From d5673018a8d8d08a5f3bed14297c2279a293418d Mon Sep 17 00:00:00 2001 From: "keiran.rowell" Date: Wed, 11 Feb 2026 16:03:48 +1100 Subject: [PATCH 01/10] Clean ESMFold ouputputs and have container triton cache writeable --- conf/modules_esmfold.config | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/conf/modules_esmfold.config b/conf/modules_esmfold.config index 3468718f..d9626377 100644 --- a/conf/modules_esmfold.config +++ b/conf/modules_esmfold.config @@ -12,19 +12,19 @@ process { withName: 'RUN_ESMFOLD' { - ext.args = {params.use_gpu ? '' : '--cpu-only'} + ext.args = '' + containerOptions = '--nv --env TRITON_CACHE_DIR=/tmp/triton_cache --env XDG_CACHE_HOME=/tmp' publishDir = [ [ - path: { "${params.outdir}/esmfold/default" }, + path: { "${params.outdir}/esmfold/${meta.id}" }, mode: 'copy', - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - pattern: '*.*' + pattern: '*_plddt.tsv' ], [ - path: { "${params.outdir}/esmfold/default/top_ranked_structures" }, + path: { "${params.outdir}/esmfold/top_ranked_structures" }, mode: 'copy', saveAs: { "${meta.id}.pdb" }, - pattern: '*.pdb' + pattern: '*_esmfold.pdb' ] ] } From d3b67b6376de1deb91f40b2f23ba88334fbce1ee Mon Sep 17 00:00:00 2001 From: "keiran.rowell" Date: Wed, 11 Feb 2026 16:12:09 +1100 Subject: [PATCH 02/10] Update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e1e8ce5b..a08d1d15 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -92,6 +92,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [[#417](https://github.com/nf-core/proteinfold/issues/417)] - Add `boltz_use_kernels` parameter to enable/disable using optimized Triton-based CUDA kernels CUDA kernels for Boltz inference. - [[#417](https://github.com/nf-core/proteinfold/issues/417)] - Handle incompatible CUDA kernel errors in Boltz by automatically retrying with `--no_kernels` false. - [[PR #454](https://github.com/nf-core/proteinfold/pulls/454)] - Update publishdir patterns for alphafold2 modules +- [[PR #464](https://github.com/nf-core/proteinfold/pulls/464)] - Update module conf and publishdir patterns for ESMFold, pass through container args ### Parameters From a118637bdccb5bd3beadeb854c488505ae14a5aa Mon Sep 17 00:00:00 2001 From: "keiran.rowell" Date: Wed, 11 Feb 2026 16:13:38 +1100 Subject: [PATCH 03/10] Whitespace.. --- conf/modules_esmfold.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules_esmfold.config b/conf/modules_esmfold.config index d9626377..7eca02f6 100644 --- a/conf/modules_esmfold.config +++ b/conf/modules_esmfold.config @@ -13,7 +13,7 @@ process { withName: 'RUN_ESMFOLD' { ext.args = '' - containerOptions = '--nv --env TRITON_CACHE_DIR=/tmp/triton_cache --env XDG_CACHE_HOME=/tmp' + containerOptions = '--nv --env TRITON_CACHE_DIR=/tmp/triton_cache --env XDG_CACHE_HOME=/tmp' publishDir = [ [ path: { "${params.outdir}/esmfold/${meta.id}" }, From 3c8e1bb56025cc6b9468e297799d8f7974d0dd28 Mon Sep 17 00:00:00 2001 From: Keiran Rowell <54380465+keiran-rowell-unsw@users.noreply.github.com> Date: Thu, 12 Feb 2026 08:56:04 +1100 Subject: [PATCH 04/10] Update conf/modules_esmfold.config Reinstate fallback to CPU, particular with as a last-ditch fallback on later CC GPUs Co-authored-by: Jose Espinosa-Carrasco --- conf/modules_esmfold.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules_esmfold.config b/conf/modules_esmfold.config index 7eca02f6..8d8ee606 100644 --- a/conf/modules_esmfold.config +++ b/conf/modules_esmfold.config @@ -12,7 +12,7 @@ process { withName: 'RUN_ESMFOLD' { - ext.args = '' + ext.args = {params.use_gpu ? '' : '--cpu-only'} containerOptions = '--nv --env TRITON_CACHE_DIR=/tmp/triton_cache --env XDG_CACHE_HOME=/tmp' publishDir = [ [ From e81fcafbefd92c0a6b60187b6035bebcdd9c758a Mon Sep 17 00:00:00 2001 From: "keiran.rowell" Date: Thu, 12 Feb 2026 08:57:36 +1100 Subject: [PATCH 05/10] remove containerOptions, prefer to add paths in-container for v2 --- conf/modules_esmfold.config | 1 - 1 file changed, 1 deletion(-) diff --git a/conf/modules_esmfold.config b/conf/modules_esmfold.config index 8d8ee606..7ddffefb 100644 --- a/conf/modules_esmfold.config +++ b/conf/modules_esmfold.config @@ -13,7 +13,6 @@ process { withName: 'RUN_ESMFOLD' { ext.args = {params.use_gpu ? '' : '--cpu-only'} - containerOptions = '--nv --env TRITON_CACHE_DIR=/tmp/triton_cache --env XDG_CACHE_HOME=/tmp' publishDir = [ [ path: { "${params.outdir}/esmfold/${meta.id}" }, From 72a54bd3580c47e7b89c3324326371d5e4674fbf Mon Sep 17 00:00:00 2001 From: "keiran.rowell" Date: Thu, 12 Feb 2026 09:01:41 +1100 Subject: [PATCH 06/10] fix mis-number and typo in changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index bb9e7b76..9023059e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -91,6 +91,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [[PR #451](https://github.com/nf-core/proteinfold/pulls/451)] - Remove af2 multimer padding from msa plots. - [[#417](https://github.com/nf-core/proteinfold/issues/417)] - Add `boltz_use_kernels` parameter to enable/disable using optimized Triton-based CUDA kernels CUDA kernels for Boltz inference. - [[#285](https://github.com/nf-core/proteinfold/issues/285)] - Adding contributors to manifest. +- [[PR #460](https://github.com/nf-core/proteinfold/pulls/460)] - Use `nvidia-smi` to obtain number of SM. - [[PR #454](https://github.com/nf-core/proteinfold/pulls/454)] - Update publishdir patterns for alphafold2 modules. - [[PR #458](https://github.com/nf-core/proteinfold/pulls/458)] - Update publishdir patterns for colabfold module. - [[#313](https://github.com/nf-core/proteinfold/issues/313)] - Harmonize colabfold metrics extraction with other modes. From 6ad9d236a84cf5ef004b1027011a7646c6968e9b Mon Sep 17 00:00:00 2001 From: "keiran.rowell" Date: Thu, 12 Feb 2026 19:30:15 +1100 Subject: [PATCH 07/10] pass through --env paths only if singularity or apptainer --- conf/modules_esmfold.config | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/conf/modules_esmfold.config b/conf/modules_esmfold.config index 7ddffefb..193d63eb 100644 --- a/conf/modules_esmfold.config +++ b/conf/modules_esmfold.config @@ -13,6 +13,11 @@ process { withName: 'RUN_ESMFOLD' { ext.args = {params.use_gpu ? '' : '--cpu-only'} + containerOptions = { + workflow.containerEngine in ['singularity', 'apptainer'] ? + '--nv --env TRITON_CACHE_DIR=/tmp/triton_cache --env XDG_CACHE_HOME=/tmp' : + '' + } publishDir = [ [ path: { "${params.outdir}/esmfold/${meta.id}" }, From 6760dc0855e6b6c001cce11795b58e35f4a6247d Mon Sep 17 00:00:00 2001 From: "keiran.rowell" Date: Thu, 12 Feb 2026 19:31:51 +1100 Subject: [PATCH 08/10] Fix Boltz output PR # --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0590295c..65441300 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -101,7 +101,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [[PR #461](https://github.com/nf-core/proteinfold/pulls/461)] - Update publishdir patterns for HelixFold3 module - [[PR #462](https://github.com/nf-core/proteinfold/pulls/462)] - Update publishdir patterns for RoseTTAFold-All-Atom modules - [[PR #464](https://github.com/nf-core/proteinfold/pulls/454)] - Update publishdir patterns for Boltz module -- [[PR #464](https://github.com/nf-core/proteinfold/pulls/464)] - Update module conf and publishdir patterns for ESMFold, pass through container args +- [[PR #466](https://github.com/nf-core/proteinfold/pulls/464)] - Update module conf and publishdir patterns for ESMFold, pass through container args - [[PR #469](https://github.com/nf-core/proteinfold/pulls/454)] - HTML reports now in /reports output directory ### Parameters From d753a06c7c811823b7a5512e0bedb400771f2952 Mon Sep 17 00:00:00 2001 From: "keiran.rowell" Date: Thu, 12 Feb 2026 19:34:11 +1100 Subject: [PATCH 09/10] run pre-commit --- conf/modules | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 conf/modules diff --git a/conf/modules b/conf/modules new file mode 100644 index 00000000..e69de29b From 4f938ab8e0d033552a2640b3f3b35964c850803b Mon Sep 17 00:00:00 2001 From: "keiran.rowell" Date: Thu, 12 Feb 2026 19:35:48 +1100 Subject: [PATCH 10/10] trailing whitespace.. --- conf/modules_esmfold.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/conf/modules_esmfold.config b/conf/modules_esmfold.config index 193d63eb..258e8f17 100644 --- a/conf/modules_esmfold.config +++ b/conf/modules_esmfold.config @@ -14,8 +14,8 @@ process { withName: 'RUN_ESMFOLD' { ext.args = {params.use_gpu ? '' : '--cpu-only'} containerOptions = { - workflow.containerEngine in ['singularity', 'apptainer'] ? - '--nv --env TRITON_CACHE_DIR=/tmp/triton_cache --env XDG_CACHE_HOME=/tmp' : + workflow.containerEngine in ['singularity', 'apptainer'] ? + '--nv --env TRITON_CACHE_DIR=/tmp/triton_cache --env XDG_CACHE_HOME=/tmp' : '' } publishDir = [