From e94558ba2819f347699d3b3fedffe40fa0f89f87 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 23 Oct 2024 19:23:46 +0200 Subject: [PATCH 1/8] update CHANGELOG --- CHANGELOG.md | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 51374d1e8..c3011a087 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -22,6 +22,37 @@ Special thanks to the following for their contributions to the release: - [PR #1425](https://github.com/nf-core/rnaseq/pull/1425) - Add profile for ARM compatibility - [PR #1432](https://github.com/nf-core/rnaseq/pull/1432) - Bump versions for 3.17.0 release - [PR #1434](https://github.com/nf-core/rnaseq/pull/1434) - Default registry is quay.io for all containers +- [PR #1437](https://github.com/nf-core/rnaseq/pull/1437) - Update software dependencies + +### Software dependencies + +| Dependency | Old version | New version | +| ----------------------------- | ----------- | ----------- | +| `bbmap` | 39.01 | 39.10 | +| `coreutils` | 8.30 | 9.5 | +| `fq` | 0.9.1 | 0.12.0 | +| `python (catadditionalfasta)` | 3.9.5 | 3.12.2 | +| `python (tx2gene)` | 3.9.5 | 3.10.4 | +| `cutadapt` | 3.4 | 4.9 | +| `htslib (star)` | 1.18 | 1.20 | +| `htslib` | 1.20 | 1.21 | +| `kallisto` | 0.48.0 | 0.51.1 | +| `preseq` | 3.1.2 | 3.2.0 | +| `salmon` | 1.10.1 | 1.10.3 | +| `samtools (star)` | 1.18 | 1.20 | +| `samtools` | 1.20 | 1.21 | +| `sortmerna` | 4.3.6 | 4.3.7 | +| `star` | 2.7.10a | =2.7.11b | +| `stringtie` | 2.2.1 | 2.2.3 | +| `subread` | 2.0.1 | 2.0.6 | +| `trim-galore` | 0.6.7 | 0.6.10 | +| `ucsc-bedgraphtobigwig` | 445 | 469 | + +> **NB:** Dependency has been **updated** if both old and new version information is present. +> +> **NB:** Dependency has been **added** if just the new version information is present. +> +> **NB:** Dependency has been **removed** if new version information isn't present. ## [[3.16.1](https://github.com/nf-core/rnaseq/releases/tag/3.16.1)] - 2024-10-16 From b5f530fc8fa20fcbe6c7eb3a4ffbd64eb2f53bf5 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 23 Oct 2024 19:28:19 +0200 Subject: [PATCH 2/8] fix CI --- .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 6346287ac..a02a316a5 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -44,7 +44,7 @@ jobs: test: name: "Run tests (${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }})" needs: [nf-test-changes] - if: needs.nf-test-changes.outputs.nf_test_files != '[]' + if: nf-test-changes.outputs.nf_test_files != '[]' runs-on: ubuntu-latest strategy: fail-fast: false From 97d3697b36ba84f399b4c76b4f07b72c0ea35d7d Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 23 Oct 2024 19:29:21 +0200 Subject: [PATCH 3/8] update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c3011a087..abc9cd032 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,6 +23,7 @@ Special thanks to the following for their contributions to the release: - [PR #1432](https://github.com/nf-core/rnaseq/pull/1432) - Bump versions for 3.17.0 release - [PR #1434](https://github.com/nf-core/rnaseq/pull/1434) - Default registry is quay.io for all containers - [PR #1437](https://github.com/nf-core/rnaseq/pull/1437) - Update software dependencies +- [PR #1437](https://github.com/nf-core/rnaseq/pull/1437) - Fix CI triggers ### Software dependencies From 23d3ee75a7a8c8753b441b9b9034391784aa6b6e Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 23 Oct 2024 19:31:26 +0200 Subject: [PATCH 4/8] fix GHA --- .github/workflows/ci.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index a02a316a5..40125fbb2 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -44,7 +44,6 @@ jobs: test: name: "Run tests (${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }})" needs: [nf-test-changes] - if: nf-test-changes.outputs.nf_test_files != '[]' runs-on: ubuntu-latest strategy: fail-fast: false From b55c81a42af1788920e0405e4cf8a9ca9d399832 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 23 Oct 2024 19:35:20 +0200 Subject: [PATCH 5/8] revert GHA --- .github/workflows/ci.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 40125fbb2..6346287ac 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -44,6 +44,7 @@ jobs: test: name: "Run tests (${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }})" needs: [nf-test-changes] + if: needs.nf-test-changes.outputs.nf_test_files != '[]' runs-on: ubuntu-latest strategy: fail-fast: false From 9690d295a68dca62217409ff266fa719a062f8ac Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 23 Oct 2024 19:35:33 +0200 Subject: [PATCH 6/8] revert CHANGELOG --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index abc9cd032..c3011a087 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,7 +23,6 @@ Special thanks to the following for their contributions to the release: - [PR #1432](https://github.com/nf-core/rnaseq/pull/1432) - Bump versions for 3.17.0 release - [PR #1434](https://github.com/nf-core/rnaseq/pull/1434) - Default registry is quay.io for all containers - [PR #1437](https://github.com/nf-core/rnaseq/pull/1437) - Update software dependencies -- [PR #1437](https://github.com/nf-core/rnaseq/pull/1437) - Fix CI triggers ### Software dependencies From ac1b7e08517665e0f8b372ee4912056858a79831 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 23 Oct 2024 20:42:58 +0200 Subject: [PATCH 7/8] update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c3011a087..fc825f839 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,6 +23,7 @@ Special thanks to the following for their contributions to the release: - [PR #1432](https://github.com/nf-core/rnaseq/pull/1432) - Bump versions for 3.17.0 release - [PR #1434](https://github.com/nf-core/rnaseq/pull/1434) - Default registry is quay.io for all containers - [PR #1437](https://github.com/nf-core/rnaseq/pull/1437) - Update software dependencies +- [PR #1437](https://github.com/nf-core/rnaseq/pull/1437) - Remove conda from test matrix ### Software dependencies From 38903446cbfeed8d1dd62b8780cbf86cc2df5515 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 23 Oct 2024 20:43:07 +0200 Subject: [PATCH 8/8] remove conda from matrix --- .github/workflows/ci.yml | 38 -------------------------------------- 1 file changed, 38 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 6346287ac..3660947b7 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -54,37 +54,14 @@ jobs: - "latest-everything" nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"] profile: - - "conda" - "docker" - "singularity" isMaster: - ${{ github.base_ref == 'master' }} # Exclude conda and singularity on dev exclude: - - isMaster: false - profile: "conda" - isMaster: false profile: "singularity" - - profile: "conda" - nf_test_files: "tests/default.nf.test" - - profile: "conda" - nf_test_files: "tests/featurecounts_group_type.nf.test" - - profile: "conda" - nf_test_files: "tests/hisat2.nf.test" - - profile: "conda" - nf_test_files: "tests/kallisto.nf.test" - - profile: "conda" - nf_test_files: "tests/min_mapped_reads.nf.test" - - profile: "conda" - nf_test_files: "tests/remove_ribo_rna.nf.test" - - profile: "conda" - nf_test_files: "tests/salmon.nf.test" - - profile: "conda" - nf_test_files: "tests/skip_qc.nf.test" - - profile: "conda" - nf_test_files: "tests/skip_trimming.nf.test" - - profile: "conda" - nf_test_files: "tests/star_rsem.nf.test" steps: - name: Check out pipeline code uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 @@ -104,21 +81,6 @@ jobs: mkdir -p $NXF_SINGULARITY_CACHEDIR mkdir -p $NXF_SINGULARITY_LIBRARYDIR - - name: Set up Miniconda - if: matrix.profile == 'conda' - uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 - with: - miniconda-version: "latest" - auto-update-conda: true - conda-solver: libmamba - channels: conda-forge,bioconda - - - name: Set up Conda - if: matrix.profile == 'conda' - run: | - echo $(realpath $CONDA)/condabin >> $GITHUB_PATH - echo $(realpath python) >> $GITHUB_PATH - - name: Install nf-test uses: nf-core/setup-nf-test@v1 with: