Update to the latest template

[olgabot]

Description of the bug

Linting is failing here: #5

should be nf-core pipelines lint not nf-core lint

Command used and terminal output

Run nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md


                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\ 
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 3.0.2 - https://nf-co.re


DeprecationWarning: The command 'lint' is deprecated.
WARNING  The `nf-core lint` command is deprecated. Use `nf-core pipelines lint` 
         instead.                                                               

INFO     Testing pipeline: /home/runner/work/nf-core-kmerseek/nf-core-kmerseek  

25l
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 0 of 4 » fastqc
Linting nf-core modules ━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1 of 4 » fastqc
Linting nf-core modules ━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1 of 4 » fastqc
Linting nf-core modules ━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1 of 4 » fastqc
Linting nf-core modules ━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1 of 4 » fastqc
Linting nf-core modules ━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1 of 4 » fastqc
Linting nf-core modules ━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1 of 4 » fastqc
Linting nf-core modules ━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1 of 4 » fastqc
Linting nf-core modules ━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1 of 4 » fastqc
Linting nf-core modules ━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1 of 4 » fastqc
Linting nf-core modules ━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1 of 4 » fastqc
Linting nf-core modules ━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1 of 4 » fastqc
Linting nf-core modules ━━━━━━━━━━╺━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1 of 4 » fastqc
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━ 2 of 4 » multiqc
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━ 2 of 4 » multiqc
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━ 2 of 4 » multiqc
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━ 2 of 4 » multiqc
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━ 2 of 4 » multiqc
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━ 2 of 4 » multiqc
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━ 2 of 4 » multiqc
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━ 2 of 4 » multiqc
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━ 2 of 4 » multiqc
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━ 2 of 4 » multiqc
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━ 2 of 4 » multiqc
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━ 2 of 4 » multiqc
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━ 2 of 4 » multiqc
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━ 2 of 4 » multiqc
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━ 2 of 4 » multiqc
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━ 2 of 4 » multiqc
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━╸━━━━━━━━━━━━━━━━━━━ 2 of 4 » multiqc
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━ 3 of 4 » seqkit/split2
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━ 3 of 4 » seqkit/split2
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━ 3 of 4 » seqkit/split2
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━ 3 of 4 » seqkit/split2
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━ 3 of 4 » seqkit/split2
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━ 3 of 4 » seqkit/split2
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━ 3 of 4 » seqkit/split2
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━ 3 of 4 » seqkit/split2
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━ 3 of 4 » seqkit/split2
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━ 3 of 4 » seqkit/split2
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━ 3 of 4 » seqkit/split2
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━ 3 of 4 » seqkit/split2
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━╸━━━━━━━━ 3 of 4 » seqkit/split2
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4 of 4 » sourmash/sketch
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4 of 4 » sourmash/sketch
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4 of 4 » sourmash/sketch
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4 of 4 » sourmash/sketch
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4 of 4 » sourmash/sketch
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4 of 4 » sourmash/sketch
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4 of 4 » sourmash/sketch
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4 of 4 » sourmash/sketch
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4 of 4 » sourmash/sketch
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4 of 4 » sourmash/sketch
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4 of 4 » sourmash/sketch
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4 of 4 » sourmash/sketch
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4 of 4 » sourmash/sketch
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4 of 4 » sourmash/sketch
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4 of 4 » sourmash/sketch
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4 of 4 » sourmash/sketch
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4 of 4 » sourmash/sketch
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4 of 4 » sourmash/sketch
Linting nf-core modules ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4 of 4 » sourmash/sketch
25h
25l
Linting local subworkflows ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 0 of 2 » kmerize
Linting local subworkflows ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2 of 2 » search
25h
25l
Linting nf-core subworkflows ━━━━━━━━━━━━━━━━━━ 0 of 3 » utils_nextflow_pipeline
Linting nf-core subworkflows ━━━━━━╺━━━━━━━━━━━ 1 of 3 » utils_nextflow_pipeline
Linting nf-core subworkflows ━━━━━━╺━━━━━━━━━━━ 1 of 3 » utils_nextflow_pipeline
Linting nf-core subworkflows ━━━━━━╺━━━━━━━━━━━ 1 of 3 » utils_nextflow_pipeline
Linting nf-core subworkflows ━━━━━━╺━━━━━━━━━━━ 1 of 3 » utils_nextflow_pipeline
Linting nf-core subworkflows ━━━━━━╺━━━━━━━━━━━ 1 of 3 » utils_nextflow_pipeline
Linting nf-core subworkflows ━━━━━━╺━━━━━━━━━━━ 1 of 3 » utils_nextflow_pipeline
Linting nf-core subworkflows ━━━━━━╺━━━━━━━━━━━ 1 of 3 » utils_nextflow_pipeline
Linting nf-core subworkflows ━━━━━━╺━━━━━━━━━━━ 1 of 3 » utils_nextflow_pipeline
Linting nf-core subworkflows ━━━━━━╺━━━━━━━━━━━ 1 of 3 » utils_nextflow_pipeline
Linting nf-core subworkflows ━━━━━━╺━━━━━━━━━━━ 1 of 3 » utils_nextflow_pipeline
Linting nf-core subworkflows ━━━━━━╺━━━━━━━━━━━ 1 of 3 » utils_nextflow_pipeline
Linting nf-core subworkflows ━━━━━━╺━━━━━━━━━━━ 1 of 3 » utils_nextflow_pipeline
Linting nf-core subworkflows ━━━━━━╺━━━━━━━━━━━ 1 of 3 » utils_nextflow_pipeline
Linting nf-core subworkflows ━━━━━━╺━━━━━━━━━━━ 1 of 3 » utils_nextflow_pipeline
Linting nf-core subworkflows ━━━━━━╺━━━━━━━━━━━ 1 of 3 » utils_nextflow_pipeline
Linting nf-core subworkflows ━━━━━━━━━━━━━╺━━━━━━ 2 of 3 » utils_nfcore_pipeline
Linting nf-core subworkflows ━━━━━━━━━━━━━╺━━━━━━ 2 of 3 » utils_nfcore_pipeline
Linting nf-core subworkflows ━━━━━━━━━━━━━╺━━━━━━ 2 of 3 » utils_nfcore_pipeline
Linting nf-core subworkflows ━━━━━━━━━━━━━╺━━━━━━ 2 of 3 » utils_nfcore_pipeline
Linting nf-core subworkflows ━━━━━━━━━━━━━╺━━━━━━ 2 of 3 » utils_nfcore_pipeline
Linting nf-core subworkflows ━━━━━━━━━━━━━╺━━━━━━ 2 of 3 » utils_nfcore_pipeline
Linting nf-core subworkflows ━━━━━━━━━━━━━╺━━━━━━ 2 of 3 » utils_nfcore_pipeline
Linting nf-core subworkflows ━━━━━━━━━━━━━╺━━━━━━ 2 of 3 » utils_nfcore_pipeline
Linting nf-core subworkflows ━━━━━━━━━━━━━╺━━━━━━ 2 of 3 » utils_nfcore_pipeline
Linting nf-core subworkflows ━━━━━━━━━━━━━╺━━━━━━ 2 of 3 » utils_nfcore_pipeline
Linting nf-core subworkflows ━━━━━━━━━━━━━╺━━━━━━ 2 of 3 » utils_nfcore_pipeline
Linting nf-core subworkflows ━━━━━━━━━━━━━╺━━━━━━ 2 of 3 » utils_nfcore_pipeline
Linting nf-core subworkflows ━━━━━━━━━━━━━╺━━━━━━ 2 of 3 » utils_nfcore_pipeline
Linting nf-core subworkflows ━━━━━━━━━━━━━╺━━━━━━ 2 of 3 » utils_nfcore_pipeline
Linting nf-core subworkflows ━━━━━━━━━━━━━━━━ 3 of 3 » utils_nfvalidation_plugin
Linting nf-core subworkflows ━━━━━━━━━━━━━━━━ 3 of 3 » utils_nfvalidation_plugin
Linting nf-core subworkflows ━━━━━━━━━━━━━━━━ 3 of 3 » utils_nfvalidation_plugin
Linting nf-core subworkflows ━━━━━━━━━━━━━━━━ 3 of 3 » utils_nfvalidation_plugin
Linting nf-core subworkflows ━━━━━━━━━━━━━━━━ 3 of 3 » utils_nfvalidation_plugin
Linting nf-core subworkflows ━━━━━━━━━━━━━━━━ 3 of 3 » utils_nfvalidation_plugin
Linting nf-core subworkflows ━━━━━━━━━━━━━━━━ 3 of 3 » utils_nfvalidation_plugin
Linting nf-core subworkflows ━━━━━━━━━━━━━━━━ 3 of 3 » utils_nfvalidation_plugin
Linting nf-core subworkflows ━━━━━━━━━━━━━━━━ 3 of 3 » utils_nfvalidation_plugin
Linting nf-core subworkflows ━━━━━━━━━━━━━━━━ 3 of 3 » utils_nfvalidation_plugin
Linting nf-core subworkflows ━━━━━━━━━━━━━━━━ 3 of 3 » utils_nfvalidation_plugin
Linting nf-core subworkflows ━━━━━━━━━━━━━━━━ 3 of 3 » utils_nfvalidation_plugin
Linting nf-core subworkflows ━━━━━━━━━━━━━━━━ 3 of 3 » utils_nfvalidation_plugin
Linting nf-core subworkflows ━━━━━━━━━━━━━━━━ 3 of 3 » utils_nfvalidation_plugin
Linting nf-core subworkflows ━━━━━━━━━━━━━━━━ 3 of 3 » utils_nfvalidation_plugin
25h

╭─ [?] 1 Pipeline Test Ignored ────────────────────────────────────────────────╮
│                                                                              │
│ files_unchanged: File ignored due to lint config:                            │
│ docs/images/nf-core-kmerseek_logo_dark.png                                   │
│                                                                              │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ [!] 33 Pipeline Test Warnings ──────────────────────────────────────────────╮
│                                                                              │
│ files_exist: File not found: conf/igenomes_ignored.config                    │
│ nextflow_config: nf-validation has been detected in the pipeline. Please     │
│ migrate to nf-schema:                                                        │
│ https://nextflow-io.github.io/nf-schema/latest/migration_guide/              │
│ readme: README contains the placeholder zenodo.XXXXXXX. This should be       │
│ replaced with the zenodo doi (after the first release).                      │
│ pipeline_todos: TODO string in main.nf: Remove this line if you don't need a │
│ FASTA file                                                                   │
│ pipeline_todos: TODO string in nextflow.config: Specify your pipeline's      │
│ command line flags                                                           │
│ pipeline_todos: TODO string in README.md: TODO nf-core:                      │
│ pipeline_todos: TODO string in README.md: Include a figure that guides the   │
│ user through the major workflow steps. Many nf-core                          │
│ pipeline_todos: TODO string in README.md: Fill in short bullet-pointed list  │
│ of the default steps in the pipeline                                         │
│ pipeline_todos: TODO string in README.md: Describe the minimum required      │
│ steps to execute the pipeline, e.g. how to prepare samplesheets.             │
│ pipeline_todos: TODO string in README.md: update the following command to    │
│ include all required parameters for a minimal example                        │
│ pipeline_todos: TODO string in README.md: If applicable, make list of people │
│ who have also contributed                                                    │
│ pipeline_todos: TODO string in README.md: Add citation for pipeline after    │
│ first release. Uncomment lines below and update Zenodo doi and badge at the  │
│ top of this file.                                                            │
│ pipeline_todos: TODO string in README.md: Add bibliography of tools and data │
│ used in your pipeline                                                        │
│ pipeline_todos: TODO string in output.md: Write this documentation           │
│ describing your workflow's output                                            │
│ pipeline_todos: TODO string in usage.md: Add documentation about anything    │
│ specific to running your pipeline. For general topics, please point to (and  │
│ add to) the main nf-core website.                                            │
│ pipeline_todos: TODO string in search.nf: If in doubt look at other          │
│ nf-core/subworkflows to see how we are doing things! :)                      │
│ pipeline_todos: TODO string in search.nf: A subworkflow SHOULD import at     │
│ least two modules                                                            │
│ pipeline_todos: TODO string in search.nf: edit input (take) channels         │
│ pipeline_todos: TODO string in search.nf: substitute modules here for the    │
│ modules of your subworkflow                                                  │
│ pipeline_todos: TODO string in search.nf: edit emitted channels              │
│ pipeline_todos: TODO string in main.nf: Optionally add in-text citation      │
│ tools to this list.                                                          │
│ pipeline_todos: TODO string in main.nf: Optionally add bibliographic entries │
│ to this list.                                                                │
│ pipeline_todos: TODO string in main.nf: Only uncomment below if logic in     │
│ toolCitationText/toolBibliographyText has been filled!                       │
│ pipeline_todos: TODO string in test_full.config: Specify the paths to your   │
│ full test data ( on nf-core/test-datasets or directly in repositories, e.g.  │
│ SRA)                                                                         │
│ pipeline_todos: TODO string in test_full.config: Give any required params    │
│ for the test so that command line flags are not needed                       │
│ pipeline_todos: TODO string in test.config: Specify the paths to your test   │
│ data on nf-core/test-datasets                                                │
│ pipeline_todos: TODO string in test.config: Give any required params for the │
│ test so that command line flags are not needed                               │
│ pipeline_todos: TODO string in base.config: Check the defaults for all       │
│ processes                                                                    │
│ pipeline_todos: TODO string in base.config: Customise requirements for       │
│ specific processes.                                                          │
│ pipeline_todos: TODO string in methods_description_template.yml: #Update the │
│ HTML below to your preferred methods description, e.g. add publication       │
│ citation for this pipeline                                                   │
│ pipeline_todos: TODO string in awsfulltest.yml: You can customise AWS full   │
│ pipeline tests as required                                                   │
│ pipeline_todos: TODO string in ci.yml: You can customise CI pipeline run     │
│ tests as required                                                            │
│ nfcore_yml: nf-core version in .nf-core.yml is not set to the latest         │
│ version. Should be 3.0.2 but was 2.14.1                                      │
│                                                                              │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ [✗] 9 Pipeline Tests Failed ────────────────────────────────────────────────╮
│                                                                              │
│ nextflow_config: Config variable (incorrectly) found: params.max_cpus        │
│ nextflow_config: Config variable (incorrectly) found: params.max_memory      │
│ nextflow_config: Config variable (incorrectly) found: params.max_time        │
│ nextflow_config: Old lines for loading custom profiles found. File should    │
│ contain:  // Load nf-core custom profiles from different            │
│ Institutions includeConfig !System.getenv('NXF_OFFLINE') &&                  │
│ params.custom_config_base ?                                                  │
│ "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"            │
│ files_unchanged: .github/CONTRIBUTING.md does not match the template         │
│ files_unchanged: .github/PULL_REQUEST_TEMPLATE.md does not match the         │
│ template                                                                     │
│ files_unchanged: .github/workflows/linting_comment.yml does not match the    │
│ template                                                                     │
│ files_unchanged: .github/workflows/linting.yml does not match the template   │
│ actions_awsfulltest: .github/workflows/awsfulltest.yml is not triggered      │
│ correctly                                                                    │
│                                                                              │
╰──────────────────────────────────────────────────────────────────────────────╯

╭─ [!] 4 Module Test Warnings ─────────────────────────────────────────────────╮
│                  ╷                             ╷                             │
│ Module name      │ File path                   │ Test message                │
│╶─────────────────┼─────────────────────────────┼────────────────────────────╴│
│ fastqc           │ modules/nf-core/fastqc      │ New version available       │
│ multiqc          │ modules/nf-core/multiqc     │ New version available       │
│ seqkit/split2    │ modules/nf-core/seqkit/spl… │ New version available       │
│ sourmash/sketch  │ modules/nf-core/sourmash/s… │ New version available       │
│                  ╵                             ╵                             │
╰──────────────────────────────────────────────────────────────────────────────╯

╭─ [!] 5 Subworkflow Test Warnings ────────────────────────────────────────────╮
│                            ╷                        ╷                        │
│ Subworkflow name           │ File path              │ Test message           │
│╶───────────────────────────┼────────────────────────┼───────────────────────╴│
│ search                     │ subworkflows/local/se… │ Subworkflow includes   │
│                            │                        │ less than two modules  │
│ search                     │ subworkflows/local/se… │ Included component     │
│                            │                        │ 'SOURMASH_MULTISEARCH' │
│                            │                        │ versions are not added │
│                            │                        │ in main.nf             │
│ utils_nextflow_pipeline    │ subworkflows/nf-core/… │ New version available  │
│ utils_nfcore_pipeline      │ subworkflows/nf-core/… │ New version available  │
│ utils_nfvalidation_plugin  │ subworkflows/nf-core/… │ New version available  │
│                            ╵                        ╵                        │
╰──────────────────────────────────────────────────────────────────────────────╯
INFO     Writing lint results to lint_results.md                                
╭───────────────────────╮
│ LINT RESULTS SUMMARY  │
├───────────────────────┤
│ [✔] 210 Tests Passed  │
│ [?]   1 Test Ignored  │
│ [!]  42 Test Warnings │
│ [✗]   9 Tests Failed  │
╰───────────────────────╯

Tip: Some of these linting errors can automatically be resolved with the 
following command:

    nf-core pipelines lint --dir 
/home/runner/work/nf-core-kmerseek/nf-core-kmerseek  --fix files_unchanged

### Relevant files

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### System information

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