Nextflow lint results

Generated: 2026-03-12T00:16:28.793339385Z
Nextflow version: 26.02.0-edge
Summary: 150 errors, 135 warnings

❌ Errors

Error: conf/test.config:26:13: pipelines_testdata_base_path is not defined

    input = pipelines_testdata_base_path + 'testdata-bcr/Metadata_small_test_airr.tsv'
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test.config:27:16: pipelines_testdata_base_path is not defined

    cprimers = pipelines_testdata_base_path + 'testdata-bcr/C_primers.fasta'
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test.config:28:16: pipelines_testdata_base_path is not defined

    vprimers = pipelines_testdata_base_path + 'testdata-bcr/V_primers.fasta'
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test.config:29:23: pipelines_testdata_base_path is not defined

    reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test.config:30:25: pipelines_testdata_base_path is not defined

    reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_10x_sc.config:29:13: pipelines_testdata_base_path is not defined

    input = pipelines_testdata_base_path + 'testdata-sc/10x_sc_raw.tsv'
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_10x_sc.config:30:21: pipelines_testdata_base_path is not defined

    reference_10x = pipelines_testdata_base_path + 'testdata-sc/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0.tar.gz'
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_assembled_hs.config:24:13: pipelines_testdata_base_path is not defined

    input = pipelines_testdata_base_path + 'testdata-reveal/test_assembled_metadata_hs.tsv'
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_assembled_hs.config:25:23: pipelines_testdata_base_path is not defined

    reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_assembled_hs.config:26:25: pipelines_testdata_base_path is not defined

    reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_assembled_immcantation_devel_hs.config:24:13: pipelines_testdata_base_path is not defined

    input = pipelines_testdata_base_path + 'testdata-reveal/test_assembled_metadata_hs.tsv'
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_assembled_immcantation_devel_hs.config:25:23: pipelines_testdata_base_path is not defined

    reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_assembled_immcantation_devel_hs.config:26:25: pipelines_testdata_base_path is not defined

    reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_assembled_immcantation_devel_mm.config:24:13: pipelines_testdata_base_path is not defined

    input = pipelines_testdata_base_path + 'testdata-reveal/test_assembled_metadata_mm.tsv'
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_assembled_immcantation_devel_mm.config:25:23: pipelines_testdata_base_path is not defined

    reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_assembled_immcantation_devel_mm.config:26:25: pipelines_testdata_base_path is not defined

    reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_assembled_mm.config:24:13: pipelines_testdata_base_path is not defined

    input = pipelines_testdata_base_path + 'testdata-reveal/test_assembled_metadata_mm.tsv'
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_assembled_mm.config:25:23: pipelines_testdata_base_path is not defined

    reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_assembled_mm.config:26:25: pipelines_testdata_base_path is not defined

    reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_embeddings_H.config:27:13: pipelines_testdata_base_path is not defined

    input = pipelines_testdata_base_path + 'testdata-reveal/test_assembled_metadata_tiny.tsv'
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_embeddings_H.config:28:23: pipelines_testdata_base_path is not defined

    reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_embeddings_H.config:29:25: pipelines_testdata_base_path is not defined

    reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_embeddings_HL.config:27:13: pipelines_testdata_base_path is not defined

    input = pipelines_testdata_base_path + 'testdata-reveal/test_assembled_metadata_tiny.tsv'
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_embeddings_HL.config:28:23: pipelines_testdata_base_path is not defined

    reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_embeddings_HL.config:29:25: pipelines_testdata_base_path is not defined

    reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_fetchimgt.config:26:13: pipelines_testdata_base_path is not defined

    input = pipelines_testdata_base_path + 'testdata-reveal/test_assembled_metadata_hs.tsv'
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_full.config:25:13: pipelines_testdata_base_path is not defined

    input = pipelines_testdata_base_path + 'testdata-bcr/metadata_pcr_umi_airr_300.tsv'
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_full.config:28:23: pipelines_testdata_base_path is not defined

    reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_full.config:29:25: pipelines_testdata_base_path is not defined

    reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_maskprimers_align.config:25:13: pipelines_testdata_base_path is not defined

    input = pipelines_testdata_base_path + 'testdata-bcr/Metadata_small_test_airr.tsv'
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_maskprimers_align.config:26:16: pipelines_testdata_base_path is not defined

    cprimers = pipelines_testdata_base_path + 'testdata-bcr/C_primers.fasta'
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_maskprimers_align.config:27:16: pipelines_testdata_base_path is not defined

    vprimers = pipelines_testdata_base_path + 'testdata-bcr/V_primers.fasta'
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_maskprimers_align.config:28:23: pipelines_testdata_base_path is not defined

    reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_maskprimers_align.config:29:25: pipelines_testdata_base_path is not defined

    reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_maskprimers_extract.config:25:13: pipelines_testdata_base_path is not defined

    input = pipelines_testdata_base_path + 'testdata-bcr/Metadata_small_test_airr.tsv'
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_maskprimers_extract.config:26:23: pipelines_testdata_base_path is not defined

    reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_maskprimers_extract.config:27:25: pipelines_testdata_base_path is not defined

    reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_nebnext_umi.config:28:13: pipelines_testdata_base_path is not defined

    input = pipelines_testdata_base_path + 'testdata-neb/samplesheet.tsv'
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_nebnext_umi.config:30:23: pipelines_testdata_base_path is not defined

    reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_nebnext_umi.config:31:25: pipelines_testdata_base_path is not defined

    reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_no_umi.config:31:13: pipelines_testdata_base_path is not defined

    input = pipelines_testdata_base_path + 'testdata-no-umi/Metadata_test-no-umi_airr.tsv'
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_no_umi.config:32:16: pipelines_testdata_base_path is not defined

    cprimers = pipelines_testdata_base_path + 'testdata-no-umi/Greiff2014_CPrimers.fasta'
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_no_umi.config:33:16: pipelines_testdata_base_path is not defined

    vprimers = pipelines_testdata_base_path + 'testdata-no-umi/Greiff2014_VPrimers.fasta'
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_no_umi.config:34:23: pipelines_testdata_base_path is not defined

    reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_no_umi.config:35:25: pipelines_testdata_base_path is not defined

    reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_nocluster.config:25:13: pipelines_testdata_base_path is not defined

    input = pipelines_testdata_base_path + 'testdata-bcr/Metadata_small_test_airr.tsv'
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_nocluster.config:26:16: pipelines_testdata_base_path is not defined

    cprimers = pipelines_testdata_base_path + 'testdata-bcr/C_primers.fasta'
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_nocluster.config:27:16: pipelines_testdata_base_path is not defined

    vprimers = pipelines_testdata_base_path + 'testdata-bcr/V_primers.fasta'
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_nocluster.config:28:23: pipelines_testdata_base_path is not defined

    reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_nocluster.config:29:25: pipelines_testdata_base_path is not defined

    reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_raw_immcantation_devel.config:25:13: pipelines_testdata_base_path is not defined

    input = pipelines_testdata_base_path + 'testdata-bcr/Metadata_small_test_airr.tsv'
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_raw_immcantation_devel.config:26:16: pipelines_testdata_base_path is not defined

    cprimers = pipelines_testdata_base_path + 'testdata-bcr/C_primers.fasta'
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_raw_immcantation_devel.config:27:16: pipelines_testdata_base_path is not defined

    vprimers = pipelines_testdata_base_path + 'testdata-bcr/V_primers.fasta'
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_raw_immcantation_devel.config:29:23: pipelines_testdata_base_path is not defined

    reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_raw_immcantation_devel.config:30:25: pipelines_testdata_base_path is not defined

    reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_reassign_false.config:24:13: pipelines_testdata_base_path is not defined

    input = pipelines_testdata_base_path + 'testdata-reveal/test_assembled_metadata_assigned.tsv'
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_reassign_false.config:25:23: pipelines_testdata_base_path is not defined

    reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_reassign_false.config:26:25: pipelines_testdata_base_path is not defined

    reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_takara_smartseq_umi_bcr.config:27:13: pipelines_testdata_base_path is not defined

    input = pipelines_testdata_base_path +'testdata-clontech/samplesheet.tsv'
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_takara_smartseq_umi_bcr.config:29:23: pipelines_testdata_base_path is not defined

    reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_takara_smartseq_umi_bcr.config:30:25: pipelines_testdata_base_path is not defined

    reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_tcr.config:34:13: pipelines_testdata_base_path is not defined

    input = pipelines_testdata_base_path + 'testdata-tcr/TCR_metadata_airr.tsv'
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_tcr.config:35:16: pipelines_testdata_base_path is not defined

    cprimers = pipelines_testdata_base_path + 'testdata-tcr/cprimers.fasta'
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_tcr.config:36:19: pipelines_testdata_base_path is not defined

    race_linker = pipelines_testdata_base_path + 'testdata-tcr/linker.fasta'
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_tcr.config:37:23: pipelines_testdata_base_path is not defined

    reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: conf/test_tcr.config:38:25: pipelines_testdata_base_path is not defined

    reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: modules/local/airrflow_report/airrflow_report.nf:6:5: Invalid process directive

    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
    ^

Error: modules/local/enchantr/clonal_assignment.nf:6:13: for loops are no longer supported
```
            for (param in args.keySet().sort()){
            ^^^
```

Error: modules/local/enchantr/clonal_assignment.nf:6:18: param is not defined

            for (param in args.keySet().sort()){
                 ^^^^^

Error: modules/local/enchantr/clonal_assignment.nf:7:29: param is not defined

                value = args[param].toString()
                            ^^^^^^^

Error: modules/local/enchantr/clonal_assignment.nf:11:30: param is not defined

                s = s + ",'"+param+"'="+value
                             ^^^^^

Error: modules/local/enchantr/clonal_assignment.nf:25:5: Invalid process directive

    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
    ^

Error: modules/local/enchantr/collapse_duplicates.nf:8:5: Invalid process directive

    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
    ^

Error: modules/local/enchantr/detect_contamination.nf:8:5: Invalid process directive

    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
    ^

Error: modules/local/enchantr/dowser_lineages.nf:6:13: for loops are no longer supported
```
            for (param in args.keySet().sort()){
            ^^^
```

Error: modules/local/enchantr/dowser_lineages.nf:6:18: param is not defined

            for (param in args.keySet().sort()){
                 ^^^^^

Error: modules/local/enchantr/dowser_lineages.nf:7:29: param is not defined

                value = args[param].toString()
                            ^^^^^^^

Error: modules/local/enchantr/dowser_lineages.nf:11:30: param is not defined

                s = s + ",'"+param+"'="+value
                             ^^^^^

Error: modules/local/enchantr/dowser_lineages.nf:25:5: Invalid process directive

    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
    ^

Error: modules/local/enchantr/find_threshold.nf:6:13: for loops are no longer supported
```
            for (param in args.keySet().sort()){
            ^^^
```

Error: modules/local/enchantr/find_threshold.nf:6:18: param is not defined

            for (param in args.keySet().sort()){
                 ^^^^^

Error: modules/local/enchantr/find_threshold.nf:7:29: param is not defined

                value = args[param].toString()
                            ^^^^^^^

Error: modules/local/enchantr/find_threshold.nf:11:30: param is not defined

                s = s + ",'"+param+"'="+value
                             ^^^^^

Error: modules/local/enchantr/find_threshold.nf:25:5: Invalid process directive

    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
    ^

Error: modules/local/enchantr/remove_chimeric.nf:9:5: Invalid process directive

    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
    ^

Error: modules/local/enchantr/report_file_size.nf:10:5: Invalid process directive

    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
    ^

Error: modules/local/enchantr/single_cell_qc.nf:6:13: for loops are no longer supported
```
            for (param in args.keySet().sort()){
            ^^^
```

Error: modules/local/enchantr/single_cell_qc.nf:6:18: param is not defined

            for (param in args.keySet().sort()){
                 ^^^^^

Error: modules/local/enchantr/single_cell_qc.nf:7:29: param is not defined

                value = args[param].toString()
                            ^^^^^^^

Error: modules/local/enchantr/single_cell_qc.nf:11:30: param is not defined

                s = s + ",'"+param+"'="+value
                             ^^^^^

Error: modules/local/enchantr/single_cell_qc.nf:24:5: Invalid process directive

    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
    ^

Error: modules/local/enchantr/validate_input.nf:10:5: Invalid process directive

    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
    ^

Error: modules/local/presto/presto_maskprimers_align.nf:28:9: barcode is already declared
```
    def barcode = barcode ? '--barcode' : ''
        ^^^^^^^
```
Error: modules/local/presto/presto_maskprimers_extract.nf:28:9: barcode is already declared
```
    def barcode = barcode ? '--barcode' : ''
        ^^^^^^^
```
Error: modules/local/presto/presto_maskprimers_score.nf:32:9: barcode is already declared
```
    def barcode = barcode ? '--barcode' : ''
        ^^^^^^^
```

Error: modules/local/reveal/add_meta_to_tab.nf:7:5: Invalid process directive

    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
    ^

Error: modules/local/reveal/filter_junction_mod3.nf:7:5: Invalid process directive

    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
    ^

Error: modules/local/reveal/filter_quality.nf:7:5: Invalid process directive

    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
    ^

Error: nextflow.config:88:25: pipelines_testdata_base_path is not defined

    reference_igblast = pipelines_testdata_base_path + 'database-cache/igblast_base.zip'
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: nextflow.config:89:23: pipelines_testdata_base_path is not defined

    reference_fasta = pipelines_testdata_base_path + 'database-cache/imgtdb_base.zip'
                      ^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: subworkflows/local/clonal_analysis.nf:83:38: Unexpected input: '"'

    ch_repertoire.map{ it -> [ it[0]."${params.cloneby}",
                                     ^

Error: subworkflows/local/databases.nf:5:1: Invalid workflow definition -- check for missing or out-of-order section labels
```
workflow DATABASES {
^
```

Error: subworkflows/local/fastq_input_check.nf:66:35: Unexpected input: '"'

    meta.collapseby_group   = col."${params.collapseby}"
                                  ^

Error: subworkflows/local/presto_sans_umi.nf:67:13: Incorrect number of call arguments, expected 8 but received 6
```
            PRESTO_MASKPRIMERS_ALIGN_SANSUMI_FWD(
            ^
```
Error: subworkflows/local/presto_sans_umi.nf:75:13: Incorrect number of call arguments, expected 8 but received 6
```
            PRESTO_MASKPRIMERS_ALIGN_SANSUMI_REV(
            ^
```
Error: subworkflows/local/presto_sans_umi.nf:84:13: Incorrect number of call arguments, expected 8 but received 6
```
            PRESTO_MASKPRIMERS_ALIGN_SANSUMI_FWD(
            ^
```
Error: subworkflows/local/presto_sans_umi.nf:92:13: Incorrect number of call arguments, expected 8 but received 6
```
            PRESTO_MASKPRIMERS_ALIGN_SANSUMI_REV(
            ^
```

Error: subworkflows/local/rnaseq_input.nf:3:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/airrflow/subworkflows/local/fastq_input_check.nf'

include { FASTQ_INPUT_CHECK                                             } from '../../subworkflows/local/fastq_input_check'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: subworkflows/local/rnaseq_input.nf:25:5: FASTQ_INPUT_CHECK is not defined
```
    FASTQ_INPUT_CHECK(
    ^^^^^^^^^^^^^^^^^
```

Error: subworkflows/local/rnaseq_input.nf:28:35: FASTQ_INPUT_CHECK is not defined

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

Error: subworkflows/local/rnaseq_input.nf:30:16: FASTQ_INPUT_CHECK is not defined

    ch_reads = FASTQ_INPUT_CHECK.out.reads
               ^^^^^^^^^^^^^^^^^

Error: subworkflows/local/rnaseq_input.nf:129:19: FASTQ_INPUT_CHECK is not defined

    samplesheet = FASTQ_INPUT_CHECK.out.samplesheet
                  ^^^^^^^^^^^^^^^^^

Error: subworkflows/local/sc_raw_input.nf:5:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/airrflow/subworkflows/local/fastq_input_check.nf'

include { FASTQ_INPUT_CHECK                                             } from '../../subworkflows/local/fastq_input_check'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: subworkflows/local/sc_raw_input.nf:21:5: FASTQ_INPUT_CHECK is not defined
```
    FASTQ_INPUT_CHECK(
    ^^^^^^^^^^^^^^^^^
```

Error: subworkflows/local/sc_raw_input.nf:24:35: FASTQ_INPUT_CHECK is not defined

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

Error: subworkflows/local/sc_raw_input.nf:26:16: FASTQ_INPUT_CHECK is not defined

    ch_reads = FASTQ_INPUT_CHECK.out.reads
               ^^^^^^^^^^^^^^^^^

Error: subworkflows/local/sc_raw_input.nf:99:19: FASTQ_INPUT_CHECK is not defined

    samplesheet = FASTQ_INPUT_CHECK.out.samplesheet
                  ^^^^^^^^^^^^^^^^^

Error: subworkflows/local/sequence_assembly.nf:11:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
ch_report_rmd = Channel.fromPath(params.report_rmd, checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: subworkflows/local/sequence_assembly.nf:12:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
ch_report_css = Channel.fromPath(params.report_css, checkIfExists: true)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: subworkflows/local/sequence_assembly.nf:28:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/airrflow/subworkflows/local/fastq_input_check.nf'
```
include { FASTQ_INPUT_CHECK           } from '../../subworkflows/local/fastq_input_check'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: subworkflows/local/sequence_assembly.nf:178:5: FASTQ_INPUT_CHECK is not defined
```
    FASTQ_INPUT_CHECK(ch_input)
    ^^^^^^^^^^^^^^^^^
```

Error: subworkflows/local/sequence_assembly.nf:179:35: FASTQ_INPUT_CHECK is not defined

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

Error: subworkflows/local/sequence_assembly.nf:181:16: FASTQ_INPUT_CHECK is not defined
```
    ch_reads = FASTQ_INPUT_CHECK.out.reads
               ^^^^^^^^^^^^^^^^^
```

Error: subworkflows/local/sequence_assembly.nf:243:19: FASTQ_INPUT_CHECK is not defined

    samplesheet = FASTQ_INPUT_CHECK.out.samplesheet
                  ^^^^^^^^^^^^^^^^^

Error: workflows/airrflow.nf:14:1: 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/airrflow.nf:15:1: 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/airrflow.nf:16:1: 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/airrflow.nf:17:1: 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/airrflow.nf:20:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

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

Error: workflows/airrflow.nf:21:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

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

Error: workflows/airrflow.nf:22:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

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

Error: workflows/airrflow.nf:23:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function

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

Error: workflows/airrflow.nf:36:1: Included name 'DATABASES' is not defined in module '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/airrflow/subworkflows/local/databases.nf'
```
include { DATABASES                     } from '../subworkflows/local/databases'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```

Error: workflows/airrflow.nf:42:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/airrflow/subworkflows/local/clonal_analysis.nf'

include { CLONAL_ANALYSIS               } from '../subworkflows/local/clonal_analysis'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/airrflow.nf:45:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/airrflow/subworkflows/local/fastq_input_check.nf'

include { FASTQ_INPUT_CHECK             } from '../subworkflows/local/fastq_input_check'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/airrflow.nf:82:9: DATABASES is not defined
```
        DATABASES()
        ^^^^^^^^^
```

Error: workflows/airrflow.nf:119:21: DATABASES is not defined

                    DATABASES.out.igblast.collect()
                    ^^^^^^^^^

Error: workflows/airrflow.nf:144:21: DATABASES is not defined

                    DATABASES.out.igblast.collect()
                    ^^^^^^^^^

Error: workflows/airrflow.nf:214:13: DATABASES is not defined

            DATABASES.out.igblast.collect(),
            ^^^^^^^^^

Error: workflows/airrflow.nf:215:13: DATABASES is not defined

            DATABASES.out.reference_fasta.collect()
            ^^^^^^^^^

Error: workflows/airrflow.nf:251:13: CLONAL_ANALYSIS is not defined

            CLONAL_ANALYSIS(
            ^^^^^^^^^^^^^^^

Error: workflows/airrflow.nf:254:17: ch_report_logo_img is not defined

                ch_report_logo_img.collect().ifEmpty([])
                ^^^^^^^^^^^^^^^^^^

Error: workflows/airrflow.nf:256:44: CLONAL_ANALYSIS is not defined

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

Error: workflows/airrflow.nf:263:17: DATABASES is not defined

                DATABASES.out.igblast.collect()
                ^^^^^^^^^

Error: workflows/airrflow.nf:292:17: ch_report_rmd is not defined

                ch_report_rmd.collect(),
                ^^^^^^^^^^^^^

Error: workflows/airrflow.nf:293:17: ch_report_css is not defined

                ch_report_css.collect(),
                ^^^^^^^^^^^^^

Error: workflows/airrflow.nf:294:17: ch_report_logo is not defined

                ch_report_logo.collect(),
                ^^^^^^^^^^^^^^

Error: workflows/airrflow.nf:349:17: ch_multiqc_config is not defined

                ch_multiqc_config.toList(),
                ^^^^^^^^^^^^^^^^^

Error: workflows/airrflow.nf:350:17: ch_multiqc_custom_config is not defined

                ch_multiqc_custom_config.toList(),
                ^^^^^^^^^^^^^^^^^^^^^^^^

Error: workflows/airrflow.nf:351:17: ch_report_logo is not defined

                ch_report_logo.toList(),
                ^^^^^^^^^^^^^^

⚠️ Warnings

Warning: modules/local/presto/presto_maskprimers_align.nf:29:9: Variable was declared but not used
```
    def revpr = reverse_primers ? '--revpr' : ''
        ^^^^^
```
Warning: modules/nf-core/cat/fastq/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/cat/fastq/main.nf:23:59: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: modules/nf-core/cat/fastq/main.nf:54:59: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: modules/nf-core/cellranger/vdj/main.nf:47:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/nf-core/trust4/main.nf:91:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: subworkflows/local/assembled_input_check.nf:18:15: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_logs = Channel.empty()
              ^^^^^^^
```
Warning: subworkflows/local/assembled_input_check.nf:25:25: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { get_meta(it) }
                        ^^
```
Warning: subworkflows/local/bulk_qc_and_filter.nf:14:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/bulk_qc_and_filter.nf:15:15: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_logs = Channel.empty()
              ^^^^^^^
```
Warning: subworkflows/local/presto_sans_umi.nf:29:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```

Warning: subworkflows/local/presto_sans_umi.nf:207:48: Parameter was not used -- prefix with _ to suppress warning

    fastp_reads_json = FASTP.out.json.collect{ meta,json -> json }
                                               ^^^^

Warning: subworkflows/local/presto_sans_umi.nf:208:48: Parameter was not used -- prefix with _ to suppress warning

    fastp_reads_html = FASTP.out.html.collect{ meta,html -> html }
                                               ^^^^

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

Warning: subworkflows/local/presto_umi.nf:84:51: Parameter was not used -- prefix with _ to suppress warning

                                            .map{ id, meta1, R1, R2, meta2, index -> [ meta1, R1, R2, index ] }
                                                  ^^

Warning: subworkflows/local/presto_umi.nf:84:70: Parameter was not used -- prefix with _ to suppress warning

                                            .map{ id, meta1, R1, R2, meta2, index -> [ meta1, R1, R2, index ] }
                                                                     ^^^^^

Warning: subworkflows/local/presto_umi.nf:433:31: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_clustersets_logs = Channel.empty()
                              ^^^^^^^
```

Warning: subworkflows/local/presto_umi.nf:586:48: Parameter was not used -- prefix with _ to suppress warning

    fastp_reads_json = FASTP.out.json.collect{ meta,json -> json }
                                               ^^^^

Warning: subworkflows/local/presto_umi.nf:587:48: Parameter was not used -- prefix with _ to suppress warning

    fastp_reads_html = FASTP.out.html.collect{ meta,html -> html }
                                               ^^^^

Warning: subworkflows/local/repertoire_analysis_reporting.nf:31:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/repertoire_analysis_reporting.nf:51:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_parsed_logs = Channel.empty()
                         ^^^^^^^
```
Warning: subworkflows/local/rnaseq_input.nf:19:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/rnaseq_input.nf:20:5: Variable was declared but not used
```
    ch_logs = Channel.empty()
    ^^^^^^^
```
Warning: subworkflows/local/rnaseq_input.nf:20:15: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_logs = Channel.empty()
              ^^^^^^^
```

Warning: subworkflows/local/rnaseq_input.nf:96:53: Implicit closure parameter is deprecated, declare an explicit parameter instead

                    return [ meta, out_files.find { it.endsWith("${meta.id}_airr.tsv") } ]
                                                    ^^

Warning: subworkflows/local/rnaseq_input.nf:98:53: Implicit closure parameter is deprecated, declare an explicit parameter instead

                    return [ meta, out_files.find { it.endsWith("${meta.id}_barcode_airr.tsv") } ]
                                                    ^^

Warning: subworkflows/local/rnaseq_input.nf:121:48: Parameter was not used -- prefix with _ to suppress warning

    fastp_reads_json = FASTP.out.json.collect{ meta,json -> json }
                                               ^^^^

Warning: subworkflows/local/rnaseq_input.nf:122:48: Parameter was not used -- prefix with _ to suppress warning

    fastp_reads_html = FASTP.out.html.collect{ meta,html -> html }
                                               ^^^^

Warning: subworkflows/local/sc_raw_input.nf:15:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/sc_raw_input.nf:16:5: Variable was declared but not used
```
    ch_logs = Channel.empty()
    ^^^^^^^
```
Warning: subworkflows/local/sc_raw_input.nf:16:15: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_logs = Channel.empty()
              ^^^^^^^
```

Warning: subworkflows/local/sc_raw_input.nf:49:31: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_sc_reference = Channel.fromPath(params.reference_10x, checkIfExists: true)
                              ^^^^^^^

Warning: subworkflows/local/sc_raw_input.nf:66:42: Implicit closure parameter is deprecated, declare an explicit parameter instead

                [ meta, out_files.find { it.endsWith("airr_rearrangement.tsv") } ]
                                         ^^

Warning: subworkflows/local/sc_raw_input.nf:77:16: Variable was declared but not used
```
        .set { ch_renamed_tsv }
               ^^^^^^^^^^^^^^
```

Warning: subworkflows/local/sequence_assembly.nf:11:1: Variable was declared but not used

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

Warning: subworkflows/local/sequence_assembly.nf:11:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
ch_report_rmd = Channel.fromPath(params.report_rmd, checkIfExists: true)
                ^^^^^^^
```

Warning: subworkflows/local/sequence_assembly.nf:12:1: Variable was declared but not used

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

Warning: subworkflows/local/sequence_assembly.nf:12:17: The use of Channel to access channel factories is deprecated -- use channel instead
```
ch_report_css = Channel.fromPath(params.report_css, checkIfExists: true)
                ^^^^^^^
```
Warning: subworkflows/local/sequence_assembly.nf:62:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_adapter_fasta = Channel.fromPath(params.adapter_fasta, checkIfExists: true)
                           ^^^^^^^
```

Warning: subworkflows/local/sequence_assembly.nf:72:37: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: subworkflows/local/sequence_assembly.nf:77:37: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: subworkflows/local/sequence_assembly.nf:85:33: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_vprimers_fasta = Channel.of([])
                                ^^^^^^^
```
Warning: subworkflows/local/sequence_assembly.nf:86:33: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_cprimers_fasta = Channel.of([])
                                ^^^^^^^
```

Warning: subworkflows/local/sequence_assembly.nf:92:35: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: subworkflows/local/sequence_assembly.nf:94:35: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_internal_cregion = Channel.of([])
                                  ^^^^^^^
```

Warning: subworkflows/local/sequence_assembly.nf:98:33: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: subworkflows/local/sequence_assembly.nf:103:33: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: subworkflows/local/sequence_assembly.nf:122:33: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: subworkflows/local/sequence_assembly.nf:124:33: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_vprimers_fasta = Channel.of([])
                                ^^^^^^^
```

Warning: subworkflows/local/sequence_assembly.nf:129:33: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: subworkflows/local/sequence_assembly.nf:137:35: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: subworkflows/local/sequence_assembly.nf:139:35: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_internal_cregion = Channel.of([])
                                  ^^^^^^^
```

Warning: subworkflows/local/sequence_assembly.nf:145:33: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: subworkflows/local/sequence_assembly.nf:147:33: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_vprimers_fasta = Channel.of([])
                                ^^^^^^^
```

Warning: subworkflows/local/sequence_assembly.nf:152:33: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: subworkflows/local/sequence_assembly.nf:176:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/sequence_assembly.nf:203:34: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_presto_pairseq_logs = Channel.empty()
                                 ^^^^^^^
```
Warning: subworkflows/local/sequence_assembly.nf:204:38: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_presto_clustersets_logs = Channel.empty()
                                     ^^^^^^^
```
Warning: subworkflows/local/sequence_assembly.nf:205:41: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_presto_buildconsensus_logs = Channel.empty()
                                        ^^^^^^^
```
Warning: subworkflows/local/sequence_assembly.nf:206:48: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_presto_postconsensus_pairseq_logs = Channel.empty()
                                               ^^^^^^^
```
Warning: subworkflows/local/single_cell_qc_and_filtering.nf:8:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/single_cell_qc_and_filtering.nf:9:15: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_logs = Channel.empty()
              ^^^^^^^
```
Warning: subworkflows/local/translate_embed.nf:13:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_airrflow_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_airrflow_pipeline/main.nf:103:5: The use of Channel to access channel factories is deprecated -- use channel instead
```
    Channel.fromList(samplesheetToList(input, "${projectDir}/assets/schema_input.json"))
    ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_airrflow_pipeline/main.nf:105:5: The use of Channel to access channel factories is deprecated -- use channel instead
```
    Channel.fromPath(input).set{ch_samplesheet}
    ^^^^^^^
```
Warning: subworkflows/local/vdj_annotation.nf:20:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/vdj_annotation.nf:21:15: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_logs = Channel.empty()
              ^^^^^^^
```

Warning: workflows/airrflow.nf:14:1: Variable was declared but not used

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

Warning: workflows/airrflow.nf:14:28: 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/airrflow.nf:15:1: Variable was declared but not used

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

Warning: workflows/airrflow.nf:15:52: 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/airrflow.nf:15:117: 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/airrflow.nf:16:1: Variable was declared but not used

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

Warning: workflows/airrflow.nf:16:52: 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/airrflow.nf:16:115: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/airrflow.nf:17:1: 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/airrflow.nf:20:1: Variable was declared but not used

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

Warning: workflows/airrflow.nf:20:23: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/airrflow.nf:21:1: Variable was declared but not used

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

Warning: workflows/airrflow.nf:21:23: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/airrflow.nf:22:1: Variable was declared but not used

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

Warning: workflows/airrflow.nf:22:23: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/airrflow.nf:23:1: Variable was declared but not used

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

Warning: workflows/airrflow.nf:23:23: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/airrflow.nf:77:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_versions = Channel.empty()
                      ^^^^^^^
```
Warning: workflows/airrflow.nf:78:28: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_reassign_logs = Channel.empty()
                           ^^^^^^^
```
Warning: workflows/airrflow.nf:79:31: The use of Channel to access channel factories is deprecated -- use channel instead
```
        ch_input_check_logs = Channel.empty()
                              ^^^^^^^
```

Warning: workflows/airrflow.nf:95:17: Variable was declared but not used

                ch_cellranger_airr                      = SC_RAW_INPUT.out.airr
                ^^^^^^^^^^^^^^^^^^

Warning: workflows/airrflow.nf:96:17: Variable was declared but not used

                ch_cellranger_out                       = SC_RAW_INPUT.out.outs
                ^^^^^^^^^^^^^^^^^

Warning: workflows/airrflow.nf:100:59: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_presto_filterseq_logs                = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/airrflow.nf:101:59: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_presto_maskprimers_logs              = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/airrflow.nf:102:59: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_presto_pairseq_logs                  = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/airrflow.nf:103:59: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_presto_clustersets_logs              = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/airrflow.nf:104:59: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_presto_buildconsensus_logs           = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/airrflow.nf:105:59: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_presto_postconsensus_pairseq_logs    = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/airrflow.nf:106:59: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_presto_assemblepairs_logs            = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/airrflow.nf:107:59: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_presto_collapseseq_logs              = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/airrflow.nf:108:59: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_presto_splitseq_logs                 = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/airrflow.nf:109:59: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_fastp_html                           = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/airrflow.nf:110:59: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_fastp_json                           = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/airrflow.nf:111:59: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_fastqc_postassembly_mqc              = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/airrflow.nf:112:59: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_tsv_files                            = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/airrflow.nf:127:59: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_presto_filterseq_logs                = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/airrflow.nf:128:59: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_presto_maskprimers_logs              = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/airrflow.nf:129:59: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_presto_pairseq_logs                  = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/airrflow.nf:130:59: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_presto_clustersets_logs              = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/airrflow.nf:131:59: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_presto_buildconsensus_logs           = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/airrflow.nf:132:59: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_presto_postconsensus_pairseq_logs    = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/airrflow.nf:133:59: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_presto_assemblepairs_logs            = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/airrflow.nf:134:59: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_presto_collapseseq_logs              = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/airrflow.nf:135:59: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_presto_splitseq_logs                 = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/airrflow.nf:138:59: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_fastqc_postassembly_mqc              = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/airrflow.nf:139:59: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_tsv_files                            = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/airrflow.nf:162:59: The use of Channel to access channel factories is deprecated -- use channel instead

                ch_tsv_files                            = Channel.empty()
                                                          ^^^^^^^

Warning: workflows/airrflow.nf:183:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
                ch_tsv_files = Channel.empty()
                               ^^^^^^^
```
Warning: workflows/airrflow.nf:185:37: The use of Channel to access channel factories is deprecated -- use channel instead
```
                ch_fasta_from_tsv = Channel.empty()
                                    ^^^^^^^
```

Warning: workflows/airrflow.nf:192:52: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_presto_filterseq_logs             = Channel.empty()
                                                   ^^^^^^^

Warning: workflows/airrflow.nf:193:52: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_presto_maskprimers_logs           = Channel.empty()
                                                   ^^^^^^^

Warning: workflows/airrflow.nf:194:52: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_presto_pairseq_logs               = Channel.empty()
                                                   ^^^^^^^

Warning: workflows/airrflow.nf:195:52: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_presto_clustersets_logs           = Channel.empty()
                                                   ^^^^^^^

Warning: workflows/airrflow.nf:196:52: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_presto_buildconsensus_logs        = Channel.empty()
                                                   ^^^^^^^

Warning: workflows/airrflow.nf:197:52: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_presto_postconsensus_pairseq_logs = Channel.empty()
                                                   ^^^^^^^

Warning: workflows/airrflow.nf:198:52: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_presto_assemblepairs_logs         = Channel.empty()
                                                   ^^^^^^^

Warning: workflows/airrflow.nf:199:52: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_presto_collapseseq_logs           = Channel.empty()
                                                   ^^^^^^^

Warning: workflows/airrflow.nf:200:52: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_presto_splitseq_logs              = Channel.empty()
                                                   ^^^^^^^

Warning: workflows/airrflow.nf:201:52: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_fastp_html                        = Channel.empty()
                                                   ^^^^^^^

Warning: workflows/airrflow.nf:202:52: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_fastp_json                        = Channel.empty()
                                                   ^^^^^^^

Warning: workflows/airrflow.nf:203:52: The use of Channel to access channel factories is deprecated -- use channel instead

            ch_fastqc_postassembly_mqc           = Channel.empty()
                                                   ^^^^^^^

Warning: workflows/airrflow.nf:303:26: The use of Channel to access channel factories is deprecated -- use channel instead
```
    def topic_versions = Channel.topic("versions")
                         ^^^^^^^
```

Warning: workflows/airrflow.nf:334:35: The use of Channel to access channel factories is deprecated -- use channel instead

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

Warning: workflows/airrflow.nf:337:39: 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/airrflow.nf:339:32: The use of Channel to access channel factories is deprecated -- use channel instead
```
            ch_multiqc_files = Channel.empty()
                               ^^^^^^^
```

Warning: workflows/airrflow.nf:345:88: Implicit closure parameter is deprecated, declare an explicit parameter instead

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

Warning: workflows/airrflow.nf:357:30: The use of Channel to access channel factories is deprecated -- use channel instead
```
            multiqc_report = Channel.empty()
                             ^^^^^^^
```

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