Merge pull request #297 from nf-core/dev

Release 1.5.4

.github/workflows/awsfulltest.yml

@@ -19,9 +19,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: octokit/[email protected]
+        if: github.event_name != 'workflow_dispatch'
         id: check_approvals
         with:
-          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews
+          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       - id: test_variables
@@ -32,9 +33,6 @@ jobs:
           test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
-        # TODO nf-core: You can customise AWS full pipeline tests as required
-        # Add full size test data (but still relatively small datasets for few samples)
-        # on the `test_full.config` test runs with only one set of parameters
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

.nf-core.yml

@@ -17,5 +17,5 @@ template:
   outdir: .
   skip_features:
     - igenomes
-  version: 1.5.2
+  version: 1.5.4
 update: null

CHANGELOG.md

@@ -3,6 +3,20 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## 1.5.4 - 2024-12-03
+
+### `Added`
+
+### `Changed`
+
+- [#291](https://github.com/nf-core/demultiplex/pull/291) Updated `samshee` module to the latest version
+- [#296](https://github.com/nf-core/demultiplex/pull/296) Bump to version 1.5.4.
+
+### `Fixed`
+
+- [#288](https://github.com/nf-core/demultiplex/pull/288) Fix `test_full` by validating parameters in `lenientMode` and fix workflow megatest workflow dispatch.
+- [#294](https://github.com/nf-core/demultiplex/pull/294) Fix workflow.onComplete email sending feature.
+
 ## 1.5.3 - 2024-11-06
 
 ### `Added`

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/demultiplex/releases/tag/1.5.3" target="_blank">nf-core/demultiplex</a>
+  This report has been generated by the <a href="https://github.com/nf-core/demultiplex/releases/tag/1.5.4" target="_blank">nf-core/demultiplex</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/demultiplex/1.5.3/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/demultiplex/1.5.4/docs/output" target="_blank">documentation</a>.
 
 report_section_order:
   "nf-core-demultiplex-methods-description":

conf/test_full.config

@@ -19,3 +19,20 @@ params {
     demultiplexer = 'bcl2fastq'
     v1_schema     = true
 }
+
+// Load modules.config afterwards to load ext.args in samshee correctly
+process {
+    withName: SAMSHEE {
+        ext.args = [
+            params.json_schema_validator ? "--schema '${params.json_schema_validator}'" : "",
+            params.name_schema_validator ? "--schema '${params.name_schema_validator}'" : "",
+            params.v1_schema ? "--output-format sectioned" : "",
+        ].join(" ").trim()
+        errorStrategy = "terminate"
+        publishDir = [
+            path: { "${params.outdir}/" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+}

modules.json

@@ -67,7 +67,7 @@
                     },
                     "samshee": {
                         "branch": "master",
-                        "git_sha": "467c202a876d26af544fa8c4b22a050a535462a7",
+                        "git_sha": "61e2a514b2ee26847d960386431b593a3c7d094f",
                         "installed_by": ["modules"]
                     },
                     "seqtk/sample": {
@@ -106,7 +106,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba",
+                        "git_sha": "d588e574e40a8aeba3636e2b766358091bfa3aa0",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {

nextflow.config

@@ -265,7 +265,7 @@ manifest {
     description     = """Demultiplexing pipeline for Illumina sequencing data"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=24.04.2'
-    version         = '1.5.3'
+    version         = '1.5.4'
     doi             = '10.5281/zenodo.7153103'
 }
 
@@ -276,6 +276,7 @@ plugins {
 
 validation {
     defaultIgnoreParams = ["genomes"]
+    lenientMode = true
     help {
         enabled = true
         command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"

subworkflows/local/utils_nfcore_demultiplex_pipeline/main.nf

@@ -128,7 +128,13 @@ workflow PIPELINE_COMPLETION {
     //
     // Completion email and summary
     //
+    // We need to ensure that the multiqc_report is a value channel (DataflowVariable).
+    // Queue channels will not be available in the workflow.onComplete block.
+    def multiqc_reports = multiqc_report.toList()
+
     workflow.onComplete {
+        assert multiqc_reports instanceof groovyx.gpars.dataflow.DataflowVariable : "Expected a value channel (DataflowVariable) for multiqc_reports inside workflow.onComplete block."
+
         if (email || email_on_fail) {
             completionEmail(
                 summary_params,
@@ -137,7 +143,7 @@ workflow PIPELINE_COMPLETION {
                 plaintext_email,
                 outdir,
                 monochrome_logs,
-                multiqc_report.toList()
+                multiqc_reports.getVal()
             )
         }