Adding foldseek to the workflow

CHANGELOG.md

@@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [[#177](https://github.com/nf-core/proteinfold/issues/177)]- Fix typo in some instances of model preset `alphafold2_ptm`.
 - [[PR #178](https://github.com/nf-core/proteinfold/pull/178)] - Enable running multiple modes in parallel.
+- [[#179](https://github.com/nf-core/proteinfold/issues/179)]- Produce an interactive html report for the predicted structures.
+- [[#180](https://github.com/nf-core/proteinfold/issues/180)]- Implement Fooldseek.
 
 ## [[1.1.1](https://github.com/nf-core/proteinfold/releases/tag/1.1.1)] - 2025-07-30
 

conf/dbs.config

@@ -55,4 +55,9 @@ params {
 
     // Esmfold paths
     esmfold_params_path                         = "${params.esmfold_db}/*"
+
+    // Foldseek databases paths
+    foldseek_db = null
+    foldseek_db_path = null
+
 }

conf/modules.config

@@ -51,4 +51,13 @@ process {
         ]
     }
 
+    withName: 'FOLDSEEK_EASYSEARCH' {
+        ext.args   = { params.foldseek_easysearch_arg ? "$params.foldseek_easysearch_arg" : "--format-mode 3" }
+        publishDir = [
+            path: { "${params.outdir}/foldseek_easysearch" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
 }

main.nf

@@ -35,7 +35,8 @@ include { PIPELINE_COMPLETION              } from './subworkflows/local/utils_nf
 include { getColabfoldAlphafold2Params     } from './subworkflows/local/utils_nfcore_proteinfold_pipeline'
 include { getColabfoldAlphafold2ParamsPath } from './subworkflows/local/utils_nfcore_proteinfold_pipeline'
 
-include { GENERATE_REPORT } from './modules/local/generate_report'
+include { GENERATE_REPORT     } from './modules/local/generate_report'
+include { FOLDSEEK_EASYSEARCH } from './modules/nf-core/foldseek/easysearch/main'
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     COLABFOLD PARAMETER VALUES
@@ -206,6 +207,24 @@ workflow NFCORE_PROTEINFOLD {
         )
         ch_versions = ch_versions.mix(GENERATE_REPORT.out.versions)
     }
+
+    if (params.foldseek_search == "easysearch"){
+        ch_foldseek_db = channel.value([["id": params.foldseek_db],
+                                        file(params.foldseek_db_path,
+                                            checkIfExists: true)])
+
+        FOLDSEEK_EASYSEARCH(
+            ch_report_input
+            .map{
+                if (it[0].model == "esmfold")
+                    [it[0], it[1]]
+                else
+                    [it[0], it[1][0]]
+                },
+            ch_foldseek_db
+        )
+    }
+
     emit:
     multiqc_report = ch_multiqc  // channel: /path/to/multiqc_report.html
     versions       = ch_versions // channel: [version1, version2, ...]

modules.json

@@ -11,6 +11,12 @@
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/aria2/aria2.diff"
                     },
+                    "foldseek/easysearch": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/foldseek/easysearch/foldseek-easysearch.diff"
+                    },
                     "gunzip": {
                         "branch": "master",
                         "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",

nextflow.config

@@ -79,6 +79,10 @@ params {
     // Esmfold paths
     esmfold_params_path         = null
 
+    // Foldseek params
+    foldseek_search = null
+    foldseek_easysearch_arg = null
+
     // Process skipping options
     skip_multiqc               = false
     skip_visualisation         = false