318 update 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 +11,7 @@ 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 #320](https://github.com/nf-core/fetchngs/pull/20) - Update module multiqc_mappings_config and sratools/prefetch for TES compliance
 
 ### Software dependencies
 
@@ -40,6 +41,7 @@ Special thanks to the following for their contributions to the release:
 - [Maxime Garcia](https://github.com/maxulysse)
 - [Sateesh Peri](https://github.com/sateeshperi)
 - [Sebastian Uhrig](https://github.com/suhrig)
+- [Venkat Malladi](https://github.com/vsmalladi)
 
 Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
 

modules.json

@@ -18,7 +18,7 @@
  },
  "sratools/prefetch": {
  "branch": "master",
- "git_sha": "1fc29f92e439d5631fdf34b8ac4687297d70f5ec",
+ "git_sha": "368e6c90b91adbd171e7c0a1c85a700b86a915af",
  "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
  },
  "untar": {

modules/local/aspera_cli/tests/main.nf.test.snap

@@ -67,9 +67,9 @@
  }
  ],
  "meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.10.1"
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.4"
  },
- "timestamp": "2024-02-28T11:52:00.601018"
+ "timestamp": "2024-09-17T09:16:31.501413"
  }
 }

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:

modules/local/multiqc_mappings_config/tests/main.nf.test.snap

@@ -3,10 +3,7 @@
  "content": [
  {
  "0": [
- [
- "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a",
- "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
- ]
+ "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a"
  ],
  "1": [
  "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
@@ -15,17 +12,14 @@
  "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
  ],
  "yml": [
- [
- "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a",
- "versions.yml:md5,dd4c66f0551d15510b36bb2e2b2fdd73"
- ]
+ "multiqc_config.yml:md5,7f3cb10fff83ba9eb3e8fa6862d1290a"
  ]
  }
  ],
  "meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.10.1"
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.4"
  },
- "timestamp": "2024-02-28T11:52:12.65888"
+ "timestamp": "2024-09-17T09:16:46.557614"
  }
 }

modules/local/sra_fastq_ftp/tests/main.nf.test.snap

@@ -67,9 +67,9 @@
  }
  ],
  "meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.10.1"
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.4"
  },
- "timestamp": "2024-02-28T11:51:51.301654"
+ "timestamp": "2024-09-17T09:16:57.715689"
  }
-}
+}

modules/local/sra_ids_to_runinfo/tests/main.nf.test.snap

@@ -17,9 +17,9 @@
  }
  ],
  "meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.10.1"
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.4"
  },
- "timestamp": "2024-02-28T11:52:05.345153"
+ "timestamp": "2024-09-17T09:17:11.040523"
  }
 }

modules/local/sra_runinfo_to_ftp/tests/main.nf.test.snap

@@ -17,9 +17,9 @@
  }
  ],
  "meta": {
- "nf-test": "0.8.4",
- "nextflow": "23.10.1"
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.4"
  },
- "timestamp": "2024-02-28T11:51:45.748227"
+ "timestamp": "2024-09-17T09:17:23.371547"
  }
 }