diff --git a/CHANGELOG.md b/CHANGELOG.md
index 704489e..b5f894b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
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).
-## 0.4.0+dev - [23-Aug-2024]
+## 0.4.0+dev - [11-Sep-2024]
### `Added`
@@ -19,15 +19,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
10. Added param `enforce_full_intron_support` to turn on/off strict model purging by TSEBRA [#21](https://github.com/plant-food-research-open/genepal/issues/21)
11. Added param `filter_liftoff_by_hints` to evaluate liftoff models with TSEBRA to make sure they have the same level of evidence as BRAKER [#28](ttps://github.com/plant-food-research-open/genepal/issues/28)
12. Added a script to automatically check module version updates
-13. Updated modules: `AGAT/CONVERTSPGFF2GTF`, `CAT_FASTQ`, `CUSTOM/DUMPSOFTWAREVERSIONS`, `EGGNOGMAPPER`, `FASTP`, `GFFREAD`, `SAMTOOLS/CAT`, `CUSTOM/RESTOREGFFIDS`, `CUSTOM/SHORTENFASTAIDS`, `EDTA/EDTA`, `CAT/CAT`, `FASTQC`, `GUNZIP`, `LIFTOFF`, `STAR/ALIGN`, `STAR/GENOMEGENERATE`, `UMITOOLS/EXTRACT`,
-14. Updated sub-workflows: `FASTQ_FASTQC_UMITOOLS_FASTP` and `FASTA_EDTA_LAI`
-15. Reduced `BRAKER3` threads to 8 [#55](https://github.com/plant-food-research-open/genepal/issues/55)
-16. Now the final annotations are stored in the `annotations` folder [#53](https://github.com/plant-food-research-open/genepal/issues/53)
-17. Added `-gff` flag to `REPEATMASKER` to save the gff file [#54](https://github.com/plant-food-research-open/genepal/issues/54)
-18. Now a single `fasta` file can be directly specified for `protein_evidence`
-19. `eggnogmapper_db_dir` is not a required parameter anymore
-20. `eggnogmapper_tax_scope` is now set to 1 (root div) by default
-21. Added a `test` profile based on public data
+13. Reduced `BRAKER3` threads to 8 [#55](https://github.com/plant-food-research-open/genepal/issues/55)
+14. Now the final annotations are stored in the `annotations` folder [#53](https://github.com/plant-food-research-open/genepal/issues/53)
+15. Added `-gff` flag to `REPEATMASKER` to save the gff file [#54](https://github.com/plant-food-research-open/genepal/issues/54)
+16. Now a single `fasta` file can be directly specified for `protein_evidence`
+17. `eggnogmapper_db_dir` is not a required parameter anymore
+18. `eggnogmapper_tax_scope` is now set to 1 (root div) by default
+19. Added a `test` profile based on public data
+20. Updated modules and sub-workflows
### `Fixed`
diff --git a/README.md b/README.md
index 3f14e6a..ef4c3ba 100644
--- a/README.md
+++ b/README.md
@@ -39,8 +39,8 @@ First, prepare an assemblysheet with your input genomes that looks as follows:
`assemblysheet.csv`:
```csv
-tag,fasta,is_masked
-a_thaliana,/path/to/genome.fa,yes
+tag ,fasta ,is_masked
+a_thaliana ,/path/to/genome.fa ,yes
```
Each row represents an input genome and the fields are:
diff --git a/docs/parameters.md b/docs/parameters.md
index 3e293ad..6de7e25 100644
--- a/docs/parameters.md
+++ b/docs/parameters.md
@@ -109,4 +109,4 @@ Less common options for the pipeline, typically set in a config file.
| `validationShowHiddenParams` | Show all params when using `--help` | `boolean` | | | True |
| `validationFailUnrecognisedParams` | Validation of parameters fails when an unrecognised parameter is found. | `boolean` | | | True |
| `validationLenientMode` | Validation of parameters in lenient more. | `boolean` | | | True |
-| `pipelines_testdata_base_path` | | `string` | https://raw.githubusercontent.com/nf-core/test-datasets/ | | True |
+| `pipelines_testdata_base_path` | Base path for pipeline test datasets | `string` | https://raw.githubusercontent.com/nf-core/test-datasets/ | | True |
diff --git a/modules.json b/modules.json
index d77d640..cb588f6 100644
--- a/modules.json
+++ b/modules.json
@@ -87,123 +87,122 @@
"nf-core": {
"agat/convertspgff2gtf": {
"branch": "master",
- "git_sha": "0a0b723d114e502207072603479b635dfbc2bf59",
+ "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"agat/convertspgxf2gxf": {
"branch": "master",
- "git_sha": "0a0b723d114e502207072603479b635dfbc2bf59",
+ "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"agat/spfilterfeaturefromkilllist": {
"branch": "master",
- "git_sha": "d1535889747781d919bc81da2344952f4bfa2be4",
+ "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"agat/spmergeannotations": {
"branch": "master",
- "git_sha": "8e30f5d09155b45ddafc2d1357fc5f447f1aaa03",
+ "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"cat/cat": {
"branch": "master",
- "git_sha": "5bb8ca085e17549e185e1823495ab8d20727a805",
+ "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"cat/fastq": {
"branch": "master",
- "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
+ "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"eggnogmapper": {
"branch": "master",
- "git_sha": "b34fb117e397e72a070cde8adf21b758670c90f5",
+ "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"fastavalidator": {
"branch": "master",
- "git_sha": "90dad5491658049282ceb287a3d7732c1ce39837",
+ "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"fastp": {
"branch": "master",
- "git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
+ "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["fastq_fastqc_umitools_fastp"]
},
"fastqc": {
"branch": "master",
- "git_sha": "b49b8992e5271ce427f3a7cdb29628fc58400eb5",
+ "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
},
"gffcompare": {
"branch": "master",
- "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+ "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"gffread": {
"branch": "master",
- "git_sha": "6c996d7fbe0816dcbb68ce587ad5f873313682a1",
+ "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"gt/gff3": {
"branch": "master",
- "git_sha": "9a8bba5910982ae637dedb8664e3121db77e173f",
+ "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"gunzip": {
"branch": "master",
- "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
- "installed_by": ["modules"],
- "patch": "modules/nf-core/gunzip/gunzip.diff"
+ "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
+ "installed_by": ["modules"]
},
"liftoff": {
"branch": "master",
- "git_sha": "b34fb117e397e72a070cde8adf21b758670c90f5",
+ "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"orthofinder": {
"branch": "master",
- "git_sha": "07f10f34d88408af7c71f13227d11f23b7f53b50",
+ "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"repeatmodeler/builddatabase": {
"branch": "master",
- "git_sha": "52507581f62929f98dd6e6c5c5824583fa6ef94d",
+ "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"repeatmodeler/repeatmodeler": {
"branch": "master",
- "git_sha": "52507581f62929f98dd6e6c5c5824583fa6ef94d",
+ "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"samtools/cat": {
"branch": "master",
- "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
+ "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"sortmerna": {
"branch": "master",
- "git_sha": "df05c8db5195867c0bc7b92c1788115b66f0d17d",
+ "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"star/align": {
"branch": "master",
- "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+ "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"star/genomegenerate": {
"branch": "master",
- "git_sha": "46eca555142d6e597729fcb682adcc791796f514",
+ "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"tsebra": {
"branch": "master",
- "git_sha": "0995f9cd0cc5e4eb60f7870280b75ecdb5ab0db2",
+ "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["modules"]
},
"umitools/extract": {
"branch": "master",
- "git_sha": "b4919e9a2b4d8b71061e601633db4600a3858fa1",
+ "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"installed_by": ["fastq_fastqc_umitools_fastp"]
}
}
@@ -217,12 +216,12 @@
},
"utils_nextflow_pipeline": {
"branch": "master",
- "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+ "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352",
"installed_by": ["subworkflows"]
},
"utils_nfcore_pipeline": {
"branch": "master",
- "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
+ "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab",
"installed_by": ["subworkflows"]
},
"utils_nfvalidation_plugin": {
diff --git a/modules/nf-core/agat/convertspgff2gtf/environment.yml b/modules/nf-core/agat/convertspgff2gtf/environment.yml
index 6747331..0410ee7 100644
--- a/modules/nf-core/agat/convertspgff2gtf/environment.yml
+++ b/modules/nf-core/agat/convertspgff2gtf/environment.yml
@@ -1,7 +1,5 @@
-name: agat_convertspgff2gtf
channels:
- conda-forge
- bioconda
- - defaults
dependencies:
- bioconda::agat=1.4.0
diff --git a/modules/nf-core/agat/convertspgxf2gxf/environment.yml b/modules/nf-core/agat/convertspgxf2gxf/environment.yml
index 6ed34fa..0410ee7 100644
--- a/modules/nf-core/agat/convertspgxf2gxf/environment.yml
+++ b/modules/nf-core/agat/convertspgxf2gxf/environment.yml
@@ -1,7 +1,5 @@
-name: agat_convertspgxf2gxf
channels:
- conda-forge
- bioconda
- - defaults
dependencies:
- bioconda::agat=1.4.0
diff --git a/modules/nf-core/agat/spfilterfeaturefromkilllist/environment.yml b/modules/nf-core/agat/spfilterfeaturefromkilllist/environment.yml
index fb2df48..a6b5f2b 100644
--- a/modules/nf-core/agat/spfilterfeaturefromkilllist/environment.yml
+++ b/modules/nf-core/agat/spfilterfeaturefromkilllist/environment.yml
@@ -1,9 +1,7 @@
---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-name: "agat_spfilterfeaturefromkilllist"
channels:
- conda-forge
- bioconda
- - defaults
dependencies:
- "bioconda::agat=1.4.0"
diff --git a/modules/nf-core/agat/spmergeannotations/environment.yml b/modules/nf-core/agat/spmergeannotations/environment.yml
index 5644e08..a6b5f2b 100644
--- a/modules/nf-core/agat/spmergeannotations/environment.yml
+++ b/modules/nf-core/agat/spmergeannotations/environment.yml
@@ -1,9 +1,7 @@
---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-name: "agat_spmergeannotations"
channels:
- conda-forge
- bioconda
- - defaults
dependencies:
- "bioconda::agat=1.4.0"
diff --git a/modules/nf-core/cat/cat/environment.yml b/modules/nf-core/cat/cat/environment.yml
index 17a04ef..9b01c86 100644
--- a/modules/nf-core/cat/cat/environment.yml
+++ b/modules/nf-core/cat/cat/environment.yml
@@ -1,7 +1,5 @@
-name: cat_cat
channels:
- conda-forge
- bioconda
- - defaults
dependencies:
- conda-forge::pigz=2.3.4
diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml
index 8c69b12..c7eb9bd 100644
--- a/modules/nf-core/cat/fastq/environment.yml
+++ b/modules/nf-core/cat/fastq/environment.yml
@@ -1,7 +1,5 @@
-name: cat_fastq
channels:
- conda-forge
- bioconda
- - defaults
dependencies:
- conda-forge::coreutils=8.30
diff --git a/modules/nf-core/eggnogmapper/environment.yml b/modules/nf-core/eggnogmapper/environment.yml
index f4fb6fd..2092ea5 100644
--- a/modules/nf-core/eggnogmapper/environment.yml
+++ b/modules/nf-core/eggnogmapper/environment.yml
@@ -1,7 +1,5 @@
-name: eggnogmapper
channels:
- conda-forge
- bioconda
- - defaults
dependencies:
- bioconda::eggnog-mapper=2.1.12
diff --git a/modules/nf-core/fastavalidator/environment.yml b/modules/nf-core/fastavalidator/environment.yml
index 70f346e..44d55c1 100644
--- a/modules/nf-core/fastavalidator/environment.yml
+++ b/modules/nf-core/fastavalidator/environment.yml
@@ -1,9 +1,7 @@
---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-name: "fastavalidator"
channels:
- conda-forge
- bioconda
- - defaults
dependencies:
- "bioconda::py_fasta_validator=0.6"
diff --git a/modules/nf-core/fastp/environment.yml b/modules/nf-core/fastp/environment.yml
index 70389e6..26d4aca 100644
--- a/modules/nf-core/fastp/environment.yml
+++ b/modules/nf-core/fastp/environment.yml
@@ -1,7 +1,5 @@
-name: fastp
channels:
- conda-forge
- bioconda
- - defaults
dependencies:
- bioconda::fastp=0.23.4
diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml
index 1787b38..691d4c7 100644
--- a/modules/nf-core/fastqc/environment.yml
+++ b/modules/nf-core/fastqc/environment.yml
@@ -1,7 +1,5 @@
-name: fastqc
channels:
- conda-forge
- bioconda
- - defaults
dependencies:
- bioconda::fastqc=0.12.1
diff --git a/modules/nf-core/gffcompare/environment.yml b/modules/nf-core/gffcompare/environment.yml
index bcd633e..2b52417 100644
--- a/modules/nf-core/gffcompare/environment.yml
+++ b/modules/nf-core/gffcompare/environment.yml
@@ -1,7 +1,5 @@
-name: gffcompare
channels:
- conda-forge
- bioconda
- - defaults
dependencies:
- bioconda::gffcompare=0.12.6
diff --git a/modules/nf-core/gffcompare/meta.yml b/modules/nf-core/gffcompare/meta.yml
index 674f08c..dd944f2 100644
--- a/modules/nf-core/gffcompare/meta.yml
+++ b/modules/nf-core/gffcompare/meta.yml
@@ -89,3 +89,4 @@ authors:
- "@jemten"
maintainers:
- "@jemten"
+ - "@gallvp"
diff --git a/modules/nf-core/gffcompare/tests/main.nf.test b/modules/nf-core/gffcompare/tests/main.nf.test
new file mode 100644
index 0000000..258733a
--- /dev/null
+++ b/modules/nf-core/gffcompare/tests/main.nf.test
@@ -0,0 +1,103 @@
+
+nextflow_process {
+
+ name "Test Process GFFCOMPARE"
+ script "../main.nf"
+ process "GFFCOMPARE"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "gffcompare"
+
+ test("test-gffcompare") {
+
+ when {
+ process {
+ """
+ input[0] = [
+ [ id:'test' ], // meta map
+ [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) ],
+ ]
+ input[1] = [
+ [ id:'sarscov2' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+ ]
+ input[2] = [
+ [ id:'sarscov2' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
+ ]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+ test("test-gffcompare-combine") {
+
+ when {
+ process {
+ """
+ input[0] = [ [ id:'test' ], // meta map
+ [
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
+ ]
+ ]
+ input[1] = [
+ [ id:'sarscov2' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+ ]
+ input[2] = [[id:'sarscov2'], []]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+ test("test-gffcompare-combine-stub") {
+ options '-stub'
+ when {
+ process {
+ """
+ input[0] = [ [ id:'test' ], // meta map
+ [
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true)
+ ]
+ ]
+ input[1] = [
+ [ id:'sarscov2' ], // meta map
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true),
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+ ]
+ input[2] = [[id:'sarscov2'], []]
+
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+}
diff --git a/modules/nf-core/gffcompare/tests/main.nf.test.snap b/modules/nf-core/gffcompare/tests/main.nf.test.snap
new file mode 100644
index 0000000..9db3c0a
--- /dev/null
+++ b/modules/nf-core/gffcompare/tests/main.nf.test.snap
@@ -0,0 +1,365 @@
+{
+ "test-gffcompare": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test"
+ },
+ "test.annotated.gtf:md5,9fdcea941cb003026e1ab04a45c3944c"
+ ]
+ ],
+ "1": [
+
+ ],
+ "2": [
+ [
+ {
+ "id": "test"
+ },
+ "test.genome.gff3.tmap:md5,8935511caaf122288167f8d908eb2632"
+ ]
+ ],
+ "3": [
+ [
+ {
+ "id": "test"
+ },
+ "test.genome.gff3.refmap:md5,60461ca3548615db12d31c53c5356ee5"
+ ]
+ ],
+ "4": [
+ [
+ {
+ "id": "test"
+ },
+ "test.loci:md5,b637f88bbedda47aee859f7bc20c36ab"
+ ]
+ ],
+ "5": [
+ [
+ {
+ "id": "test"
+ },
+ "test.stats:md5,a7c5a8cd8aa7188a2152e894f2355f10"
+ ]
+ ],
+ "6": [
+ [
+ {
+ "id": "test"
+ },
+ "test.tracking:md5,344cd0bea36e5aab3a0824f2aaf7b824"
+ ]
+ ],
+ "7": [
+ "versions.yml:md5,6f40a0e2547d9e3f4cf8e142ae5c17b6"
+ ],
+ "annotated_gtf": [
+ [
+ {
+ "id": "test"
+ },
+ "test.annotated.gtf:md5,9fdcea941cb003026e1ab04a45c3944c"
+ ]
+ ],
+ "combined_gtf": [
+
+ ],
+ "loci": [
+ [
+ {
+ "id": "test"
+ },
+ "test.loci:md5,b637f88bbedda47aee859f7bc20c36ab"
+ ]
+ ],
+ "refmap": [
+ [
+ {
+ "id": "test"
+ },
+ "test.genome.gff3.refmap:md5,60461ca3548615db12d31c53c5356ee5"
+ ]
+ ],
+ "stats": [
+ [
+ {
+ "id": "test"
+ },
+ "test.stats:md5,a7c5a8cd8aa7188a2152e894f2355f10"
+ ]
+ ],
+ "tmap": [
+ [
+ {
+ "id": "test"
+ },
+ "test.genome.gff3.tmap:md5,8935511caaf122288167f8d908eb2632"
+ ]
+ ],
+ "tracking": [
+ [
+ {
+ "id": "test"
+ },
+ "test.tracking:md5,344cd0bea36e5aab3a0824f2aaf7b824"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,6f40a0e2547d9e3f4cf8e142ae5c17b6"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-29T19:08:50.819004"
+ },
+ "test-gffcompare-combine-stub": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "test"
+ },
+ "test.annotated.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "1": [
+ [
+ {
+ "id": "test"
+ },
+ "test.combined.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "2": [
+ [
+ {
+ "id": "test"
+ },
+ "test.tmap:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "3": [
+ [
+ {
+ "id": "test"
+ },
+ "test.refmap:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "4": [
+ [
+ {
+ "id": "test"
+ },
+ "test.loci:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "5": [
+ [
+ {
+ "id": "test"
+ },
+ "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "6": [
+ [
+ {
+ "id": "test"
+ },
+ "test.tracking:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "7": [
+ "versions.yml:md5,6f40a0e2547d9e3f4cf8e142ae5c17b6"
+ ],
+ "annotated_gtf": [
+ [
+ {
+ "id": "test"
+ },
+ "test.annotated.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "combined_gtf": [
+ [
+ {
+ "id": "test"
+ },
+ "test.combined.gtf:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "loci": [
+ [
+ {
+ "id": "test"
+ },
+ "test.loci:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "refmap": [
+ [
+ {
+ "id": "test"
+ },
+ "test.refmap:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "stats": [
+ [
+ {
+ "id": "test"
+ },
+ "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "tmap": [
+ [
+ {
+ "id": "test"
+ },
+ "test.tmap:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "tracking": [
+ [
+ {
+ "id": "test"
+ },
+ "test.tracking:md5,d41d8cd98f00b204e9800998ecf8427e"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,6f40a0e2547d9e3f4cf8e142ae5c17b6"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-29T19:10:25.943352"
+ },
+ "test-gffcompare-combine": {
+ "content": [
+ {
+ "0": [
+
+ ],
+ "1": [
+ [
+ {
+ "id": "test"
+ },
+ "test.combined.gtf:md5,deebda20162eddb07b53d1da393a92a1"
+ ]
+ ],
+ "2": [
+ [
+ {
+ "id": "test"
+ },
+ [
+ "test.genome.gff3.tmap:md5,6f3866608c9d2b45d169dbc15a6372c4",
+ "test.genome.gtf.tmap:md5,6f3866608c9d2b45d169dbc15a6372c4"
+ ]
+ ]
+ ],
+ "3": [
+
+ ],
+ "4": [
+ [
+ {
+ "id": "test"
+ },
+ "test.loci:md5,2c020db4486b1997f68555825065c28d"
+ ]
+ ],
+ "5": [
+ [
+ {
+ "id": "test"
+ },
+ "test.stats:md5,040cf90e0d649479173a5c846928cd67"
+ ]
+ ],
+ "6": [
+ [
+ {
+ "id": "test"
+ },
+ "test.tracking:md5,55b10c257c1a07224cb5d995c799f782"
+ ]
+ ],
+ "7": [
+ "versions.yml:md5,6f40a0e2547d9e3f4cf8e142ae5c17b6"
+ ],
+ "annotated_gtf": [
+
+ ],
+ "combined_gtf": [
+ [
+ {
+ "id": "test"
+ },
+ "test.combined.gtf:md5,deebda20162eddb07b53d1da393a92a1"
+ ]
+ ],
+ "loci": [
+ [
+ {
+ "id": "test"
+ },
+ "test.loci:md5,2c020db4486b1997f68555825065c28d"
+ ]
+ ],
+ "refmap": [
+
+ ],
+ "stats": [
+ [
+ {
+ "id": "test"
+ },
+ "test.stats:md5,040cf90e0d649479173a5c846928cd67"
+ ]
+ ],
+ "tmap": [
+ [
+ {
+ "id": "test"
+ },
+ [
+ "test.genome.gff3.tmap:md5,6f3866608c9d2b45d169dbc15a6372c4",
+ "test.genome.gtf.tmap:md5,6f3866608c9d2b45d169dbc15a6372c4"
+ ]
+ ]
+ ],
+ "tracking": [
+ [
+ {
+ "id": "test"
+ },
+ "test.tracking:md5,55b10c257c1a07224cb5d995c799f782"
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,6f40a0e2547d9e3f4cf8e142ae5c17b6"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.8.4",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-08-29T19:10:21.420587"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/gffread/environment.yml b/modules/nf-core/gffread/environment.yml
index c6df58a..ee23984 100644
--- a/modules/nf-core/gffread/environment.yml
+++ b/modules/nf-core/gffread/environment.yml
@@ -1,7 +1,5 @@
-name: gffread
channels:
- conda-forge
- bioconda
- - defaults
dependencies:
- bioconda::gffread=0.12.7
diff --git a/modules/nf-core/gt/gff3/environment.yml b/modules/nf-core/gt/gff3/environment.yml
index 8289fb3..666eb47 100644
--- a/modules/nf-core/gt/gff3/environment.yml
+++ b/modules/nf-core/gt/gff3/environment.yml
@@ -1,9 +1,7 @@
---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-name: "gt_gff3"
channels:
- conda-forge
- bioconda
- - defaults
dependencies:
- "bioconda::genometools-genometools=1.6.5"
diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml
index dfc02a7..c779485 100644
--- a/modules/nf-core/gunzip/environment.yml
+++ b/modules/nf-core/gunzip/environment.yml
@@ -1,8 +1,6 @@
-name: gunzip
channels:
- conda-forge
- bioconda
- - defaults
dependencies:
- conda-forge::grep=3.11
- conda-forge::sed=4.8
diff --git a/modules/nf-core/liftoff/environment.yml b/modules/nf-core/liftoff/environment.yml
index 7f3eadf..94c10a3 100644
--- a/modules/nf-core/liftoff/environment.yml
+++ b/modules/nf-core/liftoff/environment.yml
@@ -1,9 +1,6 @@
-name: liftoff
-
channels:
- conda-forge
- bioconda
- - defaults
dependencies:
- bioconda::liftoff=1.6.3
diff --git a/modules/nf-core/orthofinder/environment.yml b/modules/nf-core/orthofinder/environment.yml
index f93b9bb..68c475f 100644
--- a/modules/nf-core/orthofinder/environment.yml
+++ b/modules/nf-core/orthofinder/environment.yml
@@ -1,9 +1,6 @@
----
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-name: "orthofinder"
channels:
- conda-forge
- bioconda
- - defaults
dependencies:
- - "bioconda::orthofinder=2.5.5"
+ - bioconda::diamond=2.1.9
+ - bioconda::orthofinder=2.5.5
diff --git a/modules/nf-core/orthofinder/main.nf b/modules/nf-core/orthofinder/main.nf
index 2971fc0..a47c4de 100644
--- a/modules/nf-core/orthofinder/main.nf
+++ b/modules/nf-core/orthofinder/main.nf
@@ -9,31 +9,40 @@ process ORTHOFINDER {
input:
tuple val(meta), path(fastas, stageAs: 'input/')
+ tuple val(meta2), path(prior_run)
output:
- tuple val(meta), path("$prefix") , emit: orthofinder
- path "versions.yml" , emit: versions
+ tuple val(meta), path("$prefix") , emit: orthofinder
+ tuple val(meta), path("$prefix/WorkingDirectory") , emit: working
+ path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
- def args = task.ext.args ?: ''
- prefix = task.ext.prefix ?: "${meta.id}"
+ def args = task.ext.args ?: ''
+ prefix = task.ext.prefix ?: "${meta.id}"
+ def include_command = prior_run ? "-b $prior_run" : ''
+
"""
mkdir temp_pickle
orthofinder \\
- $args \\
-t $task.cpus \\
-a $task.cpus \\
-p temp_pickle \\
-f input \\
- -n $prefix
+ -n $prefix \\
+ $include_command \\
+ $args
+
+ if [ -e input/OrthoFinder/Results_$prefix ]; then
+ mv input/OrthoFinder/Results_$prefix $prefix
+ fi
- mv \\
- input/OrthoFinder/Results_$prefix \\
- $prefix
+ if [ -e ${prior_run}/OrthoFinder/Results_$prefix ]; then
+ mv ${prior_run}/OrthoFinder/Results_$prefix $prefix
+ fi
cat <<-END_VERSIONS > versions.yml
"${task.process}":
@@ -42,8 +51,10 @@ process ORTHOFINDER {
"""
stub:
- def args = task.ext.args ?: ''
- prefix = task.ext.prefix ?: "${meta.id}"
+ def args = task.ext.args ?: ''
+ prefix = task.ext.prefix ?: "${meta.id}"
+ def include_command = prior_run ? "-b $prior_run" : ''
+
"""
mkdir -p $prefix/Comparative_Genomics_Statistics
mkdir $prefix/Gene_Duplication_Events
diff --git a/modules/nf-core/orthofinder/meta.yml b/modules/nf-core/orthofinder/meta.yml
index 23cc532..8c7689b 100644
--- a/modules/nf-core/orthofinder/meta.yml
+++ b/modules/nf-core/orthofinder/meta.yml
@@ -29,6 +29,15 @@ input:
type: list
description: Input fasta files
pattern: "*.{fa,faa,fasta,fas,pep}"
+ - meta2:
+ type: map
+ description: |
+ Groovy Map containing a name
+ e.g. `[ id:'folder1' ]`
+ - prior_run:
+ type: directory
+ description: |
+ A folder container containing a previous WorkingDirectory from Orthofinder.
output:
- meta:
@@ -43,6 +52,9 @@ output:
- orthofinder:
type: directory
description: Orthofinder output directory
+ - working:
+ type: directory
+ description: Orthofinder output WorkingDirectory (used for the orthofinder resume function)
authors:
- "@GallVp"
diff --git a/modules/nf-core/orthofinder/tests/main.nf.test b/modules/nf-core/orthofinder/tests/main.nf.test
index 2d64800..aa68d1d 100644
--- a/modules/nf-core/orthofinder/tests/main.nf.test
+++ b/modules/nf-core/orthofinder/tests/main.nf.test
@@ -9,6 +9,7 @@ nextflow_process {
tag "modules"
tag "modules_nfcore"
tag "orthofinder"
+ tag "untar"
test("sarscov2 - candidatus_portiera_aleyrodidarum - proteome") {
@@ -28,6 +29,10 @@ nextflow_process {
[ id:'test', single_end:false ],
[ file_a, file_b ]
]
+ input[1] = [
+ [],
+ []
+ ]
"""
}
}
@@ -41,8 +46,6 @@ nextflow_process {
all_files << file
}
- def all_file_names = all_files.collect { it.name }.sort(false)
-
def stable_file_names = [
'Statistics_PerSpecies.tsv',
'SpeciesTree_Gene_Duplications_0.5_Support.txt',
@@ -52,8 +55,66 @@ nextflow_process {
def stable_files = all_files.findAll { it.name in stable_file_names }
assert snapshot(
- all_file_names,
- stable_files,
+ stable_files.toSorted(),
+ process.out.versions[0]
+ ).match()
+ }
+
+ }
+
+
+ test("sarscov2 - candidatus_portiera_aleyrodidarum - proteome - resume") {
+
+
+ setup {
+ run("UNTAR") {
+ script "../../untar/main.nf"
+ process {
+ """
+ input[0] = [ [ id:'test1' ], // meta map
+ file(params.modules_testdata_base_path + 'delete_me/orthofinder/WorkingDirectory.tar.gz', checkIfExists: true)
+ ]
+ """
+ }
+ }
+ }
+
+ when {
+ process {
+ """
+ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true)
+ .copyTo("${workDir}/sarscov2.fasta")
+
+ def file_a = file("https://raw.githubusercontent.com/nf-core/test-datasets/proteinfold/testdata/sequences/H1065.fasta")
+ def file_c = UNTAR.out.untar
+ input[0] = [
+ [ id:'test_2', single_end:false ],
+ [ file_a ]
+ ]
+ input[1] = UNTAR.out.untar
+ """
+ }
+ }
+
+ then {
+ assert process.success
+
+ def all_files = []
+
+ file(process.out.orthofinder[0][1]).eachFileRecurse (FileType.FILES) { file ->
+ all_files << file
+ }
+
+ def stable_file_names = [
+ 'Statistics_PerSpecies.tsv',
+ 'OrthologuesStats_Totals.tsv',
+ 'Duplications_per_Species_Tree_Node.tsv'
+ ]
+
+ def stable_files = all_files.findAll { it.name in stable_file_names }
+
+ assert snapshot(
+ stable_files.toSorted(),
process.out.versions[0]
).match()
}
@@ -80,6 +141,10 @@ nextflow_process {
[ id:'test', single_end:false ],
[ file_a, file_b ]
]
+ input[1] = [
+ [],
+ []
+ ]
"""
}
}
diff --git a/modules/nf-core/orthofinder/tests/main.nf.test.snap b/modules/nf-core/orthofinder/tests/main.nf.test.snap
index 8b621c0..f2c7b91 100644
--- a/modules/nf-core/orthofinder/tests/main.nf.test.snap
+++ b/modules/nf-core/orthofinder/tests/main.nf.test.snap
@@ -1,310 +1,6 @@
{
"sarscov2 - candidatus_portiera_aleyrodidarum - proteome": {
"content": [
- [
- "Blast0_0.txt.gz",
- "Blast0_1.txt.gz",
- "Blast1_0.txt.gz",
- "Blast1_1.txt.gz",
- "Citation.txt",
- "Duplications.tsv",
- "Duplications_per_Orthogroup.tsv",
- "Duplications_per_Species_Tree_Node.tsv",
- "Log.txt",
- "N0.tsv",
- "OG0000000.fa",
- "OG0000000_tree.txt",
- "OG0000000_tree.txt",
- "OG0000000_tree_id.txt",
- "OG0000001.fa",
- "OG0000001_tree.txt",
- "OG0000001_tree.txt",
- "OG0000001_tree_id.txt",
- "OG0000002.fa",
- "OG0000003.fa",
- "OG0000004.fa",
- "OG0000005.fa",
- "OG0000006.fa",
- "OG0000007.fa",
- "OG0000008.fa",
- "OG0000009.fa",
- "OG0000010.fa",
- "OG0000011.fa",
- "OG0000012.fa",
- "OG0000013.fa",
- "OG0000014.fa",
- "OG0000015.fa",
- "OG0000016.fa",
- "OG0000017.fa",
- "OG0000018.fa",
- "OG0000019.fa",
- "OG0000020.fa",
- "OG0000021.fa",
- "OG0000022.fa",
- "OG0000023.fa",
- "OG0000024.fa",
- "OG0000025.fa",
- "OG0000026.fa",
- "OG0000027.fa",
- "OG0000028.fa",
- "OG0000029.fa",
- "OG0000030.fa",
- "OG0000031.fa",
- "OG0000032.fa",
- "OG0000033.fa",
- "OG0000034.fa",
- "OG0000035.fa",
- "OG0000036.fa",
- "OG0000037.fa",
- "OG0000038.fa",
- "OG0000039.fa",
- "OG0000040.fa",
- "OG0000041.fa",
- "OG0000042.fa",
- "OG0000043.fa",
- "OG0000044.fa",
- "OG0000045.fa",
- "OG0000046.fa",
- "OG0000047.fa",
- "OG0000048.fa",
- "OG0000049.fa",
- "OG0000050.fa",
- "OG0000051.fa",
- "OG0000052.fa",
- "OG0000053.fa",
- "OG0000054.fa",
- "OG0000055.fa",
- "OG0000056.fa",
- "OG0000057.fa",
- "OG0000058.fa",
- "OG0000059.fa",
- "OG0000060.fa",
- "OG0000061.fa",
- "OG0000062.fa",
- "OG0000063.fa",
- "OG0000064.fa",
- "OG0000065.fa",
- "OG0000066.fa",
- "OG0000067.fa",
- "OG0000068.fa",
- "OG0000069.fa",
- "OG0000070.fa",
- "OG0000071.fa",
- "OG0000072.fa",
- "OG0000073.fa",
- "OG0000074.fa",
- "OG0000075.fa",
- "OG0000076.fa",
- "OG0000077.fa",
- "OG0000078.fa",
- "OG0000079.fa",
- "OG0000080.fa",
- "OG0000081.fa",
- "OG0000082.fa",
- "OG0000083.fa",
- "OG0000084.fa",
- "OG0000085.fa",
- "OG0000086.fa",
- "OG0000087.fa",
- "OG0000088.fa",
- "OG0000089.fa",
- "OG0000090.fa",
- "OG0000091.fa",
- "OG0000092.fa",
- "OG0000093.fa",
- "OG0000094.fa",
- "OG0000095.fa",
- "OG0000096.fa",
- "OG0000097.fa",
- "OG0000098.fa",
- "OG0000099.fa",
- "OG0000100.fa",
- "OG0000101.fa",
- "OG0000102.fa",
- "OG0000103.fa",
- "OG0000104.fa",
- "OG0000105.fa",
- "OG0000106.fa",
- "OG0000107.fa",
- "OG0000108.fa",
- "OG0000109.fa",
- "OG0000110.fa",
- "OG0000111.fa",
- "OG0000112.fa",
- "OG0000113.fa",
- "OG0000114.fa",
- "OG0000115.fa",
- "OG0000116.fa",
- "OG0000117.fa",
- "OG0000118.fa",
- "OG0000119.fa",
- "OG0000120.fa",
- "OG0000121.fa",
- "OG0000122.fa",
- "OG0000123.fa",
- "OG0000124.fa",
- "OG0000125.fa",
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- "OG0000137.fa",
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- "OG0000139.fa",
- "OG0000140.fa",
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- "OG0000206.fa",
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- "OG0000210.fa",
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- "OG0000214.fa",
- "OG0000215.fa",
- "OG0000216.fa",
- "OG0000217.fa",
- "OG0000218.fa",
- "OG0000219.fa",
- "OG0000220.fa",
- "OG0000221.fa",
- "OG0000222.fa",
- "OG0000223.fa",
- "OG0000224.fa",
- "OG0000225.fa",
- "OG0000226.fa",
- "OG0000227.fa",
- "OG0000228.fa",
- "OG0000229.fa",
- "OG0000230.fa",
- "OG0000231.fa",
- "OG0000232.fa",
- "OG0000233.fa",
- "OG0000234.fa",
- "OG0000235.fa",
- "OG0000236.fa",
- "OG0000237.fa",
- "OG0000238.fa",
- "OG0000239.fa",
- "OG0000240.fa",
- "OG0000241.fa",
- "OG0000242.fa",
- "OG0000243.fa",
- "OG0000244.fa",
- "OG0000245.fa",
- "OrthoFinder_graph.txt",
- "Orthogroups.GeneCount.tsv",
- "Orthogroups.tsv",
- "Orthogroups.txt",
- "Orthogroups_SingleCopyOrthologues.txt",
- "Orthogroups_SpeciesOverlaps.tsv",
- "Orthogroups_UnassignedGenes.tsv",
- "OrthologuesStats_Totals.tsv",
- "OrthologuesStats_many-to-many.tsv",
- "OrthologuesStats_many-to-one.tsv",
- "OrthologuesStats_one-to-many.tsv",
- "OrthologuesStats_one-to-one.tsv",
- "SequenceIDs.txt",
- "SimpleTest.phy",
- "SimpleTest.phy_fastme_stat.txt",
- "SimpleTest.tre",
- "Species0.fa",
- "Species0.fa",
- "Species1.fa",
- "SpeciesIDs.txt",
- "SpeciesTree_Gene_Duplications_0.5_Support.txt",
- "SpeciesTree_rooted.txt",
- "SpeciesTree_rooted_ids.txt",
- "SpeciesTree_rooted_node_labels.txt",
- "SpeciesTree_unrooted.txt",
- "SpeciesTree_unrooted_ids.txt",
- "Statistics_Overall.tsv",
- "Statistics_PerSpecies.tsv",
- "candidatus_portiera_aleyrodidarum.tsv",
- "candidatus_portiera_aleyrodidarum.tsv",
- "candidatus_portiera_aleyrodidarum__v__sarscov2.tsv",
- "clusters_OrthoFinder_I1.5.txt",
- "clusters_OrthoFinder_I1.5.txt_id_pairs.txt",
- "diamondDBSpecies0.dmnd",
- "diamondDBSpecies0.dmnd",
- "diamondDBSpecies1.dmnd",
- "sarscov2.tsv",
- "sarscov2.tsv",
- "sarscov2__v__candidatus_portiera_aleyrodidarum.tsv",
- "test_search_results.txt.gz"
- ],
[
"Statistics_PerSpecies.tsv:md5,984b5011a34d54527fe17896bfa36a2d",
"SpeciesTree_Gene_Duplications_0.5_Support.txt:md5,8b7a673e2e8b6d1aeb697f2bb88afa18",
@@ -313,10 +9,10 @@
"versions.yml:md5,86b472c85626aac1840eec0769016f5c"
],
"meta": {
- "nf-test": "0.8.4",
- "nextflow": "24.04.2"
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.4"
},
- "timestamp": "2024-06-07T21:33:50.902329"
+ "timestamp": "2024-09-03T10:59:02.895708598"
},
"sarscov2 - candidatus_portiera_aleyrodidarum - proteome - stub": {
"content": [
@@ -372,6 +68,17 @@
]
],
"1": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ [
+
+ ]
+ ]
+ ],
+ "2": [
"versions.yml:md5,86b472c85626aac1840eec0769016f5c"
],
"orthofinder": [
@@ -426,13 +133,39 @@
],
"versions": [
"versions.yml:md5,86b472c85626aac1840eec0769016f5c"
+ ],
+ "working": [
+ [
+ {
+ "id": "test",
+ "single_end": false
+ },
+ [
+
+ ]
+ ]
]
}
],
"meta": {
- "nf-test": "0.8.4",
- "nextflow": "24.04.2"
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-09-03T11:07:31.319665056"
+ },
+ "sarscov2 - candidatus_portiera_aleyrodidarum - proteome - resume": {
+ "content": [
+ [
+ "Duplications_per_Species_Tree_Node.tsv:md5,addc6f5ceec40bd82b00038d1872a27c",
+ "OrthologuesStats_Totals.tsv:md5,20d243abef226051a43cb37e922fc3eb",
+ "Statistics_PerSpecies.tsv:md5,83174c383b6c6828d1cc9b3be1679890"
+ ],
+ "versions.yml:md5,86b472c85626aac1840eec0769016f5c"
+ ],
+ "meta": {
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.4"
},
- "timestamp": "2024-06-07T16:00:56.530716"
+ "timestamp": "2024-09-03T11:04:10.916947006"
}
}
\ No newline at end of file
diff --git a/modules/nf-core/repeatmodeler/builddatabase/environment.yml b/modules/nf-core/repeatmodeler/builddatabase/environment.yml
index ecc282e..5314307 100644
--- a/modules/nf-core/repeatmodeler/builddatabase/environment.yml
+++ b/modules/nf-core/repeatmodeler/builddatabase/environment.yml
@@ -1,9 +1,7 @@
---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-name: "repeatmodeler_builddatabase"
channels:
- conda-forge
- bioconda
- - defaults
dependencies:
- "bioconda::repeatmodeler=2.0.5"
diff --git a/modules/nf-core/repeatmodeler/repeatmodeler/environment.yml b/modules/nf-core/repeatmodeler/repeatmodeler/environment.yml
index 2422071..5314307 100644
--- a/modules/nf-core/repeatmodeler/repeatmodeler/environment.yml
+++ b/modules/nf-core/repeatmodeler/repeatmodeler/environment.yml
@@ -1,9 +1,7 @@
---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-name: "repeatmodeler_repeatmodeler"
channels:
- conda-forge
- bioconda
- - defaults
dependencies:
- "bioconda::repeatmodeler=2.0.5"
diff --git a/modules/nf-core/samtools/cat/environment.yml b/modules/nf-core/samtools/cat/environment.yml
index a368198..da2df5e 100644
--- a/modules/nf-core/samtools/cat/environment.yml
+++ b/modules/nf-core/samtools/cat/environment.yml
@@ -1,8 +1,6 @@
-name: samtools_cat
channels:
- conda-forge
- bioconda
- - defaults
dependencies:
- bioconda::samtools=1.20
- bioconda::htslib=1.20
diff --git a/modules/nf-core/sortmerna/environment.yml b/modules/nf-core/sortmerna/environment.yml
index f40f995..fab4408 100644
--- a/modules/nf-core/sortmerna/environment.yml
+++ b/modules/nf-core/sortmerna/environment.yml
@@ -1,7 +1,5 @@
-name: sortmerna
channels:
- conda-forge
- bioconda
- - defaults
dependencies:
- bioconda::sortmerna=4.3.6
diff --git a/modules/nf-core/star/align/environment.yml b/modules/nf-core/star/align/environment.yml
index 8bd58cf..e3d1c71 100644
--- a/modules/nf-core/star/align/environment.yml
+++ b/modules/nf-core/star/align/environment.yml
@@ -1,8 +1,6 @@
-name: star_align
channels:
- conda-forge
- bioconda
- - defaults
dependencies:
- bioconda::star=2.7.10a
- bioconda::samtools=1.18
diff --git a/modules/nf-core/star/genomegenerate/environment.yml b/modules/nf-core/star/genomegenerate/environment.yml
index 791f255..38611df 100644
--- a/modules/nf-core/star/genomegenerate/environment.yml
+++ b/modules/nf-core/star/genomegenerate/environment.yml
@@ -1,8 +1,6 @@
-name: star_genomegenerate
channels:
- conda-forge
- bioconda
- - defaults
dependencies:
- bioconda::samtools=1.18
- bioconda::htslib=1.18
diff --git a/modules/nf-core/tsebra/environment.yml b/modules/nf-core/tsebra/environment.yml
index 657cd82..f189f6b 100644
--- a/modules/nf-core/tsebra/environment.yml
+++ b/modules/nf-core/tsebra/environment.yml
@@ -1,9 +1,7 @@
---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-name: "tsebra"
channels:
- conda-forge
- bioconda
- - defaults
dependencies:
- "bioconda::tsebra=1.1.2.5"
diff --git a/modules/nf-core/umitools/extract/environment.yml b/modules/nf-core/umitools/extract/environment.yml
index aab452d..9f9e03c 100644
--- a/modules/nf-core/umitools/extract/environment.yml
+++ b/modules/nf-core/umitools/extract/environment.yml
@@ -1,7 +1,5 @@
-name: umitools_extract
channels:
- conda-forge
- bioconda
- - defaults
dependencies:
- bioconda::umi_tools=1.1.5
diff --git a/subworkflows/local/fasta_orthofinder.nf b/subworkflows/local/fasta_orthofinder.nf
index 715d78e..a39e26d 100644
--- a/subworkflows/local/fasta_orthofinder.nf
+++ b/subworkflows/local/fasta_orthofinder.nf
@@ -24,7 +24,10 @@ workflow FASTA_ORTHOFINDER {
| collect
| filter { it.size() > 1 }
- ORTHOFINDER ( ch_orthofinder_peps.map { fastas -> [ [ id: 'genepal' ], fastas ] } )
+ ORTHOFINDER(
+ ch_orthofinder_peps.map { fastas -> [ [ id: 'genepal' ], fastas ] },
+ [ [], [] ]
+ )
ch_versions = ch_versions.mix(ORTHOFINDER.out.versions)
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
index ac31f28..28e32b2 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
@@ -2,10 +2,6 @@
// Subworkflow with functionality that may be useful for any Nextflow pipeline
//
-import org.yaml.snakeyaml.Yaml
-import groovy.json.JsonOutput
-import nextflow.extension.FilesEx
-
/*
========================================================================================
SUBWORKFLOW DEFINITION
@@ -58,7 +54,7 @@ workflow UTILS_NEXTFLOW_PIPELINE {
// Generate version string
//
def getWorkflowVersion() {
- String version_string = ""
+ def version_string = "" as String
if (workflow.manifest.version) {
def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
version_string += "${prefix_v}${workflow.manifest.version}"
@@ -79,10 +75,10 @@ def dumpParametersToJSON(outdir) {
def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
def filename = "params_${timestamp}.json"
def temp_pf = new File(workflow.launchDir.toString(), ".${filename}")
- def jsonStr = JsonOutput.toJson(params)
- temp_pf.text = JsonOutput.prettyPrint(jsonStr)
+ def jsonStr = groovy.json.JsonOutput.toJson(params)
+ temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr)
- FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
+ nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json")
temp_pf.delete()
}
@@ -90,7 +86,7 @@ def dumpParametersToJSON(outdir) {
// When running with -profile conda, warn if channels have not been set-up appropriately
//
def checkCondaChannels() {
- Yaml parser = new Yaml()
+ def parser = new org.yaml.snakeyaml.Yaml()
def channels = []
try {
def config = parser.load("conda config --show channels".execute().text)
@@ -102,14 +98,16 @@ def checkCondaChannels() {
// Check that all channels are present
// This channel list is ordered by required channel priority.
- def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
+ def required_channels_in_order = ['conda-forge', 'bioconda']
def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
// Check that they are in the right order
def channel_priority_violation = false
- def n = required_channels_in_order.size()
- for (int i = 0; i < n - 1; i++) {
- channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1]))
+
+ required_channels_in_order.eachWithIndex { channel, index ->
+ if (index < required_channels_in_order.size() - 1) {
+ channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index+1]))
+ }
}
if (channels_missing | channel_priority_violation) {
diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
index d0a926b..a09572e 100644
--- a/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
+++ b/subworkflows/nf-core/utils_nextflow_pipeline/tests/nextflow.config
@@ -3,7 +3,7 @@ manifest {
author = """nf-core"""
homePage = 'https://127.0.0.1'
description = """Dummy pipeline"""
- nextflowVersion = '!>=23.04.0'
+ nextflowVersion = '!>=23.04.0'
version = '9.9.9'
doi = 'https://doi.org/10.5281/zenodo.5070524'
}
diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
index 14558c3..cbd8495 100644
--- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
+++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf
@@ -2,9 +2,6 @@
// Subworkflow with utility functions specific to the nf-core pipeline template
//
-import org.yaml.snakeyaml.Yaml
-import nextflow.extension.FilesEx
-
/*
========================================================================================
SUBWORKFLOW DEFINITION
@@ -34,7 +31,7 @@ workflow UTILS_NFCORE_PIPELINE {
// Warn if a -profile or Nextflow config has not been provided to run the pipeline
//
def checkConfigProvided() {
- valid_config = true
+ def valid_config = true as Boolean
if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) {
log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" +
"This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" +
@@ -66,11 +63,13 @@ def checkProfileProvided(nextflow_cli_args) {
//
def workflowCitation() {
def temp_doi_ref = ""
- String[] manifest_doi = workflow.manifest.doi.tokenize(",")
+ def manifest_doi = workflow.manifest.doi.tokenize(",")
// Using a loop to handle multiple DOIs
// Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers
// Removing ` ` since the manifest.doi is a string and not a proper list
- for (String doi_ref: manifest_doi) temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
+ manifest_doi.each { doi_ref ->
+ temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n"
+ }
return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
"* The pipeline\n" +
temp_doi_ref + "\n" +
@@ -84,7 +83,7 @@ def workflowCitation() {
// Generate workflow version string
//
def getWorkflowVersion() {
- String version_string = ""
+ def version_string = "" as String
if (workflow.manifest.version) {
def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : ''
version_string += "${prefix_v}${workflow.manifest.version}"
@@ -102,8 +101,8 @@ def getWorkflowVersion() {
// Get software versions for pipeline
//
def processVersionsFromYAML(yaml_file) {
- Yaml yaml = new Yaml()
- versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
+ def yaml = new org.yaml.snakeyaml.Yaml()
+ def versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] }
return yaml.dumpAsMap(versions).trim()
}
@@ -124,7 +123,7 @@ def workflowVersionToYAML() {
def softwareVersionsToYAML(ch_versions) {
return ch_versions
.unique()
- .map { processVersionsFromYAML(it) }
+ .map { version -> processVersionsFromYAML(version) }
.unique()
.mix(Channel.of(workflowVersionToYAML()))
}
@@ -134,19 +133,19 @@ def softwareVersionsToYAML(ch_versions) {
//
def paramsSummaryMultiqc(summary_params) {
def summary_section = ''
- for (group in summary_params.keySet()) {
+ summary_params.keySet().each { group ->
def group_params = summary_params.get(group) // This gets the parameters of that particular group
if (group_params) {
summary_section += " $group
\n"
summary_section += " \n"
- for (param in group_params.keySet()) {
+ group_params.keySet().sort().each { param ->
summary_section += " - $param
- ${group_params.get(param) ?: 'N/A'}
\n"
}
summary_section += "
\n"
}
}
- String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n"
+ def yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" as String
yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n"
yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
@@ -161,7 +160,7 @@ def paramsSummaryMultiqc(summary_params) {
// nf-core logo
//
def nfCoreLogo(monochrome_logs=true) {
- Map colors = logColours(monochrome_logs)
+ def colors = logColours(monochrome_logs) as Map
String.format(
"""\n
${dashedLine(monochrome_logs)}
@@ -180,7 +179,7 @@ def nfCoreLogo(monochrome_logs=true) {
// Return dashed line
//
def dashedLine(monochrome_logs=true) {
- Map colors = logColours(monochrome_logs)
+ def colors = logColours(monochrome_logs) as Map
return "-${colors.dim}----------------------------------------------------${colors.reset}-"
}
@@ -188,7 +187,7 @@ def dashedLine(monochrome_logs=true) {
// ANSII colours used for terminal logging
//
def logColours(monochrome_logs=true) {
- Map colorcodes = [:]
+ def colorcodes = [:] as Map
// Reset / Meta
colorcodes['reset'] = monochrome_logs ? '' : "\033[0m"
@@ -287,7 +286,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
}
def summary = [:]
- for (group in summary_params.keySet()) {
+ summary_params.keySet().sort().each { group ->
summary << summary_params[group]
}
@@ -344,10 +343,10 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
def sendmail_html = sendmail_template.toString()
// Send the HTML e-mail
- Map colors = logColours(monochrome_logs)
+ def colors = logColours(monochrome_logs) as Map
if (email_address) {
try {
- if (plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
+ if (plaintext_email) { throw new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') }
// Try to send HTML e-mail using sendmail
def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
sendmail_tf.withWriter { w -> w << sendmail_html }
@@ -364,13 +363,13 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
// Write summary e-mail HTML to a file
def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
output_hf.withWriter { w -> w << email_html }
- FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html");
+ nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html");
output_hf.delete()
// Write summary e-mail TXT to a file
def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt")
output_tf.withWriter { w -> w << email_txt }
- FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
+ nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt");
output_tf.delete()
}
@@ -378,7 +377,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi
// Print pipeline summary on completion
//
def completionSummary(monochrome_logs=true) {
- Map colors = logColours(monochrome_logs)
+ def colors = logColours(monochrome_logs) as Map
if (workflow.success) {
if (workflow.stats.ignoredCount == 0) {
log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
@@ -395,7 +394,7 @@ def completionSummary(monochrome_logs=true) {
//
def imNotification(summary_params, hook_url) {
def summary = [:]
- for (group in summary_params.keySet()) {
+ summary_params.keySet().sort().each { group ->
summary << summary_params[group]
}