Add nf-core-utils plugin v0.5.0 for pipeline utilities

CHANGELOG.md

@@ -48,6 +48,9 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #382](https://github.com/nf-core/fetchngs/pull/382) - Use csv.reader to fix stray quote and comma handling in multiqc_mappings_config (#375)
 - [PR #383](https://github.com/nf-core/fetchngs/pull/383) - Add ampliseq pipeline support
 - [PR #384](https://github.com/nf-core/fetchngs/pull/384) - Add mag pipeline support
+- [PR #385](https://github.com/nf-core/fetchngs/pull/385) - Add nf-core-utils plugin, replacing utils subworkflows
+- [PR #385](https://github.com/nf-core/fetchngs/pull/385) - Update nf-schema and nf-test plugins
+- [PR #385](https://github.com/nf-core/fetchngs/pull/385) - Simplify topic version handling
 
 ### Software dependencies
 
@@ -57,6 +60,23 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 | `sratools` | 2.11.0      | 3.2.1       |
 | `wget`     | 1.20.1      | 1.25.0      |
 
+### Plugins
+
+| Dependency    | Old version | New version |
+| ------------- | ----------- | ----------- |
+| nf-core-utils |             | 0.5.0       |
+| nf-schema     | 2.5.1       | 2.7.3       |
+| nft-bam       | 0.4.0       | 0.7.0       |
+| nft-utils     | 0.0.9       | 1.0.0       |
+
+### Modules / Subworkflows
+
+| Dependency   | Old name                | New name |
+| ------------ | ----------------------- | -------- |
+| Subworkflows | utils_nextflow_pipeline |          |
+| Subworkflows | utils_nfcore_pipeline   |          |
+| Subworkflows | utils_nfschema_plugin   |          |
+
 ## [[1.12.0](https://github.com/nf-core/fetchngs/releases/tag/1.12.0)] - 2024-02-29
 
 ### :warning: Major enhancements

modules.json

@@ -33,21 +33,6 @@
                         "branch": "master",
                         "git_sha": "8e6139dbf4f3ca01bbac6152d2833e04edff18df",
                         "installed_by": ["subworkflows"]
-                    },
-                    "utils_nextflow_pipeline": {
-                        "branch": "master",
-                        "git_sha": "1a545fcbd762911c21a64ced3dbef99b2b51ac75",
-                        "installed_by": ["subworkflows"]
-                    },
-                    "utils_nfcore_pipeline": {
-                        "branch": "master",
-                        "git_sha": "a3fb7351b1fdb2b1de282b765816bbea190e86a8",
-                        "installed_by": ["subworkflows"]
-                    },
-                    "utils_nfschema_plugin": {
-                        "branch": "master",
-                        "git_sha": "a7b27fd25bfa8dcc07d299e88bd790585901a436",
-                        "installed_by": ["subworkflows"]
                     }
                 }
             }

nextflow.config

@@ -327,7 +327,8 @@ manifest {
 
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.5.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-core-utils@0.5.0' // nf-core-utils is a collection of utilities for Nextflow pipelines
+    id 'nf-schema@2.7.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 validation {

nf-test.config

@@ -33,8 +33,8 @@ config {
 
     // load the necessary plugins
     plugins {
-        load "nft-bam@0.4.0"
+        load "nft-bam@0.7.0"
         load "nft-csv@0.1.0"
-        load "nft-utils@0.0.9"
+        load "nft-utils@1.0.0"
     }
 }

subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf

@@ -8,14 +8,19 @@
 ========================================================================================
 */
 
-include { UTILS_NFSCHEMA_PLUGIN   } from '../../nf-core/utils_nfschema_plugin'
-include { paramsSummaryMap        } from 'plugin/nf-schema'
-include { samplesheetToList       } from 'plugin/nf-schema'
-include { paramsHelp              } from 'plugin/nf-schema'
-include { completionEmail         } from '../../nf-core/utils_nfcore_pipeline'
-include { completionSummary       } from '../../nf-core/utils_nfcore_pipeline'
-include { UTILS_NFCORE_PIPELINE   } from '../../nf-core/utils_nfcore_pipeline'
-include { UTILS_NEXTFLOW_PIPELINE } from '../../nf-core/utils_nextflow_pipeline'
+include { checkCondaChannels   } from 'plugin/nf-core-utils'
+include { checkConfigProvided  } from 'plugin/nf-core-utils'
+include { checkProfileProvided } from 'plugin/nf-core-utils'
+include { completionEmail      } from 'plugin/nf-core-utils'
+include { completionSummary    } from 'plugin/nf-core-utils'
+include { dumpParametersToJSON } from 'plugin/nf-core-utils'
+include { getWorkflowVersion   } from 'plugin/nf-core-utils'
+
+include { paramsHelp           } from 'plugin/nf-schema'
+include { paramsSummaryLog     } from 'plugin/nf-schema'
+include { paramsSummaryMap     } from 'plugin/nf-schema'
+include { samplesheetToList    } from 'plugin/nf-schema'
+include { validateParameters   } from 'plugin/nf-schema'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -41,12 +46,18 @@ workflow PIPELINE_INITIALISATION {
     //
     // Print version and exit if required and dump pipeline parameters to JSON file
     //
-    UTILS_NEXTFLOW_PIPELINE(
-        version,
-        true,
-        outdir,
-        workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1,
-    )
+    if (version) {
+        log.info("${workflow.manifest.name} ${getWorkflowVersion()}")
+        System.exit(0)
+    }
+
+    if (outdir) {
+        dumpParametersToJSON(outdir, params)
+    }
+
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        checkCondaChannels()
+    }
 
     //
     // Validate parameters and generate parameter summary to stdout
@@ -77,25 +88,37 @@ workflow PIPELINE_INITIALISATION {
 
     command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
 
-    UTILS_NFSCHEMA_PLUGIN(
-        workflow,
-        validate_params,
-        null,
-        help,
-        help_full,
-        show_hidden,
-        before_text,
-        after_text,
-        command,
-        null,
-    )
+    if (help || help_full) {
+        help_options = [
+            beforeText: before_text,
+            afterText: after_text,
+            command: command,
+            showHidden: show_hidden,
+            fullHelp: help_full,
+        ]
+        log.info(
+            paramsHelp(
+                help_options,
+                (help instanceof String && help != "true") ? help : "",
+            )
+        )
+        exit(0)
+    }
+
+    checkProfileProvided(nextflow_cli_args)
+
+    log.info(before_text)
+    log.info(paramsSummaryLog([:], workflow))
+    log.info(after_text)
+
+    if (validate_params) {
+        validateParameters([:])
+    }
 
     //
     // Check config provided to the pipeline
     //
-    UTILS_NFCORE_PIPELINE(
-        nextflow_cli_args
-    )
+    checkConfigProvided()
 
     //
     // Create channel from input file provided through params.input
@@ -203,6 +226,7 @@ def sraCheckENAMetadataFields(ena_metadata_fields) {
         error("Invalid option: '${ena_metadata_fields}'. Minimally required fields for '--ena_metadata_fields': '${valid_ena_metadata_fields.join(',')}'")
     }
 }
+
 //
 // Print a warning after pipeline has completed
 //