Update AMPcombi modules

CHANGELOG.md

@@ -3,7 +3,11 @@
 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).
 
-## v3.1.0dev - [date]
+## v4.0.0dev - [date]
+
+### `Breaking change`
+
+- [](https://github.com/nf-core/funcscan/pull/) Updated AMPcombi, changed parameter `amp_ampcombi_cluster_removesingletons` into `amp_ampcombi_cluster_keepsingletons`. (by @jasmezz)
 
 ### `Added`
 
@@ -20,7 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
-- [#501](https://github.com/nf-core/funcscan/pull/501) Fixed issue with BAKTA HMMs not being staged correctly (reported by Yusuke Hioki, fix by @jfy133)
+- [#501](https://github.com/nf-core/funcscan/pull/501) Fixed issue with BAKTA HMMs not being staged correctly. (reported by Yusuke Hioki, fix by @jfy133)
 
 ### `Dependencies`
 
@@ -31,14 +35,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | Bakta     | 1.10.4           | 1.11.4      |
 | BiG-SLiCE |                  | 2.0.2       |
 | nf-core   | 3.3.2            | 4.0.2       |
+| AMPcombi  | 2.0.1            | 3.0.0       |
 
 ### `Deprecated`
 
 ## v3.0.0 - French Chocolatine - [2025-10-04]
 
 ### `Added`
 
-- [#477](https://github.com/nf-core/funcscan/pull/477), [#480](https://github.com/nf-core/funcscan/pull/477), [#484](https://github.com/nf-core/funcscan/pull/484) Updated to nf-core template 3.2.1., 3.3.1, 3.3.2 (by @jasmezz, @jfy133)
+- [#477](https://github.com/nf-core/funcscan/pull/477), [#480](https://github.com/nf-core/funcscan/pull/477), [#484](https://github.com/nf-core/funcscan/pull/484) Updated to nf-core template 3.2.1., 3.3.1, 3.3.2. (by @jasmezz, @jfy133)
 - [#482](https://github.com/nf-core/funcscan/pull/482) Added vertical workflow diagram. (by @jasmezz)
 
 ### `Fixed`
@@ -130,7 +135,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#322](https://github.com/nf-core/funcscan/pull/322) Updated all modules: introduce environment.yml files. (by @jasmezz)
 - [#324](https://github.com/nf-core/funcscan/pull/324) Removed separate DeepARG test profile because database download is now stable. (by @jasmezz)
-- [#332](https://github.com/nf-core/funcscan/pull/332) & [#327](https://github.com/nf-core/funcscan/pull/327) Merged pipeline template of nf-core/tools version 2.12.1 (by @jfy133, @jasmezz)
+- [#332](https://github.com/nf-core/funcscan/pull/332) & [#327](https://github.com/nf-core/funcscan/pull/327) Merged pipeline template of nf-core/tools version 2.12.1. (by @jfy133, @jasmezz)
 - [#338](https://github.com/nf-core/funcscan/pull/338) Set `--meta` parameter to default for Bakta, with singlemode optional. (by @jasmezz)
 - [#343](https://github.com/nf-core/funcscan/pull/343) Added contig taxonomic classification using [MMseqs2](https://github.com/soedinglab/MMseqs2/). (by @darcy220606)
 - [#358](https://github.com/nf-core/funcscan/pull/358) Improved RGI databases handling, users can supply their own CARD now. (by @jasmezz)
@@ -203,7 +208,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
-- [#346](https://github.com/nf-core/funcscan/pull/346) Pinned version of nf-validation to 1.1.3
+- [#346](https://github.com/nf-core/funcscan/pull/346) Pinned version of nf-validation to 1.1.3.
 
 ### `Dependencies`
 
@@ -312,7 +317,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#237](https://github.com/nf-core/funcscan/pull/237) Reactivate DeepARG automatic database downloading and CI tests as server is now back up. (by @jfy133)
 - [#235](https://github.com/nf-core/funcscan/pull/235) Improved annotation speed by switching off pipeline-irrelevant Bakta annotation steps by default. (by @jasmezz)
 - [#235](https://github.com/nf-core/funcscan/pull/235) Renamed parameter `annotation_bakta_db` to `annotation_bakta_db_localpath`. (by @jasmezz)
-- [#242](https://github.com/nf-core/funcscan/pull/242) Fixed MACREL '.faa' issue that was generated when it was run on its own and upgraded MACREL from version `1.1.0` to `1.2.0` (by @Darcy220606)
+- [#242](https://github.com/nf-core/funcscan/pull/242) Fixed MACREL '.faa' issue that was generated when it was run on its own and upgraded MACREL from version `1.1.0` to `1.2.0`. (by @Darcy220606)
 - [#248](https://github.com/nf-core/funcscan/pull/248) Applied best-practice `error("message")` to all (sub)workflow files. (by @jasmezz)
 - [#254](https://github.com/nf-core/funcscan/pull/254) Further resource optimisation based on feedback from 'real world' datasets. (ongoing, reported by @alexhbnr and @Darcy220606, fix by @jfy133)
 - [#266](https://github.com/nf-core/funcscan/pull/266) Fixed wrong process name in base.config. (reported by @Darcy220606, fix by @jasmezz)

bin/ampcombi_download.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 
 #########################################
-# Authors: [Anan Ibrahim](https://github.com/paleobiotechnology/AMPcombi), [Louisa Perelo](https://github.com/louperelo)
+# Authors: [Anan Ibrahim](https://github.com/Darcy220606), [Louisa Perelo](https://github.com/louperelo)
 # File: amp_database.py
 # Source: https://github.com/paleobiotechnology/AMPcombi/blob/main/ampcombi/amp_database.py
 # This source code is licensed under the MIT license

conf/modules.config

@@ -648,7 +648,7 @@ process {
             "--amplify_file ${params.amp_ampcombi_parsetables_amplify}",
             "--macrel_file ${params.amp_ampcombi_parsetables_macrel}",
             "--hmmsearch_file ${params.amp_ampcombi_parsetables_hmmsearch}",
-            "--ampgram_file '.tsv' --amptransformer_file '.txt' --neubi_file '.fasta' --log TRUE",
+            "--ampgram_file '.tsv' --amptransformer_file '.txt' --neubi_file '.fasta' --log",
             "--hmm_evalue ${params.amp_ampcombi_parsetables_hmmevalue}",
             "--window_size_stop_codon ${params.amp_ampcombi_parsetables_windowstopcodon}",
             "--window_size_transporter ${params.amp_ampcombi_parsetables_windowtransport}",
@@ -669,7 +669,7 @@ process {
                 }
             },
         ]
-        ext.args   = "--log TRUE"
+        ext.args   = "--log"
     }
 
     withName: AMPCOMBI2_CLUSTER {
@@ -692,8 +692,9 @@ process {
             "--cluster_seq_id ${params.amp_ampcombi_cluster_seqid}",
             "--cluster_sensitivity ${params.amp_ampcombi_cluster_sensitivity}",
             "--cluster_min_member ${params.amp_ampcombi_cluster_minmembers}",
-            "--log TRUE",
-            params.amp_ampcombi_cluster_removesingletons ? '--cluster_remove_singletons' : '',
+            "--log",
+            params.amp_ampcombi_cluster_keepsingletons ? '--cluster_keep_singletons' : '',
+
         ].join(' ').trim()
     }
 

conf/test.config

@@ -11,11 +11,7 @@
 */
 
 process {
-    resourceLimits = [
-        cpus: 4,
-        memory: '15.GB',
-        time: '1.h'
-    ]
+    resourceLimits = [cpus: 4, memory: '15.GB', time: '1.h']
 }
 
 params {
@@ -33,6 +29,7 @@ params {
     run_amp_screening          = true
     amp_run_hmmsearch          = true
     amp_hmmsearch_models       = params.pipelines_testdata_base_path + 'funcscan/hmms/mybacteriocin.hmm'
+    amp_ampcombi_db_id         = 'APD'
 
     run_cazyme_screening       = true
 }

conf/test_bakta.config

@@ -31,6 +31,7 @@ params {
     run_amp_screening                = true
     amp_run_hmmsearch                = true
     amp_hmmsearch_models             = params.pipelines_testdata_base_path + 'funcscan/hmms/mybacteriocin.hmm'
+    amp_ampcombi_db_id               = 'APD'
 
     run_arg_screening                = true
     arg_skip_deeparg                 = true

conf/test_preannotated.config

@@ -11,11 +11,7 @@
 */
 
 process {
-    resourceLimits = [
-        cpus: 4,
-        memory: '15.GB',
-        time: '1.h'
-    ]
+    resourceLimits = [cpus: 4, memory: '15.GB', time: '1.h']
 }
 
 params {
@@ -33,4 +29,5 @@ params {
     run_amp_screening          = true
     amp_run_hmmsearch          = true
     amp_hmmsearch_models       = params.pipelines_testdata_base_path + 'funcscan/hmms/mybacteriocin.hmm'
+    amp_ampcombi_db_id         = 'APD'
 }

conf/test_preannotated_cazyme.config

@@ -11,11 +11,7 @@
 */
 
 process {
-    resourceLimits = [
-        cpus: 4,
-        memory: '15.GB',
-        time: '1.h'
-    ]
+    resourceLimits = [cpus: 4, memory: '15.GB', time: '1.h']
 }
 
 params {
@@ -32,6 +28,8 @@ params {
     run_bgc_screening          = false
     run_cazyme_screening       = true
 
-    dbcan_skip_cgc             = false   // CGC annotation enabled as .gff is provided in samplesheet
-    dbcan_skip_substrate       = false   // Substrate annotation enabled as .gff is provided in samplesheet
+    dbcan_skip_cgc             = false
+    // CGC annotation enabled as .gff is provided in samplesheet
+    dbcan_skip_substrate       = false
+    // Substrate annotation enabled as .gff is provided in samplesheet
 }

conf/test_prokka.config

@@ -11,11 +11,7 @@
 */
 
 process {
-    resourceLimits = [
-        cpus: 4,
-        memory: '15.GB',
-        time: '1.h'
-    ]
+    resourceLimits = [cpus: 4, memory: '15.GB', time: '1.h']
 }
 
 params {
@@ -33,4 +29,5 @@ params {
     run_amp_screening          = true
     amp_run_hmmsearch          = true
     amp_hmmsearch_models       = params.pipelines_testdata_base_path + 'funcscan/hmms/mybacteriocin.hmm'
+    amp_ampcombi_db_id         = 'APD'
 }

conf/test_taxonomy_bakta.config

@@ -41,6 +41,8 @@ params {
 
     run_amp_screening                = true
     amp_run_hmmsearch                = true
+    amp_ampcombi_db_id               = 'APD'
+
 
     run_bgc_screening                = true
     bgc_mincontiglength              = 1000

conf/test_taxonomy_prokka.config

@@ -40,6 +40,7 @@ params {
 
     run_amp_screening             = true
     amp_run_hmmsearch             = true
+    amp_ampcombi_db_id            = 'APD'
 
     run_bgc_screening             = true
     bgc_mincontiglength           = 1000

conf/test_taxonomy_pyrodigal.config

@@ -40,6 +40,7 @@ params {
 
     run_amp_screening             = true
     amp_run_hmmsearch             = true
+    amp_ampcombi_db_id            = 'APD'
 
     run_bgc_screening             = true
     bgc_mincontiglength           = 1000

modules.json

@@ -12,17 +12,17 @@
                     },
                     "ampcombi2/cluster": {
                         "branch": "master",
-                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "git_sha": "be790aafaa178554b403f862164eb27042f0b35a",
                         "installed_by": ["modules"]
                     },
                     "ampcombi2/complete": {
                         "branch": "master",
-                        "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+                        "git_sha": "be790aafaa178554b403f862164eb27042f0b35a",
                         "installed_by": ["modules"]
                     },
                     "ampcombi2/parsetables": {
                         "branch": "master",
-                        "git_sha": "637c3e1796ab13d4c91f3030932598aed94a4f87",
+                        "git_sha": "c1a390166649d20c9c9ee8c8e849721e5d28836c",
                         "installed_by": ["modules"]
                     },
                     "ampir": {

modules/local/amp_database_download.nf

@@ -1,10 +1,10 @@
 process AMP_DATABASE_DOWNLOAD {
     label 'process_single'
 
-    conda "bioconda::ampcombi=2.0.1"
+    conda "bioconda::ampcombi=3.0.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ampcombi:2.0.1--pyhdfd78af_0':
-        'biocontainers/ampcombi:2.0.1--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/ampcombi:3.0.0--pyhdfd78af_0':
+        'biocontainers/ampcombi:3.0.0--pyhdfd78af_0' }"
 
     input:
     val database_id