Nextflow lint results

Generated: 2026-01-29T00:20:45.876401071Z
Nextflow version: 25.12.0-edge
Summary: 44 errors, 84 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( 1                  , 'cpus'    ) }
                   ^^^^^^^^^

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

        memory = { check_max( 6.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( 2     * task.attempt, 'cpus'    ) }
                   ^^^^^^^^^

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

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

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

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

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

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

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

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

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

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

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

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

Error: conf/base.config:51:20: check_max is not defined

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

Error: conf/base.config:52:20: check_max is not defined

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

Error: conf/base.config:55:20: check_max is not defined

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

Error: conf/base.config:58:20: check_max is not defined

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

Error: modules/local/grab_all_pairs.nf:66:40: meta is not defined

    def prefix = task.ext.prefix ?: "${meta.id}"
                                       ^^^^

Error: modules/local/psradd_calibrate_clean.nf:22:167: SNR is not defined

    tuple val(meta), path(ephemeris), path(template), path("${meta.pulsar}_${meta.utc}_raw*.ar", includeInputs: true), path("${meta.pulsar}_${meta.utc}_zap.ar"), env(SNR), env(FLUX)
                                                                                                                                                                      ^^^

Error: modules/local/psradd_calibrate_clean.nf:22:177: FLUX is not defined

    tuple val(meta), path(ephemeris), path(template), path("${meta.pulsar}_${meta.utc}_raw*.ar", includeInputs: true), path("${meta.pulsar}_${meta.utc}_zap.ar"), env(SNR), env(FLUX)
                                                                                                                                                                                ^^^^

Error: nextflow.config:111:5: Unexpected input: 'includeConfig'

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

Error: subworkflows/local/utils_nfcore_meerpipe_pipeline/main.nf:14:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/meerpipe/subworkflows/nf-core/utils_nextflow_pipeline/main.nf'
```
include { UTILS_NEXTFLOW_PIPELINE   } from '../../nf-core/utils_nextflow_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: subworkflows/local/utils_nfcore_meerpipe_pipeline/main.nf:15:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/meerpipe/subworkflows/nf-core/utils_nfcore_pipeline/main.nf'
```
include { completionEmail           } from '../../nf-core/utils_nfcore_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: subworkflows/local/utils_nfcore_meerpipe_pipeline/main.nf:16:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/meerpipe/subworkflows/nf-core/utils_nfcore_pipeline/main.nf'
```
include { completionSummary         } from '../../nf-core/utils_nfcore_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: subworkflows/local/utils_nfcore_meerpipe_pipeline/main.nf:17:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/meerpipe/subworkflows/nf-core/utils_nfcore_pipeline/main.nf'
```
include { dashedLine                } from '../../nf-core/utils_nfcore_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: subworkflows/local/utils_nfcore_meerpipe_pipeline/main.nf:18:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/meerpipe/subworkflows/nf-core/utils_nfcore_pipeline/main.nf'
```
include { nfCoreLogo                } from '../../nf-core/utils_nfcore_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: subworkflows/local/utils_nfcore_meerpipe_pipeline/main.nf:19:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/meerpipe/subworkflows/nf-core/utils_nfcore_pipeline/main.nf'
```
include { imNotification            } from '../../nf-core/utils_nfcore_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: subworkflows/local/utils_nfcore_meerpipe_pipeline/main.nf:20:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/meerpipe/subworkflows/nf-core/utils_nfcore_pipeline/main.nf'
```
include { UTILS_NFCORE_PIPELINE     } from '../../nf-core/utils_nfcore_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: subworkflows/local/utils_nfcore_meerpipe_pipeline/main.nf:21:1: Module could not be parsed: '/home/runner/work/strict-syntax-health/strict-syntax-health/pipelines/meerpipe/subworkflows/nf-core/utils_nfcore_pipeline/main.nf'
```
include { workflowCitation          } from '../../nf-core/utils_nfcore_pipeline'
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
```
Error: subworkflows/local/utils_nfcore_meerpipe_pipeline/main.nf:47:5: UTILS_NEXTFLOW_PIPELINE is not defined
```
    UTILS_NEXTFLOW_PIPELINE (
    ^^^^^^^^^^^^^^^^^^^^^^^
```
Error: subworkflows/local/utils_nfcore_meerpipe_pipeline/main.nf:57:21: nfCoreLogo is not defined
```
    pre_help_text = nfCoreLogo(monochrome_logs)
                    ^^^^^^^^^^
```

Error: subworkflows/local/utils_nfcore_meerpipe_pipeline/main.nf:58:29: workflowCitation is not defined

    post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs)
                            ^^^^^^^^^^^^^^^^

Error: subworkflows/local/utils_nfcore_meerpipe_pipeline/main.nf:58:57: dashedLine is not defined

    post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs)
                                                        ^^^^^^^^^^

Error: subworkflows/local/utils_nfcore_meerpipe_pipeline/main.nf:72:5: UTILS_NFCORE_PIPELINE is not defined
```
    UTILS_NFCORE_PIPELINE (
    ^^^^^^^^^^^^^^^^^^^^^
```

Error: subworkflows/local/utils_nfcore_meerpipe_pipeline/main.nf:133:13: completionEmail is not defined

            completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs)
            ^^^^^^^^^^^^^^^

Error: subworkflows/local/utils_nfcore_meerpipe_pipeline/main.nf:136:9: completionSummary is not defined
```
        completionSummary(monochrome_logs)
        ^^^^^^^^^^^^^^^^^
```
Error: subworkflows/local/utils_nfcore_meerpipe_pipeline/main.nf:139:13: imNotification is not defined
```
            imNotification(summary_params, hook_url)
            ^^^^^^^^^^^^^^
```
Error: subworkflows/nf-core/utils_nextflow_pipeline/main.nf:111:14: Unexpected input: 'i'
```
    for (int i = 0; i < n - 1; i++) {
             ^
```

Error: subworkflows/nf-core/utils_nfcore_pipeline/main.nf:73:17: Unexpected input: 'doi_ref'

    for (String doi_ref: manifest_doi) temp_doi_ref += "  https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
                ^

Error: tests/nextflow.config:9:20: PSRDB_URL is not defined (hint: use env('...') to access environment variable)
```
    psrdb_url   = "$PSRDB_URL"
                   ^^^^^^^^^^
```
Error: tests/nextflow.config:10:20: PSRDB_TOKEN is not defined (hint: use env('...') to access environment variable)
```
    psrdb_token = "$PSRDB_TOKEN"
                   ^^^^^^^^^^^^
```

⚠️ Warnings

Warning: modules/local/decimate.nf:28:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/local/decimate.nf:29:9: Variable was declared but not used

    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^

Warning: modules/local/decimate.nf:89:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/local/decimate.nf:90:9: Variable was declared but not used

    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^

Warning: modules/local/dm_rm_calc.nf:24:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/local/dm_rm_calc.nf:25:9: Variable was declared but not used

    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^

Warning: modules/local/dm_rm_calc.nf:171:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/local/dm_rm_calc.nf:172:9: Variable was declared but not used

    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^

Warning: modules/local/generate_image_results.nf:29:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/generate_image_results.nf:30:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/generate_image_results.nf:105:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/generate_residuals.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/generate_residuals.nf:22:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/generate_residuals.nf:51:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/generate_residuals.nf:52:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/generate_toas.nf:27:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/local/generate_toas.nf:28:9: Variable was declared but not used

    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^

Warning: modules/local/generate_toas.nf:64:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/local/generate_toas.nf:65:9: Variable was declared but not used

    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^

Warning: modules/local/grab_all_pairs.nf:24:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/local/grab_all_pairs.nf:25:9: Variable was declared but not used

    def prefix = task.ext.prefix ?: "${pulsar}"
        ^^^^^^

Warning: modules/local/grab_all_pairs.nf:65:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/local/grab_all_pairs.nf:66:9: Variable was declared but not used

    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^

Warning: modules/local/psradd_calibrate_clean.nf:28:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/psradd_calibrate_clean.nf:29:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/psradd_calibrate_clean.nf:186:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/psradd_calibrate_clean.nf:187:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/upload_dm_rm_results.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/upload_dm_rm_results.nf:22:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/upload_dm_rm_results.nf:103:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```
Warning: modules/local/upload_dm_rm_results.nf:104:9: Variable was declared but not used
```
    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^
```
Warning: modules/local/upload_results.nf:21:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/local/upload_results.nf:22:9: Variable was declared but not used

    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^

Warning: modules/local/upload_results.nf:116:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/local/upload_results.nf:117:9: Variable was declared but not used

    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^

Warning: modules/local/upload_toas.nf:24:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/local/upload_toas.nf:25:9: Variable was declared but not used

    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^

Warning: modules/local/upload_toas.nf:110:9: Variable was declared but not used
```
    def args = task.ext.args ?: ''
        ^^^^
```

Warning: modules/local/upload_toas.nf:111:9: Variable was declared but not used

    def prefix = task.ext.prefix ?: "${meta.id}"
        ^^^^^^

Warning: subworkflows/local/utils_nfcore_meerpipe_pipeline/main.nf:38:5: Parameter was not used -- prefix with _ to suppress warning
```
    input             //  string: Path to input samplesheet
    ^^^^^
```
Warning: subworkflows/local/utils_nfcore_meerpipe_pipeline/main.nf:42:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
    ch_versions = Channel.empty()
                  ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_meerpipe_pipeline/main.nf:83:5: The use of Channel to access channel factories is deprecated -- use channel instead
```
    Channel
    ^^^^^^^
```
Warning: subworkflows/local/utils_nfcore_meerpipe_pipeline/main.nf:95:38: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            validateInputSamplesheet(it)
                                     ^^
```

Warning: subworkflows/local/utils_nfcore_meerpipe_pipeline/main.nf:163:39: Implicit closure parameter is deprecated, declare an explicit parameter instead

    def endedness_ok = metas.collect{ it.single_end }.unique().size == 1
                                      ^^

Warning: workflows/meerpipe.nf:40:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
        obs_csv = Channel.fromPath("none_given")
                  ^^^^^^^
```
Warning: workflows/meerpipe.nf:42:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
        obs_csv = Channel.fromPath(params.obs_csv)
                  ^^^^^^^
```

Warning: workflows/meerpipe.nf:74:89: Parameter was not used -- prefix with _ to suppress warning

            pulsar, utc, project_short, beam, band, dur, mode_dur, obs_nchan, obs_nbin, cal_loc, pipe_id, ephemeris, template, n_obs, snr, flux, percent_rfi_zapped, raw_archive, cleaned_archive ->
                                                                                        ^^^^^^^

Warning: workflows/meerpipe.nf:88:64: Implicit closure parameter is deprecated, declare an explicit parameter instead

                    nchans: params.nchans.split(',').collect { it.toInteger() },
                                                               ^^

Warning: workflows/meerpipe.nf:89:62: Implicit closure parameter is deprecated, declare an explicit parameter instead

                    npols:params.npols.split(',').collect  { it.toInteger() },
                                                             ^^

Warning: workflows/meerpipe.nf:119:64: Implicit closure parameter is deprecated, declare an explicit parameter instead

                    nchans: params.nchans.split(',').collect { it.toInteger() },
                                                               ^^

Warning: workflows/meerpipe.nf:120:62: Implicit closure parameter is deprecated, declare an explicit parameter instead

                    npols:params.npols.split(',').collect  { it.toInteger() },
                                                             ^^

Warning: workflows/meerpipe.nf:150:64: Implicit closure parameter is deprecated, declare an explicit parameter instead

                    nchans: params.nchans.split(',').collect { it.toInteger() },
                                                               ^^

Warning: workflows/meerpipe.nf:151:62: Implicit closure parameter is deprecated, declare an explicit parameter instead

                    npols:params.npols.split(',').collect  { it.toInteger() },
                                                             ^^

Warning: workflows/meerpipe.nf:215:22: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .map { [ it[0] ] }
                     ^^
```
Warning: workflows/meerpipe.nf:224:19: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter { it[2].baseName != "no_template" }
                  ^^
```

Warning: workflows/meerpipe.nf:227:19: Parameter was not used -- prefix with _ to suppress warning

            meta, ephemeris, template, raw_archive, cleaned_archive ->
                  ^^^^^^^^^

Warning: workflows/meerpipe.nf:227:40: Parameter was not used -- prefix with _ to suppress warning

            meta, ephemeris, template, raw_archive, cleaned_archive ->
                                       ^^^^^^^^^^^

Warning: workflows/meerpipe.nf:231:19: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter { it[2].baseName == "no_template" }
                  ^^
```

Warning: workflows/meerpipe.nf:234:19: Parameter was not used -- prefix with _ to suppress warning

            meta, ephemeris, template, raw_archive, cleaned_archive ->
                  ^^^^^^^^^

Warning: workflows/meerpipe.nf:234:53: Parameter was not used -- prefix with _ to suppress warning

            meta, ephemeris, template, raw_archive, cleaned_archive ->
                                                    ^^^^^^^^^^^^^^^

Warning: workflows/meerpipe.nf:251:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                .filter { it[1].baseName != "no_template" }
                          ^^
```

Warning: workflows/meerpipe.nf:253:27: Parameter was not used -- prefix with _ to suppress warning

                    meta, template, decimated_archives ->
                          ^^^^^^^^

Warning: workflows/meerpipe.nf:297:21: Parameter was not used -- prefix with _ to suppress warning

                    id, meta, ephem -> [ meta[0], ephem[0] ]
                    ^^

Warning: workflows/only_dm_rm_calc.nf:33:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
        obs_csv = Channel.fromPath("none_given")
                  ^^^^^^^
```
Warning: workflows/only_dm_rm_calc.nf:35:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
        obs_csv = Channel.fromPath(params.obs_csv)
                  ^^^^^^^
```

Warning: workflows/only_dm_rm_calc.nf:73:85: Parameter was not used -- prefix with _ to suppress warning

        pulsar, utc, project_short, beam, band, dur, mode_dur, obs_nchan, obs_nbin, cal_loc, pipe_id, ephemeris, template, n_obs, snr, flux, percent_rfi_zapped, raw_archive, cleaned_archive ->
                                                                                    ^^^^^^^

Warning: workflows/only_dm_rm_calc.nf:87:60: Implicit closure parameter is deprecated, declare an explicit parameter instead

                nchans: params.nchans.split(',').collect { it.toInteger() },
                                                           ^^

Warning: workflows/only_dm_rm_calc.nf:88:58: Implicit closure parameter is deprecated, declare an explicit parameter instead

                npols:params.npols.split(',').collect  { it.toInteger() },
                                                         ^^

Warning: workflows/only_dm_rm_calc.nf:108:23: Parameter was not used -- prefix with _ to suppress warning

                meta, ephemeris, template, raw_archive, cleaned_archive, results_json, rm_image, dm_image ->
                      ^^^^^^^^^

Warning: workflows/only_dm_rm_calc.nf:108:34: Parameter was not used -- prefix with _ to suppress warning

                meta, ephemeris, template, raw_archive, cleaned_archive, results_json, rm_image, dm_image ->
                                 ^^^^^^^^

Warning: workflows/only_dm_rm_calc.nf:108:44: Parameter was not used -- prefix with _ to suppress warning

                meta, ephemeris, template, raw_archive, cleaned_archive, results_json, rm_image, dm_image ->
                                           ^^^^^^^^^^^

Warning: workflows/only_dm_rm_calc.nf:108:57: Parameter was not used -- prefix with _ to suppress warning

                meta, ephemeris, template, raw_archive, cleaned_archive, results_json, rm_image, dm_image ->
                                                        ^^^^^^^^^^^^^^^

Warning: workflows/only_toas_and_residuals.nf:46:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
        obs_csv = Channel.fromPath("none_given")
                  ^^^^^^^
```
Warning: workflows/only_toas_and_residuals.nf:48:19: The use of Channel to access channel factories is deprecated -- use channel instead
```
        obs_csv = Channel.fromPath(params.obs_csv)
                  ^^^^^^^
```

Warning: workflows/only_toas_and_residuals.nf:80:89: Parameter was not used -- prefix with _ to suppress warning

            pulsar, utc, project_short, beam, band, dur, mode_dur, obs_nchan, obs_nbin, cal_loc, pipe_id, ephemeris, template, n_obs, snr, flux, percent_rfi_zapped, raw_archive, cleaned_archive ->
                                                                                        ^^^^^^^

Warning: workflows/only_toas_and_residuals.nf:94:64: Implicit closure parameter is deprecated, declare an explicit parameter instead

                    nchans: params.nchans.split(',').collect { it.toInteger() },
                                                               ^^

Warning: workflows/only_toas_and_residuals.nf:95:62: Implicit closure parameter is deprecated, declare an explicit parameter instead

                    npols:params.npols.split(',').collect  { it.toInteger() },
                                                             ^^

Warning: workflows/only_toas_and_residuals.nf:113:22: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
            .map { [ it[0] ] }
                     ^^
```
Warning: workflows/only_toas_and_residuals.nf:122:19: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
        .filter { it[2].baseName != "no_template" }
                  ^^
```

Warning: workflows/only_toas_and_residuals.nf:125:19: Parameter was not used -- prefix with _ to suppress warning

            meta, ephemeris, template, raw_archive, cleaned_archive ->
                  ^^^^^^^^^

Warning: workflows/only_toas_and_residuals.nf:125:40: Parameter was not used -- prefix with _ to suppress warning

            meta, ephemeris, template, raw_archive, cleaned_archive ->
                                       ^^^^^^^^^^^

Warning: workflows/only_toas_and_residuals.nf:140:27: Implicit closure parameter is deprecated, declare an explicit parameter instead
```
                .filter { it[1].baseName != "no_template" }
                          ^^
```

Warning: workflows/only_toas_and_residuals.nf:142:27: Parameter was not used -- prefix with _ to suppress warning

                    meta, template, decimated_archives ->
                          ^^^^^^^^

Warning: workflows/only_toas_and_residuals.nf:186:21: Parameter was not used -- prefix with _ to suppress warning
```
                    id, meta, ephem -> [ meta[0], ephem[0] ]
                    ^^
```

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