Merge pull request #223 from nf-core/dev

Bogatell Patch Release - v.1.1.1

Author: luisas

.github/workflows/awsfulltest.yml

@@ -4,57 +4,36 @@ name: nf-core AWS full size tests
 # It runs the -profile 'test_full' on AWS batch
 
 on:
-  pull_request:
-    branches:
-      - main
-      - master
   workflow_dispatch:
   pull_request_review:
     types: [submitted]
+  release:
+    types: [published]
 
 jobs:
   run-platform:
     name: Run AWS full tests
-    # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered
-    if: github.repository == 'nf-core/multiplesequencealign' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
+    # 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/multiplesequencealign' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     steps:
-      - name: Get PR reviews
-        uses: octokit/request-action@v2.x
-        if: github.event_name != 'workflow_dispatch'
-        id: check_approvals
-        continue-on-error: true
-        with:
-          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Check for approvals
-        if: ${{ failure() && github.event_name != 'workflow_dispatch' }}
-        run: |
-          echo "No review approvals found. At least 2 approvals are required to run this action automatically."
-          exit 1
-
-      - name: Check for enough approvals (>=2)
-        id: test_variables
-        if: github.event_name != 'workflow_dispatch'
+      - name: Set revision variable
+        id: revision
         run: |
-          JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
-          CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
-          test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
+          echo "revision=${{ (github.event_name == 'workflow_dispatch' || github.event_name == 'release') && github.sha || 'dev' }}" >> "$GITHUB_OUTPUT"
 
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
-          revision: ${{ github.sha }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/multiplesequencealign/work-${{ github.sha }}
+          revision: ${{ steps.revision.outputs.revision }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/multiplesequencealign/work-${{ steps.revision.outputs.revision }}
           parameters: |
             {
               "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/multiplesequencealign/results-${{ github.sha }}"
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/multiplesequencealign/results-${{ steps.revision.outputs.revision }}"
             }
           profiles: test_full
 

.github/workflows/ci.yml

@@ -22,7 +22,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "24.10.4"
+          - "25.04.2"
           - "latest-everything"
         profile:
           - "docker"
@@ -52,7 +52,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "24.10.4"
+          - "25.04.2"
           - "latest-everything"
         profile:
           - "docker"
@@ -75,5 +75,6 @@ jobs:
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
       - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
+        continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,${{ matrix.profile }} ${{ matrix.params }}  --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -stub-run -profile ${{ matrix.test_name }},${{ matrix.profile }} ${{ matrix.params }}  --outdir ./results

.github/workflows/ci_master.yml

@@ -24,7 +24,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "24.10.4"
+          - "25.04.2"
           - "latest-everything"
         profile:
           - "docker"
@@ -75,7 +75,7 @@ jobs:
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
       - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
-        if: "${{ (matrix.test_name != 'test' && matrix.profile == 'conda') || (matrix.test_name != 'test_conda' && matrix.profile != 'conda') }}"
+        if: ${{ (matrix.test_name != 'test' && (matrix.profile == 'conda' || matrix.profile == 'singularity')) || (matrix.test_name != 'test_conda' && matrix.profile != 'conda' && matrix.profile != 'singularity') }}
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results
 
@@ -86,7 +86,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "24.10.4"
+          - "25.04.2"
           - "latest-everything"
         profile:
           - "docker"
@@ -101,6 +101,7 @@ jobs:
           - "--skip_shiny"
         test_name:
           - "test"
+          - "test_conda"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
@@ -121,10 +122,13 @@ jobs:
         run: |
           mkdir -p $NXF_SINGULARITY_CACHEDIR
           mkdir -p $NXF_SINGULARITY_LIBRARYDIR
+          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
+          echo $(realpath python) >> $GITHUB_PATH
 
       - name: Clean up Disk space
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
       - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
+        if: ${{ (matrix.test_name != 'test' && (matrix.profile == 'conda' || matrix.profile == 'singularity')) || (matrix.test_name != 'test_conda' && matrix.profile != 'conda' && matrix.profile != 'singularity') }}
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,${{ matrix.profile }} ${{ matrix.params }}  --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -stub-run -profile ${{ matrix.test_name }},${{ matrix.profile }} ${{ matrix.params }}  --outdir ./results

.github/workflows/download_pipeline.yml

@@ -52,7 +52,7 @@ jobs:
       - name: Setup Apptainer
         uses: eWaterCycle/setup-apptainer@4bb22c52d4f63406c49e94c804632975787312b3 # v2.0.0
         with:
-          apptainer-version: 1.3.4
+          apptainer-version: 1.4.1
 
       - name: Install dependencies
         run: |

.nf-core.yml

@@ -1,12 +1,12 @@
 lint:
+  actions_ci: false # TODO: remove this with nf-core template version 3.3.0
   files_exist:
     - conf/igenomes.config
     - conf/igenomes_ignored.config
   files_unchanged:
     - .github/CONTRIBUTING.md
   multiqc_config: false
-  actions_ci: false # TODO: remove this with nf-core template version 3.3.0
-nf_core_version: 3.2.0
+nf_core_version: 3.2.1
 repository_type: pipeline
 template:
   author: Luisa Santus, Jose Espinosa-Carrasco
@@ -16,4 +16,4 @@ template:
   name: multiplesequencealign
   org: nf-core
   outdir: .
-  version: 1.1.0
+  version: 1.1.1

CHANGELOG.md

@@ -3,6 +3,17 @@
 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).
 
+## [1.1.1 - Bogatell](https://github.com/nf-core/multiplesequencealign/releases/tag/1.1.1)
+
+Patch release with minor improvements in docs and validation of the pipeline.
+
+### Enhancements & fixes
+
+- [[#218](https://github.com/nf-core/multiplesequencealign/pull/218)] - Improve the input validation of the pipeline. This will prevent multiple downstream errors
+- [[#221](https://github.com/nf-core/multiplesequencealign/pull/218)] - Update pipeline documentation for Shiny.
+
+### Parameters
+
 ## [1.1.0 - Nova Icaria](https://github.com/nf-core/multiplesequencealign/releases/tag/1.1.0)
 
 Nova Icaria is a beach in Barcelona. We started from Somorrostro (beach in front of CRG) and we are going up the way to Costa Brava.
@@ -61,10 +72,10 @@ Initial release of nf-core/multiplesequencealign, created with the [nf-core](htt
 - [[#35](https://github.com/nf-core/multiplesequencealign/issues/35)] - Add module MUSCLE5_SUPER5.
 - [[#59](https://github.com/nf-core/multiplesequencealign/issues/59)] - Add support for passing structure template in samplesheet.
 - [[#77](https://github.com/nf-core/multiplesequencealign/issues/77)] - Add module zip.
-- [[#93](https://github.com/nf-core/multiplesequencealign/pull/93)] - Add multiqc basic support. Add custom params validation. Add basic shiny app.
+- [[#93](https://github.com/nf-core/multiplesequencealign/pull/93)] - Add multiqc basic support. Add custom params validation. Add basic Shiny app.
 - [[#100](https://github.com/nf-core/multiplesequencealign/pull/100)] - Add support for optional stats and evals. Clean tests.
 - [[#110](https://github.com/nf-core/multiplesequencealign/issues/110)] - Add Readme documentation. Add nf-test for the pipeline.
-- [[#76](https://github.com/nf-core/multiplesequencealign/issues/76)] - Add reading of trace files for shiny app.
+- [[#76](https://github.com/nf-core/multiplesequencealign/issues/76)] - Add reading of trace files for Shiny app.
 - [[#99](https://github.com/nf-core/multiplesequencealign/issues/99)] - Add check for conflicting input parameters for stats and eval.
 - [[#117](https://github.com/nf-core/multiplesequencealign/issues/117)] - Add data for full datasets.
 - [[#90](https://github.com/nf-core/multiplesequencealign/issues/90)] - Add TCS evaluation metric.
@@ -74,7 +85,7 @@ Initial release of nf-core/multiplesequencealign, created with the [nf-core](htt
 - [[#139](https://github.com/nf-core/multiplesequencealign/pull/139)] - Add Foldmason.
 - [[#146](https://github.com/nf-core/multiplesequencealign/pull/146)] - Only show additional process tags when they exists and use the same ubuntu version in all modules.
 - [[#145](https://github.com/nf-core/multiplesequencealign/pull/145)] - Add consensus MSA.
-- [[#147](https://github.com/nf-core/multiplesequencealign/pull/147)] - Add small testing profile + some fixes of the shiny app.
+- [[#147](https://github.com/nf-core/multiplesequencealign/pull/147)] - Add small testing profile + some fixes of the Shiny app.
 - [[#148](https://github.com/nf-core/multiplesequencealign/pull/148)] - Add UPP module.
 - [[#150](https://github.com/nf-core/multiplesequencealign/pull/150)] - Update modules and readme for pre-release.
 
@@ -91,7 +102,7 @@ Initial release of nf-core/multiplesequencealign, created with the [nf-core](htt
 - [[#134](https://github.com/nf-core/multiplesequencealign/pull/134)] - Code revision for release preparation.
 - [[#138](https://github.com/nf-core/multiplesequencealign/pull/138)] - MultiQC as nf-core module and fix visualization.
 - [[#152](https://github.com/nf-core/multiplesequencealign/pull/152)] - Ignore kalign error 132 and print a warning (incompatibility with some CPU types).
-- [[#153](https://github.com/nf-core/multiplesequencealign/pull/153)] - Fix time parser in shiny app.
+- [[#153](https://github.com/nf-core/multiplesequencealign/pull/153)] - Fix time parser in Shiny app.
 - [[#154](https://github.com/nf-core/multiplesequencealign/pull/154)] - Fix metromap.
 - [[#155](https://github.com/nf-core/multiplesequencealign/pull/155)] - Fix typos.
 

README.md

@@ -9,7 +9,7 @@
 [![GitHub Actions Linting Status](https://github.com/nf-core/multiplesequencealign/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/multiplesequencealign/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/multiplesequencealign/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.13889386-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.13889386)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.10.4-23aa62.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A525.04.2-23aa62.svg)](https://www.nextflow.io/)
 [![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/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
@@ -21,7 +21,7 @@
 
 Use **nf-core/multiplesequencealign** to:
 
-1. **Deploy** one (or many in parallel) of the most popular Multiple Sequence Alignment (MSA) tools.
+1. **Deploy** one (or many) of the most popular Multiple Sequence Alignment (MSA) tools.
 2. **Benchmark** MSA tools (and their inputs) using various metrics.
 
 Main steps:
@@ -53,7 +53,7 @@ Main steps:
 
 <br>
 
-More introductory material: [talk](https://www.youtube.com/watch?v=suNulysHIN0) from the nextlow summit, [poster](https://github.com/nf-core/multiplesequencealign/blob/dev/docs/images/poster-nf-msa.pdf).
+More introductory material: [bytesize talk](https://youtu.be/iRY-Y1p5gtc), [nextflow summit talk](https://www.youtube.com/watch?v=suNulysHIN0), [poster](https://github.com/nf-core/multiplesequencealign/blob/dev/docs/images/poster-nf-msa.pdf).
 
 ![Alt text](docs/images/nf-core-msa_metro_map.png?raw=true "nf-core-msa metro map")
 

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/multiplesequencealign/releases/tag/1.1.0"
+  This report has been generated by the <a href="https://github.com/nf-core/multiplesequencealign/releases/tag/1.1.1"
   target="_blank">nf-core/multiplesequencealign</a> analysis pipeline. For information
-  about how to interpret these results, please see the <a href="https://nf-co.re/multiplesequencealign/1.1.0/docs/output"
+  about how to interpret these results, please see the <a href="https://nf-co.re/multiplesequencealign/1.1.1/docs/output"
   target="_blank">documentation</a>.
 report_section_order:
   "nf-core-multiplesequencealign-methods-description":

assets/schema_input.json

@@ -10,26 +10,41 @@
             "id": {
                 "type": "string",
                 "pattern": "^\\S+$",
-                "errorMessage": "Sample name must be provided and cannot contain spaces",
+                "errorMessage": "Sample name must be provided, has to be a string and cannot contain spaces",
                 "meta": ["id"]
             },
             "fasta": {
                 "type": "string",
-                "pattern": "^\\S+\\.f(ast)?a$",
-                "errorMessage": "fasta file. Must end with .fa or .fasta",
-                "default": ""
+                "pattern": "^\\S+\\.f(n|ast)?a$",
+                "exists": true,
+                "format": "file-path",
+                "errorMessage": "The fasta file has to exist and has to end in either '.fasta', '.fna' or '.fa'"
             },
             "reference": {
                 "type": "string",
-                "default": ""
+                "pattern": "^\\S+\\.(f(n|ast)?a|ref)$",
+                "exists": true,
+                "format": "file-path",
+                "errorMessage": "The reference file has to exist and has to end in either '.fasta', '.fna', '.fa' or '.ref'"
             },
             "optional_data": {
                 "type": "string",
-                "default": ""
+                "anyOf": [
+                    {
+                        "format": "file-path",
+                        "pattern": "^\\S+\\.tar\\.gz$"
+                    },
+                    {
+                        "format": "directory-path"
+                    }
+                ],
+                "exists": true
             },
             "template": {
                 "type": "string",
-                "default": ""
+                "pattern": "^\\S+\\.txt$",
+                "exists": true,
+                "format": "file-path"
             }
         },
         "required": ["id"],

assets/schema_tools.json

@@ -10,7 +10,7 @@
             "tree": {
                 "type": "string",
                 "pattern": "^\\S+$",
-                "errorMessage": "tree name cannot contain spaces",
+                "errorMessage": "tree name cannot contain spaces and must be a string",
                 "meta": ["tree"],
                 "default": ""
             },
@@ -23,7 +23,22 @@
                 "type": "string",
                 "meta": ["aligner"],
                 "pattern": "^\\S+$",
-                "errorMessage": "align name must be provided and cannot contain spaces",
+                "enum": [
+                    "CLUSTALO",
+                    "FAMSA",
+                    "KALIGN",
+                    "LEARNMSA",
+                    "MAFFT",
+                    "MAGUS",
+                    "MUSCLE5",
+                    "TCOFFEE",
+                    "REGRESSIVE",
+                    "UPP",
+                    "3DCOFFEE",
+                    "MTMALIGN",
+                    "FOLDMASON"
+                ],
+                "errorMessage": "align name must be provided, has to be a string, cannot contain spaces and must be one of: CLUSTALO, FAMSA, KALIGN, LEARNMSA, MAFFT, MAGUS, MUSCLES, TCOFFEE, REGRESSIVE, UPP, 3DCOFFE, MTMALIGN or FOLDMASON",
                 "default": ""
             },
             "args_aligner": {