318 update some modeles for tes compliance

.github/PULL_REQUEST_TEMPLATE.md

@@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/fetc
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/fetchngs/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/fetchngs _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.

.github/workflows/linting.yml

@@ -14,13 +14,12 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Set up Python 3.12
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
-          cache: "pip"
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -32,14 +31,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
 
       - name: Install dependencies
@@ -60,7 +59,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:
           name: linting-logs
           path: |

.github/workflows/linting_comment.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
+        uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
         with:
           workflow: linting.yml
           workflow_conclusion: completed

CHANGELOG.md

@@ -11,6 +11,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [PR #300](https://github.com/nf-core/fetchngs/pull/300) - Use file paths instead of tags for testing matrix, should make matrices more efficient
 - [PR #303](https://github.com/nf-core/fetchngs/pull/303) - Update wget container for SRA_FASTQ_FTP from 1.20.1 to 1.21.4
 - [PR #305](https://github.com/nf-core/fetchngs/pull/305) - Update module sratools/prefetch for reliable download integrity check
+- [PR #319](https://github.com/nf-core/fetchngs/pull/319) - Update subworkflows and modules to be TES compliance.
+
+### :warning: Major enhancements
+
+- All the subworkflows and modules have been updated to newest main branch of `nf-core/modules`
+- Add support for tags
+- Updated `multiqc_mappings_config` to have different matching pattern for `config.yml` vs `versions.yml`
 
 ### Software dependencies
 

modules.json

@@ -7,23 +7,23 @@
                 "nf-core": {
                     "custom/sratoolsncbisettings": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/fasterqdump": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"],
                         "patch": "modules/nf-core/sratools/fasterqdump/sratools-fasterqdump.diff"
                     },
                     "sratools/prefetch": {
                         "branch": "master",
-                        "git_sha": "1fc29f92e439d5631fdf34b8ac4687297d70f5ec",
+                        "git_sha": "368e6c90b91adbd171e7c0a1c85a700b86a915af",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
                         "installed_by": ["modules"]
                     }
                 }
@@ -37,12 +37,12 @@
                     },
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfvalidation_plugin": {

modules/local/multiqc_mappings_config/main.nf

@@ -10,7 +10,7 @@ process MULTIQC_MAPPINGS_CONFIG {
     path csv
 
     output:
-    path "*yml"        , emit: yml
+    path "*config.yml"        , emit: yml
     path "versions.yml", emit: versions
 
     script: