                                                                                                ^^^^^^^

Warning: workflows/reportho.nf:39:49: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_oma_refseq    = params.oma_refseq_path ? Channel.value(file(params.oma_refseq_path)) : Channel.empty()
                                                ^^^^^^^

Warning: workflows/reportho.nf:39:95: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_oma_refseq    = params.oma_refseq_path ? Channel.value(file(params.oma_refseq_path)) : Channel.empty()
                                                                                              ^^^^^^^

Warning: workflows/reportho.nf:40:46: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_panther       = params.panther_path ? Channel.value(file(params.panther_path)) : Channel.empty()
                                             ^^^^^^^

Warning: workflows/reportho.nf:40:89: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_panther       = params.panther_path ? Channel.value(file(params.panther_path)) : Channel.empty()
                                                                                        ^^^^^^^

Warning: workflows/reportho.nf:41:45: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_eggnog        = params.eggnog_path ? Channel.value(file(params.eggnog_path)) : Channel.empty()
                                            ^^^^^^^

Warning: workflows/reportho.nf:41:87: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_eggnog        = params.eggnog_path ? Channel.value(file(params.eggnog_path)) : Channel.empty()
                                                                                      ^^^^^^^

Warning: workflows/reportho.nf:42:51: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_eggnog_idmap  = params.eggnog_idmap_path ? Channel.value(file(params.eggnog_idmap_path)) : Channel.empty()
                                                  ^^^^^^^

Warning: workflows/reportho.nf:42:99: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_eggnog_idmap  = params.eggnog_idmap_path ? Channel.value(file(params.eggnog_idmap_path)) : Channel.empty()
                                                                                                  ^^^^^^^

Warning: workflows/reportho.nf:44:52: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_seqhits       = ch_samplesheet_query.map { [it[0], []] }
                                                   ^^

Warning: workflows/reportho.nf:45:52: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_seqmisses     = ch_samplesheet_query.map { [it[0], []] }
                                                   ^^

Warning: workflows/reportho.nf:61:43: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    ch_seqs = ch_samplesheet_query.map { [it[0], []] }
                                          ^^
```
Warning: workflows/reportho.nf:77:41: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    ch_id_map   = ch_fasta_query.map { [it[0], []] }
                                        ^^
```
Warning: workflows/reportho.nf:78:41: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    ch_clusters = ch_fasta_query.map { [it[0], []] }
                                        ^^
```

Warning: workflows/reportho.nf:103:5: Variable was declared but not used

    ch_samplesheet = ch_samplesheet_query.mix (ch_samplesheet_fasta)
    ^^^^^^^^^^^^^^

Warning: workflows/reportho.nf:105:87: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_multiqc_files = ch_multiqc_files.mix(SCORE_ORTHOLOGS.out.aggregated_stats.map {it[1]})
                                                                                      ^^

Warning: workflows/reportho.nf:106:86: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_multiqc_files = ch_multiqc_files.mix(SCORE_ORTHOLOGS.out.aggregated_hits.map {it[1]})
                                                                                     ^^

Warning: workflows/reportho.nf:107:87: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_multiqc_files = ch_multiqc_files.mix(SCORE_ORTHOLOGS.out.aggregated_merge.map {it[1]})
                                                                                      ^^

Warning: workflows/reportho.nf:123:54: Implicit closure parameter is deprecated, declare an explicit parameter instead

            SCORE_ORTHOLOGS.out.supports_plot.map { [it[0], it[2]]},
                                                     ^^

Warning: workflows/reportho.nf:123:61: Implicit closure parameter is deprecated, declare an explicit parameter instead

            SCORE_ORTHOLOGS.out.supports_plot.map { [it[0], it[2]]},
                                                            ^^

Warning: workflows/reportho.nf:124:50: Implicit closure parameter is deprecated, declare an explicit parameter instead

            SCORE_ORTHOLOGS.out.venn_plot.map { [it[0], it[2]]},
                                                 ^^

Warning: workflows/reportho.nf:124:57: Implicit closure parameter is deprecated, declare an explicit parameter instead

            SCORE_ORTHOLOGS.out.venn_plot.map { [it[0], it[2]]},
                                                        ^^

Warning: workflows/reportho.nf:125:53: Implicit closure parameter is deprecated, declare an explicit parameter instead

            SCORE_ORTHOLOGS.out.jaccard_plot.map { [it[0], it[2]]},
                                                    ^^

Warning: workflows/reportho.nf:125:60: Implicit closure parameter is deprecated, declare an explicit parameter instead

            SCORE_ORTHOLOGS.out.jaccard_plot.map { [it[0], it[2]]},
                                                           ^^

Warning: workflows/reportho.nf:151:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_report = Channel.empty()
                        ^^^^^^^
```
Warning: workflows/reportho.nf:153:36: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_multiqc_config        = Channel.fromPath(
                                   ^^^^^^^
```
Warning: workflows/reportho.nf:157:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.fromPath(params.multiqc_config, checkIfExists: true) :
            ^^^^^^^
```
Warning: workflows/reportho.nf:158:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.empty()
            ^^^^^^^
```
Warning: workflows/reportho.nf:161:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
            ^^^^^^^
```
Warning: workflows/reportho.nf:162:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.empty()
            ^^^^^^^
```

Warning: workflows/reportho.nf:166:31: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params))
                              ^^^^^^^

Warning: workflows/reportho.nf:172:49: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_methods_description                = Channel.value(
                                                ^^^^^^^

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Nextflow lint results

❌ Errors

⚠️ Warnings

FilesExpand file tree

reportho_lint.md

Latest commit

History

reportho_lint.md

File metadata and controls

Nextflow lint results

❌ Errors

⚠️ Warnings