Nextflow lint results

Generated: 2026-01-16T10:17:19.744355002Z
Nextflow version: 25.12.0-edge
Summary: 56 errors, 205 warnings

❌ Errors

Error: conf/modules.config:136:1: If statements cannot be mixed with config statements
```
if (!(params.skip_fastqc || params.skip_qc)) {
^
```
Error: conf/modules.config:156:1: If statements cannot be mixed with config statements
```
if (!params.skip_trimming) {
^
```
Error: conf/modules.config:228:1: If statements cannot be mixed with config statements
```
if (params.aligner == 'bwa') {
^
```
Error: conf/modules.config:250:1: If statements cannot be mixed with config statements
```
if (params.aligner == 'bowtie2') {
^
```
Error: conf/modules.config:278:1: If statements cannot be mixed with config statements
```
if (params.aligner == 'chromap') {
^
```
Error: conf/modules.config:306:1: If statements cannot be mixed with config statements
```
if (params.aligner == 'star') {
^
```
Error: conf/modules.config:527:1: If statements cannot be mixed with config statements
```
if (!params.skip_picard_metrics) {
^
```
Error: conf/modules.config:548:1: If statements cannot be mixed with config statements
```
if (!params.skip_preseq) {
^
```
Error: conf/modules.config:562:1: If statements cannot be mixed with config statements
```
if (!params.skip_plot_profile) {
^
```
Error: conf/modules.config:604:1: If statements cannot be mixed with config statements
```
if (!params.skip_plot_fingerprint) {
^
```
Error: conf/modules.config:660:1: If statements cannot be mixed with config statements
```
if (!params.skip_peak_annotation) {
^
```
Error: conf/modules.config:697:1: If statements cannot be mixed with config statements
```
if (!params.skip_consensus_peaks) {
^
```
Error: conf/modules.config:740:1: If statements cannot be mixed with config statements
```
if (!params.skip_peak_annotation) {
^
```
Error: conf/modules.config:754:1: If statements cannot be mixed with config statements
```
if (!params.skip_ataqv) {
^
```
Error: conf/modules.config:774:1: If statements cannot be mixed with config statements
```
if (!params.skip_merge_replicates) {
^
```
Error: conf/modules.config:1009:1: If statements cannot be mixed with config statements
```
if (!params.skip_igv) {
^
```
Error: conf/modules.config:1028:1: If statements cannot be mixed with config statements
```
if (!params.skip_multiqc) {
^
```

Error: modules/nf-core/bwa/index/main.nf:14:27: bwa is not defined

    tuple val(meta), path(bwa) , emit: index
                          ^^^

Error: subworkflows/local/prepare_genome.nf:213:48: UNTAR is not defined

                ch_versions  = ch_versions.mix(UNTAR.out.versions)
                                               ^^^^^

Error: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:59:31: reads is already declared

                        meta, reads ->
                              ^^^^^

Error: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:88:23: reads is already declared

                meta, reads, trim_log ->
                      ^^^^^

Error: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:88:30: trim_log is already declared

                meta, reads, trim_log ->
                             ^^^^^^^^

Error: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:90:25: Variables in a closure should be declared with def

                        num_reads = getTrimGaloreReadsAfterFiltering(meta.single_end ? trim_log : trim_log[-1])
                        ^^^^^^^^^

Error: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:99:29: reads is already declared

            .filter { meta, reads, num_reads -> num_reads >= min_trimmed_reads.toFloat() }
                            ^^^^^

Error: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:99:36: num_reads is already declared

            .filter { meta, reads, num_reads -> num_reads >= min_trimmed_reads.toFloat() }
                                   ^^^^^^^^^

Error: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:100:26: reads is already declared

            .map { meta, reads, num_reads -> [ meta, reads ] }
                         ^^^^^

Error: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:100:33: num_reads is already declared

            .map { meta, reads, num_reads -> [ meta, reads ] }
                                ^^^^^^^^^

Error: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:104:26: reads is already declared

            .map { meta, reads, num_reads -> [ meta, num_reads ] }
                         ^^^^^

Error: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:104:33: num_reads is already declared

            .map { meta, reads, num_reads -> [ meta, num_reads ] }
                                ^^^^^^^^^

Error: workflows/atacseq.nf:70:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

ch_bamtools_filter_se_config = file(params.bamtools_filter_se_config)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/atacseq.nf:71:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

ch_bamtools_filter_pe_config = file(params.bamtools_filter_pe_config)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/atacseq.nf:74:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

ch_multiqc_merged_library_peak_count_header        = file("$projectDir/assets/multiqc/merged_library_peak_count_header.txt", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/atacseq.nf:75:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

ch_multiqc_merged_library_frip_score_header        = file("$projectDir/assets/multiqc/merged_library_frip_score_header.txt", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/atacseq.nf:76:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

ch_multiqc_merged_library_peak_annotation_header   = file("$projectDir/assets/multiqc/merged_library_peak_annotation_header.txt", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/atacseq.nf:77:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

ch_multiqc_merged_library_deseq2_pca_header        = file("$projectDir/assets/multiqc/merged_library_deseq2_pca_header.txt", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/atacseq.nf:78:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

ch_multiqc_merged_library_deseq2_clustering_header = file("$projectDir/assets/multiqc/merged_library_deseq2_clustering_header.txt", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/atacseq.nf:80:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

ch_multiqc_merged_replicate_peak_count_header        = file("$projectDir/assets/multiqc/merged_replicate_peak_count_header.txt", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/atacseq.nf:81:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

ch_multiqc_merged_replicate_frip_score_header        = file("$projectDir/assets/multiqc/merged_replicate_frip_score_header.txt", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/atacseq.nf:82:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

ch_multiqc_merged_replicate_peak_annotation_header   = file("$projectDir/assets/multiqc/merged_replicate_peak_annotation_header.txt", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/atacseq.nf:83:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

ch_multiqc_merged_replicate_deseq2_pca_header        = file("$projectDir/assets/multiqc/merged_replicate_deseq2_pca_header.txt", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/atacseq.nf:84:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

ch_multiqc_merged_replicate_deseq2_clustering_header = file("$projectDir/assets/multiqc/merged_replicate_deseq2_clustering_header.txt", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/atacseq.nf:87:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
ataqv_mito_reference = params.ataqv_mito_reference
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/atacseq.nf:88:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
if (!params.ataqv_mito_reference && params.mito_name) {
^
```

Error: workflows/atacseq.nf:310:9: ch_bamtools_filter_se_config is not defined

        ch_bamtools_filter_se_config,
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/atacseq.nf:311:9: ch_bamtools_filter_pe_config is not defined

        ch_bamtools_filter_pe_config
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/atacseq.nf:472:9: ch_multiqc_merged_library_peak_count_header is not defined

        ch_multiqc_merged_library_peak_count_header,
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/atacseq.nf:473:9: ch_multiqc_merged_library_frip_score_header is not defined

        ch_multiqc_merged_library_frip_score_header,
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/atacseq.nf:474:9: ch_multiqc_merged_library_peak_annotation_header is not defined

        ch_multiqc_merged_library_peak_annotation_header,
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/atacseq.nf:494:13: ch_multiqc_merged_library_deseq2_pca_header is not defined

            ch_multiqc_merged_library_deseq2_pca_header,
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/atacseq.nf:495:13: ch_multiqc_merged_library_deseq2_clustering_header is not defined

            ch_multiqc_merged_library_deseq2_clustering_header,
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/atacseq.nf:531:13: ataqv_mito_reference is not defined

            ataqv_mito_reference ?: '',
            ^^^^^^^^^^^^^^^^^^^^

Error: workflows/atacseq.nf:680:13: ch_multiqc_merged_replicate_peak_count_header is not defined

            ch_multiqc_merged_replicate_peak_count_header,
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/atacseq.nf:681:13: ch_multiqc_merged_replicate_frip_score_header is not defined

            ch_multiqc_merged_replicate_frip_score_header,
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/atacseq.nf:682:13: ch_multiqc_merged_replicate_peak_annotation_header is not defined

            ch_multiqc_merged_replicate_peak_annotation_header,
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/atacseq.nf:702:17: ch_multiqc_merged_replicate_deseq2_pca_header is not defined

                ch_multiqc_merged_replicate_deseq2_pca_header,
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/atacseq.nf:703:17: ch_multiqc_merged_replicate_deseq2_clustering_header is not defined

                ch_multiqc_merged_replicate_deseq2_clustering_header,
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

⚠️ Warnings

Warning: conf/modules.config:403:77: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: main.nf:54:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

Warning: main.nf:81:22: The use of Channel to access channel factories is deprecated -- use channel instead

    ch_samplesheet = Channel.value(file(params.input, checkIfExists: true))
                     ^^^^^^^

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/trimgalore/main.nf:41:31: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        args_list.removeAll { it.toLowerCase().contains('_r2 ') }
                              ^^
```
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/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:60:67: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_fasta    = GUNZIP_FASTA ( [ [:], fasta ] ).gunzip.map{ it[1] }
                                                                  ^^

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))
                   ^^^^^^^
```

Warning: subworkflows/local/prepare_genome.nf:71:67: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

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))
                     ^^^^^^^
```

Warning: subworkflows/local/prepare_genome.nf:78:67: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_gff      = GUNZIP_GFF ( [ [:], gff ] ).gunzip.map{ it[1] }
                                                                  ^^

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))
                     ^^^^^^^
```
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:93:80: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_blacklist = GUNZIP_BLACKLIST ( [ [:], blacklist ] ).gunzip.map{ it[1] }
                                                                               ^^

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))
                           ^^^^^^^
```

Warning: subworkflows/local/prepare_genome.nf:118:84: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

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))
                          ^^^^^^^
```

Warning: subworkflows/local/prepare_genome.nf:130:74: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_tss_bed = GUNZIP_TSS_BED ( [ [:], tss_bed ] ).gunzip.map{ it[1] }
                                                                         ^^

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))
                         ^^^^^^^
```
Warning: subworkflows/local/prepare_genome.nf:140:50: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    CUSTOM_GETCHROMSIZES ( ch_fasta.map { [ [:], it ] } )
                                                 ^^
```

Warning: subworkflows/local/prepare_genome.nf:141:59: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_chrom_sizes = CUSTOM_GETCHROMSIZES.out.sizes.map { it[1] }
                                                          ^^

Warning: subworkflows/local/prepare_genome.nf:142:56: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_fai         = CUSTOM_GETCHROMSIZES.out.fai.map{ it[1] }
                                                       ^^

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:182:62: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_bwa_index = BWA_INDEX ( ch_fasta.map { [ [:], it ] } ).index
                                                             ^^

Warning: subworkflows/local/prepare_genome.nf:190:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_bowtie2_index = Channel.empty()
                       ^^^^^^^
```

Warning: subworkflows/local/prepare_genome.nf:200:70: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_bowtie2_index = BOWTIE2_BUILD ( ch_fasta.map { [ [:], it ] } ).index
                                                                     ^^

Warning: subworkflows/local/prepare_genome.nf:208:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_chromap_index = Channel.empty()
                       ^^^^^^^
```

Warning: subworkflows/local/prepare_genome.nf:218:70: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_chromap_index = CHROMAP_INDEX ( ch_fasta.map { [ [:], it ] } ).index
                                                                     ^^

Warning: subworkflows/local/prepare_genome.nf:226:21: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_star_index = Channel.empty()
                    ^^^^^^^
```

Warning: subworkflows/local/prepare_genome.nf:230:85: Implicit closure parameter is deprecated, declare an explicit parameter instead

                ch_star_index = UNTAR_STAR_INDEX ( [ [:], star_index ] ).untar.map{ it[1] }
                                                                                    ^^

Warning: subworkflows/local/prepare_genome.nf:233:33: The use of Channel to access channel factories is deprecated -- use channel instead
```
                ch_star_index = Channel.value(file(star_index))
                                ^^^^^^^
```

Warning: subworkflows/local/prepare_genome.nf:250:59: Implicit closure parameter is deprecated, declare an explicit parameter instead

        ch_macs_gsize = KHMER_UNIQUEKMERS.out.kmers.map { it.text.trim() }
                                                          ^^

Warning: subworkflows/local/utils_nfcore_atacseq_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_atacseq_pipeline/main.nf:35:5: Parameter was not used -- prefix with _ to suppress warning
```
    input             //  string: Path to input samplesheet
    ^^^^^
```
Warning: subworkflows/local/utils_nfcore_atacseq_pipeline/main.nf:42:5: 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: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:35:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:36:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    fastqc_html = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:37:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    fastqc_zip  = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:46:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
    umi_log   = Channel.empty()
                ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:67:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    trim_unpaired   = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:68:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    trim_html       = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:69:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    trim_zip        = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:70:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    trim_log        = Channel.empty()
                      ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:71:23: 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_trimgalore/main.nf:99:23: Parameter was not used -- prefix with _ to suppress warning
```
            .filter { meta, reads, num_reads -> num_reads >= min_trimmed_reads.toFloat() }
                      ^^^^
```

Warning: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:99:29: Parameter was not used -- prefix with _ to suppress warning

            .filter { meta, reads, num_reads -> num_reads >= min_trimmed_reads.toFloat() }
                            ^^^^^

Warning: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:100:33: Parameter was not used -- prefix with _ to suppress warning
```
            .map { meta, reads, num_reads -> [ meta, reads ] }
                                ^^^^^^^^^
```
Warning: subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf:104:26: Parameter was not used -- prefix with _ to suppress warning
```
            .map { meta, reads, num_reads -> [ meta, num_reads ] }
                         ^^^^^
```

Warning: workflows/atacseq.nf:70:1: Variable was declared but not used

ch_bamtools_filter_se_config = file(params.bamtools_filter_se_config)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Warning: workflows/atacseq.nf:71:1: Variable was declared but not used

ch_bamtools_filter_pe_config = file(params.bamtools_filter_pe_config)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Warning: workflows/atacseq.nf:74:1: Variable was declared but not used

ch_multiqc_merged_library_peak_count_header        = file("$projectDir/assets/multiqc/merged_library_peak_count_header.txt", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Warning: workflows/atacseq.nf:75:1: Variable was declared but not used

ch_multiqc_merged_library_frip_score_header        = file("$projectDir/assets/multiqc/merged_library_frip_score_header.txt", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Warning: workflows/atacseq.nf:76:1: Variable was declared but not used

ch_multiqc_merged_library_peak_annotation_header   = file("$projectDir/assets/multiqc/merged_library_peak_annotation_header.txt", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Warning: workflows/atacseq.nf:77:1: Variable was declared but not used

ch_multiqc_merged_library_deseq2_pca_header        = file("$projectDir/assets/multiqc/merged_library_deseq2_pca_header.txt", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Warning: workflows/atacseq.nf:78:1: Variable was declared but not used

ch_multiqc_merged_library_deseq2_clustering_header = file("$projectDir/assets/multiqc/merged_library_deseq2_clustering_header.txt", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Warning: workflows/atacseq.nf:80:1: Variable was declared but not used

ch_multiqc_merged_replicate_peak_count_header        = file("$projectDir/assets/multiqc/merged_replicate_peak_count_header.txt", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Warning: workflows/atacseq.nf:81:1: Variable was declared but not used

ch_multiqc_merged_replicate_frip_score_header        = file("$projectDir/assets/multiqc/merged_replicate_frip_score_header.txt", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Warning: workflows/atacseq.nf:82:1: Variable was declared but not used

ch_multiqc_merged_replicate_peak_annotation_header   = file("$projectDir/assets/multiqc/merged_replicate_peak_annotation_header.txt", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Warning: workflows/atacseq.nf:83:1: Variable was declared but not used

ch_multiqc_merged_replicate_deseq2_pca_header        = file("$projectDir/assets/multiqc/merged_replicate_deseq2_pca_header.txt", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Warning: workflows/atacseq.nf:84:1: Variable was declared but not used

ch_multiqc_merged_replicate_deseq2_clustering_header = file("$projectDir/assets/multiqc/merged_replicate_deseq2_clustering_header.txt", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Warning: workflows/atacseq.nf:112:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_files = Channel.empty()
                       ^^^^^^^
```

Warning: workflows/atacseq.nf:134:29: Parameter was not used -- prefix with _ to suppress warning

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

Warning: workflows/atacseq.nf:162:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_genome_bam        = Channel.empty()
                           ^^^^^^^
```
Warning: workflows/atacseq.nf:163:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_samtools_stats    = Channel.empty()
                           ^^^^^^^
```
Warning: workflows/atacseq.nf:164:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_samtools_flagstat = Channel.empty()
                           ^^^^^^^
```
Warning: workflows/atacseq.nf:165:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_samtools_idxstats = Channel.empty()
                           ^^^^^^^
```
Warning: workflows/atacseq.nf:173:32: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                        [ [:], it ]
                               ^^
```
Warning: workflows/atacseq.nf:194:28: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    [ [:], it ]
                           ^^
```
Warning: workflows/atacseq.nf:213:28: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    [ [:], it ]
                           ^^
```

Warning: workflows/atacseq.nf:221:9: Variable was declared but not used

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

Warning: workflows/atacseq.nf:231:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_star_multiqc = Channel.empty()
                      ^^^^^^^
```
Warning: workflows/atacseq.nf:238:28: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    [ [:], it ]
                           ^^
```
Warning: workflows/atacseq.nf:281:24: 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:308:24: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                [ [:], it ]
                       ^^
```
Warning: workflows/atacseq.nf:318:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_preseq_multiqc = Channel.empty()
                        ^^^^^^^
```

Warning: workflows/atacseq.nf:330:47: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/atacseq.nf:337:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    [ it[0], it[1], [] ]
                      ^^
```
Warning: workflows/atacseq.nf:337:30: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    [ it[0], it[1], [] ]
                             ^^
```
Warning: workflows/atacseq.nf:341:28: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    [ [:], it ]
                           ^^
```
Warning: workflows/atacseq.nf:345:28: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    [ [:], it ]
                           ^^
```
Warning: workflows/atacseq.nf:365:24: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                [ [:], it ]
                       ^^
```
Warning: workflows/atacseq.nf:391:39: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_deeptoolsplotprofile_multiqc = Channel.empty()
                                      ^^^^^^^
```
Warning: workflows/atacseq.nf:437:43: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_deeptoolsplotfingerprint_multiqc = Channel.empty()
                                          ^^^^^^^
```

Warning: workflows/atacseq.nf:450:29: Parameter was not used -- prefix with _ to suppress warning

                meta, bams, bais ->
                            ^^^^

Warning: workflows/atacseq.nf:457:28: Parameter was not used -- prefix with _ to suppress warning

                meta, bam, bai ->
                           ^^^

Warning: workflows/atacseq.nf:484:44: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/atacseq.nf:485:44: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/atacseq.nf:486:44: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/atacseq.nf:487:44: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_deseq2_clustering_library_multiqc = Channel.empty()
                                           ^^^^^^^
```

Warning: workflows/atacseq.nf:539:57: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/atacseq.nf:547:59: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/atacseq.nf:548:59: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/atacseq.nf:549:59: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/atacseq.nf:550:59: The use of Channel to access channel factories is deprecated -- use channel instead

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

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

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

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

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

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

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

Warning: workflows/atacseq.nf:554:59: 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:555:59: 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:556:59: The use of Channel to access channel factories is deprecated -- use channel instead

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

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

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

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

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

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

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

Warning: workflows/atacseq.nf:575:17: Parameter was not used -- prefix with _ to suppress warning
```
                id, metas, bams ->
                ^^
```
Warning: workflows/atacseq.nf:597:28: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    [ [:], it ]
                           ^^
```
Warning: workflows/atacseq.nf:601:28: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    [ [:], it ]
                           ^^
```
Warning: workflows/atacseq.nf:624:28: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                    [ [:], it ]
                           ^^
```

Warning: workflows/atacseq.nf:723:61: 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:724:66: 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:725:52: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/atacseq.nf:726:63: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/atacseq.nf:727:46: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/atacseq.nf:728:54: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/atacseq.nf:752:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
    def topic_versions = Channel.topic("versions")
                         ^^^^^^^
```

Warning: workflows/atacseq.nf:783:49: 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/atacseq.nf:784:73: 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) : Channel.empty()
                                                                        ^^^^^^^

Warning: workflows/atacseq.nf:784:115: 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) : Channel.empty()
                                                                                                                  ^^^^^^^

Warning: workflows/atacseq.nf:785:73: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/atacseq.nf:785:115: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/atacseq.nf:787:49: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/atacseq.nf:789:49: 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/atacseq.nf:800:69: 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:801:67: 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:802:67: 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:804:39: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            ch_samtools_stats.collect{it[1]}.ifEmpty([]),
                                      ^^
```

Warning: workflows/atacseq.nf:805:42: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/atacseq.nf:806:42: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/atacseq.nf:808:68: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/atacseq.nf:809:71: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/atacseq.nf:810:71: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/atacseq.nf:811:70: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/atacseq.nf:813:57: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/atacseq.nf:814:60: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/atacseq.nf:815:60: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/atacseq.nf:816:61: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/atacseq.nf:818:39: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            ch_preseq_multiqc.collect{it[1]}.ifEmpty([]),
                                      ^^
```

Warning: workflows/atacseq.nf:820:53: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/atacseq.nf:821:57: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/atacseq.nf:823:73: 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:824:79: 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:826:54: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/atacseq.nf:828:55: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/atacseq.nf:829:58: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/atacseq.nf:830:58: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/atacseq.nf:831:57: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/atacseq.nf:833:53: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/atacseq.nf:834:59: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/atacseq.nf:836:56: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

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