Merge pull request #1433 from nf-core/dev

Dev -> Master for 3.17.0

Author: pinin4fjords

.github/workflows/ci.yml

@@ -54,37 +54,16 @@ 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"
+          - NXF_VER: "latest-everything"
+            profile: "singularity"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
@@ -104,21 +83,6 @@ 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:

CHANGELOG.md

@@ -3,6 +3,60 @@
 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).
 
+## [[3.17.0](https://github.com/nf-core/rnaseq/releases/tag/3.17.0)] - 2024-10-23
+
+### Credits
+
+Special thanks to the following for their contributions to the release:
+
+- [Maxime Garcia](https://github.com/maxulysse)
+- [Jonathan Manning](https://github.com/pinin4fjords)
+- [Pablo Gonzalez de Aledo](https://github.com/pabloaledo)
+
+### Enhancements & fixes
+
+- [PR #1418](https://github.com/nf-core/rnaseq/pull/1418) - Bump versions back to 3.17.0 after release
+- [PR #1422](https://github.com/nf-core/rnaseq/pull/1422) - Bump lots of modules so that conda versions have ARM builds
+- [PR #1423](https://github.com/nf-core/rnaseq/pull/1423) - Bump STAR version for version with ARM Conda build
+- [PR #1424](https://github.com/nf-core/rnaseq/pull/1424) - Patch sortmerna to 4.3.7 for ARM compatibility
+- [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
+- [PR #1437](https://github.com/nf-core/rnaseq/pull/1437) - Remove conda from test matrix
+- [PR #1440](https://github.com/nf-core/rnaseq/pull/1440) - Further reduce matrix
+- [PR #1441](https://github.com/nf-core/rnaseq/pull/1441) - Force some containers to be converted from docker to singularity to fix nf-core download tests
+
+### 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
 
 ### Credits