Adapt pipeline to NF strict syntax

.github/workflows/awsfulltest_screening.yml

@@ -14,7 +14,7 @@ jobs:
   run-platform:
     name: Run AWS full tests
     # run only if the PR is approved by at least 2 reviewers and against the master/main branch or manually triggered
-    if: github.repository == 'nf-core/crisprseq' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch'
+    if: github.repository == 'nf-core/crisprseq' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch'  || github.event_name == 'release'
     runs-on: ubuntu-latest
     steps:
       - name: Set revision variable
@@ -26,19 +26,19 @@ jobs:
         uses: seqeralabs/action-tower-launch@v2
 
         with:
-          workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
+          workspace_id: ${{ vars.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
-          compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          compute_env: ${{ vars.TOWER_COMPUTE_ENV }}
           revision: ${{ steps.revision.outputs.revision }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/crisprseq/work-${{ steps.revision.outputs.revision }}
+          workdir: s3://${{ vars.AWS_S3_BUCKET }}/work/crisprseq/work-${{ steps.revision.outputs.revision }}
           parameters: |
             {
               "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/crisprseq/results-${{ steps.revision.outputs.revision }}/screening_test"
+              "outdir": "s3://${{ vars.AWS_S3_BUCKET }}/crisprseq/results-${{ steps.revision.outputs.revision }}/screening_test"
             }
           profiles: test_screening_full
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5
         with:
           name: Seqera Platform debug log file
           path: |

.github/workflows/nf-test.yml

@@ -78,7 +78,7 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "25.04.0"
+          - "25.10.3"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false

.nf-core.yml

@@ -6,7 +6,7 @@ lint:
     - tests/default.nf.test
   files_unchanged:
     - .github/PULL_REQUEST_TEMPLATE.md
-nf_core_version: 3.5.1
+nf_core_version: 3.5.2
 repository_type: pipeline
 template:
   author: "J\xFAlia Mir Pedrol, Laurence Kuhlburger"

README.md

@@ -10,7 +10,7 @@
 [![GitHub Actions Linting Status](https://github.com/nf-core/crisprseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/crisprseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/crisprseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![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%A525.04.0-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%A525.10.3-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-3.5.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.1)
 [![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/modules.config

@@ -23,7 +23,6 @@ process {
         publishDir = [
             path: { "${params.outdir}/preprocessing/sequences" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: false
         ]
     }
@@ -32,39 +31,34 @@ process {
         publishDir = [
             path: { "${params.outdir}/preprocessing/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
     withName: PEAR {
         publishDir = [
             path: { "${params.outdir}/preprocessing/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
     withName: BAGEL2_BF {
         publishDir = [
             path: { "${params.outdir}/bagel2/bayes_factor/" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
     withName: BAGEL2_PR {
         publishDir = [
             path: { "${params.outdir}/bagel2/precision_recall/" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
     withName: BAGEL2_FC {
         publishDir = [
             path: { "${params.outdir}/bagel2/fold_change/" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
     withName: DRUGZ {
@@ -73,15 +67,13 @@ process {
         publishDir = [
             path: { "${params.outdir}/drugz/" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
     withName: BAGEL2_GRAPH {
         publishDir = [
             path: { "${params.outdir}/bagel2/graphs/" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -90,15 +82,13 @@ process {
         publishDir = [
             path: { "${params.outdir}/preprocessing/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
     withName: FIND_ADAPTERS {
         publishDir = [
             path: { "${params.outdir}/preprocessing/adapters" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -118,15 +108,13 @@ process {
         publishDir       = [
             path: { "${params.outdir}/bowtie/" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
     withName: MAGECK_COUNT {
         publishDir       = [
             path: { "${params.outdir}/mageck/count/" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
         ext.prefix = 'count_table'
     }
@@ -135,7 +123,6 @@ process {
         publishDir       = [
             path: { "${params.outdir}/mageck/mle/${meta.id}/" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
         ext.args   =
             params.crisprcleanr ? '--norm-method none' : ''
@@ -147,7 +134,6 @@ process {
         publishDir       = [
             path: { "${params.outdir}/mageck/rra/" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -160,7 +146,6 @@ process {
         publishDir       = [
             path: { "${params.outdir}/mageck/FluteMLE/" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
     }
 
@@ -169,7 +154,6 @@ process {
         publishDir       = [
             path: { "${params.outdir}/hitselection/drugz/" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
     }
 
@@ -178,7 +162,6 @@ process {
         publishDir       = [
             path: { "${params.outdir}/hitselection/mle/" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
     }
 
@@ -188,7 +171,6 @@ process {
         publishDir       = [
             path: { "${params.outdir}/hitselection/bagel2/" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
     }
 
@@ -197,7 +179,6 @@ process {
         publishDir       = [
             path: { "${params.outdir}/hitselection/rra/" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
             ]
     }
 
@@ -206,7 +187,6 @@ process {
         publishDir       = [
             path: { "${params.outdir}/venndiagram/${meta.id}/" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -215,15 +195,13 @@ process {
         publishDir = [
             path: { "${params.outdir}/mageck/mle/day0/" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
     withName: CRISPRCLEANR_NORMALIZE {
         publishDir       = [
             path: { "${params.outdir}/crisprcleanr/normalization/" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -232,7 +210,6 @@ process {
         publishDir = [
             path: { "${params.outdir}/preprocessing/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -241,7 +218,6 @@ process {
         publishDir = [
             path: { "${params.outdir}/preprocessing/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -250,7 +226,6 @@ process {
         publishDir = [
             path: { "${params.outdir}/preprocessing/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -259,7 +234,6 @@ process {
         publishDir = [
             path: { "${params.outdir}/preprocessing/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -283,7 +257,6 @@ process {
         publishDir = [
             path: { "${params.outdir}/summary/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: false
         ]
     }
@@ -292,7 +265,6 @@ process {
         publishDir = [
             path: { "${params.outdir}/design_matrix" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -302,7 +274,6 @@ process {
         publishDir = [
             path: { "${params.outdir}/minimap2_umi" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -312,7 +283,6 @@ process {
         publishDir = [
             path: { "${params.outdir}/minimap2_umi" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -322,7 +292,6 @@ process {
         publishDir = [
             path: { "${params.outdir}/racon_umi" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -332,7 +301,6 @@ process {
         publishDir = [
             path: { "${params.outdir}/racon_umi" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -346,7 +314,6 @@ process {
         publishDir = [
             path: { "${params.outdir}/preprocessing/UMI" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: false
         ]
     }
@@ -355,7 +322,6 @@ process {
         publishDir = [
             path: { "${params.outdir}/summary/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
             enabled: false
         ]
     }
@@ -368,23 +334,20 @@ process {
         publishDir = [
             path: { "${params.outdir}/summary/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
     withName: SAMTOOLS_INDEX {
         publishDir = [
             path: { "${params.outdir}/${params.aligner}" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
     withName: TEMPLATE_REFERENCE {
         publishDir = [
             path: { "${params.outdir}/preprocessing/sequences" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -394,7 +357,6 @@ process {
         publishDir = [
             path: { "${params.outdir}/preprocessing/sequences" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -407,7 +369,6 @@ process {
         publishDir = [
             path: { "${params.outdir}/plots" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
@@ -416,7 +377,6 @@ process {
         publishDir = [
             path: { "${params.outdir}/multiqc" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 

conf/test_targeted_full.config

@@ -24,3 +24,9 @@ params {
     // Steps
     overrepresented = true
 }
+
+process {
+    withName: 'MULTIQC' {
+        memory = '12.GB'
+    }
+}

main.nf

@@ -83,7 +83,6 @@ workflow {
     PIPELINE_INITIALISATION (
         params.version,
         params.validate_params,
-        params.monochrome_logs,
         args,
         params.outdir,
         params.input,