Some more liniting issues fixed

.github/CONTRIBUTING.md

@@ -43,7 +43,7 @@ If any failures or warnings are encountered, please follow the listed URL for mo
 
 ### Pipeline tests
 
-Each `nf-core` pipeline should be set up with a minimal set of test-data.
+Each of the Microbiome Informatics pipelines should be set up with a minimal set of test-data.
 `GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully.
 If there are any failures then the automated tests fail.
 These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code.

.nf-core.yml

@@ -1,32 +1,48 @@
+repository_type: pipeline
+template:
+  prefix: ebi-metagenomics
+  skip:
+    - ci
+    - github_badges
 lint:
   files_exist:
     - CODE_OF_CONDUCT.md
     - assets/nf-core-miassembler_logo_light.png
     - docs/images/nf-core-miassembler_logo_light.png
     - docs/images/nf-core-miassembler_logo_dark.png
+    - docs/output.md
+    - docs/usage.md
     - .github/ISSUE_TEMPLATE/config.yml
     - .github/workflows/awstest.yml
     - .github/workflows/awsfulltest.yml
     - .github/workflows/branch.yml
     - .github/workflows/ci.yml
     - .github/workflows/linting_comment.yml
     - .github/workflows/linting.yml
+    - conf/test_full.config
+    - lib/Utils.groovy
+    - lib/WorkflowMain.groovy
+    - lib/NfcoreTemplate.groovy
+    - lib/WorkflowMiassembler.groovy
+    - lib/nfcore_external_java_deps.jar
   files_unchanged:
     - CODE_OF_CONDUCT.md
     - assets/nf-core-miassembler_logo_light.png
     - docs/images/nf-core-miassembler_logo_light.png
     - docs/images/nf-core-miassembler_logo_dark.png
     - .github/ISSUE_TEMPLATE/bug_report.yml
+    - .github/CONTRIBUTING.md
+    - LICENSE
+    - docs/README.md
+    - .gitignore
   multiqc_config:
     - report_comment
-  nextflow_config:
+  nextflow_config: False
+    - params.input
+    - params.validationSchemaIgnoreParams
+    - params.custom_config_version
+    - params.custom_config_base
     - manifest.name
     - manifest.homePage
   readme:
     - nextflow_badge
-repository_type: pipeline
-template:
-  prefix: ebi-metagenomics
-  skip:
-    - ci
-    - github_badges

README.md

@@ -10,6 +10,9 @@
 
 This pipeline is still in early development. It's mostly a direct port of the mi-automation assembly generation pipeline. Some of the bespoke scripts used to remove contaminated contigs or to calculate the coverage of the assembly were replaced with tools provided by the community ([SeqKit](https://doi.org/10.1371/journal.pone.0163962) and [quast](https://doi.org/10.1093/bioinformatics/btu153) respectively).
 
+> [!NOTE]
+> This pipeline uses the nf-core template with some tweaks, but it's not part of nf-core.
+
 ## Usage
 
 > [!WARNING]

conf/modules.config

@@ -12,16 +12,6 @@
 
 process {
 
-    withName: 'SAMPLESHEET_CHECK' {
-        publishDir = [
-            [
-                path: "${params.outdir}/pipeline_info",
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        ]
-    }
-
     withName: 'FETCHTOOL*' {
         cpus   = { check_max( 1                  , 'cpus'    ) }
         memory = { check_max( 6.GB * task.attempt, 'memory'  ) }