Merge pull request nf-cmgg#31 from nf-cmgg/final-fixes

Final fixes
ToonRosseel · Dec 12, 2024 · d748611 · d748611
2 parents 9bb0ed7 + 4a3d3ea
commit d748611
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v1.2.1dev
 
+### `Improvements`
+
+- Added a `WES` profile to make it easier to run the pipeline on our infrastructure
+- Pin the VEP version to v105
+
 ### `Bug Fixes`
 
 - Fixed an issue where the bedgovcf yaml wasn't being given

diff --git a/conf/test.config b/conf/test.config
@@ -35,9 +35,9 @@ params {
     roi_auto = "https://raw.githubusercontent.com/nf-cmgg/test-datasets/exomecnv/data/genomics/homo_sapiens/genome/roi/Homo_sapiens.GRCh38.105.chr21_protein_coding_basic_sorted_merged_autosomal.bed"
     roi_chrx = "https://raw.githubusercontent.com/nf-cmgg/test-datasets/exomecnv/data/genomics/homo_sapiens/genome/roi/Homo_sapiens.GRCh38.105.chrX_protein_coding_basic_sorted_merged.bed"
 
-    yamlconfig = "${projectDir}/assets/exomedepth.yaml"
     exomedepth = true
-
+    igenomes_ignore = true
+    genomes_ignore = true
 
     // VEP options
     annotate            = false

diff --git a/conf/wes.config b/conf/wes.config
@@ -0,0 +1,12 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running the pipeline on the CMGG infrastructure
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
+params {
+    exomedepth = true
+    annotate = true
+    roi_auto = "${params.genomes_base}/Hsapiens/GRCh38/regions/Homo_sapiens.GRCh38.105.chr_protein_coding_basic_sorted_merged_autosomal.bed"
+    roi_chrx = "${params.genomes_base}/Hsapiens/GRCh38/regions/Homo_sapiens.GRCh38.105.chrX_protein_coding_basic_sorted_merged.bed"
+}
diff --git a/main.nf b/main.nf
@@ -16,8 +16,9 @@
 //  from igenomes.config using `--genome`
 include { getGenomeAttribute      } from './subworkflows/local/utils_nfcore_exomecnv_pipeline'
 
-params.fasta = getGenomeAttribute('fasta')
-params.fai   = getGenomeAttribute('fai')
+params.fasta     = getGenomeAttribute('fasta')
+params.fai       = getGenomeAttribute('fai')
+params.vep_cache = getGenomeAttribute('vep_cache')
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

diff --git a/modules.json b/modules.json
@@ -14,7 +14,8 @@
                     "ensemblvep/download": {
                         "branch": "master",
                         "git_sha": "6e3585d9ad20b41adc7d271009f8cb5e191ecab4",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/ensemblvep/download/ensemblvep-download.diff"
                     },
                     "ensemblvep/vep": {
                         "branch": "master",

diff --git a/modules/nf-core/ensemblvep/download/ensemblvep-download.diff b/modules/nf-core/ensemblvep/download/ensemblvep-download.diff
diff --git a/modules/nf-core/ensemblvep/download/main.nf b/modules/nf-core/ensemblvep/download/main.nf
diff --git a/modules/nf-core/ensemblvep/download/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/download/tests/main.nf.test.snap
diff --git a/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff b/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff
diff --git a/modules/nf-core/ensemblvep/vep/main.nf b/modules/nf-core/ensemblvep/vep/main.nf
diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test b/modules/nf-core/ensemblvep/vep/tests/main.nf.test
diff --git a/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/vep/tests/main.nf.test.snap
diff --git a/nextflow.config b/nextflow.config
@@ -13,13 +13,13 @@ params {
     // Input options
     input                      = null
 
-
     // References
     genome                     = "GRCh38"
     cmgg_config_base           = "/conf/"
     igenomes_base              = null //'s3://ngi-igenomes/igenomes/'
     igenomes_ignore            = true
-
+    genomes_base               = "/references/"
+    genomes_ignore             = false
 
     // MultiQC options
     multiqc_config             = null
@@ -62,8 +62,7 @@ params {
     // VEP Parameters
     vep_cache_version = 105
     species = "homo_sapiens"
-    vep_cache = null
-    annotate = null
+    annotate = false
     vep_assembly = "GRCh38"
 
 
@@ -173,6 +172,7 @@ profiles {
     }
     test      { includeConfig 'conf/test.config'      }
     nf_test   { includeConfig 'conf/nf_test.config'   }
+    WES       { includeConfig 'conf/wes.config'       }
 }
 
 // Load nf-core custom profiles from different Institutions
@@ -197,7 +197,7 @@ plugins {
 }
 
 // Load igenomes.config if required
-includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'
+includeConfig !params.igenomes_ignore ? "conf/igenomes.config" : !params.genomes_ignore ? "https://raw.githubusercontent.com/nf-cmgg/configs/main/conf/Hsapiens/genomes.config" : "conf/igenomes_ignored.config"
 
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container
 // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.