Merge pull request #311 from danilodileo/update-modules

Update modules
nf-core · Jan 24, 2025 · 033c178 · 033c178
2 parents ab820df + af9a097
commit 033c178
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Showing 63 changed files with 2,103 additions and 541 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,6 +16,7 @@ Initial release of nf-core/metatdenovo, created with the [nf-core](https://nf-co
 
 ### `Changed`
 
+- [#311](<[https://github.com/nf-core/metatdenovo/pull/311](https://github.com/nf-core/metatdenovo/pull/311)>) - update modules and subworkflows
 - [#295](<[https://github.com/nf-core/metatdenovo/pull/295](https://github.com/nf-core/metatdenovo/pull/295)>) - Update documentation
 - [#292](<[https://github.com/nf-core/metatdenovo/pull/292](https://github.com/nf-core/metatdenovo/pull/292)>) - Specify memory to Megahit process
 - [#290](<[https://github.com/nf-core/metatdenovo/pull/290](https://github.com/nf-core/metatdenovo/pull/290)>) - Template update to v2.14.1

diff --git a/conf/test.config b/conf/test.config
@@ -21,10 +21,6 @@ process {
 params {
     config_profile_name        = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
 
     // Input data
     input    = params.pipelines_testdata_base_path + 'metatdenovo/samplesheet/samplesheet.csv'

diff --git a/conf/test_eggnog.config b/conf/test_eggnog.config
@@ -13,10 +13,6 @@
 params {
     config_profile_name        = 'Test eggnog profile'
     config_profile_description = 'Minimal test dataset to check pipeline with eggnog function added'
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 8
-    max_memory = '24.GB'
-    max_time   = '6.h'
 
     // Input data
     input    = 'https://raw.githubusercontent.com/nf-core/test-datasets/metatdenovo/samplesheet/samplesheet.csv'

diff --git a/conf/test_eukulele.config b/conf/test_eukulele.config
@@ -14,11 +14,6 @@ params {
     config_profile_name        = 'Test profile for eukulele taxonomic annotation'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 8
-    max_memory = '24.GB'
-    max_time   = '6.h'
-
     // Input data
     input    = 'https://raw.githubusercontent.com/nf-core/test-datasets/metatdenovo/samplesheet/samplesheet.csv'
 

diff --git a/conf/test_filter.config b/conf/test_filter.config
@@ -14,11 +14,6 @@ params {
     config_profile_name        = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function, including removal of contaminating sequences (e.g. rRNA)'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = 6.GB
-    max_time   = 6.h
-
     // Input data
     input    = 'https://raw.githubusercontent.com/nf-core/test-datasets/metatdenovo/samplesheet/samplesheet.csv'
 

diff --git a/conf/test_full.config b/conf/test_full.config
@@ -17,9 +17,6 @@ params {
     // Input data for full size test
     input = params.pipelines_testdata_base_path + 'metatdenovo/samplesheet/samplesheet_full_test.csv'
 
-    // Genome references
-    genome = 'R64-1-1'
-
     // parameters
     skip_eukulele   = false
     skip_eggnog     = false

diff --git a/conf/test_kofamscan.config b/conf/test_kofamscan.config
@@ -14,11 +14,6 @@ params {
     config_profile_name        = 'Test kofamscan profile'
     config_profile_description = 'Minimal test dataset to check pipeline with kofamscan function added'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 8
-    max_memory = '24.GB'
-    max_time   = '6.h'
-
     // Input data
     input    = 'https://raw.githubusercontent.com/nf-core/test-datasets/metatdenovo/samplesheet/samplesheet.csv'
 

diff --git a/conf/test_prokka.config b/conf/test_prokka.config
@@ -14,11 +14,6 @@ params {
     config_profile_name        = 'Test profile for prokka orf caller'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = 6.GB
-    max_time   = 6.h
-
     // Input data
     input    = 'https://raw.githubusercontent.com/nf-core/test-datasets/metatdenovo/samplesheet/samplesheet.csv'
 

diff --git a/conf/test_spades.config b/conf/test_spades.config
@@ -13,10 +13,6 @@
 params {
     config_profile_name        = 'Test spades assembler profile'
     config_profile_description = 'Minimal test dataset to check pipeline function'
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
-    max_time   = '6.h'
 
     // Input data
     input    = 'https://raw.githubusercontent.com/nf-core/test-datasets/metatdenovo/samplesheet/samplesheet.csv'

diff --git a/conf/test_transdecoder.config b/conf/test_transdecoder.config
@@ -14,11 +14,6 @@ params {
     config_profile_name        = 'Test profile for transdecoder  orf caller'
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
-    // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = 6.GB
-    max_time   = 6.h
-
     // Input data
     input    = 'https://raw.githubusercontent.com/nf-core/test-datasets/metatdenovo/samplesheet/samplesheet.csv'
 

diff --git a/modules.json b/modules.json
@@ -7,27 +7,27 @@
                 "nf-core": {
                     "bbmap/align": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "49780ab7ba87906103c8810044008a042748fd4f",
                         "installed_by": ["modules"]
                     },
                     "bbmap/bbduk": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc",
                         "installed_by": ["modules"]
                     },
                     "bbmap/bbnorm": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "bbmap/index": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "49780ab7ba87906103c8810044008a042748fd4f",
                         "installed_by": ["modules"]
                     },
                     "cat/cat": {
                         "branch": "master",
-                        "git_sha": "9437e6053dccf4aafa022bfd6e7e9de67e625af8",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "cat/fastq": {
@@ -37,37 +37,37 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "dc94b6ee04a05ddb9f7ae050712ff30a13149164",
+                        "git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296",
                         "installed_by": ["modules"]
                     },
                     "hmmer/hmmsearch": {
                         "branch": "master",
-                        "git_sha": "b046a286c8240ebe3412ddf8ae901d47008d1ca7",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
+                        "git_sha": "f80914f78fb7fa1c00b14cfeb29575ee12240d9c",
                         "installed_by": ["modules"]
                     },
                     "pigz/compress": {
                         "branch": "master",
-                        "git_sha": "0eab94fc1e48703c1b0a8704bd665f554905c39d",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "prodigal": {
                         "branch": "master",
-                        "git_sha": "2a196d6bfea8b6b5f49fc1885e39fae5f50bc2a0",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "prokka": {
                         "branch": "master",
-                        "git_sha": "49ebda931c36c2b282f7958d00e1236b751f1031",
+                        "git_sha": "bcfb2f7efd4444ab442ffc8a248afbd62bca5ae7",
                         "installed_by": ["modules"]
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
+                        "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/idxstats": {

diff --git a/modules/nf-core/bbmap/align/environment.yml b/modules/nf-core/bbmap/align/environment.yml
diff --git a/modules/nf-core/bbmap/align/main.nf b/modules/nf-core/bbmap/align/main.nf
diff --git a/modules/nf-core/bbmap/align/meta.yml b/modules/nf-core/bbmap/align/meta.yml