Convert to typed params

.github/workflows/nf-test.yml

@@ -9,7 +9,7 @@ on:
       - "**/*.svg"
   release:
     types: [published]
-  workflow_dispatch:
+  workflow_dispatch: null
 
 # Cancel if a newer run is started
 concurrency:
@@ -78,8 +78,8 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "25.10.4"
-          - "latest-everything"
+          - 26.04.6
+          - latest-everything
     env:
       NXF_ANSI_LOG: false
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}

.nf-core.yml

@@ -4,6 +4,8 @@ lint:
   files_unchanged:
     - .github/PULL_REQUEST_TEMPLATE.md
     - docs/images/nf-core-reportho_logo_light.png
+  nextflow_config: false # ported to typed params
+  schema_params: false # ported to typed params
 nf_core_version: 4.0.3
 repository_type: pipeline
 template:

CHANGELOG.md

@@ -11,9 +11,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
-- [#107](https://github.com/nf-core/reportho/pull/107) - Update nf-core template to version 4.0.2
-- [#124](https://github.com/nf-core/reportho/pull/124) - Update nf-core modules to topics and clean up subworkflows.
-- [#127](https://github.com/nf-core/reportho/pull/127) - Convert local modules to topics
 - [#132](https://github.com/nf-core/reportho/pull/132) - Fetch pairwise orthologs instead of OMA group from OMA
 
 ### Fixed
@@ -53,13 +50,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 #### Changed
 
 - [#100](https://github.com/nf-core/reportho/pull/100) - Back to dev (1.2.0dev)
+- [#107](https://github.com/nf-core/reportho/pull/107) - Update nf-core template to version 4.0.2
 - [#107](https://github.com/nf-core/reportho/pull/107) - Module structure migrated to nf-core standard directory format
 - [#116](https://github.com/nf-core/reportho/pull/116) - Migrate modules to use module binaries instead of global bin/
 - [#123](https://github.com/nf-core/reportho/pull/123) - Switch local Python helper scripts and module invocations to named argparse options instead of positional sys.argv ordering
+- [#124](https://github.com/nf-core/reportho/pull/124) - Update nf-core modules to topics and clean up subworkflows.
+- [#127](https://github.com/nf-core/reportho/pull/127) - Convert local modules to topics
 - [#130](https://github.com/nf-core/reportho/pull/130) - Update local subworkflow metas with meaningful information
 - [#131](https://github.com/nf-core/reportho/pull/131) - Make syntax more consistent in workflows
 - [#132](https://github.com/nf-core/reportho/pull/132) - Migrate OMA modules to pyomadb
+- [#137](https://github.com/nf-core/reportho/pull/137) - Update nf-core template to version 4.0.3
 - [#138](https://github.com/nf-core/reportho/pull/138) - Remove params from subworkflows
+- [#141](https://github.com/nf-core/reportho/pull/141) - Convert to typed params
 
 #### Fixed
 

README.md

@@ -11,7 +11,7 @@
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.11574565-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.11574565)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.4-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A526.04.6-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
 [![nf-core template version](https://img.shields.io/badge/nf--core_template-4.0.3-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/4.0.3)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)

conf/test_offline.config

@@ -37,6 +37,5 @@ params {
     eggnog_path       = params.pipelines_testdata_base_path + 'reportho/testdata/databases/1_members-mini.tsv.gz'
     eggnog_idmap_path = params.pipelines_testdata_base_path + 'reportho/testdata/databases/latest.Eukaryota-mini.tsv.gz'
     min_score         = 2
-    skip_downstream   = true
     skip_samplesheets = true
 }

main.nf

@@ -17,10 +17,94 @@ nextflow.enable.moduleBinaries = true
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { REPORTHO  } from './workflows/reportho'
+include { REPORTHO                } from './workflows/reportho'
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_reportho_pipeline/main'
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_reportho_pipeline/main'
 
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    PARAMETER DECLARATIONS
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+params {
+    // Input options
+    input: Path = null
+    output_intermediates: Boolean = false
+
+    // MultiQC options
+    multiqc_config: Path? = null
+    multiqc_title: String? = null
+    multiqc_logo: Path? = null
+    max_multiqc_email_size: String = "25.MB"
+    multiqc_methods_description: String? = null
+
+
+    // Ortholog options
+    use_all: Boolean = false
+    offline_run: Boolean = false
+    local_databases: Boolean = false
+
+    // Ortholog fetching options
+    skip_oma: Boolean = false
+    oma_path: Path? = null
+    oma_uniprot_path: Path? = null
+    oma_ensembl_path: Path? = null
+    oma_refseq_path: Path? = null
+    skip_panther: Boolean = false
+    panther_path: Path? = null
+    skip_orthoinspector: Boolean = false
+    orthoinspector_path: Path? = null
+    orthoinspector_version: String = 'Eukaryota2023'
+    skip_eggnog: Boolean = false
+    eggnog_path: Path? = null
+    eggnog_idmap_path: Path? = null
+
+    // ID merging options
+    skip_merge: Boolean = false
+    min_identity: Integer = 90
+    min_coverage: Integer = 80
+
+    // Ortholog scoring options
+    use_centroid: Boolean = false
+    min_score: Integer = 2
+
+    // Process skipping options
+    skip_orthoplots: Boolean = false
+    skip_report: Boolean = false
+    skip_multiqc: Boolean = false
+    skip_samplesheets: Boolean = false
+
+    // Infrastructure options
+    array_size: Integer = 10
+
+    // Boilerplate options
+    outdir: Path = null
+    publish_dir_mode: String = 'copy'
+    email: String? = null
+    email_on_fail: String? = null
+    plaintext_email: Boolean = false
+    monochrome_logs: Boolean = false
+    help: Boolean = false
+    help_full: Boolean = false
+    show_hidden: Boolean = false
+    version: Boolean = false
+    pipelines_testdata_base_path: String = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
+    trace_report_suffix: String = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')
+
+    // Config options
+    config_profile_name: String? = null
+    config_profile_description: String? = null
+
+    custom_config_version: String = 'master'
+    custom_config_base: String = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
+    config_profile_contact: String? = null
+    config_profile_url: String? = null
+
+    // Schema validation default options
+    validate_params: Boolean = true
+}
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     NAMED WORKFLOWS FOR PIPELINE
@@ -31,10 +115,9 @@ include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_repo
 // WORKFLOW: Run main analysis pipeline depending on type of input
 //
 workflow NFCORE_REPORTHO {
-
     take:
-    samplesheet_query   // channel: samplesheet read in from --input with query
-    samplesheet_fasta   // channel: samplesheet read in from --input with fasta
+    samplesheet_query // channel: samplesheet read in from --input with query
+    samplesheet_fasta // channel: samplesheet read in from --input with fasta
     offline_run
     use_all
     use_centroid
@@ -53,7 +136,6 @@ workflow NFCORE_REPORTHO {
     eggnog_idmap_path
     min_score
     skip_merge
-    skip_downstream
     skip_orthoplots
     skip_samplesheets
     skip_report
@@ -69,7 +151,7 @@ workflow NFCORE_REPORTHO {
     //
     // WORKFLOW: Run pipeline
     //
-    REPORTHO (
+    REPORTHO(
         samplesheet_query,
         samplesheet_fasta,
         offline_run,
@@ -90,7 +172,6 @@ workflow NFCORE_REPORTHO {
         eggnog_idmap_path,
         min_score,
         skip_merge,
-        skip_downstream,
         skip_orthoplots,
         skip_samplesheets,
         skip_report,
@@ -112,35 +193,29 @@ workflow NFCORE_REPORTHO {
 */
 
 workflow {
-
-    main:
     effective_local_databases = params.local_databases
-    effective_skip_downstream = params.containsKey('skip_downstream') ? params['skip_downstream'] : false
 
     if (params.offline_run) {
         if (!effective_local_databases) {
             effective_local_databases = true
             log.warn("Offline mode enabled, setting 'local_databases' to 'true'")
         }
-        if (!effective_skip_downstream) {
-            effective_skip_downstream = true
-            log.warn("Offline mode enabled, setting 'skip_downstream' to 'true'")
-        }
         if (params.use_all) {
             log.warn("Offline run set with 'use_all', only local databases will be used")
         }
-    } else if (params.use_all && effective_local_databases) {
+    }
+    else if (params.use_all && effective_local_databases) {
         log.warn("Local databases set with 'use_all', only local databases will be used")
     }
 
-    if (!params.skip_samplesheets && (params.offline_run || (params.skip_merge && effective_skip_downstream))) {
+    if (!params.skip_samplesheets && (params.offline_run || params.skip_merge)) {
         log.error("Samplesheet generation for nf-core/multiplesequencealign requires fetched sequences. Set '--skip_samplesheets' to true or disable offline/no-fetch settings.")
     }
 
     //
     // SUBWORKFLOW: Run initialisation tasks
     //
-    PIPELINE_INITIALISATION (
+    PIPELINE_INITIALISATION(
         params.version,
         params.validate_params,
         params.monochrome_logs,
@@ -149,13 +224,13 @@ workflow {
         params.input,
         params.help,
         params.help_full,
-        params.show_hidden
+        params.show_hidden,
     )
 
     //
     // WORKFLOW: Run main workflow
     //
-    NFCORE_REPORTHO (
+    NFCORE_REPORTHO(
         PIPELINE_INITIALISATION.out.samplesheet_query,
         PIPELINE_INITIALISATION.out.samplesheet_fasta,
         params.offline_run,
@@ -176,7 +251,6 @@ workflow {
         params.eggnog_idmap_path,
         params.min_score,
         params.skip_merge,
-        effective_skip_downstream,
         params.skip_orthoplots,
         params.skip_samplesheets,
         params.skip_report,
@@ -185,24 +259,18 @@ workflow {
         params.multiqc_config,
         params.multiqc_logo,
         params.multiqc_methods_description,
-        params.outdir
+        params.outdir,
     )
     //
     // SUBWORKFLOW: Run completion tasks
     //
-    PIPELINE_COMPLETION (
+    PIPELINE_COMPLETION(
         params.email,
         params.email_on_fail,
         params.plaintext_email,
         params.max_multiqc_email_size,
         params.outdir,
         params.monochrome_logs,
-        NFCORE_REPORTHO.out
+        NFCORE_REPORTHO.out,
     )
 }
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    THE END
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/

modules.json

@@ -41,7 +41,7 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
+                        "git_sha": "1a545fcbd762911c21a64ced3dbef99b2b51ac75",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
@@ -51,7 +51,7 @@
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "fdc08b8b1ae74f56686ce21f7ea11ad11990ce57",
+                        "git_sha": "a7b27fd25bfa8dcc07d299e88bd790585901a436",
                         "installed_by": ["subworkflows"]
                     }
                 }