Nextflow lint results

Generated: 2026-05-21T00:39:30.845320457Z
Nextflow version: 26.04.1
Summary: 161 warnings

⚠️ Warnings

Warning: conf/modules.config:391:77: Implicit closure parameter is deprecated, declare an explicit parameter instead

            saveAs: { (meta.single_end || params.save_align_intermeds) ? "${it}" : null }
                                                                            ^^

Warning: modules/local/macs3_consensus.nf:33:46: Implicit closure parameter is deprecated, declare an explicit parameter instead

    sort -T '.' -k1,1 -k2,2n ${peaks.collect{it.toString()}.sort().join(' ')} \\
                                             ^^

Warning: modules/local/macs3_consensus.nf:38:25: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ${peaks.collect{it.toString()}.sort().join(',').replaceAll("_peaks.${peak_type}","")} \\
                        ^^

Warning: modules/nf-core/bowtie2/align/main.nf:93:9: Variable was declared but not used

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

Warning: modules/nf-core/bwa/mem/main.nf:56:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/bwa/mem/main.nf:59:9: Variable was declared but not used

    def samtools_command = sort_bam ? 'sort' : 'view'
        ^^^^^^^^^^^^^^^^

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/macs3/callpeak/main.nf:34:40: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        def id = args_list.findIndexOf{it=='--format'}
                                       ^^
```
Warning: modules/nf-core/macs3/callpeak/main.nf:56:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
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/bedgraphtobigwig/main.nf:23:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: subworkflows/local/align_star.nf:17:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/bam_bedgraph_bigwig_bedtools_ucsc.nf:16:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/bam_filter_bamtools.nf:19:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/bam_peaks_call_qc_annotate_macs3_homer.nf:29:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/bam_peaks_call_qc_annotate_macs3_homer.nf:47:13: Parameter was not used -- prefix with _ to suppress warning
```
            meta, peaks ->
            ^^^^
```
Warning: subworkflows/local/bam_peaks_call_qc_annotate_macs3_homer.nf:56:27: Parameter was not used -- prefix with _ to suppress warning
```
            meta, ip_bam, control_bam, peaks ->
                          ^^^^^^^^^^^
```
Warning: subworkflows/local/bam_peaks_call_qc_annotate_macs3_homer.nf:73:19: Parameter was not used -- prefix with _ to suppress warning
```
            meta, ip_bam, peaks, frip ->
                  ^^^^^^
```
Warning: subworkflows/local/bam_peaks_call_qc_annotate_macs3_homer.nf:88:39: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_homer_annotatepeaks          = Channel.empty()
                                      ^^^^^^^
```
Warning: subworkflows/local/bam_peaks_call_qc_annotate_macs3_homer.nf:89:39: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_plot_macs3_qc_txt            = Channel.empty()
                                      ^^^^^^^
```
Warning: subworkflows/local/bam_peaks_call_qc_annotate_macs3_homer.nf:90:39: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_plot_macs3_qc_pdf            = Channel.empty()
                                      ^^^^^^^
```
Warning: subworkflows/local/bam_peaks_call_qc_annotate_macs3_homer.nf:91:39: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_plot_homer_annotatepeaks_txt = Channel.empty()
                                      ^^^^^^^
```
Warning: subworkflows/local/bam_peaks_call_qc_annotate_macs3_homer.nf:92:39: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_plot_homer_annotatepeaks_pdf = Channel.empty()
                                      ^^^^^^^
```
Warning: subworkflows/local/bam_peaks_call_qc_annotate_macs3_homer.nf:93:39: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_plot_homer_annotatepeaks_tsv = Channel.empty()
                                      ^^^^^^^
```
Warning: subworkflows/local/bam_peaks_call_qc_annotate_macs3_homer.nf:111:40: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                ch_macs3_peaks.collect{it[1]},
                                       ^^
```
Warning: subworkflows/local/bam_peaks_call_qc_annotate_macs3_homer.nf:122:53: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                HOMER_ANNOTATEPEAKS.out.txt.collect{it[1]},
                                                    ^^
```
Warning: subworkflows/local/bam_shift_reads.nf:12:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf:25:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf:30:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .collect { it[1] }
                   ^^
```
Warning: subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf:31:19: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter { it.size() > 1 }
                  ^^
```
Warning: subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf:50:30: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_homer_annotatepeaks = Channel.empty()
                             ^^^^^^^
```
Warning: subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf:64:20: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .collect { it[1] }
                   ^^
```
Warning: subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf:65:19: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter { it.size() > 1 }
                  ^^
```
Warning: subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf:66:18: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { [ it ] }
                 ^^
```
Warning: subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf:69:19: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter { it.size() == 3 }
                  ^^
```
Warning: subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf:87:34: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_deseq2_qc_pdf           = Channel.empty()
                                 ^^^^^^^
```
Warning: subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf:88:34: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_deseq2_qc_rdata         = Channel.empty()
                                 ^^^^^^^
```
Warning: subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf:89:34: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_deseq2_qc_rds           = Channel.empty()
                                 ^^^^^^^
```
Warning: subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf:90:34: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_deseq2_qc_pca_txt       = Channel.empty()
                                 ^^^^^^^
```
Warning: subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf:91:34: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_deseq2_qc_pca_multiqc   = Channel.empty()
                                 ^^^^^^^
```
Warning: subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf:92:34: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_deseq2_qc_dists_txt     = Channel.empty()
                                 ^^^^^^^
```
Warning: subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf:93:34: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_deseq2_qc_dists_multiqc = Channel.empty()
                                 ^^^^^^^
```
Warning: subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf:94:34: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_deseq2_qc_log           = Channel.empty()
                                 ^^^^^^^
```
Warning: subworkflows/local/bed_consensus_quantify_qc_bedtools_featurecounts_deseq2.nf:95:34: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_deseq2_qc_size_factors  = Channel.empty()
                                 ^^^^^^^
```
Warning: subworkflows/local/bigwig_plot_deeptools.nf:19:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/input_check.nf:11:5: Parameter was not used -- prefix with _ to suppress warning
```
    with_control // boolean: samplesheet contains controls
    ^^^^^^^^^^^^
```
Warning: subworkflows/local/input_check.nf:18:37: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { create_fastq_channel(it, seq_center) }
                                    ^^
```
Warning: subworkflows/local/input_check.nf:19:16: Variable was declared but not used
```
        .set { reads }
               ^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:53:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:58:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_fasta = Channel.empty()
               ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:63:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_fasta = Channel.value(file(fasta, checkIfExists: true))
                   ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:74:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_gtf = Channel.value(file(gtf, checkIfExists: true))
                     ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:81:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_gff = Channel.value(file(gff, checkIfExists: true))
                     ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:90:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_blacklist = Channel.empty()
                   ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:96:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_blacklist = Channel.value(file(blacklist, checkIfExists: true))
                           ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:121:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_gene_bed = Channel.value(file(gene_bed, checkIfExists: true))
                          ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:133:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_tss_bed = Channel.value(file(tss_bed, checkIfExists: true))
                         ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:148:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_genome_autosomes = Channel.empty()
                          ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:159:30: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_genome_filtered_bed = Channel.empty()
                             ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:172:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_bwa_index = Channel.empty()
                   ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:189:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_bowtie2_index = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:207:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_chromap_index = Channel.empty()
                       ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:225:21: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_star_index = Channel.empty()
                    ^^^^^^^
```

Warning: subworkflows/local/prepare_genome.nf:232:33: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_star_index = Channel.value(file(star_index, checkIfExists: true))
                                ^^^^^^^

Warning: subworkflows/local/utils_nfcore_atacseq_pipeline/main.nf:34:5: Parameter was not used -- prefix with _ to suppress warning
```
    input             //  string: Path to input samplesheet
    ^^^^^
```
Warning: subworkflows/local/utils_nfcore_atacseq_pipeline/main.nf:41:5: Variable was declared but not used
```
    ch_versions = channel.empty()
    ^^^^^^^^^^^
```
Warning: subworkflows/nf-core/bam_markduplicates_picard/main.nf:18:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
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/fastq_align_bowtie2/main.nf:18:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_align_bwa/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/fastq_align_chromap/main.nf:19:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

Warning: workflows/atacseq.nf:139:29: Parameter was not used -- prefix with _ to suppress warning

            .filter { meta, reads -> meta.single_end }
                            ^^^^^

Warning: workflows/atacseq.nf:166:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_genome_bam        = Channel.empty()
                           ^^^^^^^
```
Warning: workflows/atacseq.nf:167:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_samtools_stats    = Channel.empty()
                           ^^^^^^^
```
Warning: workflows/atacseq.nf:168:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_samtools_flagstat = Channel.empty()
                           ^^^^^^^
```
Warning: workflows/atacseq.nf:169:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_samtools_idxstats = Channel.empty()
                           ^^^^^^^
```
Warning: workflows/atacseq.nf:177:32: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                        [ [:], it ]
                               ^^
```
Warning: workflows/atacseq.nf:198:28: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    [ [:], it ]
                           ^^
```
Warning: workflows/atacseq.nf:217:28: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    [ [:], it ]
                           ^^
```

Warning: workflows/atacseq.nf:225:9: Variable was declared but not used

        ch_genome_bam_index  = FASTQ_ALIGN_CHROMAP.out.bai
        ^^^^^^^^^^^^^^^^^^^

Warning: workflows/atacseq.nf:235:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_star_multiqc = Channel.empty()
                      ^^^^^^^
```
Warning: workflows/atacseq.nf:242:28: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    [ [:], it ]
                           ^^
```
Warning: workflows/atacseq.nf:285:24: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                [ [:], it ]
                       ^^
```
Warning: workflows/atacseq.nf:289:24: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                [ [:], it ]
                       ^^
```
Warning: workflows/atacseq.nf:312:24: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                [ [:], it ]
                       ^^
```
Warning: workflows/atacseq.nf:322:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_preseq_multiqc = Channel.empty()
                        ^^^^^^^
```

Warning: workflows/atacseq.nf:334:47: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_picardcollectmultiplemetrics_multiqc = Channel.empty()
                                              ^^^^^^^

Warning: workflows/atacseq.nf:341:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    [ it[0], it[1], [] ]
                      ^^
```
Warning: workflows/atacseq.nf:341:30: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    [ it[0], it[1], [] ]
                             ^^
```
Warning: workflows/atacseq.nf:345:28: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    [ [:], it ]
                           ^^
```
Warning: workflows/atacseq.nf:349:28: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    [ [:], it ]
                           ^^
```
Warning: workflows/atacseq.nf:369:24: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                [ [:], it ]
                       ^^
```
Warning: workflows/atacseq.nf:395:39: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_deeptoolsplotprofile_multiqc = Channel.empty()
                                      ^^^^^^^
```
Warning: workflows/atacseq.nf:441:43: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_deeptoolsplotfingerprint_multiqc = Channel.empty()
                                          ^^^^^^^
```

Warning: workflows/atacseq.nf:454:29: Parameter was not used -- prefix with _ to suppress warning

                meta, bams, bais ->
                            ^^^^

Warning: workflows/atacseq.nf:461:28: Parameter was not used -- prefix with _ to suppress warning

                meta, bam, bai ->
                           ^^^

Warning: workflows/atacseq.nf:488:44: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_macs3_consensus_library_bed       = Channel.empty()
                                           ^^^^^^^

Warning: workflows/atacseq.nf:489:44: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_featurecounts_library_multiqc     = Channel.empty()
                                           ^^^^^^^

Warning: workflows/atacseq.nf:490:44: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_deseq2_pca_library_multiqc        = Channel.empty()
                                           ^^^^^^^

Warning: workflows/atacseq.nf:491:44: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_deseq2_clustering_library_multiqc = Channel.empty()
                                           ^^^^^^^
```

Warning: workflows/atacseq.nf:543:57: Implicit closure parameter is deprecated, declare an explicit parameter instead

            MERGED_LIBRARY_ATAQV_ATAQV.out.json.collect{it[1]}
                                                        ^^

Warning: workflows/atacseq.nf:551:59: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_markduplicates_replicate_stats                   = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/atacseq.nf:552:59: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_markduplicates_replicate_flagstat                = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/atacseq.nf:553:59: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_markduplicates_replicate_idxstats                = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/atacseq.nf:554:59: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_markduplicates_replicate_metrics                 = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/atacseq.nf:555:59: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_ucsc_bedgraphtobigwig_replicate_bigwig           = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/atacseq.nf:556:59: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_macs3_replicate_peaks                            = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/atacseq.nf:557:59: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_macs3_frip_replicate_multiqc                     = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/atacseq.nf:558:59: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_macs3_peak_count_replicate_multiqc               = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/atacseq.nf:559:59: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_macs3_plot_homer_annotatepeaks_replicate_multiqc = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/atacseq.nf:560:59: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_macs3_consensus_replicate_bed                    = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/atacseq.nf:561:59: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_featurecounts_replicate_multiqc                  = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/atacseq.nf:562:59: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_deseq2_pca_replicate_multiqc                     = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/atacseq.nf:563:59: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_deseq2_clustering_replicate_multiqc              = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/atacseq.nf:579:17: Parameter was not used -- prefix with _ to suppress warning
```
                id, metas, bams ->
                ^^
```
Warning: workflows/atacseq.nf:601:28: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    [ [:], it ]
                           ^^
```
Warning: workflows/atacseq.nf:605:28: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    [ [:], it ]
                           ^^
```
Warning: workflows/atacseq.nf:628:28: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    [ [:], it ]
                           ^^
```

Warning: workflows/atacseq.nf:727:61: Implicit closure parameter is deprecated, declare an explicit parameter instead

            MERGED_LIBRARY_BAM_TO_BIGWIG.out.bigwig.collect{it[1]}.ifEmpty([]),
                                                            ^^

Warning: workflows/atacseq.nf:728:66: Implicit closure parameter is deprecated, declare an explicit parameter instead

            MERGED_LIBRARY_CALL_ANNOTATE_PEAKS.out.peaks.collect{it[1]}.ifEmpty([]),
                                                                 ^^

Warning: workflows/atacseq.nf:729:52: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_macs3_consensus_library_bed.collect{it[1]}.ifEmpty([]),
                                                   ^^

Warning: workflows/atacseq.nf:730:63: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_ucsc_bedgraphtobigwig_replicate_bigwig.collect{it[1]}.ifEmpty([]),
                                                              ^^

Warning: workflows/atacseq.nf:731:46: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_macs3_replicate_peaks.collect{it[1]}.ifEmpty([]),
                                             ^^

Warning: workflows/atacseq.nf:732:54: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_macs3_consensus_replicate_bed.collect{it[1]}.ifEmpty([]),
                                                     ^^

Warning: workflows/atacseq.nf:788:53: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/atacseq.nf:789:70: The use of Channel to access channel factories is deprecated -- use channel instead

        def ch_multiqc_custom_config              = multiqc_config ? Channel.fromPath(multiqc_config) : Channel.empty()
                                                                     ^^^^^^^

Warning: workflows/atacseq.nf:789:105: The use of Channel to access channel factories is deprecated -- use channel instead

        def ch_multiqc_custom_config              = multiqc_config ? Channel.fromPath(multiqc_config) : Channel.empty()
                                                                                                        ^^^^^^^

Warning: workflows/atacseq.nf:790:70: The use of Channel to access channel factories is deprecated -- use channel instead

        def ch_multiqc_logo                       = multiqc_logo   ? Channel.fromPath(multiqc_logo)   : Channel.empty()
                                                                     ^^^^^^^

Warning: workflows/atacseq.nf:790:105: The use of Channel to access channel factories is deprecated -- use channel instead

        def ch_multiqc_logo                       = multiqc_logo   ? Channel.fromPath(multiqc_logo)   : Channel.empty()
                                                                                                        ^^^^^^^

Warning: workflows/atacseq.nf:792:53: The use of Channel to access channel factories is deprecated -- use channel instead

        def ch_workflow_summary                   = Channel.value(paramsSummaryMultiqc(ch_summary_params))
                                                    ^^^^^^^

Warning: workflows/atacseq.nf:794:53: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/atacseq.nf:805:69: Implicit closure parameter is deprecated, declare an explicit parameter instead

            FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.fastqc_zip.collect{it[1]}.ifEmpty([]),
                                                                    ^^

Warning: workflows/atacseq.nf:806:67: Implicit closure parameter is deprecated, declare an explicit parameter instead

            FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.trim_zip.collect{it[1]}.ifEmpty([]),
                                                                  ^^

Warning: workflows/atacseq.nf:807:67: Implicit closure parameter is deprecated, declare an explicit parameter instead

            FASTQ_FASTQC_UMITOOLS_TRIMGALORE.out.trim_log.collect{it[1]}.ifEmpty([]),
                                                                  ^^

Warning: workflows/atacseq.nf:809:39: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            ch_samtools_stats.collect{it[1]}.ifEmpty([]),
                                      ^^
```

Warning: workflows/atacseq.nf:810:42: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_samtools_flagstat.collect{it[1]}.ifEmpty([]),
                                         ^^

Warning: workflows/atacseq.nf:811:42: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_samtools_idxstats.collect{it[1]}.ifEmpty([]),
                                         ^^

Warning: workflows/atacseq.nf:813:68: Implicit closure parameter is deprecated, declare an explicit parameter instead

            MERGED_LIBRARY_MARKDUPLICATES_PICARD.out.stats.collect{it[1]}.ifEmpty([]),
                                                                   ^^

Warning: workflows/atacseq.nf:814:71: Implicit closure parameter is deprecated, declare an explicit parameter instead

            MERGED_LIBRARY_MARKDUPLICATES_PICARD.out.flagstat.collect{it[1]}.ifEmpty([]),
                                                                      ^^

Warning: workflows/atacseq.nf:815:71: Implicit closure parameter is deprecated, declare an explicit parameter instead

            MERGED_LIBRARY_MARKDUPLICATES_PICARD.out.idxstats.collect{it[1]}.ifEmpty([]),
                                                                      ^^

Warning: workflows/atacseq.nf:816:70: Implicit closure parameter is deprecated, declare an explicit parameter instead

            MERGED_LIBRARY_MARKDUPLICATES_PICARD.out.metrics.collect{it[1]}.ifEmpty([]),
                                                                     ^^

Warning: workflows/atacseq.nf:818:57: Implicit closure parameter is deprecated, declare an explicit parameter instead

            MERGED_LIBRARY_FILTER_BAM.out.stats.collect{it[1]}.ifEmpty([]),
                                                        ^^

Warning: workflows/atacseq.nf:819:60: Implicit closure parameter is deprecated, declare an explicit parameter instead

            MERGED_LIBRARY_FILTER_BAM.out.flagstat.collect{it[1]}.ifEmpty([]),
                                                           ^^

Warning: workflows/atacseq.nf:820:60: Implicit closure parameter is deprecated, declare an explicit parameter instead

            MERGED_LIBRARY_FILTER_BAM.out.idxstats.collect{it[1]}.ifEmpty([]),
                                                           ^^

Warning: workflows/atacseq.nf:821:61: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_picardcollectmultiplemetrics_multiqc.collect{it[1]}.ifEmpty([]),
                                                            ^^

Warning: workflows/atacseq.nf:823:39: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            ch_preseq_multiqc.collect{it[1]}.ifEmpty([]),
                                      ^^
```

Warning: workflows/atacseq.nf:825:53: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_deeptoolsplotprofile_multiqc.collect{it[1]}.ifEmpty([]),
                                                    ^^

Warning: workflows/atacseq.nf:826:57: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_deeptoolsplotfingerprint_multiqc.collect{it[1]}.ifEmpty([]),
                                                        ^^

Warning: workflows/atacseq.nf:828:73: Implicit closure parameter is deprecated, declare an explicit parameter instead

            MERGED_LIBRARY_CALL_ANNOTATE_PEAKS.out.frip_multiqc.collect{it[1]}.ifEmpty([]),
                                                                        ^^

Warning: workflows/atacseq.nf:829:79: Implicit closure parameter is deprecated, declare an explicit parameter instead

            MERGED_LIBRARY_CALL_ANNOTATE_PEAKS.out.peak_count_multiqc.collect{it[1]}.ifEmpty([]),
                                                                              ^^

Warning: workflows/atacseq.nf:831:54: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_featurecounts_library_multiqc.collect{it[1]}.ifEmpty([]),
                                                     ^^

Warning: workflows/atacseq.nf:833:55: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_markduplicates_replicate_stats.collect{it[1]}.ifEmpty([]),
                                                      ^^

Warning: workflows/atacseq.nf:834:58: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_markduplicates_replicate_flagstat.collect{it[1]}.ifEmpty([]),
                                                         ^^

Warning: workflows/atacseq.nf:835:58: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_markduplicates_replicate_idxstats.collect{it[1]}.ifEmpty([]),
                                                         ^^

Warning: workflows/atacseq.nf:836:57: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_markduplicates_replicate_metrics.collect{it[1]}.ifEmpty([]),
                                                        ^^

Warning: workflows/atacseq.nf:838:53: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_macs3_frip_replicate_multiqc.collect{it[1]}.ifEmpty([]),
                                                    ^^

Warning: workflows/atacseq.nf:839:59: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_macs3_peak_count_replicate_multiqc.collect{it[1]}.ifEmpty([]),
                                                          ^^

Warning: workflows/atacseq.nf:841:56: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_featurecounts_replicate_multiqc.collect{it[1]}.ifEmpty([]),
                                                       ^^

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