Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update modules #311

Merged
merged 4 commits into from
Jan 24, 2025
Merged

Update modules #311

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
023c734
modules update
Jan 24, 2025
27f67b8
removed unused parameters
Jan 24, 2025
aae3cf5
subworkflows update
Jan 24, 2025
af9a097
prettier
Jan 24, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
4 changes: 0 additions & 4 deletions conf/test.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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'
Expand Down
4 changes: 0 additions & 4 deletions conf/test_eggnog.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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'
Expand Down
5 changes: 0 additions & 5 deletions conf/test_eukulele.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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'

Expand Down
5 changes: 0 additions & 5 deletions conf/test_filter.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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'

Expand Down
3 changes: 0 additions & 3 deletions conf/test_full.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
5 changes: 0 additions & 5 deletions conf/test_kofamscan.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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'

Expand Down
5 changes: 0 additions & 5 deletions conf/test_prokka.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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'

Expand Down
4 changes: 0 additions & 4 deletions conf/test_spades.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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'
Expand Down
5 changes: 0 additions & 5 deletions conf/test_transdecoder.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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'

Expand Down
24 changes: 12 additions & 12 deletions modules.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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": {
Expand All @@ -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": {
Expand Down
2 changes: 0 additions & 2 deletions modules/nf-core/bbmap/align/environment.yml
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

15 changes: 14 additions & 1 deletion modules/nf-core/bbmap/align/main.nf
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

72 changes: 43 additions & 29 deletions modules/nf-core/bbmap/align/meta.yml
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

Loading
Loading