From 11f7a939e2989a50f85e84660c73e68ac7b54a2f Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 21 Jun 2024 11:09:20 +0200 Subject: [PATCH 1/4] Discriminate between num_recycles of esmfold and colabfold (default value different) --- docs/usage.md | 6 +++--- main.nf | 4 ++-- nextflow.config | 4 ++-- nextflow_schema.json | 6 +++--- workflows/colabfold.nf | 8 ++++---- workflows/esmfold.nf | 6 +++--- 6 files changed, 17 insertions(+), 17 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index fd8b4392..12e47552 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -234,7 +234,7 @@ nextflow run nf-core/proteinfold \ --mode colabfold \ --colabfold_server local \ --colabfold_db \ - --num_recycle 3 \ + --num_recycles_colabfold 3 \ --use_amber \ --colabfold_model_preset "AlphaFold2-ptm" \ --use_gpu \ @@ -252,7 +252,7 @@ nextflow run nf-core/proteinfold \ --colabfold_server webserver \ --host_url \ --colabfold_db \ - --num_recycle 3 \ + --num_recycles_colabfold 3 \ --use_amber \ --colabfold_model_preset "AlphaFold2-ptm" \ --use_gpu \ @@ -407,7 +407,7 @@ nextflow run nf-core/proteinfold \ --outdir \ --mode esmfold --esmfold_db \ - --num_recycles 4 \ + --num_recycles_esmfold 4 \ --esmfold_model_preset \ --use_gpu \ -profile diff --git a/main.nf b/main.nf index 49b524d2..d6da0f09 100644 --- a/main.nf +++ b/main.nf @@ -144,7 +144,7 @@ workflow NFCORE_PROTEINFOLD { PREPARE_COLABFOLD_DBS.out.params, PREPARE_COLABFOLD_DBS.out.colabfold_db, PREPARE_COLABFOLD_DBS.out.uniref30, - params.num_recycle + params.num_recycles_colabfold ) ch_multiqc = COLABFOLD.out.multiqc_report ch_versions = ch_versions.mix(COLABFOLD.out.versions) @@ -172,7 +172,7 @@ workflow NFCORE_PROTEINFOLD { ESMFOLD ( ch_versions, PREPARE_ESMFOLD_DBS.out.params, - params.num_recycle + params.num_recycles_esmfold ) ch_multiqc = ESMFOLD.out.multiqc_report ch_versions = ch_versions.mix(ESMFOLD.out.versions) diff --git a/nextflow.config b/nextflow.config index d39fccd2..7ca395f2 100644 --- a/nextflow.config +++ b/nextflow.config @@ -50,7 +50,7 @@ params { // Colabfold parameters colabfold_server = "webserver" colabfold_model_preset = "alphafold2_ptm" // {'auto', 'alphafold2', 'alphafold2_ptm', 'alphafold2_multimer_v1', 'alphafold2_multimer_v2', 'alphafold2_multimer_v3'} - num_recycle = 3 + num_recycles_colabfold = 3 use_amber = true colabfold_db = null db_load_mode = 0 @@ -69,7 +69,7 @@ params { // Esmfold parameters esmfold_db = null esmfold_model_preset = "monomer" - num_recycles = 4 + num_recycles_esmfold = 4 // Esmfold links esmfold_3B_v1 = null diff --git a/nextflow_schema.json b/nextflow_schema.json index 962a23ec..df0bbfe3 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -130,10 +130,10 @@ ], "fa_icon": "fas fa-stream" }, - "num_recycle": { + "num_recycles_colabfold": { "type": "integer", "default": 3, - "description": "Number of recycles", + "description": "Number of recycles for Colabfold", "fa_icon": "fas fa-recycle" }, "use_amber": { @@ -180,7 +180,7 @@ "description": "Specifies the PARAMS path used by 'esmfold' mode", "fa_icon": "fas fa-folder-open" }, - "num_recycles": { + "num_recycles_esmfold": { "type": "integer", "default": 4, "description": "Specifies the number of recycles used by Esmfold", diff --git a/workflows/colabfold.nf b/workflows/colabfold.nf index 459637ce..3d2829f3 100644 --- a/workflows/colabfold.nf +++ b/workflows/colabfold.nf @@ -45,7 +45,7 @@ workflow COLABFOLD { ch_colabfold_params // channel: path(colabfold_params) ch_colabfold_db // channel: path(colabfold_db) ch_uniref30 // channel: path(uniref30) - num_recycle // int: Number of recycles for esmfold + num_recycles // int: Number of recycles for esmfold main: ch_multiqc_files = Channel.empty() @@ -72,7 +72,7 @@ workflow COLABFOLD { ch_colabfold_params, [], [], - num_recycle + num_recycles ) ch_versions = ch_versions.mix(COLABFOLD_BATCH.out.versions) } else { @@ -82,7 +82,7 @@ workflow COLABFOLD { ch_colabfold_params, [], [], - num_recycle + num_recycles ) ch_versions = ch_versions.mix(COLABFOLD_BATCH.out.versions) } @@ -122,7 +122,7 @@ workflow COLABFOLD { ch_colabfold_params, ch_colabfold_db, ch_uniref30, - num_recycle + num_recycles ) ch_versions = ch_versions.mix(COLABFOLD_BATCH.out.versions) } diff --git a/workflows/esmfold.nf b/workflows/esmfold.nf index 355aa021..962c01a1 100644 --- a/workflows/esmfold.nf +++ b/workflows/esmfold.nf @@ -41,7 +41,7 @@ workflow ESMFOLD { take: ch_versions // channel: [ path(versions.yml) ] ch_esmfold_params // directory: /path/to/esmfold/params/ - ch_num_recycle // int: Number of recycles for esmfold + ch_num_recycles // int: Number of recycles for esmfold main: ch_multiqc_files = Channel.empty() @@ -64,14 +64,14 @@ workflow ESMFOLD { RUN_ESMFOLD( MULTIFASTA_TO_SINGLEFASTA.out.input_fasta, ch_esmfold_params, - ch_num_recycle + ch_num_recycles ) ch_versions = ch_versions.mix(RUN_ESMFOLD.out.versions) } else { RUN_ESMFOLD( ch_fasta, ch_esmfold_params, - ch_num_recycle + ch_num_recycles ) ch_versions = ch_versions.mix(RUN_ESMFOLD.out.versions) } From ae73c37d4ab09f40c59fb412dd02eb508ae735b6 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 21 Jun 2024 11:10:36 +0200 Subject: [PATCH 2/4] Update readme --- README.md | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index a7554366..f21278b1 100644 --- a/README.md +++ b/README.md @@ -95,7 +95,7 @@ The pipeline takes care of downloading the databases and parameters required by --mode colabfold \ --colabfold_server local \ --colabfold_db \ - --num_recycle 3 \ + --num_recycles_colabfold 3 \ --use_amber \ --colabfold_model_preset "AlphaFold2-ptm" \ --use_gpu \ @@ -113,7 +113,7 @@ The pipeline takes care of downloading the databases and parameters required by --colabfold_server webserver \ --host_url \ --colabfold_db \ - --num_recycle 3 \ + --num_recycles_colabfold 3 \ --use_amber \ --colabfold_model_preset "AlphaFold2-ptm" \ --use_gpu \ @@ -133,7 +133,7 @@ The pipeline takes care of downloading the databases and parameters required by --mode esmfold \ --esmfold_model_preset \ --esmfold_db \ - --num_recycles 4 \ + --num_recycles_esmfold 4 \ --use_gpu \ -profile ``` @@ -154,8 +154,6 @@ For more details about the output files and reports, please refer to the nf-core/proteinfold was originally written by Athanasios Baltzis ([@athbaltzis](https://github.com/athbaltzis)), Jose Espinosa-Carrasco ([@JoseEspinosa](https://github.com/JoseEspinosa)), Luisa Santus ([@luisas](https://github.com/luisas)) and Leila Mansouri ([@l-mansouri](https://github.com/l-mansouri)) from [The Comparative Bioinformatics Group](https://www.crg.eu/en/cedric_notredame) at [The Centre for Genomic Regulation, Spain](https://www.crg.eu/) under the umbrella of the [BovReg project](https://www.bovreg.eu/) and Harshil Patel ([@drpatelh](https://github.com/drpatelh)) from [Seqera Labs, Spain](https://seqera.io/). -We thank the following people for their extensive assistance in the development of this pipeline: - Many thanks to others who have helped out and contributed along the way too, including (but not limited to): Norman Goodacre and Waleed Osman from Interline Therapeutics ([@interlinetx](https://github.com/interlinetx)), Martin Steinegger ([@martin-steinegger](https://github.com/martin-steinegger)) and Raoul J.P. Bonnal ([@rjpbonnal](https://github.com/rjpbonnal)) ## Contributions and Support From 12fb738dfedd181aef6643a457a9e280b14094c1 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 21 Jun 2024 11:13:26 +0200 Subject: [PATCH 3/4] Add mention to AWS Open Data Sponsorship Program --- README.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/README.md b/README.md index f21278b1..63a92f26 100644 --- a/README.md +++ b/README.md @@ -156,6 +156,8 @@ nf-core/proteinfold was originally written by Athanasios Baltzis ([@athbaltzis]( Many thanks to others who have helped out and contributed along the way too, including (but not limited to): Norman Goodacre and Waleed Osman from Interline Therapeutics ([@interlinetx](https://github.com/interlinetx)), Martin Steinegger ([@martin-steinegger](https://github.com/martin-steinegger)) and Raoul J.P. Bonnal ([@rjpbonnal](https://github.com/rjpbonnal)) +We would also like to thanks to the AWS Open Data Sponsorship Program for generously providing the resources necessary to host the data utilized in the testing, development, and deployment of nf-core proteinfold. + ## Contributions and Support If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md). From e30e250e393034a760a4ed785915b77af0908f48 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 21 Jun 2024 11:56:19 +0200 Subject: [PATCH 4/4] Update changelog --- CHANGELOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 92777261..4dcf3305 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -37,6 +37,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [[#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. - [[PR ##163](https://github.com/nf-core/proteinfold/pull/163)] - Fix full test CI. +- [[#150]](https://github.com/nf-core/proteinfold/issues/150)] - Add thanks to the AWS Open Data Sponsorship program in `README.md`. +- [[PR ##166](https://github.com/nf-core/proteinfold/pull/166)] - Create 2 different parameters for Colabfold and ESMfold number of recycles. ### Parameters @@ -57,6 +59,8 @@ 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` | +| `--num_recycle` | `--num_recycles_colabfold` | +| | `--num_recycles_esmfold` | | | `--uniref30_alphafold2_link` | | | `--esmfold_db` | | | `--esmfold_model_preset` |