Nextflow lint results

Generated: 2026-01-16T10:28:47.639887306Z
Nextflow version: 25.12.0-edge
Summary: 21 errors, 148 warnings

❌ Errors

Error: conf/modules.config:40:17: Unexpected input: ':'

        withName: 'TRIMMOMATIC' {
                ^

Error: modules/nf-core/untarfiles/main.nf:1:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
def deprecation_message = """
^^^
```
Error: modules/nf-core/untarfiles/main.nf:27:18: deprecation_message is not defined
```
    assert true: deprecation_message
                 ^^^^^^^^^^^^^^^^^^^
```
Error: modules/nf-core/untarfiles/main.nf:49:18: deprecation_message is not defined
```
    assert true: deprecation_message
                 ^^^^^^^^^^^^^^^^^^^
```

Error: subworkflows/local/cat_fractions/main.nf:22:13: Variables in a closure should be declared with def

            meta2 = meta[0].clone()  // take first map only and create a copy
            ^^^^^

Error: subworkflows/local/deeptools_qc/main.nf:71:26: bam is already declared

            .map { meta, bam, bai ->
                         ^^^

Error: subworkflows/local/deeptools_qc/main.nf:71:31: bai is already declared

            .map { meta, bam, bai ->
                              ^^^

Error: workflows/sammyseq.nf:50:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

if (params.fasta) { ch_fasta =  Channel.fromPath(params.fasta) } else { exit 1, 'Fasta reference genome not specified!' }
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/sammyseq.nf:53:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

ch_fasta_meta = ch_fasta.map{ it -> [[id:it[0].baseName], it] }.collect()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/sammyseq.nf:61:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

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

Error: workflows/sammyseq.nf:62:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

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

Error: workflows/sammyseq.nf:63:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

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

Error: workflows/sammyseq.nf:64:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/sammyseq.nf:160:21: Variables in a closure should be declared with def

                    newid=id.id + "_trim"
                    ^^^^^

Error: workflows/sammyseq.nf:161:21: Variables in a closure should be declared with def

                    sng=meta.subMap('single_end').single_end
                    ^^^

Error: workflows/sammyseq.nf:162:21: Variables in a closure should be declared with def

                    newmeta=[id: newid, single_end: sng]
                    ^^^^^^^

Error: workflows/sammyseq.nf:195:13: ch_fasta_meta is not defined

            ch_fasta_meta,
            ^^^^^^^^^^^^^

Error: workflows/sammyseq.nf:205:13: ch_fasta_meta is not defined

            ch_fasta_meta,
            ^^^^^^^^^^^^^

Error: workflows/sammyseq.nf:224:9: ch_fasta_meta is not defined
```
        ch_fasta_meta,
        ^^^^^^^^^^^^^
```
Error: workflows/sammyseq.nf:245:9: ch_fasta_meta is not defined
```
        ch_fasta_meta
        ^^^^^^^^^^^^^
```

Error: workflows/sammyseq.nf:260:21: ch_fasta_meta is not defined

    ch_fasta_path = ch_fasta_meta.map { it[1] }
                    ^^^^^^^^^^^^^

⚠️ Warnings

Warning: modules/local/differential_enrichment/main.nf:29:5: Variable was declared but not used
```
    test_group = contrast_data[0]
    ^^^^^^^^^^
```
Warning: modules/local/differential_enrichment/main.nf:30:5: Variable was declared but not used
```
    ref_group = contrast_data[1]
    ^^^^^^^^^
```
Warning: modules/local/differential_enrichment/main.nf:31:5: Variable was declared but not used
```
    contrast_name = "${contrast_data[0]}vs${contrast_data[1]}"
    ^^^^^^^^^^^^^
```

Warning: modules/nf-core/cat/fastq/main.nf:22:60: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

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

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

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

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

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

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

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

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

Warning: modules/nf-core/gunzip/main.nf:43:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/trimgalore/main.nf:47:31: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        args_list.removeAll { it.toLowerCase().contains('_r2 ') }
                              ^^
```
Warning: modules/nf-core/untarfiles/main.nf:1:5: Variable was declared but not used
```
def deprecation_message = """
    ^^^^^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/bigwig_plot_deeptools/main.nf:15:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/cat_fractions/main.nf:12:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/cat_fractions/main.nf:29:19: Parameter was not used -- prefix with _ to suppress warning
```
        .filter { meta, fastq -> fastq.size() > 1 }
                  ^^^^
```
Warning: subworkflows/local/cat_fractions/main.nf:42:23: Variable was declared but not used
```
        ).reads.set { cat_fastq_output }
                      ^^^^^^^^^^^^^^^^
```
Warning: subworkflows/local/deeptools_qc/main.nf:20:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/deeptools_qc/main.nf:62:36: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_fingerprint_matrix_global = Channel.empty()
                                   ^^^^^^^
```
Warning: subworkflows/local/deeptools_qc/main.nf:63:37: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_fingerprint_metrics_global = Channel.empty()
                                    ^^^^^^^
```
Warning: subworkflows/local/deeptools_qc/main.nf:64:36: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_fingerprint_region_matrix = Channel.empty()
                                   ^^^^^^^
```
Warning: subworkflows/local/deeptools_qc/main.nf:65:37: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_fingerprint_region_metrics = Channel.empty()
                                    ^^^^^^^
```
Warning: subworkflows/local/differential_solubility_analysis/main.nf:20:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/differential_solubility_analysis/main.nf:26:29: Parameter was not used -- prefix with _ to suppress warning
```
        .filter { csv_meta, mle_file -> csv_meta.csv_expid_filter }
                            ^^^^^^^^
```
Warning: subworkflows/local/differential_solubility_analysis/main.nf:35:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_contrasts = Channel
                   ^^^^^^^
```
Warning: subworkflows/local/filter_bam_samtools/main.nf:15:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/filter_bam_samtools/main.nf:24:23: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        bam_bai.map { it[2].getName().tokenize('.')[-1] }
                      ^^
```
Warning: subworkflows/local/generate_comparisons/main.nf:17:29: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_comparison_results = Channel.empty()
                            ^^^^^^^
```
Warning: subworkflows/local/generate_comparisons/main.nf:18:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/generate_comparisons/main.nf:21:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    comparisons_ch_s1 = Channel.empty()
                        ^^^^^^^
```
Warning: subworkflows/local/generate_comparisons/main.nf:22:25: The use of Channel to access channel factories is deprecated -- use channel instead
```
    comparisons_ch_s2 = Channel.empty()
                        ^^^^^^^
```
Warning: subworkflows/local/generate_comparisons/main.nf:26:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel
        ^^^^^^^
```

Warning: subworkflows/local/generate_comparisons/main.nf:40:70: Implicit closure parameter is deprecated, declare an explicit parameter instead

        def comparison_list = params.comparison.split(',').collect { it.trim() }
                                                                     ^^

Warning: subworkflows/local/generate_comparisons/main.nf:44:26: Parameter was not used -- prefix with _ to suppress warning
```
            .map { meta, fastqs -> meta }
                         ^^^^^^
```

Warning: subworkflows/local/generate_comparisons/main.nf:49:64: Implicit closure parameter is deprecated, declare an explicit parameter instead

                    def samples_by_expID = meta_list.groupBy { it.experimentalID } // Group samples by experimental ID
                                                               ^^

Warning: subworkflows/local/generate_comparisons/main.nf:52:49: Implicit closure parameter is deprecated, declare an explicit parameter instead

                        def s1 = samples.find { it.fraction == frac1 }?.id
                                                ^^

Warning: subworkflows/local/generate_comparisons/main.nf:53:49: Implicit closure parameter is deprecated, declare an explicit parameter instead

                        def s2 = samples.find { it.fraction == frac2 }?.id
                                                ^^

Warning: subworkflows/local/generate_comparisons/main.nf:85:16: Parameter was not used -- prefix with _ to suppress warning
```
        .map { sample1, comparison, file, meta ->
               ^^^^^^^
```
Warning: subworkflows/local/generate_comparisons/main.nf:92:16: Parameter was not used -- prefix with _ to suppress warning
```
        .map { sample2, comparison, file, meta ->
               ^^^^^^^
```
Warning: subworkflows/local/generate_comparisons/main.nf:100:16: Parameter was not used -- prefix with _ to suppress warning
```
        .map { comparison, f1, meta1, f2, meta2 ->
               ^^^^^^^^^^
```
Warning: subworkflows/local/generate_comparisons/main.nf:137:15: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ? Channel.value([[:], file(params.blacklist)])
              ^^^^^^^
```
Warning: subworkflows/local/generate_comparisons/main.nf:138:15: The use of Channel to access channel factories is deprecated -- use channel instead
```
            : Channel.value([[:], []])
              ^^^^^^^
```
Warning: subworkflows/local/genome_binning/main.nf:18:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/genome_binning/main.nf:23:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_keep_regions_bed = Channel.empty()
                          ^^^^^^^
```
Warning: subworkflows/local/genome_binning/main.nf:29:28: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            ).gunzip.map { it[1] }
                           ^^
```

Warning: subworkflows/local/genome_binning/main.nf:32:35: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_keep_regions_bed = Channel.fromPath(keep_regions_bed_param, checkIfExists: true)
                                  ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:33:5: Parameter was not used -- prefix with _ to suppress warning
```
    fasta              //    path: path to genome fasta file
    ^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:34:5: Parameter was not used -- prefix with _ to suppress warning
```
    aligner            //    string: aligner name
    ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:35:5: Parameter was not used -- prefix with _ to suppress warning
```
    gtf                //    file: /path/to/genome.gtf
    ^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:36:5: Parameter was not used -- prefix with _ to suppress warning
```
    tss_bed            //    file: /path/to/tss.bed
    ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:38:5: Parameter was not used -- prefix with _ to suppress warning
```
    blacklist          //    file: /path/to/blacklist.bed
    ^^^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:39:5: Parameter was not used -- prefix with _ to suppress warning
```
    gene_bed           //    file: /path/to/gene.bed
    ^^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:40:5: Parameter was not used -- prefix with _ to suppress warning
```
    bwa_index          //    file: /path/to/bwa/index/
    ^^^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:41:5: Parameter was not used -- prefix with _ to suppress warning
```
    bowtie2_index      //    file: /path/to/bowtie2/index/
    ^^^^^^^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:42:5: Parameter was not used -- prefix with _ to suppress warning
```
    chrom_sizes        //    file: /path/to/genome.sizes
    ^^^^^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:43:5: Parameter was not used -- prefix with _ to suppress warning
```
    fai                //    file: /path/to/genome.fai
    ^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:44:5: Parameter was not used -- prefix with _ to suppress warning
```
    binsize            //    binsize: genome binning
    ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:47:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:52:16: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_fasta = Channel.empty()
               ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:54:74: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: subworkflows/local/prepare_genome/main.nf:57:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_fasta = Channel.value(file(params.fasta))
                   ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:72:14: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_gtf = Channel.empty()
             ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:75:74: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: subworkflows/local/prepare_genome/main.nf:78:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_gtf = Channel.value(file(params.gtf))
                     ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:85:18: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_tss_bed = Channel.empty()
                 ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:88:81: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: subworkflows/local/prepare_genome/main.nf:91:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_tss_bed = Channel.value(file(params.tss_bed))
                         ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:98:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_blacklist = Channel.empty()
                   ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:101:87: Parameter was not used -- prefix with _ to suppress warning

            ch_blacklist = GUNZIP_BLACKLIST ( [ [:], params.blacklist ] ).gunzip.map{ meta, file -> tuple([id: 'blacklist'], file) }
                                                                                      ^^^^

Warning: subworkflows/local/prepare_genome/main.nf:104:28: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_blacklist = Channel.value(tuple([id: 'blacklist'], file(params.blacklist)))
                           ^^^^^^^

Warning: subworkflows/local/prepare_genome/main.nf:111:14: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_fai = Channel.empty()
             ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:114:66: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_fai = GUNZIP_FAI([ [:], params.fai ]).gunzip.map{ it[1] }
                                                                 ^^

Warning: subworkflows/local/prepare_genome/main.nf:117:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_fai = Channel.value(file(params.fai))
                     ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:121:39: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            ch_fasta.map { tuple([:], it) },
                                      ^^
```
Warning: subworkflows/local/prepare_genome/main.nf:125:51: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        ch_fai = SAMTOOLS_FAIDX_FAI.out.fai.map { it[1] }
                                                  ^^
```
Warning: subworkflows/local/prepare_genome/main.nf:132:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_chrom_sizes = Channel.empty()
                     ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:135:90: Implicit closure parameter is deprecated, declare an explicit parameter instead

            ch_chrom_sizes = GUNZIP_CHROM_SIZES([ [:], params.chrom_sizes ]).gunzip.map{ it[1] }
                                                                                         ^^

Warning: subworkflows/local/prepare_genome/main.nf:138:30: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_chrom_sizes = Channel.value(file(params.chrom_sizes))
                             ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:142:39: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            ch_fasta.map { tuple([:], it) },
                                      ^^
```

Warning: subworkflows/local/prepare_genome/main.nf:146:69: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: subworkflows/local/prepare_genome/main.nf:154:30: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_genome_filtered_bed = Channel.empty()
                             ^^^^^^^
```
Warning: subworkflows/local/prepare_genome/main.nf:167:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_bwa_index = Channel.empty()
                   ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:177:62: 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/main.nf:185:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_bowtie2_index = Channel.empty()
                       ^^^^^^^
```

Warning: subworkflows/local/prepare_genome/main.nf:195:70: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: subworkflows/local/utils_nfcore_sammyseq_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_sammyseq_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_sammyseq_pipeline/main.nf:42:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

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

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

Warning: subworkflows/local/utils_nfcore_sammyseq_pipeline/main.nf:104:5: The use of Channel to access channel factories is deprecated -- use channel instead
```
    Channel
    ^^^^^^^
```
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_bwaaln/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_dna/main.nf:27:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_bam_index    = Channel.empty()
                          ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_align_dna/main.nf:28:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_bam          = Channel.empty()
                          ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_align_dna/main.nf:29:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_reports      = Channel.empty()
                          ^^^^^^^
```
Warning: subworkflows/nf-core/fastq_align_dna/main.nf:30:27: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_versions     = Channel.empty()
                          ^^^^^^^
```

Warning: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:101:98: The use of Channel to access channel factories is deprecated -- use channel instead

    return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML()))
                                                                                                 ^^^^^^^

Warning: workflows/sammyseq.nf:50:33: The use of Channel to access channel factories is deprecated -- use channel instead

if (params.fasta) { ch_fasta =  Channel.fromPath(params.fasta) } else { exit 1, 'Fasta reference genome not specified!' }
                                ^^^^^^^

Warning: workflows/sammyseq.nf:53:1: Variable was declared but not used

ch_fasta_meta = ch_fasta.map{ it -> [[id:it[0].baseName], it] }.collect()
^^^^^^^^^^^^^

Warning: workflows/sammyseq.nf:61:1: Variable was declared but not used

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

Warning: workflows/sammyseq.nf:61:30: 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/sammyseq.nf:62:1: Variable was declared but not used

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

Warning: workflows/sammyseq.nf:62:54: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/sammyseq.nf:62:119: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/sammyseq.nf:63:1: Variable was declared but not used

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

Warning: workflows/sammyseq.nf:63:54: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/sammyseq.nf:63:117: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/sammyseq.nf:64:1: Variable was declared but not used

ch_multiqc_custom_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Warning: workflows/sammyseq.nf:79:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: workflows/sammyseq.nf:80:24: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_files = Channel.empty()
                       ^^^^^^^
```
Warning: workflows/sammyseq.nf:146:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_trimmed= Channel.empty()
                ^^^^^^^
```

Warning: workflows/sammyseq.nf:176:68: Implicit closure parameter is deprecated, declare an explicit parameter instead

    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]})
                                                                   ^^

Warning: workflows/sammyseq.nf:183:22: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_aligned_bam = Channel.empty()
                     ^^^^^^^
```

Warning: workflows/sammyseq.nf:225:59: Implicit closure parameter is deprecated, declare an explicit parameter instead

        PREPARE_GENOME.out.fai.collect { [ [id: 'fasta'], it ] }
                                                          ^^

Warning: workflows/sammyseq.nf:229:5: Variable was declared but not used
```
    ch_mle_in = BAM_MARKDUPLICATES_PICARD.out.bam
    ^^^^^^^^^
```
Warning: workflows/sammyseq.nf:258:48: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    ch_fai_path = PREPARE_GENOME.out.fai.map { it[1] }
                                               ^^
```
Warning: workflows/sammyseq.nf:260:41: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
    ch_fasta_path = ch_fasta_meta.map { it[1] }
                                        ^^
```

Warning: workflows/sammyseq.nf:267:59: The use of Channel to access channel factories is deprecated -- use channel instead

        params.blacklist ? PREPARE_GENOME.out.blacklist : Channel.value(tuple([ id:'no_blacklist' ], []))
                                                          ^^^^^^^

Warning: workflows/sammyseq.nf:280:55: The use of Channel to access channel factories is deprecated -- use channel instead

    params.blacklist ? PREPARE_GENOME.out.blacklist : Channel.value(tuple([ id:'no_blacklist' ], []))
                                                      ^^^^^^^

Warning: workflows/sammyseq.nf:282:5: Variable was declared but not used

    ch_dt_corrmatrix     = DEEPTOOLS_QC.out.correlation_matrix
    ^^^^^^^^^^^^^^^^

Warning: workflows/sammyseq.nf:283:5: Variable was declared but not used

    ch_dt_pcadata        = DEEPTOOLS_QC.out.pca_data
    ^^^^^^^^^^^^^

Warning: workflows/sammyseq.nf:285:9: Variable was declared but not used

        ch_dt_fpmatrix_global = DEEPTOOLS_QC.out.fingerprint_matrix_global
        ^^^^^^^^^^^^^^^^^^^^^

Warning: workflows/sammyseq.nf:286:9: Variable was declared but not used

        ch_dt_fpmetrics_global = DEEPTOOLS_QC.out.fingerprint_metrics_global
        ^^^^^^^^^^^^^^^^^^^^^^

Warning: workflows/sammyseq.nf:288:13: Variable was declared but not used

            ch_dt_fpmatrix_region = DEEPTOOLS_QC.out.fingerprint_matrix_region
            ^^^^^^^^^^^^^^^^^^^^^

Warning: workflows/sammyseq.nf:289:13: Variable was declared but not used

            ch_dt_fpmetrics_region = DEEPTOOLS_QC.out.fingerprint_metrics_region
            ^^^^^^^^^^^^^^^^^^^^^^

Warning: workflows/sammyseq.nf:299:44: Implicit closure parameter is deprecated, declare an explicit parameter instead

                def sorted = values.sort { it[1].getBaseName() }
                                           ^^

Warning: workflows/sammyseq.nf:300:50: Implicit closure parameter is deprecated, declare an explicit parameter instead

                def sorted_bw = sorted.collect { it[1] }
                                                 ^^

Warning: workflows/sammyseq.nf:301:54: Implicit closure parameter is deprecated, declare an explicit parameter instead

                def sorted_labels = sorted.collect { it[0].id }
                                                     ^^

Warning: workflows/sammyseq.nf:328:24: Parameter was not used -- prefix with _ to suppress warning
```
                .map { meta, bed -> bed }
                       ^^^^
```
Warning: workflows/sammyseq.nf:340:33: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_comparison_results = Channel.empty()
                                ^^^^^^^
```
Warning: workflows/sammyseq.nf:395:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_multiqc_config        = Channel.fromPath(
                               ^^^^^^^
```
Warning: workflows/sammyseq.nf:398:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath(params.multiqc_config, checkIfExists: true) :
        ^^^^^^^
```
Warning: workflows/sammyseq.nf:399:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.empty()
        ^^^^^^^
```
Warning: workflows/sammyseq.nf:401:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.fromPath(params.multiqc_logo, checkIfExists: true) :
        ^^^^^^^
```
Warning: workflows/sammyseq.nf:402:9: The use of Channel to access channel factories is deprecated -- use channel instead
```
        Channel.empty()
        ^^^^^^^
```

Warning: workflows/sammyseq.nf:406:27: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/sammyseq.nf:412:45: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/sammyseq.nf:424:91: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/sammyseq.nf:428:83: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/sammyseq.nf:429:86: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/sammyseq.nf:430:86: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/sammyseq.nf:432:89: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/sammyseq.nf:433:79: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/sammyseq.nf:436:100: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/sammyseq.nf:437:101: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/sammyseq.nf:441:100: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/sammyseq.nf:442:102: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/sammyseq.nf:455:75: The use of Channel to access channel factories is deprecated -- use channel instead

    multiqc_report = !params.skip_multiqc ? MULTIQC.out.report.toList() : Channel.empty() // channel: /path/to/multiqc_report.html
                                                                          ^^^^^^^

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