Merge pull request #20 from Ferlab-Ste-Justine/Feat/genotypeGVCFtoModule

Feat: Added nf-core module GATK4_GENOTYPEGVCFS
Ferlab-Ste-Justine · Sep 23, 2024 · 6ff06ac · 6ff06ac
2 parents 08284c4 + 225cfaf
commit 6ff06ac
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 
 ## v2.0.0dev - [date]
+### Known issues:
+
+[#20](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/20) The nf-core module genotypeGVCFs has a potential performance flaw. The output glob specifies for vcf and tbi *.vcf and *.vcf.tbi respectively. This regex will also include the inputs, which can cause unnecessary file transfers. This has already proven to cause issues on fusion. One fix could be to transfer the whole module to local to perform the small change necessary to fix this (change the globs to *${prefix}.vcf)
+
 
 ## v1.0dev
 
@@ -18,7 +22,8 @@ Initial release of ferlab/postprocessing, created with the [nf-core](https://nf-
 - [#10](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/10) Converted the exclude_MNPs function into a nf-core subworkflow containing 2 nf-core modules. Also added test profile test data (but it fails at VQSR for now)
 - [#17](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/17) Save nextflow log file to output directory on workflow completion
 - [#17](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/17) Allow to run nf-tests check in github workflow
-- [#18](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/19) Added local module COMBINEGVCFS to replace local function importGVCFs, mostly equivalent to nf-core module GATK4_COMBINEGVCFS
+- [#19](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/19) Added local module COMBINEGVCFS to replace local function importGVCFs, mostly equivalent to nf-core module GATK4_COMBINEGVCFS
+- [#20](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/20) Added nf-core module GATK4_GENOTYPEGVCFS to replace local function genotype_gvcf
 - [#21](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/21) Added nextflow docker image
 - [#22](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/22) Added exomiser docker image
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -33,4 +33,9 @@ process {
     withName: COMBINEGVCFS {
         container = 'broadinstitute/gatk:4.5.0.0'
     }
+
+    withName: GATK4_GENOTYPEGVCFS {
+        container = 'broadinstitute/gatk:4.5.0.0'
+        ext.prefix = {meta.id + ".genotyped"}
+    }
 }
diff --git a/modules.json b/modules.json
@@ -14,6 +14,11 @@
             "branch": "master",
             "git_sha": "33ef773a7ea36e88323902f63662aa53c9b88988",
             "installed_by": ["modules"]
+          },
+          "gatk4/genotypegvcfs": {
+            "branch": "master",
+            "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
+            "installed_by": ["modules"]
           }
         }
       },

diff --git a/modules/nf-core/gatk4/genotypegvcfs/environment.yml b/modules/nf-core/gatk4/genotypegvcfs/environment.yml
diff --git a/modules/nf-core/gatk4/genotypegvcfs/main.nf b/modules/nf-core/gatk4/genotypegvcfs/main.nf
diff --git a/modules/nf-core/gatk4/genotypegvcfs/meta.yml b/modules/nf-core/gatk4/genotypegvcfs/meta.yml