allowed un-compressed input formats

.github/workflows/linting.yml

@@ -53,7 +53,7 @@ jobs:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
-        run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
+        run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
       - name: Save PR number
         if: ${{ always() }}

.github/workflows/linting_comment.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
+        uses: dawidd6/action-download-artifact@bf251b5aa9c2f7eeb574a96ee720e24f801b7c11 # v6
         with:
           workflow: linting.yml
           workflow_conclusion: completed

.gitignore

@@ -23,3 +23,4 @@ docs/TODO.md
 assets/schema_input_nfv2.0.0.json
 nextflow_schema_nfv2.json
 .vscode
+.nf-test.log

.nf-core.yml

@@ -1,5 +1,5 @@
 repository_type: pipeline
-nf_core_version: "2.14.1"
+nf_core_version: "3.0.2"
 lint:
   files_exist:
     - CODE_OF_CONDUCT.md
@@ -27,6 +27,9 @@ lint:
   nextflow_config:
     - manifest.name
     - manifest.homePage
+    - params.max_cpus
+    - params.max_memory
+    - params.max_time
   multiqc_config: False
 template:
   prefix: phac-nml

.wordlist.txt

@@ -174,4 +174,5 @@ downsampling
 Christy
 Marinier
 Petkau
+gzipped
 

CHANGELOG.md

@@ -15,6 +15,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Documentation and Readme has been updated. [PR 126](https://github.com/phac-nml/mikrokondo/pull/126)
 
+- Adjusted `schema_input.json` to allow for non-gzipped inputs. [PR 137](https://github.com/phac-nml/mikrokondo/pull/137)
+
+- Updated github actions workflows for nf-core version 3.0.1. [PR 137](https://github.com/phac-nml/mikrokondo/pull/137)
+
 ## [0.4.2] - 2024-09-25
 
 ### `Fixed`

assets/schema_input.json

@@ -1,5 +1,5 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft-07/schema",
     "$id": "https://raw.githubusercontent.com/mk-kondo/mikrokondo/master/assets/schema_input.json",
     "title": "Samplesheet schema validation",
     "description": "Schema for the file provided with params.input",
@@ -15,7 +15,7 @@
             },
             "fastq_1": {
                 "type": "string",
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
+                "pattern": "^\\S+\\.f(ast)?q(\\.gz)?$",
                 "format": "file-path",
                 "errorMessage": "FastQ file for reads 1 (forward reads) must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'. If this is meant to be a run of mikrokondo with long read data please specify the paths under long_reads",
                 "dependentRequired": ["fastq_2"],
@@ -24,23 +24,23 @@
             },
             "fastq_2": {
                 "type": "string",
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
+                "pattern": "^\\S+\\.f(ast)?q(\\.gz)?$",
                 "format": "file-path",
                 "errorMessage": "FastQ file for reads 2 (reverse reads) cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
                 "meta": ["fastq_2"],
                 "unique": true
             },
             "long_reads": {
                 "type": "string",
-                "pattern": "^\\S+\\.f(ast)?q\\.gz$",
+                "pattern": "^\\S+\\.f(ast)?q(\\.gz)?$",
                 "format": "file-path",
                 "errorMessage": "FastQ file for long reads must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'.",
                 "meta": ["long_reads"],
                 "unique": true
             },
             "assembly": {
                 "type": "string",
-                "pattern": "^\\S+\\.f(ast)?n?a\\.gz$",
+                "pattern": "^\\S+\\.f(ast)?n?a(\\.gz)?$",
                 "format": "file-path",
                 "errorMessage": "Fasta file, cannot contain spaces and must have extension '.fa.gz' or '.fasta.gz'.",
                 "meta": ["assembly"],

nextflow.config

@@ -1029,21 +1029,26 @@ params {
 // Load base.config by default for all pipelines
 includeConfig 'conf/base.config'
 
+
+/*
+
+Below options require additional parametrs to be added.
+
+config_profile_name        = null
+config_profile_description = null
+
+custom_config_version      = 'master'
+custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
+config_profile_contact     = null
+config_profile_url         = null
+
 // Load nf-core custom profiles from different Institutions
-try {
-    includeConfig "${params.custom_config_base}/nfcore_custom.config"
-} catch (Exception e) {
-    System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
-}
+includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
 
-// Load mk-kondo/mikrokondo custom profiles from different institutions.
-// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
-// try {
-//   includeConfig "${params.custom_config_base}/pipeline/mikrokondo.config"
-// } catch (Exception e) {
-//   System.err.println("WARNING: Could not load nf-core/config/mikrokondo profiles: ${params.custom_config_base}/pipeline/mikrokondo.config")
-// }
+// Load nf-core/viralrecon custom profiles from different institutions.
+includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/mikrokondo.config" : "/dev/null"
 
+*/
 
 profiles {
     debug {
@@ -1141,7 +1146,7 @@ process.ext.override_configured_container_registry = true
 plugins {
     //id '[email protected]'
     id '[email protected]'
-    id 'nf-prov'
+    id 'nf-prov@1.2.4'
     id '[email protected]'
 }
 

nextflow_schema.json

@@ -1,5 +1,5 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft-07/schema",
     "$id": "https://raw.githubusercontent.com/phac-nml/mikrokondo/main/nextflow_schema.json",
     "title": "phac-nml/mikrokondo pipeline parameters",
     "description": "Mikrokondo beta",