Nextflow lint results

Generated: 2026-01-16T10:24:53.971076257Z
Nextflow version: 25.12.0-edge
Summary: 44 errors, 30 warnings

❌ Errors

Error: conf/base.config:14:16: check_max is not defined

    cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
               ^^^^^^^^^

Error: conf/base.config:15:16: check_max is not defined

    memory = { check_max( 6.GB * task.attempt, 'memory' ) }
               ^^^^^^^^^

Error: conf/base.config:16:16: check_max is not defined

    time   = { check_max( 4.h  * task.attempt, 'time'   ) }
               ^^^^^^^^^

Error: conf/base.config:30:20: check_max is not defined

        cpus   = { check_max( 1                  , 'cpus'    ) }
                   ^^^^^^^^^

Error: conf/base.config:31:20: check_max is not defined

        memory = { check_max( 6.GB * task.attempt, 'memory'  ) }
                   ^^^^^^^^^

Error: conf/base.config:32:20: check_max is not defined

        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
                   ^^^^^^^^^

Error: conf/base.config:35:20: check_max is not defined

        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
                   ^^^^^^^^^

Error: conf/base.config:36:20: check_max is not defined

        memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
                   ^^^^^^^^^

Error: conf/base.config:37:20: check_max is not defined

        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
                   ^^^^^^^^^

Error: conf/base.config:40:20: check_max is not defined

        cpus   = { check_max( 6     * task.attempt, 'cpus'    ) }
                   ^^^^^^^^^

Error: conf/base.config:41:20: check_max is not defined

        memory = { check_max( 36.GB * task.attempt, 'memory'  ) }
                   ^^^^^^^^^

Error: conf/base.config:42:20: check_max is not defined

        time   = { check_max( 8.h   * task.attempt, 'time'    ) }
                   ^^^^^^^^^

Error: conf/base.config:45:20: check_max is not defined

        cpus   = { check_max( 12    * task.attempt, 'cpus'    ) }
                   ^^^^^^^^^

Error: conf/base.config:46:20: check_max is not defined

        memory = { check_max( 72.GB * task.attempt, 'memory'  ) }
                   ^^^^^^^^^

Error: conf/base.config:47:20: check_max is not defined

        time   = { check_max( 16.h  * task.attempt, 'time'    ) }
                   ^^^^^^^^^

Error: conf/base.config:50:20: check_max is not defined

        time   = { check_max( 20.h  * task.attempt, 'time'    ) }
                   ^^^^^^^^^

Error: conf/base.config:53:20: check_max is not defined

        memory = { check_max( 200.GB * task.attempt, 'memory' ) }
                   ^^^^^^^^^

Error: main.nf:30:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
if (params.help) {
^
```

Error: main.nf:31:16: NfcoreTemplate is not defined

    def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
               ^^^^^^^^^^^^^^

Error: main.nf:32:27: WorkflowMain is not defined

    def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
                          ^^^^^^^^^^^^

Error: main.nf:34:54: NfcoreTemplate is not defined

    log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs)
                                                     ^^^^^^^^^^^^^^

Error: main.nf:43:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
WorkflowMain.initialise(workflow, params, log, args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```

Error: main.nf:43:1: WorkflowMain is not defined

WorkflowMain.initialise(workflow, params, log, args)
^^^^^^^^^^^^

Error: modules/nf-core/multiqc/main.nf:28:31: Unexpected input: '/'

    def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : ''
                              ^

Error: nextflow.config:71:5: Unexpected input: 'includeConfig'

    includeConfig "${params.custom_config_base}/nfcore_custom.config"
    ^

Error: subworkflows/local/mmap.nf:21:21: Unexpected input: '->'

        .map ( gene -> gene.trim() )
                    ^

Error: workflows/omicsgenetraitassociation.nf:9:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```

Error: workflows/omicsgenetraitassociation.nf:9:12: NfcoreTemplate is not defined

def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
           ^^^^^^^^^^^^^^

Error: workflows/omicsgenetraitassociation.nf:10:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```

Error: workflows/omicsgenetraitassociation.nf:10:23: WorkflowMain is not defined

def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
                      ^^^^^^^^^^^^

Error: workflows/omicsgenetraitassociation.nf:11:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
def summary_params = paramsSummaryMap(workflow)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/omicsgenetraitassociation.nf:14:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
log.info logo + paramsSummaryLog(workflow) + citation
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/omicsgenetraitassociation.nf:16:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
WorkflowOmicsgenetraitassociation.initialise(params, log)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/omicsgenetraitassociation.nf:16:1: WorkflowOmicsgenetraitassociation is not defined
```
WorkflowOmicsgenetraitassociation.initialise(params, log)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/omicsgenetraitassociation.nf:52:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/omicsgenetraitassociation/subworkflows/local/mmap.nf'
```
include { MMAP_SUBWORKFLOW }            from '../subworkflows/local/mmap'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: workflows/omicsgenetraitassociation.nf:120:5: MMAP_SUBWORKFLOW is not defined
```
    MMAP_SUBWORKFLOW (
    ^^^^^^^^^^^^^^^^
```

Error: workflows/omicsgenetraitassociation.nf:127:22: MMAP_SUBWORKFLOW is not defined

    ch_mmap_parsed = MMAP_SUBWORKFLOW.out.parsed_mmap_output
                     ^^^^^^^^^^^^^^^^

Error: workflows/omicsgenetraitassociation.nf:128:26: MMAP_SUBWORKFLOW is not defined

    ch_mmap_cma_format = MMAP_SUBWORKFLOW.out.cma_format_output
                         ^^^^^^^^^^^^^^^^

Error: workflows/omicsgenetraitassociation.nf:129:35: MMAP_SUBWORKFLOW is not defined

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

Error: workflows/omicsgenetraitassociation.nf:248:1: Statements cannot be mixed with script declarations -- move statements into a process, workflow, or function
```
workflow.onComplete {
^
```

Error: workflows/omicsgenetraitassociation.nf:250:9: NfcoreTemplate is not defined

        NfcoreTemplate.email(workflow, params, summary_params, projectDir, log)
        ^^^^^^^^^^^^^^

Error: workflows/omicsgenetraitassociation.nf:252:5: NfcoreTemplate is not defined
```
    NfcoreTemplate.dump_parameters(workflow, params)
    ^^^^^^^^^^^^^^
```
Error: workflows/omicsgenetraitassociation.nf:253:5: NfcoreTemplate is not defined
```
    NfcoreTemplate.summary(workflow, params, log)
    ^^^^^^^^^^^^^^
```

Error: workflows/omicsgenetraitassociation.nf:255:9: NfcoreTemplate is not defined

        NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log)
        ^^^^^^^^^^^^^^

⚠️ Warnings

Warning: modules/local/cma/cma/main.nf:24:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/cma/format_cma_input/main.nf:26:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/mea/go_analysis/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/mea/merge_ora_and_summary/main.nf:25:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/mea/pascal/main.nf:20:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/mea/postprocess/main.nf:28:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/mea/preprocess/main.nf:24:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/mmap/mmap/main.nf:23:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/mmap/mmap_parse/main.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/pascal/main.nf:22:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/nf-core/custom/dumpsoftwareversions/main.nf:22:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/nf-core/fastqc/main.nf:27:48: Parameter was not used -- prefix with _ to suppress warning

    def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
                                               ^^^^^^^^

Warning: subworkflows/local/cma.nf:15:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/cma.nf:16:15: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_pval = Channel.empty()
              ^^^^^^^
```
Warning: subworkflows/local/cma.nf:17:20: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_tetrachor = Channel.empty()
                   ^^^^^^^
```

Warning: subworkflows/local/cma.nf:20:23: The use of Channel to access channel factories is deprecated -- use channel instead

        input_files = Channel.fromPath("${params.cma_two_traits}/*.csv").toList()
                      ^^^^^^^

Warning: subworkflows/local/input_check.nf:15:37: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .map { create_fastq_channel(it) }
                                    ^^
```
Warning: subworkflows/local/pascal.nf:14:31: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions             = Channel.empty()
                              ^^^^^^^
```
Warning: subworkflows/local/pascal.nf:15:31: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_pascal_out           = Channel.empty()
                              ^^^^^^^
```
Warning: subworkflows/local/pascal.nf:21:16: Parameter was not used -- prefix with _ to suppress warning
```
        .map { meta, file -> file}
               ^^^^
```
Warning: workflows/omicsgenetraitassociation.nf:79:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: workflows/omicsgenetraitassociation.nf:80:31: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_mea_preprocess_input = Channel.empty()
                              ^^^^^^^
```
Warning: workflows/omicsgenetraitassociation.nf:86:5: The use of Channel to access channel factories is deprecated -- use channel instead
```
    Channel.fromSamplesheet("input")
    ^^^^^^^
```
Warning: workflows/omicsgenetraitassociation.nf:111:5: Variable was declared but not used
```
    ch_pascal_output = PASCAL_SUBWORKFLOW.out.pascal_output
    ^^^^^^^^^^^^^^^^
```
Warning: workflows/omicsgenetraitassociation.nf:127:5: Variable was declared but not used
```
    ch_mmap_parsed = MMAP_SUBWORKFLOW.out.parsed_mmap_output
    ^^^^^^^^^^^^^^
```
Warning: workflows/omicsgenetraitassociation.nf:160:23: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_module_files = Channel.fromPath("${params.module_file_dir}/*.txt")
                      ^^^^^^^
```

Warning: workflows/omicsgenetraitassociation.nf:225:5: Variable was declared but not used

    ch_merge_summary_dir = MERGE_ORA_AND_SUMMARY.out.summary_dir
    ^^^^^^^^^^^^^^^^^^^^

Warning: workflows/omicsgenetraitassociation.nf:227:5: Variable was declared but not used
```
    ch_merge_meta = MERGE_ORA_AND_SUMMARY.out.meta
    ^^^^^^^^^^^^^
```
Warning: workflows/omicsgenetraitassociation.nf:228:5: Variable was declared but not used
```
    ch_merge_trait = MERGE_ORA_AND_SUMMARY.out.trait
    ^^^^^^^^^^^^^^
```
Warning: workflows/omicsgenetraitassociation.nf:233:5: Variable was declared but not used
```
    ch_master_summary = ch_merge_summary_files
    ^^^^^^^^^^^^^^^^^
```

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Nextflow lint results

❌ Errors

⚠️ Warnings

FilesExpand file tree

omicsgenetraitassociation_lint.md

Latest commit

History

omicsgenetraitassociation_lint.md

File metadata and controls

Nextflow lint results

❌ Errors

⚠️ Warnings