Nextflow lint results

Generated: 2026-03-19T00:25:03.977218403Z
Nextflow version: 26.03.0-edge
Summary: 13 errors, 116 warnings

❌ Errors

Error: modules/nf-core/samtools/sort/main.nf:68:9: reference is already declared

    def reference = fasta ? "--reference ${fasta}" : ""
        ^^^^^^^^^

Error: nextflow.config:383:33: manifest is not defined

\033[0;35m  nf-core/rnafusion ${manifest.version}\033[0m
                                ^^^^^^^^

Error: nextflow.config:386:26: manifest is not defined

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

Error: nextflow.config:386:69: manifest is not defined

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

Error: nextflow.config:386:186: manifest is not defined

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

Error: nextflow.config:395:22: validation is not defined

        beforeText = validation.help.beforeText
                     ^^^^^^^^^^

Error: nextflow.config:396:21: validation is not defined

        afterText = validation.help.afterText
                    ^^^^^^^^^^

Error: tests/nextflow.config:27:38: pipelines_testdata_base_path is not defined

    dfam_hmm                    = "${pipelines_testdata_base_path}/testdata/human/test_starfusion_dfam.hmm"
                                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: tests/nextflow.config:28:38: pipelines_testdata_base_path is not defined

    dfam_h3f                    = "${pipelines_testdata_base_path}/testdata/human/test_starfusion_dfam.hmm.h3f"
                                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: tests/nextflow.config:29:38: pipelines_testdata_base_path is not defined

    dfam_h3i                    = "${pipelines_testdata_base_path}/testdata/human/test_starfusion_dfam.hmm.h3i"
                                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: tests/nextflow.config:30:38: pipelines_testdata_base_path is not defined

    dfam_h3m                    = "${pipelines_testdata_base_path}/testdata/human/test_starfusion_dfam.hmm.h3m"
                                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: tests/nextflow.config:31:38: pipelines_testdata_base_path is not defined

    dfam_h3p                    = "${pipelines_testdata_base_path}/testdata/human/test_starfusion_dfam.hmm.h3p"
                                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: tests/nextflow.config:32:38: pipelines_testdata_base_path is not defined

    pfam_file                   = "${pipelines_testdata_base_path}/testdata/human/Pfam-A.hmm.gz"
                                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

⚠️ Warnings

Warning: modules/nf-core/agat/convertgff2bed/main.nf:36:9: Variable was declared but not used
```
    def args   = task.ext.args   ?: ''
        ^^^^
```
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/cat/fastq/main.nf:22:60: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def readList = reads instanceof List ? reads.collect { it.toString() } : [reads.toString()]
                                                           ^^

Warning: modules/nf-core/cat/fastq/main.nf:58:60: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def readList = reads instanceof List ? reads.collect { it.toString() } : [reads.toString()]
                                                           ^^

Warning: modules/nf-core/ctatsplicing/prepgenomelib/main.nf:23:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/ctatsplicing/prepgenomelib/main.nf:24:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/nf-core/ctatsplicing/prepgenomelib/main.nf:38:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/ctatsplicing/prepgenomelib/main.nf:39:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/nf-core/gatk4/markduplicates/main.nf:33:47: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    def input_list = bam.collect { "--INPUT ${it}" }.join(' ')
                                              ^^
```

Warning: modules/nf-core/gffread/main.nf:26:103: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def extension   = args.contains("-T")       ? 'gtf' : ( ( ['-w', '-x', '-y' ].any { args.contains(it) } ) ? 'fasta' : 'gff3' )
                                                                                                      ^^

Warning: modules/nf-core/gffread/main.nf:30:61: Parameter was not used -- prefix with _ to suppress warning

    def args_sorted = args.replaceAll(/(.*)(-[wxy])(.*)/) { all, pre, param, post -> "$pre $post $param" }.trim()
                                                            ^^^

Warning: modules/nf-core/gffread/main.nf:49:103: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def extension   = args.contains("-T")       ? 'gtf' : ( ( ['-w', '-x', '-y' ].any { args.contains(it) } ) ? 'fasta' : 'gff3' )
                                                                                                      ^^

Warning: modules/nf-core/salmon/quant/main.nf:34:58: Implicit closure parameter is deprecated, declare an explicit parameter instead

    meta.single_end ? [reads].flatten().each { reads1 << it } : reads.eachWithIndex { v, ix -> (ix & 1 ? reads2 : reads1) << v }
                                                         ^^

Warning: modules/nf-core/samtools/sort/main.nf:68:9: Variable was declared but not used

    def reference = fasta ? "--reference ${fasta}" : ""
        ^^^^^^^^^

Warning: modules/nf-core/star/align/main.nf:46:56: Implicit closure parameter is deprecated, declare an explicit parameter instead

    meta.single_end ? [reads].flatten().each{reads1 << it} : reads.eachWithIndex{ v, ix -> ( ix & 1 ? reads2 : reads1) << v }
                                                       ^^

Warning: nextflow.config:386:129: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: subworkflows/local/build_references/main.nf:40:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    def ch_versions = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/local/build_references/main.nf:42:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
    def ch_fasta = Channel.empty()
                   ^^^^^^^
```
Warning: subworkflows/local/build_references/main.nf:43:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
    def ch_gtf   = Channel.empty()
                   ^^^^^^^
```
Warning: subworkflows/local/build_references/main.nf:50:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_fasta = Channel.fromPath(params.fasta).map { that -> [[id:that.Name], that] }
                   ^^^^^^^
```
Warning: subworkflows/local/build_references/main.nf:51:18: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_gtf = Channel.fromPath(params.gtf).map { that -> [[id:that.Name], that] }
                 ^^^^^^^
```
Warning: subworkflows/local/build_references/main.nf:54:18: The use of Channel to access channel factories is deprecated -- use channel instead
```
    def ch_fai = Channel.empty()
                 ^^^^^^^
```
Warning: subworkflows/local/build_references/main.nf:60:18: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_fai = Channel.fromPath(params.fai).map { that -> [[id:that.Name], that] }
                 ^^^^^^^
```
Warning: subworkflows/local/build_references/main.nf:63:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    def ch_hgnc_date = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/local/build_references/main.nf:64:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    def ch_hgnc_ref  = Channel.empty()
                       ^^^^^^^
```

Warning: subworkflows/local/build_references/main.nf:74:27: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_hgnc_ref = Channel.fromPath(params.hgnc_ref).map { that -> [[id:that.Name], that] }
                          ^^^^^^^

Warning: subworkflows/local/build_references/main.nf:75:28: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_hgnc_date = Channel.fromPath(params.hgnc_date).map { that -> [[id:that.Name], that] }
                           ^^^^^^^

Warning: subworkflows/local/build_references/main.nf:79:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    def ch_rrna_interval = Channel.empty()
                           ^^^^^^^
```

Warning: subworkflows/local/build_references/main.nf:96:32: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_rrna_interval = Channel.fromPath(params.rrna_intervals).map { that -> [[id:that.Name], that] }
                               ^^^^^^^

Warning: subworkflows/local/build_references/main.nf:100:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    def ch_refflat = Channel.empty()
                     ^^^^^^^
```

Warning: subworkflows/local/build_references/main.nf:107:26: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_refflat = Channel.fromPath(params.refflat).map { that -> [[id:that.Name], that] }
                         ^^^^^^^

Warning: subworkflows/local/build_references/main.nf:111:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
    def ch_salmon_index = Channel.empty()
                          ^^^^^^^
```
Warning: subworkflows/local/build_references/main.nf:122:35: The use of Channel to access channel factories is deprecated -- use channel instead
```
                ch_salmon_index = Channel.fromPath(params.salmon_index)
                                  ^^^^^^^
```
Warning: subworkflows/local/build_references/main.nf:127:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    def ch_starindex_ref = Channel.empty()
                           ^^^^^^^
```

Warning: subworkflows/local/build_references/main.nf:135:32: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_starindex_ref = Channel.fromPath(params.starindex_ref).map { that -> [[id:that.Name], that] }
                               ^^^^^^^

Warning: subworkflows/local/build_references/main.nf:139:71: The use of Channel to access channel factories is deprecated -- use channel instead

    def ch_arriba_ref_blacklist       = params.arriba_ref_blacklist ? Channel.fromPath(params.arriba_ref_blacklist) : Channel.empty()
                                                                      ^^^^^^^

Warning: subworkflows/local/build_references/main.nf:139:119: The use of Channel to access channel factories is deprecated -- use channel instead

    def ch_arriba_ref_blacklist       = params.arriba_ref_blacklist ? Channel.fromPath(params.arriba_ref_blacklist) : Channel.empty()
                                                                                                                      ^^^^^^^

Warning: subworkflows/local/build_references/main.nf:140:71: The use of Channel to access channel factories is deprecated -- use channel instead

    def ch_arriba_ref_cytobands       = params.arriba_ref_cytobands ? Channel.fromPath(params.arriba_ref_cytobands) : Channel.empty()
                                                                      ^^^^^^^

Warning: subworkflows/local/build_references/main.nf:140:119: The use of Channel to access channel factories is deprecated -- use channel instead

    def ch_arriba_ref_cytobands       = params.arriba_ref_cytobands ? Channel.fromPath(params.arriba_ref_cytobands) : Channel.empty()
                                                                                                                      ^^^^^^^

Warning: subworkflows/local/build_references/main.nf:141:75: The use of Channel to access channel factories is deprecated -- use channel instead

    def ch_arriba_ref_known_fusions   = params.arriba_ref_known_fusions ? Channel.fromPath(params.arriba_ref_known_fusions) : Channel.empty()
                                                                          ^^^^^^^

Warning: subworkflows/local/build_references/main.nf:141:127: The use of Channel to access channel factories is deprecated -- use channel instead

    def ch_arriba_ref_known_fusions   = params.arriba_ref_known_fusions ? Channel.fromPath(params.arriba_ref_known_fusions) : Channel.empty()
                                                                                                                              ^^^^^^^

Warning: subworkflows/local/build_references/main.nf:142:77: The use of Channel to access channel factories is deprecated -- use channel instead

    def ch_arriba_ref_protein_domains = params.arriba_ref_protein_domains ? Channel.fromPath(params.arriba_ref_protein_domains) : Channel.empty()
                                                                            ^^^^^^^

Warning: subworkflows/local/build_references/main.nf:142:131: The use of Channel to access channel factories is deprecated -- use channel instead

    def ch_arriba_ref_protein_domains = params.arriba_ref_protein_domains ? Channel.fromPath(params.arriba_ref_protein_domains) : Channel.empty()
                                                                                                                                  ^^^^^^^

Warning: subworkflows/local/build_references/main.nf:144:59: The use of Channel to access channel factories is deprecated -- use channel instead

    def ch_fusioncatcher_ref = params.fusioncatcher_ref ? Channel.fromPath(params.fusioncatcher_ref).map { it -> [[id:it.name], it] } : Channel.empty()
                                                          ^^^^^^^

Warning: subworkflows/local/build_references/main.nf:144:137: The use of Channel to access channel factories is deprecated -- use channel instead

    def ch_fusioncatcher_ref = params.fusioncatcher_ref ? Channel.fromPath(params.fusioncatcher_ref).map { it -> [[id:it.name], it] } : Channel.empty()
                                                                                                                                        ^^^^^^^

Warning: subworkflows/local/build_references/main.nf:146:29: The use of Channel to access channel factories is deprecated -- use channel instead
```
    def ch_starfusion_ref = Channel.empty()
                            ^^^^^^^
```

Warning: subworkflows/local/build_references/main.nf:154:29: The use of Channel to access channel factories is deprecated -- use channel instead

                pfam_file = Channel.fromPath(params.pfam_file, checkIfExists: true)
                            ^^^^^^^

Warning: subworkflows/local/build_references/main.nf:160:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
                dfam_hmm = Channel.fromPath(params.dfam_hmm, checkIfExists: true)
                           ^^^^^^^
```
Warning: subworkflows/local/build_references/main.nf:161:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
                dfam_h3f = Channel.fromPath(params.dfam_h3f, checkIfExists: true)
                           ^^^^^^^
```
Warning: subworkflows/local/build_references/main.nf:162:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
                dfam_h3i = Channel.fromPath(params.dfam_h3i, checkIfExists: true)
                           ^^^^^^^
```
Warning: subworkflows/local/build_references/main.nf:163:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
                dfam_h3m = Channel.fromPath(params.dfam_h3m, checkIfExists: true)
                           ^^^^^^^
```
Warning: subworkflows/local/build_references/main.nf:164:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
                dfam_h3p = Channel.fromPath(params.dfam_h3p, checkIfExists: true)
                           ^^^^^^^
```

Warning: subworkflows/local/build_references/main.nf:192:33: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_starfusion_ref = Channel.fromPath(params.starfusion_ref).map { it -> [[id:it.name], it] }
                                ^^^^^^^

Warning: subworkflows/local/build_references/main.nf:196:31: The use of Channel to access channel factories is deprecated -- use channel instead
```
    def ch_fusionreport_ref = Channel.empty()
                              ^^^^^^^
```

Warning: subworkflows/local/build_references/main.nf:206:35: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_fusionreport_ref = Channel.fromPath(params.fusionreport_ref).map { that -> [[id:that.Name], that] }
                                  ^^^^^^^

Warning: subworkflows/local/fusioncatcher_workflow/main.nf:17:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_versions   = Channel.empty()
                        ^^^^^^^
```

Warning: subworkflows/local/fusioncatcher_workflow/main.nf:21:54: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_fusioncatcher_fusions = reads.combine(Channel.value(file(fusioncatcher_fusions, checkIfExists:true)))
                                                     ^^^^^^^

Warning: subworkflows/local/fusioninspector_workflow/main.nf:27:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_versions = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/local/fusioninspector_workflow/main.nf:28:35: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_arriba_visualisation = Channel.empty()
                                  ^^^^^^^
```

Warning: subworkflows/local/fusioninspector_workflow/main.nf:33:51: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_whitelist = ch_fusion_list.combine(Channel.value(file(whitelist, checkIfExists:true)))
                                                  ^^^^^^^

Warning: subworkflows/local/qc_workflow/main.nf:18:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_versions = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf:36:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf:73:5: The use of Channel to access channel factories is deprecated -- use channel instead
```
    Channel
    ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf:170:56: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        def setDfamParams = dfamParams.findAll { params[it] }
                                                       ^^
```

Warning: subworkflows/local/utils_nfcore_rnafusion_pipeline/main.nf:228:42: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def strandedness_ok = metas.collect{ it.strandedness }.unique().size == 1
                                         ^^

Warning: subworkflows/nf-core/bam_sort_stats_samtools/main.nf:16:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/nf-core/bam_stats_samtools/main.nf:15:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/nf-core/bam_stringtie_merge/main.nf:12:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions       = Channel.empty()
                        ^^^^^^^
```
Warning: subworkflows/nf-core/bam_stringtie_merge/main.nf:13:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_stringtie_gtfs = Channel.empty()
                        ^^^^^^^
```
Warning: subworkflows/nf-core/bam_stringtie_merge/main.nf:22:16: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { it[1] }
               ^^
```
Warning: subworkflows/nf-core/fastq_align_star/main.nf:20:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf:33:22: Parameter was not used -- prefix with _ to suppress warning
```
    catch (Exception ex) {
                     ^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf:52:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf:53:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    fastqc_raw_html = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf:54:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    fastqc_raw_zip = Channel.empty()
                     ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf:55:15: The use of Channel to access channel factories is deprecated -- use channel instead
```
    umi_log = Channel.empty()
              ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf:56:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
    trim_json = Channel.empty()
                ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf:57:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
    trim_html = Channel.empty()
                ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf:58:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    trim_log = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf:59:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    trim_reads_fail = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf:60:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    trim_reads_merged = Channel.empty()
                        ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf:61:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    fastqc_trim_html = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf:62:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    fastqc_trim_zip = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf:63:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    trim_read_count = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf:64:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    adapter_seq = 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/rnafusion.nf:47:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    def ch_versions = Channel.empty()
                      ^^^^^^^
```
Warning: workflows/rnafusion.nf:48:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    def ch_multiqc_files = Channel.empty()
                           ^^^^^^^
```
Warning: workflows/rnafusion.nf:137:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
        def ch_reads = Channel.empty()
                       ^^^^^^^
```

Warning: workflows/rnafusion.nf:140:55: The use of Channel to access channel factories is deprecated -- use channel instead

        def ch_adapter_fasta = params.adapter_fasta ? Channel.fromPath(params.adapter_fasta).collect() : []
                                                      ^^^^^^^

Warning: workflows/rnafusion.nf:171:29: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_sbwf_fastp_mqc = Channel.empty()
                            ^^^^^^^
```

Warning: workflows/rnafusion.nf:172:71: Implicit closure parameter is deprecated, declare an explicit parameter instead

            .mix(FASTQ_FASTQC_UMITOOLS_FASTP.out.fastqc_raw_zip.map { it[1] })
                                                                      ^^

Warning: workflows/rnafusion.nf:173:72: Implicit closure parameter is deprecated, declare an explicit parameter instead

            .mix(FASTQ_FASTQC_UMITOOLS_FASTP.out.fastqc_trim_zip.map { it[1] })
                                                                       ^^

Warning: workflows/rnafusion.nf:174:66: Implicit closure parameter is deprecated, declare an explicit parameter instead

            .mix(FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_html.map { it[1] })
                                                                 ^^

Warning: workflows/rnafusion.nf:175:66: Implicit closure parameter is deprecated, declare an explicit parameter instead

            .mix(FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_json.map { it[1] })
                                                                 ^^

Warning: workflows/rnafusion.nf:193:88: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_multiqc_files = ch_multiqc_files.mix(SALMON_QUANT.out.json_info.collect{it[1]})
                                                                                       ^^

Warning: workflows/rnafusion.nf:227:99: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_multiqc_files        = ch_multiqc_files.mix(FASTQ_ALIGN_STAR.out.log_final.collect{it[1]}.ifEmpty([]))
                                                                                                  ^^

Warning: workflows/rnafusion.nf:228:100: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_multiqc_files        = ch_multiqc_files.mix(FASTQ_ALIGN_STAR.out.gene_count.collect{it[1]}.ifEmpty([]))
                                                                                                   ^^

Warning: workflows/rnafusion.nf:262:30: The use of Channel to access channel factories is deprecated -- use channel instead

                    .combine(Channel.value(file(params.arriba_fusions, checkIfExists: true)))
                             ^^^^^^^

Warning: workflows/rnafusion.nf:338:30: The use of Channel to access channel factories is deprecated -- use channel instead
```
        def ch_fusion_list = Channel.empty()
                             ^^^^^^^
```
Warning: workflows/rnafusion.nf:339:39: The use of Channel to access channel factories is deprecated -- use channel instead
```
        def ch_fusion_list_filtered = Channel.empty()
                                      ^^^^^^^
```
Warning: workflows/rnafusion.nf:340:38: The use of Channel to access channel factories is deprecated -- use channel instead
```
        def ch_fusionreport_report = Channel.empty()
                                     ^^^^^^^
```
Warning: workflows/rnafusion.nf:341:35: The use of Channel to access channel factories is deprecated -- use channel instead
```
        def ch_fusionreport_csv = Channel.empty()
                                  ^^^^^^^
```

Warning: workflows/rnafusion.nf:396:114: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_multiqc_files = ch_multiqc_files.mix(FUSIONINSPECTOR_WORKFLOW.out.ch_arriba_visualisation.collect{it[1]}.ifEmpty([]))
                                                                                                                 ^^

Warning: workflows/rnafusion.nf:412:92: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.rnaseq_metrics.collect{it[1]})
                                                                                           ^^

Warning: workflows/rnafusion.nf:413:95: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.duplicate_metrics.collect{it[1]})
                                                                                              ^^

Warning: workflows/rnafusion.nf:414:96: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_multiqc_files = ch_multiqc_files.mix(QC_WORKFLOW.out.insertsize_metrics.collect{it[1]})
                                                                                               ^^

Warning: workflows/rnafusion.nf:433:29: The use of Channel to access channel factories is deprecated -- use channel instead
```
    def ch_multiqc_output = Channel.empty()
                            ^^^^^^^
```
Warning: workflows/rnafusion.nf:435:36: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_multiqc_config        = Channel.fromPath(
                                   ^^^^^^^
```
Warning: workflows/rnafusion.nf:438:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.fromPath(params.multiqc_config, checkIfExists: true) :
            ^^^^^^^
```
Warning: workflows/rnafusion.nf:439:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.empty()
            ^^^^^^^
```
Warning: workflows/rnafusion.nf:441:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
            ^^^^^^^
```
Warning: workflows/rnafusion.nf:442:13: The use of Channel to access channel factories is deprecated -- use channel instead
```
            Channel.empty()
            ^^^^^^^
```

Warning: workflows/rnafusion.nf:446:31: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/rnafusion.nf:452:49: The use of Channel to access channel factories is deprecated -- use channel instead

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

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