Minor code polish

.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:
@@ -19,7 +19,7 @@ concurrency:
 env:
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
   NFT_VER: "0.9.3"
-  NFT_WORKDIR: "~"
+  # NFT_WORKDIR: "~"
   NXF_ANSI_LOG: false
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
@@ -78,8 +78,8 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "25.04.0"
-          - "latest-everything"
+          - 25.10.4
+          - latest-everything
     env:
       NXF_ANSI_LOG: false
       TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}
@@ -89,6 +89,9 @@ jobs:
         with:
           fetch-depth: 0
 
+      - name: Set NFT_WORKDIR dynamically
+        run: echo "NFT_WORKDIR=$HOME" >> $GITHUB_ENV
+
       - name: Run nf-test
         id: run_nf_test
         uses: ./.github/actions/nf-test

CHANGELOG.md

@@ -38,6 +38,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#162](https://github.com/nf-core/seqinspector/pull/162) Add tests for prepare_genome subworkflow
 - [#168](https://github.com/nf-core/seqinspector/pull/168) Add contributors list
 - [#168](https://github.com/nf-core/seqinspector/pull/168) Add logo to the pipeline logo
+- [#174](https://github.com/nf-core/seqinspector/pull/174) Add nf-core-utils 0.4.0
 
 ### `Fixed`
 
@@ -56,6 +57,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#171](https://github.com/nf-core/seqinspector/pull/171) Rescue number of tasks in the pipeline level tests
 - [#172](https://github.com/nf-core/seqinspector/pull/172) More complete conda environment for rundir parser
 - [#173](https://github.com/nf-core/seqinspector/pull/173) Fix warning message for tag name collision
+- [#174](https://github.com/nf-core/seqinspector/pull/174) Fix null message when no rundir information is available
 
 ### `Changed`
 
@@ -74,9 +76,13 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
 - [#168](https://github.com/nf-core/seqinspector/pull/168) Adhere to strict syntax
 - [#169](https://github.com/nf-core/seqinspector/pull/169) Prepare release 1.0.0
 - [#173](https://github.com/nf-core/seqinspector/pull/173) Improve documentation
+- [#174](https://github.com/nf-core/seqinspector/pull/174) Refactor tests
+- [#174](https://github.com/nf-core/seqinspector/pull/174) More strict syntax
+- [#174](https://github.com/nf-core/seqinspector/pull/174) No params included in workflows
 
 ### `Dependencies`
 
 - [#116](https://github.com/nf-core/seqinspector/pull/116) Update MultiQC to 1.28
+- [#174](https://github.com/nf-core/seqinspector/pull/174) Update nf-schema to 2.6.1
 
 ### `Deprecated`

README.md

@@ -10,7 +10,7 @@
 [![GitHub Actions Linting Status](https://github.com/nf-core/seqinspector/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/seqinspector/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/seqinspector/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%A525.10.4-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/)

main.nf

@@ -10,22 +10,22 @@
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    GENOME PARAMETER VALUES
+    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-params.fasta = getGenomeAttribute('fasta')
-
+include { SEQINSPECTOR            } from './workflows/seqinspector'
+include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
+include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
+include { getGenomeAttribute      } from 'plugin/nf-core-utils'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
+    GENOME PARAMETER VALUES
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { SEQINSPECTOR            } from './workflows/seqinspector'
-include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
-include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_seqinspector_pipeline'
+params.fasta = getGenomeAttribute('fasta')
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -45,13 +45,22 @@ workflow NFCORE_SEQINSPECTOR {
     //
     // WORKFLOW: Run pipeline
     //
-    skip_tools = params.skip_tools ? params.skip_tools.split(',') : []
-
     SEQINSPECTOR(
         samplesheet,
-        params.fasta,
-        skip_tools,
+        params.bait_intervals,
         params.bwamem2,
+        params.fasta ? channel.fromPath(params.fasta, checkIfExists: true).map { file -> tuple([id: file.name], file) }.collect() : channel.value([[:], []]),
+        params.fastq_screen_references,
+        params.multiqc_config,
+        params.multiqc_logo,
+        params.multiqc_methods_description,
+        params.outdir,
+        params.ref_dict,
+        params.run_picard_collecthsmetrics,
+        params.sample_size,
+        params.skip_tools ? params.skip_tools.split(',') : ['no_skip_tools'],
+        params.sort_bam,
+        params.target_intervals,
     )
 
     emit:
@@ -66,7 +75,6 @@ workflow NFCORE_SEQINSPECTOR {
 
 workflow {
 
-
     //
     // SUBWORKFLOW: Run initialisation tasks
     //
@@ -102,22 +110,3 @@ workflow {
         NFCORE_SEQINSPECTOR.out.global_report,
     )
 }
-
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    FUNCTIONS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
-//
-// Get attribute from genome config file e.g. fasta
-//
-
-def getGenomeAttribute(attribute) {
-    if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
-        if (params.genomes[params.genome].containsKey(attribute)) {
-            return params.genomes[params.genome][attribute]
-        }
-    }
-    return null
-}

modules.json

@@ -29,7 +29,8 @@
                     "fastqscreen/buildfromindex": {
                         "branch": "master",
                         "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/fastqscreen/buildfromindex/fastqscreen-buildfromindex.diff"
                     },
                     "fastqscreen/fastqscreen": {
                         "branch": "master",

modules/local/rundirparser/main.nf

@@ -44,6 +44,7 @@ process RUNDIRPARSER {
     fi
 
     # TODO: check what kind of seq platfrom to decide which script to use
+    # or replace with a smarter solution, like the MultiQC_SAV plugin
     parse_illumina.py ${input_dir}
     """
 

nextflow.config

@@ -405,14 +405,15 @@ manifest {
     description     = """Pipeline to QC your sequences"""
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
-    nextflowVersion = '!>=25.04.0'
+    nextflowVersion = '!>=25.10.4'
     version         = '1.0.0'
     doi             = ''
 }
 
 // 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@0.4.0' // nf-core-utils is a collection of utilities for Nextflow pipelines
+    id 'nf-schema@2.6.1'     // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 validation {

nf-test.config

@@ -20,6 +20,6 @@ config {
     // load the necessary plugins
     plugins {
         load "nft-bam@0.4.0"
-        load "nft-utils@0.0.8"
+        load "nft-utils@0.0.9"
     }
 }