From bb8334c02158a55bd53689bdac91f06869949412 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Fri, 25 Aug 2023 08:55:57 +0200 Subject: [PATCH 1/6] Fix deepARG test profile and use more stable deepARG db URL --- .github/workflows/ci.yml | 52 +++++++++++++++++++++------------------- conf/test_deeparg.config | 5 ++-- 2 files changed, 30 insertions(+), 27 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index f45e42aa..ee88aaf1 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -72,31 +72,33 @@ jobs: run: | nextflow run ${GITHUB_WORKSPACE} -profile test_bgc,docker --outdir ./results ${{ matrix.parameters }} - # test_deeparg: #Tests switched off as long as DeepARG servers are unavaiable for database download. - # name: Run pipeline with test data (DeepARG only workflow) - # # Only run on push if this is the nf-core dev branch (merged PRs) - # if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/funcscan') }}" - # runs-on: ubuntu-latest - # strategy: - # matrix: - # NXF_VER: - # - "23.04.0" - # - "latest-everything" - # parameters: - # - "--annotation_tool bakta --annotation_bakta_db_downloadtype light" - # - "--annotation_tool prodigal" - # - "--annotation_tool prokka" - # - "--annotation_tool pyrodigal" + test_deeparg: + name: Run pipeline with test data (DeepARG only workflow) + # Only run on push if this is the nf-core dev branch (merged PRs) + if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/funcscan') }}" + runs-on: ubuntu-latest + strategy: + matrix: + NXF_VER: + - "23.04.0" + - "latest-everything" + parameters: + - "--annotation_tool bakta --annotation_bakta_db_downloadtype light" + - "--annotation_tool prodigal" + - "--annotation_tool prokka" + - "--annotation_tool pyrodigal" - # steps: - # - name: Check out pipeline code - # uses: actions/checkout@v2 + steps: + - name: Check out pipeline code + uses: actions/checkout@v2 - # - name: Install Nextflow - # uses: nf-core/setup-nextflow@v1 - # with: - # version: "${{ matrix.NXF_VER }}" + - name: Install Nextflow + uses: nf-core/setup-nextflow@v1 + with: + version: "${{ matrix.NXF_VER }}" - # - name: Run pipeline with test data (DeepARG workflow) - # run: | - # nextflow run ${GITHUB_WORKSPACE} -profile test_deeparg,docker --outdir ./results ${{ matrix.parameters }} + - name: Run pipeline with test data (DeepARG workflow) + run: | + wget https://zenodo.org/record/8280582/files/deeparg.zip ## download from zenodo due to instability of deepARG server + unzip deeparg.zip + nextflow run ${GITHUB_WORKSPACE} -profile test_deeparg,docker --outdir ./results ${{ matrix.parameters }} --arg_deeparg_data 'deeparg/deeparg/'' diff --git a/conf/test_deeparg.config b/conf/test_deeparg.config index 625d8eb4..ff229340 100644 --- a/conf/test_deeparg.config +++ b/conf/test_deeparg.config @@ -30,8 +30,9 @@ params { arg_skip_fargene = true arg_skip_rgi = true arg_skip_amrfinderplus = true + arg_skip_abricate = true arg_skip_deeparg = false - run_amp_screening = false - run_bgc_screening = false + run_amp_screening = false + run_bgc_screening = false } From f651f88b372c95214add9c094fe0d26b5809fba1 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Fri, 25 Aug 2023 08:57:00 +0200 Subject: [PATCH 2/6] Reduce deepARG test annotaion tool to prevent zenodo DL throttling --- .github/workflows/ci.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ee88aaf1..2d0c597b 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -84,8 +84,6 @@ jobs: - "latest-everything" parameters: - "--annotation_tool bakta --annotation_bakta_db_downloadtype light" - - "--annotation_tool prodigal" - - "--annotation_tool prokka" - "--annotation_tool pyrodigal" steps: From edb6c978a6e35f85bb5c80adde7e2a378ca914f2 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Fri, 25 Aug 2023 09:02:45 +0200 Subject: [PATCH 3/6] Update CHANBGELOG --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e0674f20..e65ca457 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [#307](https://github.com/nf-core/funcscan/pull/307) Fixed stability of deepARG tests by using Zenodo copy of database (❤️ to Gustavo Arango and Liqing Zhang for uploading, fix by @jfy133) + ### `Dependencies` ### `Deprecated` From 079ef0f5e9e00b1b90f71c71f9125e654a9e33e5 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 25 Aug 2023 09:16:58 +0200 Subject: [PATCH 4/6] Apply suggestions from code review --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 2d0c597b..cae33590 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -99,4 +99,4 @@ jobs: run: | wget https://zenodo.org/record/8280582/files/deeparg.zip ## download from zenodo due to instability of deepARG server unzip deeparg.zip - nextflow run ${GITHUB_WORKSPACE} -profile test_deeparg,docker --outdir ./results ${{ matrix.parameters }} --arg_deeparg_data 'deeparg/deeparg/'' + nextflow run ${GITHUB_WORKSPACE} -profile test_deeparg,docker --outdir ./results ${{ matrix.parameters }} --arg_deeparg_data 'deeparg/deeparg/' From b7c5237d60095c089c44e76ff6d68aad0de82161 Mon Sep 17 00:00:00 2001 From: jasmezz Date: Fri, 25 Aug 2023 09:39:07 +0200 Subject: [PATCH 5/6] Add DeepARG Zenodo link to usage docs --- docs/usage.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index cf9ba24f..2582618c 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -185,9 +185,10 @@ You can either: 1. Install DeepARG from [bioconda](https://bioconda.github.io/recipes/deeparg/README.html?highlight=deeparg) 2. Run `deeparg download_data -o ////` -Or +Or download the files directly from -1. Download the files directly from the [DeepARG FTP site](https://bench.cs.vt.edu/ftp/data/gustavo1/deeparg/database/) +1. the [DeepARG FTP site](https://bench.cs.vt.edu/ftp/data/gustavo1/deeparg/database/) +2. the [DeepARG database Zenodo archive](https://zenodo.org/record/8280582) Note that more recent database versions maybe available from the [ARGMiner service](https://bench.cs.vt.edu/argminer/#/home). From bc4db0dee77878a0b181a62f6d3fd458fa7192c8 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 25 Aug 2023 11:13:20 +0200 Subject: [PATCH 6/6] Update .github/workflows/ci.yml --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index cae33590..c34546ec 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -99,4 +99,4 @@ jobs: run: | wget https://zenodo.org/record/8280582/files/deeparg.zip ## download from zenodo due to instability of deepARG server unzip deeparg.zip - nextflow run ${GITHUB_WORKSPACE} -profile test_deeparg,docker --outdir ./results ${{ matrix.parameters }} --arg_deeparg_data 'deeparg/deeparg/' + nextflow run ${GITHUB_WORKSPACE} -profile test_deeparg,docker --outdir ./results ${{ matrix.parameters }} --arg_deeparg_data 'deeparg/'