Merge pull request #19 from nf-core/dev

Merge upstream dev (2.0.0rc1)

Author: jscgh

.github/actions/nf-test/action.yml

@@ -54,13 +54,9 @@ runs:
         conda-solver: libmamba
         conda-remove-defaults: true
 
-      # TODO Skip failing conda tests and document their failures
-      # https://github.com/nf-core/modules/issues/7017
     - name: Run nf-test
       shell: bash
       env:
-        NFT_DIFF: ${{ env.NFT_DIFF }}
-        NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }}
         NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
       run: |
         nf-test test \

.github/workflows/linting.yml

@@ -13,7 +13,7 @@ jobs:
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
 
-      - name: Set up Python 3.12
+      - name: Set up Python 3.13
         uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5
         with:
           python-version: "3.13"

.github/workflows/linting_comment.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@4c1e823582f43b179e2cbb49c3eade4e41f992e2 # v10
+        uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11
         with:
           workflow: linting.yml
           workflow_conclusion: completed

.github/workflows/nf-test.yml

@@ -1,12 +1,5 @@
 name: Run nf-test
 on:
-  push:
-    paths-ignore:
-      - "docs/**"
-      - "**/meta.yml"
-      - "**/*.md"
-      - "**/*.png"
-      - "**/*.svg"
   pull_request:
     paths-ignore:
       - "docs/**"
@@ -35,7 +28,7 @@ jobs:
   nf-test-changes:
     name: nf-test-changes
     runs-on: # use self-hosted runners
-      - runs-on=$-nf-test-changes
+      - runs-on=${{ github.run_id }}-nf-test-changes
       - runner=4cpu-linux-x64
     outputs:
       shard: ${{ steps.set-shards.outputs.shard }}
@@ -69,7 +62,7 @@ jobs:
     needs: [nf-test-changes]
     if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }}
     runs-on: # use self-hosted runners
-      - runs-on=$-nf-test
+      - runs-on=${{ github.run_id }}-nf-test
       - runner=4cpu-linux-x64
     strategy:
       fail-fast: false
@@ -85,7 +78,7 @@ jobs:
           - isMain: false
             profile: "singularity"
         NXF_VER:
-          - "24.04.2"
+          - "24.10.5"
           - "latest-everything"
     env:
       NXF_ANSI_LOG: false
@@ -97,23 +90,39 @@ jobs:
           fetch-depth: 0
 
       - name: Run nf-test
+        id: run_nf_test
         uses: ./.github/actions/nf-test
+        continue-on-error: ${{ matrix.NXF_VER == 'latest-everything' }}
         env:
-          NFT_DIFF: ${{ env.NFT_DIFF }}
-          NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }}
           NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
         with:
           profile: ${{ matrix.profile }}
           shard: ${{ matrix.shard }}
           total_shards: ${{ env.TOTAL_SHARDS }}
+
+      - name: Report test status
+        if: ${{ always() }}
+        run: |
+          if [[ "${{ steps.run_nf_test.outcome }}" == "failure" ]]; then
+            echo "::error::Test with ${{ matrix.NXF_VER }} failed"
+            # Add to workflow summary
+            echo "## ❌ Test failed: ${{ matrix.profile }} | ${{ matrix.NXF_VER }} | Shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }}" >> $GITHUB_STEP_SUMMARY
+            if [[ "${{ matrix.NXF_VER }}" == "latest-everything" ]]; then
+              echo "::warning::Test with latest-everything failed but will not cause workflow failure. Please check if the error is expected or if it needs fixing."
+            fi
+            if [[ "${{ matrix.NXF_VER }}" != "latest-everything" ]]; then
+              exit 1
+            fi
+          fi
+
   confirm-pass:
     needs: [nf-test]
     if: always()
     runs-on: # use self-hosted runners
-      - runs-on=$-confirm-pass
+      - runs-on=${{ github.run_id }}-confirm-pass
       - runner=2cpu-linux-x64
     steps:
-      - name: One or more tests failed
+      - name: One or more tests failed (excluding latest-everything)
         if: ${{ contains(needs.*.result, 'failure') }}
         run: exit 1
 
@@ -132,11 +141,3 @@ jobs:
           echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}"
           echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
           echo "::endgroup::"
-
-      - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner
-        if: always()
-        run: |
-          ls -la ./
-          rm -rf ./* || true
-          rm -rf ./.??* || true
-          ls -la ./

.github/workflows/release-announcements.yml

@@ -30,7 +30,7 @@ jobs:
   bsky-post:
     runs-on: ubuntu-latest
     steps:
-      - uses: zentered/bluesky-post-action@4aa83560bb3eac05dbad1e5f221ee339118abdd2 # v0.2.0
+      - uses: zentered/bluesky-post-action@6461056ea355ea43b977e149f7bf76aaa572e5e8 # v0.3.0
         with:
           post: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!

.gitignore

@@ -7,3 +7,4 @@ testing/
 testing*
 *.pyc
 null/
+.nf*

.nf-core.yml

@@ -3,7 +3,7 @@ lint:
     - .github/workflows/linting.yml
     - .github/CONTRIBUTING.md
   multiqc_config: false
-nf_core_version: 3.3.1
+nf_core_version: 3.3.2
 repository_type: pipeline
 template:
   author: Athanasios Baltzis, Jose Espinosa-Carrasco, Harshil Patel

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - prettier@3.5.0
+          - prettier@3.6.2
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:

CHANGELOG.md

@@ -40,45 +40,77 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[PR #306](https://github.com/nf-core/proteinfold/pull/306)] - extract_output.py -> extract_metrics.py so pLDDT, MSA, PAE emitted as raw data .tsv files
 - [[PR #307](https://github.com/nf-core/proteinfold/pull/307)] - Update Boltz-1 boilerplate and formatting.
 - [[PR #314](https://github.com/nf-core/proteinfold/pull/314)] - Fix extract metrics for broken modules.
+- [[PR #312](https://github.com/nf-core/proteinfold/pull/312)] - pTM & ipTM metrics now extracted
 - [[PR #315](https://github.com/nf-core/proteinfold/pull/315)] - Add global db flag.
 - [[#263](https://github.com/nf-core/proteinfold/issues/263)] - Removed broken colabfold options (`auto` and `alphafold2`)
 - [[PR #316](https://github.com/nf-core/proteinfold/pull/316)] - Add process_gpu label to modules which use GPU.
 - [[PR #319](https://github.com/nf-core/proteinfold/pull/319)] - Update boltz workflow to accept YAML as input.
 - [[PR #322](https://github.com/nf-core/proteinfold/pull/322)] - Updates and reorganises the reference database directory structure.
+- [[PR #329](https://github.com/nf-core/proteinfold/pull/329)] - Updates Boltz module to include Boltz-2.
 - [[PR #332](https://github.com/nf-core/proteinfold/pull/332)] - Fix rare superposition bug in reports.
 - [[PR #333](https://github.com/nf-core/proteinfold/pull/333)] - Updates the RFAA dockerfile for better versioning and smaller image size.
 - [[PR #335](https://github.com/nf-core/proteinfold/pull/335)] - Update pipeline template to [nf-core/tools 3.3.1](https://github.com/nf-core/tools/releases/tag/3.3.1).
+- [[PR #346](https://github.com/nf-core/proteinfold/pull/346)] - Update pipeline template to [nf-core/tools 3.3.2](https://github.com/nf-core/tools/releases/tag/3.3.2).
+- [[PR #351](https://github.com/nf-core/proteinfold/pull/351)] - add chain-wise (i)pTM values and summary file for AF3-generation codes.
+- [[PR #355](https://github.com/nf-core/proteinfold/pull/355)] - Remove unneccesary params from Boltz and Helixfold3 modes.
+- [[PR #356](https://github.com/nf-core/proteinfold/pull/356)] - Update AF2 defaults to use split mode and monomer_ptm model.
+- [[PR #357](https://github.com/nf-core/proteinfold/pull/357)] - Update ColabFold module and image.
+- [[PR #359](https://github.com/nf-core/proteinfold/pull/359)] - Harmonize parameters across modes.
+- [[PR #360](https://github.com/nf-core/proteinfold/pull/360)] - Rename some DBs paths in the run modules so they are equal to those when DBs are downloaded.
+- [[PR #362](https://github.com/nf-core/proteinfold/pull/355)] - Update boltz Dockerfile and image pinning specific version (2.0.3).
+- [[#364](https://github.com/nf-core/proteinfold/issues/364)] - Move Dockerfiles to its corresponding module.
+- [[PR #370](https://github.com/nf-core/proteinfold/pull/370)] - Fix extract chain metrics.
+- [[#367](https://github.com/nf-core/proteinfold/issues/367)] - Boltz post-processing crashes.
+- [[#368](https://github.com/nf-core/proteinfold/issues/368)] - Helixfold3 iPTM output missing when dealing with monomers make the process to fail.
 
 ### Parameters
 
-| Old parameter                | New parameter                  |
-| ---------------------------- | ------------------------------ |
-|                              | `--pdb_obsolete_path`          |
-| `--small_bfd_link`           | `--alphafold2_small_bfd_link`  |
-| `--mgnify_link`              | `--alphafold2_mgnify_link`     |
-| `--pdb_mmcif_link`           | `--alphafold2_pdb_mmcif_link`  |
-| `--uniref30_alphafold2_link` | `--alphafold2_uniref30_link`   |
-| `--uniref90_link`            | `--alphafold2_uniref90_link`   |
-| `--pdb_seqres_link`          | `--alphafold2_pdb_seqres_link` |
-| `--small_bfd_path`           | `--alphafold2_small_bfd_path`  |
-| `--mgnify_path_alphafold2`   | `--alphafold2_mgnify_path`     |
-| `--pdb_mmcif_path`           | `--alphafold2_pdb_mmcif_path`  |
-| `--uniref30_alphafold2_path` | `--alphafold2_uniref30_path`   |
-| `--uniref90_path`            | `--alphafold2_uniref90_path`   |
-| `--pdb_seqres_path`          | `--alphafold2_pdb_seqres_path` |
-| `--uniprot_path`             | `--alphafold2_uniprot_path`    |
-|                              | `--alphafold3_small_bfd_link`  |
-|                              | `--alphafold3_mgnify_link`     |
-|                              | `--alphafold3_uniref90_link`   |
-|                              | `--alphafold3_pdb_seqres_link` |
-|                              | `--uniprot_link`               |
-|                              | `--alphafold3_small_bfd_path`  |
-|                              | `--alphafold3_params_path`     |
-|                              | `--alphafold3_mgnify_path`     |
-|                              | `--alphafold3_pdb_mmcif_path`  |
-|                              | `--alphafold3_uniref90_path`   |
-|                              | `--alphafold3_pdb_seqres_path` |
-|                              | `--alphafold3_uniprot_path`    |
+| Old parameter                | New parameter                    |
+| ---------------------------- | -------------------------------- |
+|                              | `--alphafold2_pdb_obsolete_path` |
+| `--small_bfd_link`           | `--alphafold2_small_bfd_link`    |
+| `--mgnify_link`              | `--alphafold2_mgnify_link`       |
+| `--pdb_mmcif_link`           | `--alphafold2_pdb_mmcif_link`    |
+| `--uniref30_alphafold2_link` | `--alphafold2_uniref30_link`     |
+| `--uniref90_link`            | `--alphafold2_uniref90_link`     |
+| `--pdb_seqres_link`          | `--alphafold2_pdb_seqres_link`   |
+| `--small_bfd_path`           | `--alphafold2_small_bfd_path`    |
+| `--mgnify_path_alphafold2`   | `--alphafold2_mgnify_path`       |
+| `--pdb_mmcif_path`           | `--alphafold2_pdb_mmcif_path`    |
+| `--uniref30_alphafold2_path` | `--alphafold2_uniref30_path`     |
+| `--uniref90_path`            | `--alphafold2_uniref90_path`     |
+| `--pdb_seqres_path`          | `--alphafold2_pdb_seqres_path`   |
+| `--uniprot_path`             | `--alphafold2_uniprot_path`      |
+|                              | `--alphafold3_small_bfd_link`    |
+|                              | `--alphafold3_mgnify_link`       |
+|                              | `--alphafold3_uniref90_link`     |
+|                              | `--alphafold3_pdb_seqres_link`   |
+|                              | `--alphafold3_uniprot_link`      |
+|                              | `--alphafold3_small_bfd_path`    |
+|                              | `--alphafold3_params_path`       |
+|                              | `--alphafold3_mgnify_path`       |
+|                              | `--alphafold3_pdb_mmcif_path`    |
+|                              | `--alphafold3_uniref90_path`     |
+|                              | `--alphafold3_pdb_seqres_path`   |
+|                              | `--alphafold3_uniprot_path`      |
+|                              | `--boltz_model`                  |
+|                              | `--boltz_out_dir`                |
+|                              | `--boltz_output_format`          |
+|                              | `--boltz_use_msa_server`         |
+|                              | `--boltz_msa_server_url`         |
+|                              | `--boltz_use_potentials`         |
+|                              | `--boltz_write_full_pae`         |
+|                              | `--boltz2_aff_path`              |
+|                              | `--boltz2_conf_path`             |
+|                              | `--boltz2_mols_path`             |
+|                              | `--boltz_model_path`             |
+|                              | `--boltz_ccd_path`               |
+|                              | `--boltz_db`                     |
+|                              | `--boltz2_aff_link`              |
+|                              | `--boltz2_conf_link`             |
+|                              | `--boltz2_mols_link`             |
+|                              | `--boltz_model_link`             |
+|                              | `--boltz_ccd_link`               |
 
 > **NB:** Parameter has been **updated** if both old and new parameter information is present.
 > **NB:** Parameter has been **added** if just the new parameter information is present.
@@ -161,8 +193,8 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 | `--uniprot_sprot`     | `--uniprot_sprot_link`                   |
 | `--uniprot_trembl`    | `--uniprot_trembl_link`                  |
 | `--uniclust30_path`   | `--uniref30_alphafold2_path`             |
-| `--uniref30`          | `--uniref30_colabfold_link`              |
-| `--uniref30_path`     | `--uniref30_colabfold_path`              |
+| `--uniref30`          | `--colabfold_uniref30_link`              |
+| `--uniref30_path`     | `--colabfold_uniref30_path`              |
 | `--num_recycle`       | `--num_recycles_colabfold`               |
 |                       | `--num_recycles_esmfold`                 |
 |                       | `--uniref30_alphafold2_link`             |

README.md

@@ -5,12 +5,11 @@
   </picture>
 </h1>
 
-[![GitHub Actions CI Status](https://github.com/nf-core/proteinfold/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/proteinfold/actions/workflows/ci.yml)
+[![GitHub Actions CI Status](https://github.com/nf-core/proteinfold/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/proteinfold/actions/workflows/nf-test.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/proteinfold/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/proteinfold/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/proteinfold/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.13135393-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.13135393)
-[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
-[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.04.2-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
-[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.1)
+[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
+[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
@@ -117,7 +116,6 @@ The pipeline takes care of downloading the databases and parameters required by
       --input samplesheet.csv \
       --outdir <OUTDIR> \
       --mode colabfold \
-      --colabfold_server local \
       --colabfold_db <null (default) | PATH> \
       --num_recycles_colabfold 3 \
       --use_amber <true/false> \
@@ -134,8 +132,8 @@ The pipeline takes care of downloading the databases and parameters required by
       --input samplesheet.csv \
       --outdir <OUTDIR> \
       --mode colabfold \
-      --colabfold_server webserver \
-      --host_url <custom MMSeqs2 API Server URL> \
+      --use_msa_server \
+      --msa_server_url <custom MMSeqs2 API Server URL> \
       --colabfold_db <null (default) | PATH> \
       --num_recycles_colabfold 3 \
       --use_amber <true/false> \