Nextflow lint results

Generated: 2026-06-16T20:20:15.714039682Z
Nextflow version: 26.04.3
Summary: 160 warnings

⚠️ Warnings

Warning: main.nf:49:74: Implicit closure parameter is deprecated, declare an explicit parameter instead

    callers = params.peakcaller ? params.peakcaller.split(',').collect { it.trim().toLowerCase() } : ['seacr']
                                                                         ^^

Warning: main.nf:59:29: The use of Channel to access channel factories is deprecated -- use channel instead

        params.blacklist ? (Channel.from(file(params.blacklist, checkIfExists: true))) : Channel.empty(),
                            ^^^^^^^

Warning: main.nf:59:90: The use of Channel to access channel factories is deprecated -- use channel instead

        params.blacklist ? (Channel.from(file(params.blacklist, checkIfExists: true))) : Channel.empty(),
                                                                                         ^^^^^^^

Warning: main.nf:67:5: Emit name should be omitted when there is only one emit

    multiqc_report = CUTANDRUN.out.multiqc_report // channel: /path/to/multiqc_report.html
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Warning: modules/local/python/igv_session.nf:33:36: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        file_list = beds.collect { it.toString() }.sort()
                                   ^^
```
Warning: modules/local/python/igv_session.nf:34:47: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        file_list += secondary_beds.collect { it.toString() }.sort()
                                              ^^
```
Warning: modules/local/python/igv_session.nf:35:39: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        file_list += bigwig.collect { it.toString() }.sort()
                                      ^^
```

Warning: modules/local/python/igv_session.nf:38:64: Implicit closure parameter is deprecated, declare an explicit parameter instead

        file_list = (bigwig + secondary_beds + beds).collect { it.toString() }.sort()
                                                               ^^

Warning: modules/nf-core/cat/fastq/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/cat/fastq/main.nf:23:59: 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:54:59: 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/custom/getchromsizes/main.nf:23:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/gunzip/main.nf:43:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/macs2/callpeak/main.nf:33:40: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        def id = args_list.findIndexOf{it=='--format'}
                                       ^^
```
Warning: modules/nf-core/samtools/flagstat/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/samtools/idxstats/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/samtools/stats/main.nf:22:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/ucsc/bedclip/main.nf:23:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/ucsc/bedgraphtobigwig/main.nf:23:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: subworkflows/local/align_bowtie2.nf:19:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/align_bowtie2.nf:24:34: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    ch_index = index.map { [[id: it.baseName], it] }
                                 ^^
```
Warning: subworkflows/local/align_bowtie2.nf:24:48: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    ch_index = index.map { [[id: it.baseName], it] }
                                               ^^
```
Warning: subworkflows/local/align_bowtie2.nf:27:28: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_index.collect { it[1] },
                           ^^
```
Warning: subworkflows/local/align_bowtie2.nf:36:50: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    ch_spikein_index = spikein_index.map { [[id: it.baseName], it] }
                                                 ^^
```

Warning: subworkflows/local/align_bowtie2.nf:36:64: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_spikein_index = spikein_index.map { [[id: it.baseName], it] }
                                                               ^^

Warning: subworkflows/local/align_bowtie2.nf:39:36: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_spikein_index.collect { it[1] },
                                   ^^
```
Warning: subworkflows/local/consensus_peaks.nf:14:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/deduplicate_linear.nf:23:14: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_bam = Channel.empty()
             ^^^^^^^
```
Warning: subworkflows/local/deduplicate_linear.nf:24:18: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_metrics = Channel.empty()
                 ^^^^^^^
```
Warning: subworkflows/local/deduplicate_linear.nf:25:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/deduplicate_linear.nf:26:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_linear_duplicates = Channel.empty()
                           ^^^^^^^
```
Warning: subworkflows/local/deeptools_qc.nf:17:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/extract_fragments.nf:15:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/extract_metadata_awk.nf:15:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/extract_metadata_awk.nf:16:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_metadata = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/fastqc_trimgalore.nf:15:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/fastqc_trimgalore.nf:17:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    fastqc_html = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/fastqc_trimgalore.nf:18:18: The use of Channel to access channel factories is deprecated -- use channel instead
```
    fastqc_zip = Channel.empty()
                 ^^^^^^^
```
Warning: subworkflows/local/fastqc_trimgalore.nf:25:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
    trim_html = Channel.empty()
                ^^^^^^^
```
Warning: subworkflows/local/fastqc_trimgalore.nf:26:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    trim_zip = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/fastqc_trimgalore.nf:27:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    trim_log = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/mark_duplicates_picard.nf:18:14: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_bam = Channel.empty()
             ^^^^^^^
```
Warning: subworkflows/local/mark_duplicates_picard.nf:19:14: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_bai = Channel.empty()
             ^^^^^^^
```
Warning: subworkflows/local/mark_duplicates_picard.nf:20:18: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_metrics = Channel.empty()
                 ^^^^^^^
```
Warning: subworkflows/local/mark_duplicates_picard.nf:21:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_stats = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/mark_duplicates_picard.nf:22:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_flagstat = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/mark_duplicates_picard.nf:23:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_idxstats = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/mark_duplicates_picard.nf:24:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/peak_qc.nf:28:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:30:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:31:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_spikein_fasta = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:41:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_fasta = Channel.from(file(params.fasta)).map { row -> [[id: "fasta"], row] }
                   ^^^^^^^
```

Warning: subworkflows/local/prepare_genome.nf:53:32: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_spikein_fasta = Channel.from(file(params.spikein_fasta)).map { row -> [[id: "spikein_fasta"], row] }
                               ^^^^^^^

Warning: subworkflows/local/prepare_genome.nf:61:14: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_gtf = Channel.empty()
             ^^^^^^^
```

Warning: subworkflows/local/prepare_genome.nf:63:61: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_gtf = GUNZIP_GTF([[:], params.gtf]).gunzip.map { it[1] }
                                                            ^^

Warning: subworkflows/local/prepare_genome.nf:67:18: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_gtf = Channel.from(file(params.gtf))
                 ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:70:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_gene_bed = Channel.empty()
                  ^^^^^^^
```

Warning: subworkflows/local/prepare_genome.nf:76:75: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_gene_bed = GUNZIP_BED([[:], params.gene_bed]).gunzip.map { it[1] }
                                                                          ^^

Warning: subworkflows/local/prepare_genome.nf:80:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_gene_bed = Channel.from(file(params.gene_bed))
                          ^^^^^^^
```

Warning: subworkflows/local/prepare_genome.nf:128:62: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_chrom_sizes = TARGET_CHROMSIZES(ch_fasta).sizes.map { it[1] }
                                                             ^^

Warning: subworkflows/local/prepare_genome.nf:134:79: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_spikein_chrom_sizes = SPIKEIN_CHROMSIZES(ch_spikein_fasta).sizes.map { it[1] }
                                                                              ^^

Warning: subworkflows/local/prepare_genome.nf:139:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_bt2_index = Channel.empty()
                   ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:140:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_bt2_spikein_index = Channel.empty()
                           ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:174:33: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_genome_include_regions = Channel.empty()
                                ^^^^^^^
```
Warning: subworkflows/local/prepare_peakcalling.nf:21:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/prepare_peakcalling.nf:22:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_bedgraph = Channel.empty()
                  ^^^^^^^
```

Warning: subworkflows/local/prepare_peakcalling.nf:42:49: Implicit closure parameter is deprecated, declare an explicit parameter instead

                def denominator = row[3].find { it.key == "bt2_total_aligned" }?.value.toInteger()
                                                ^^

Warning: subworkflows/local/prepare_peakcalling.nf:77:25: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                .map { [it[0].id, it[0].group, it[2]] }
                        ^^
```
Warning: subworkflows/local/prepare_peakcalling.nf:77:35: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                .map { [it[0].id, it[0].group, it[2]] }
                                  ^^
```
Warning: subworkflows/local/prepare_peakcalling.nf:77:48: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                .map { [it[0].id, it[0].group, it[2]] }
                                               ^^
```
Warning: subworkflows/local/prepare_peakcalling.nf:157:25: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                .map { [it[0].id, it[0].group, it[3]] }
                        ^^
```
Warning: subworkflows/local/prepare_peakcalling.nf:157:35: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                .map { [it[0].id, it[0].group, it[3]] }
                                  ^^
```
Warning: subworkflows/local/prepare_peakcalling.nf:157:48: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                .map { [it[0].id, it[0].group, it[3]] }
                                               ^^
```
Warning: subworkflows/local/samtools_view_sort_stats.nf:17:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_cutandrun_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_cutandrun_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_cutandrun_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_cutandrun_pipeline/main.nf:101:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_samplesheet = Channel.fromList(processSamplesheet(rows, params.use_control))
                     ^^^^^^^
```

Warning: subworkflows/local/utils_nfcore_cutandrun_pipeline/main.nf:188:46: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def referenced_controls = rows.collect { it[0].control_group }.findAll { it } as Set
                                             ^^

Warning: subworkflows/local/utils_nfcore_cutandrun_pipeline/main.nf:188:78: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def referenced_controls = rows.collect { it[0].control_group }.findAll { it } as Set
                                                                             ^^

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/utils_nextflow_pipeline/main.nf:43:5: Emit name should be omitted when there is only one emit
```
    dummy_emit = true
    ^^^^^^^^^^^^^^^
```
Warning: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:16:5: Variable was declared but not used
```
    valid_config = checkConfigProvided()
    ^^^^^^^^^^^^
```
Warning: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:20:5: Emit name should be omitted when there is only one emit
```
    valid_config
    ^^^^^^^^^^^^
```

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: subworkflows/nf-core/utils_nfschema_plugin/main.nf:72:5: Emit name should be omitted when there is only one emit
```
    dummy_emit = true
    ^^^^^^^^^^^^^^^
```
Warning: workflows/cutandrun.nf:94:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    def ch_versions = Channel.empty()
                      ^^^^^^^
```
Warning: workflows/cutandrun.nf:95:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    def ch_multiqc_files = Channel.empty()
                           ^^^^^^^
```

Warning: workflows/cutandrun.nf:149:92: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/cutandrun.nf:150:90: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/cutandrun.nf:151:90: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/cutandrun.nf:159:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_orig_bam = Channel.empty()
                  ^^^^^^^
```
Warning: workflows/cutandrun.nf:160:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_orig_spikein_bam = Channel.empty()
                          ^^^^^^^
```
Warning: workflows/cutandrun.nf:161:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_bowtie2_log = Channel.empty()
                     ^^^^^^^
```
Warning: workflows/cutandrun.nf:162:30: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_bowtie2_spikein_log = Channel.empty()
                             ^^^^^^^
```
Warning: workflows/cutandrun.nf:163:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_samtools_bam = Channel.empty()
                      ^^^^^^^
```
Warning: workflows/cutandrun.nf:164:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_samtools_bai = Channel.empty()
                      ^^^^^^^
```
Warning: workflows/cutandrun.nf:165:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_samtools_flagstat = Channel.empty()
                           ^^^^^^^
```
Warning: workflows/cutandrun.nf:166:31: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_samtools_spikein_bam = Channel.empty()
                              ^^^^^^^
```
Warning: workflows/cutandrun.nf:167:31: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_samtools_spikein_bai = Channel.empty()
                              ^^^^^^^
```
Warning: workflows/cutandrun.nf:168:33: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_samtools_spikein_stats = Channel.empty()
                                ^^^^^^^
```
Warning: workflows/cutandrun.nf:169:36: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_samtools_spikein_flagstat = Channel.empty()
                                   ^^^^^^^
```
Warning: workflows/cutandrun.nf:170:36: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_samtools_spikein_idxstats = Channel.empty()
                                   ^^^^^^^
```

Warning: workflows/cutandrun.nf:195:87: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_multiqc_files = ch_multiqc_files.mix(ALIGN_BOWTIE2.out.stats.collect { it[1] }.ifEmpty([]))
                                                                                      ^^

Warning: workflows/cutandrun.nf:196:90: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_multiqc_files = ch_multiqc_files.mix(ALIGN_BOWTIE2.out.idxstats.collect { it[1] }.ifEmpty([]))
                                                                                         ^^

Warning: workflows/cutandrun.nf:205:30: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_metadata_bt2_target = Channel.empty()
                             ^^^^^^^
```
Warning: workflows/cutandrun.nf:206:31: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_metadata_bt2_spikein = Channel.empty()
                              ^^^^^^^
```

Warning: workflows/cutandrun.nf:238:58: Implicit closure parameter is deprecated, declare an explicit parameter instead

            PREPARE_GENOME.out.allowed_regions.collect { it[1] }.ifEmpty([]),
                                                         ^^

Warning: workflows/cutandrun.nf:246:82: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/cutandrun.nf:247:85: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/cutandrun.nf:260:89: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/cutandrun.nf:266:33: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_markduplicates_metrics = Channel.empty()
                                ^^^^^^^
```

Warning: workflows/cutandrun.nf:281:92: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/cutandrun.nf:282:95: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/cutandrun.nf:303:88: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/cutandrun.nf:304:91: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/cutandrun.nf:312:37: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_metadata_picard_duplicates = Channel.empty()
                                    ^^^^^^^
```
Warning: workflows/cutandrun.nf:328:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_linear_metrics = Channel.empty()
                        ^^^^^^^
```

Warning: workflows/cutandrun.nf:342:88: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/cutandrun.nf:343:91: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/cutandrun.nf:344:101: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/cutandrun.nf:347:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_bedgraph = Channel.empty()
                  ^^^^^^^
```
Warning: workflows/cutandrun.nf:348:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_bigwig = Channel.empty()
                ^^^^^^^
```
Warning: workflows/cutandrun.nf:349:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_seacr_peaks = Channel.empty()
                     ^^^^^^^
```
Warning: workflows/cutandrun.nf:350:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_macs2_peaks = Channel.empty()
                     ^^^^^^^
```
Warning: workflows/cutandrun.nf:351:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_peaks_primary = Channel.empty()
                       ^^^^^^^
```
Warning: workflows/cutandrun.nf:352:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_peaks_secondary = Channel.empty()
                         ^^^^^^^
```
Warning: workflows/cutandrun.nf:353:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_peaks_summits = Channel.empty()
                       ^^^^^^^
```
Warning: workflows/cutandrun.nf:354:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_consensus_peaks = Channel.empty()
                         ^^^^^^^
```
Warning: workflows/cutandrun.nf:355:33: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_consensus_peaks_unfilt = Channel.empty()
                                ^^^^^^^
```

Warning: workflows/cutandrun.nf:590:48: Implicit closure parameter is deprecated, declare an explicit parameter instead

                PREPARE_GENOME.out.fasta.map { it[1] },
                                               ^^

Warning: workflows/cutandrun.nf:591:54: Implicit closure parameter is deprecated, declare an explicit parameter instead

                PREPARE_GENOME.out.fasta_index.map { it[1] },
                                                     ^^

Warning: workflows/cutandrun.nf:593:44: Implicit closure parameter is deprecated, declare an explicit parameter instead

                ch_peaks_primary.collect { it[1] }.filter { it -> it.size() > 1 }.ifEmpty([]),
                                           ^^

Warning: workflows/cutandrun.nf:594:46: Implicit closure parameter is deprecated, declare an explicit parameter instead

                ch_peaks_secondary.collect { it[1] }.filter { it -> it.size() > 1 }.ifEmpty([]),
                                             ^^

Warning: workflows/cutandrun.nf:595:37: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                ch_bigwig.collect { it[1] }.ifEmpty([]),
                                    ^^
```
Warning: workflows/cutandrun.nf:606:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                .filter { it[0].is_control == false }
                          ^^
```

Warning: workflows/cutandrun.nf:681:44: Implicit closure parameter is deprecated, declare an explicit parameter instead

                    ch_bigwig_no_igg.map { it[1] }.toSortedList().map { [[id: 'all_genes'], it] },
                                           ^^

Warning: workflows/cutandrun.nf:681:93: Implicit closure parameter is deprecated, declare an explicit parameter instead

                    ch_bigwig_no_igg.map { it[1] }.toSortedList().map { [[id: 'all_genes'], it] },
                                                                                            ^^

Warning: workflows/cutandrun.nf:704:99: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/cutandrun.nf:705:89: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/cutandrun.nf:706:99: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/cutandrun.nf:750:92: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/cutandrun.nf:751:93: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/cutandrun.nf:752:95: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/cutandrun.nf:753:91: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/cutandrun.nf:798:90: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/cutandrun.nf:802:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    multiqc_report = Channel.empty()
                     ^^^^^^^
```

Warning: workflows/cutandrun.nf:804:74: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_multiqc_files = ch_multiqc_files.mix(ch_bowtie2_log.collect { it[1] }.ifEmpty([]))
                                                                         ^^

Warning: workflows/cutandrun.nf:805:82: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_multiqc_files = ch_multiqc_files.mix(ch_bowtie2_spikein_log.collect { it[1] }.ifEmpty([]))
                                                                                 ^^

Warning: workflows/cutandrun.nf:806:80: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_multiqc_files = ch_multiqc_files.mix(ch_samtools_flagstat.collect { it[1] }.ifEmpty([]))
                                                                               ^^

Warning: workflows/cutandrun.nf:807:85: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_multiqc_files = ch_multiqc_files.mix(ch_markduplicates_metrics.collect { it[1] }.ifEmpty([]))
                                                                                    ^^

Warning: workflows/cutandrun.nf:819:29: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_multiqc_config = Channel.fromPath("${projectDir}/assets/multiqc_config.yml", checkIfExists: true)
                            ^^^^^^^

Warning: workflows/cutandrun.nf:820:60: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
                                                           ^^^^^^^

Warning: workflows/cutandrun.nf:820:123: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty()
                                                                                                                          ^^^^^^^

Warning: workflows/cutandrun.nf:821:49: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty()
                                                ^^^^^^^

Warning: workflows/cutandrun.nf:821:110: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath(params.multiqc_logo, checkIfExists: true) : Channel.empty()
                                                                                                             ^^^^^^^

Warning: workflows/cutandrun.nf:823:31: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/cutandrun.nf:825:34: The use of Channel to access channel factories is deprecated -- use channel instead

        ch_methods_description = Channel.value(methodsDescriptionText(ch_multiqc_custom_methods_description))
                                 ^^^^^^^

Warning: workflows/cutandrun.nf:888:98: 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()))
                                                                                                 ^^^^^^^

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