Updated deps and parameters docs

Plant-Food-Research-Open · Sep 10, 2024 · 806c7cf · 806c7cf
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diff --git 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
@@ -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
@@ -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
@@ -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
diff --git a/modules/nf-core/agat/convertspgxf2gxf/environment.yml b/modules/nf-core/agat/convertspgxf2gxf/environment.yml
diff --git a/modules/nf-core/agat/spfilterfeaturefromkilllist/environment.yml b/modules/nf-core/agat/spfilterfeaturefromkilllist/environment.yml
diff --git a/modules/nf-core/agat/spmergeannotations/environment.yml b/modules/nf-core/agat/spmergeannotations/environment.yml
diff --git a/modules/nf-core/cat/cat/environment.yml b/modules/nf-core/cat/cat/environment.yml
diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml
diff --git a/modules/nf-core/eggnogmapper/environment.yml b/modules/nf-core/eggnogmapper/environment.yml
diff --git a/modules/nf-core/fastavalidator/environment.yml b/modules/nf-core/fastavalidator/environment.yml
diff --git a/modules/nf-core/fastp/environment.yml b/modules/nf-core/fastp/environment.yml
diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml
diff --git a/modules/nf-core/gffcompare/environment.yml b/modules/nf-core/gffcompare/environment.yml
diff --git a/modules/nf-core/gffcompare/meta.yml b/modules/nf-core/gffcompare/meta.yml