Update several modules

CHANGELOG.md

@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#427](https://github.com/nf-core/funcscan/pull/427) AMPcombi now can use multiple other databases for classifications. (by @darcy220606)
 - [#429](https://github.com/nf-core/funcscan/pull/429) Updated to nf-core template 3.1.0. (by @jfy133 and @jasmezz)
 - [#433](https://github.com/nf-core/funcscan/pull/433) Updated to nf-core template 3.1.1. (by @jfy133)
+- [#431](https://github.com/nf-core/funcscan/pull/431) Updated AMPcombi, Macrel, all MMseqs2 modules, MultiQC, Pyrodigal, and seqkit, added `--taxa_classification_mmseqs_compressed` parameter. (by @jasmezz)
 
 ### `Fixed`
 
@@ -21,11 +22,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Dependencies`
 
-| Tool     | Previous version | New version |
-| -------- | ---------------- | ----------- |
-| AMPcombi | 0.2.2            | 2.0.1       |
-| Macrel   | 1.2.0            | 1.4.0       |
-| MultiQC  | 1.24.0           | 1.25.1      |
+| Tool      | Previous version | New version |
+| --------- | ---------------- | ----------- |
+| AMPcombi  | 0.2.2            | 2.0.1       |
+| Macrel    | 1.2.0            | 1.4.0       |
+| MMseqs2   | 15.6f452         | 17.b804f    |
+| MultiQC   | 1.24.0           | 1.26        |
+| Pyrodigal | 3.3.0            | 3.6.3       |
+| seqkit    | 2.8.1            | 2.9.0       |
 
 ### `Deprecated`
 
@@ -105,7 +109,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | GECCO         | 0.9.8            | 0.9.10      |
 | hAMRonization | 1.1.1            | 1.1.4       |
 | HMMER         | 3.3.2            | 3.4         |
-| MMSeqs        | NA               | 2:15.6f452  |
+| MMseqs2       | NA               | 15.6f452    |
 | MultiQC       | 1.15             | 1.24        |
 | Pyrodigal     | 2.1.0            | 3.3.0       |
 | RGI           | 5.2.1            | 6.0.3       |

conf/base.config

@@ -156,6 +156,7 @@ process {
     withName: ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
         memory = { 4.GB * task.attempt }
         cpus   = 1
+        time   = { 2.h * task.attempt }
     }
 
     withName: DEEPBGC_DOWNLOAD {

conf/modules.config

@@ -41,7 +41,8 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
         ext.args   = [
-            params.taxa_classification_mmseqs_db_savetmp ? "" : "--remove-tmp-files"
+            params.taxa_classification_mmseqs_db_savetmp ? "" : "--remove-tmp-files",
+            "--compressed ${params.taxa_classification_mmseqs_compressed}"
         ].join(' ').trim()
     }
 
@@ -52,6 +53,9 @@ process {
             enabled: params.save_db,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
+        ext.args   = [
+            "--compressed ${params.taxa_classification_mmseqs_compressed}"
+        ].join(' ').trim()
     }
 
     withName: MMSEQS_TAXONOMY {
@@ -70,6 +74,7 @@ process {
             "--orf-filter-s ${params.taxa_classification_mmseqs_taxonomy_orffilters}",
             "--lca-mode ${params.taxa_classification_mmseqs_taxonomy_lcamode}",
             "--vote-mode ${params.taxa_classification_mmseqs_taxonomy_votemode}",
+            "--compressed ${params.taxa_classification_mmseqs_compressed}"
         ].join(' ').trim()
     }
 
@@ -81,6 +86,9 @@ process {
             pattern: "*.tsv",
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
         ]
+        ext.args   = [
+            "--compressed ${params.taxa_classification_mmseqs_compressed}"
+        ].join(' ').trim()
     }
 
     withName: SEQKIT_SEQ {

modules.json

@@ -22,7 +22,7 @@
                     },
                     "ampcombi2/parsetables": {
                         "branch": "master",
-                        "git_sha": "993865fe60cb1569155fbbbe0cee113e1127abaf",
+                        "git_sha": "0e9cb409c32d3ec4f0d3804588e4778971c09b7e",
                         "installed_by": ["modules"]
                     },
                     "ampir": {
@@ -32,7 +32,7 @@
                     },
                     "amplify/predict": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "ce35ce92566b3328b405253543b9b2b4d4e5f4f7",
                         "installed_by": ["modules"]
                     },
                     "amrfinderplus/run": {
@@ -62,7 +62,7 @@
                     },
                     "bakta/bakta": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "0e9cb409c32d3ec4f0d3804588e4778971c09b7e",
                         "installed_by": ["modules"]
                     },
                     "bakta/baktadbdownload": {
@@ -82,12 +82,12 @@
                     },
                     "deepbgc/download": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "ce35ce92566b3328b405253543b9b2b4d4e5f4f7",
                         "installed_by": ["modules"]
                     },
                     "deepbgc/pipeline": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "ce35ce92566b3328b405253543b9b2b4d4e5f4f7",
                         "installed_by": ["modules"]
                     },
                     "fargene": {
@@ -102,7 +102,7 @@
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "ce35ce92566b3328b405253543b9b2b4d4e5f4f7",
                         "installed_by": ["modules"]
                     },
                     "hamronization/abricate": {
@@ -147,27 +147,27 @@
                     },
                     "mmseqs/createdb": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "2dc4c0474a77f5f8709eb970d890ad102e92af6f",
                         "installed_by": ["modules"]
                     },
                     "mmseqs/createtsv": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "2dc4c0474a77f5f8709eb970d890ad102e92af6f",
                         "installed_by": ["modules"]
                     },
                     "mmseqs/databases": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "2dc4c0474a77f5f8709eb970d890ad102e92af6f",
                         "installed_by": ["modules"]
                     },
                     "mmseqs/taxonomy": {
                         "branch": "master",
-                        "git_sha": "dc94b6ee04a05ddb9f7ae050712ff30a13149164",
+                        "git_sha": "2dc4c0474a77f5f8709eb970d890ad102e92af6f",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
+                        "git_sha": "f80914f78fb7fa1c00b14cfeb29575ee12240d9c",
                         "installed_by": ["modules"]
                     },
                     "prodigal": {
@@ -177,17 +177,17 @@
                     },
                     "prokka": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "bcfb2f7efd4444ab442ffc8a248afbd62bca5ae7",
                         "installed_by": ["modules"]
                     },
                     "pyrodigal": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "938e803109104e30773f76a7142442722498fef1",
                         "installed_by": ["modules"]
                     },
                     "rgi/cardannotation": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "3e548877f25a5980a177cc4f81d2d2e8c24164ef",
                         "installed_by": ["modules"]
                     },
                     "rgi/main": {
@@ -197,7 +197,7 @@
                     },
                     "seqkit/seq": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "60645c2b45e56579de0a0c89416805cae44c1f46",
                         "installed_by": ["modules"]
                     },
                     "tabix/bgzip": {
@@ -207,7 +207,7 @@
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "3e548877f25a5980a177cc4f81d2d2e8c24164ef",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/untar/untar.diff"
                     }