Merge pull request #52 from Ferlab-Ste-Justine/fix/CLIN-3706-support-…

…more-file-extensions-for-raw-gvcf

fix: CLIN-3706 support more input gvcf file extensions

CHANGELOG.md

@@ -18,6 +18,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Fixed`
 - [#50](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/50) Use container tag 1.20 for splitMultiAllelics process
 - [#51](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/51) Add missing ressources for exomiser process in configuration
+- [#52](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/52) Ensure .gvcf file extensions are supported in all scenarios
 
 ### `Known issues`
 - The nf-core modules that we are using have a potential performance flaw. Typically, the regex used to describe the output files also match the input files (ex: "*.vcf"), which can cause unnecessary file transfers.  This has already proven to cause issues on fusion. One fix could be to transfer the whole modules to local to perform the small change necessary to fix this.

README.md

@@ -14,15 +14,16 @@
 It performs joint genotyping, tags low-quality variants, and optionally annotates the final vcf data using vep and/or prioritize variant using exomiser.
 
 ###  Summary:
-1. Remove MNPs using bcftools 
-2. Normalize .gvcf
-3. Combine .gvcf
-4. [Joint-genotyping](https://gatk.broadinstitute.org/hc/en-us/articles/360037057852-GenotypeGVCFs)
-5. Tag false positive variants with either:
+1. Standardize input vcf files using bcftools view
+2. Remove MNPs using bcftools 
+3. Normalize .gvcf
+4. Combine .gvcf
+5. [Joint-genotyping](https://gatk.broadinstitute.org/hc/en-us/articles/360037057852-GenotypeGVCFs)
+6. Tag false positive variants with either:
   - For whole genome sequencing data: [Variant quality score recalibration (VQSR)](https://gatk.broadinstitute.org/hc/en-us/articles/360036510892-VariantRecalibrator)
   - For whole exome sequencing data: [Hard-Filtering](https://gatk.broadinstitute.org/hc/en-us/articles/360036733451-VariantFiltration)
-6. Optionnally annotate variants with [Variant effect predictor (VEP)](https://useast.ensembl.org/info/docs/tools/vep/index.html)
-7. Optionnally integrate phenotype data to annotate, filter and prioritise variants likely to be disease-causing with [exomiser](https://www.sanger.ac.uk/tool/exomiser/)
+7. Optionnally annotate variants with [Variant effect predictor (VEP)](https://useast.ensembl.org/info/docs/tools/vep/index.html)
+8. Optionnally integrate phenotype data to annotate, filter and prioritise variants likely to be disease-causing with [exomiser](https://www.sanger.ac.uk/tool/exomiser/)
 
 
 

conf/modules.config

@@ -26,6 +26,12 @@ process {
 
     publishDir = new_publish_dir()
 
+    withName: BCFTOOLS_VIEW {
+        container = 'staphb/bcftools:1.20'
+        ext.args = { '-Oz --write-index=tbi' }
+        ext.prefix = {meta.id + ".standardized.g"}
+    }
+
     withName: BCFTOOLS_FILTER {
         container = 'staphb/bcftools:1.20'
         ext.args = {'-e \'strlen(REF)>1 & strlen(REF)==strlen(ALT) & TYPE="snp"\' -Oz --write-index=tbi'}

docs/usage.md

@@ -85,10 +85,6 @@ You can optionally skip this step by setting the `exclude_mnps` parameter to `fa
 
 Note that MNPs are not supported by the VQSR procedure, so you cannot skip this step if you have whole genome data.
 
-Additionally, if you skip the exclusion of MNPs, ensure that your input GVCF files are indexed or that they are compressed with bgzip. 
-If the index file is missing, the workflow will attempt to generate it, but the input GVCF file must be compressed with bgzip for this to work.
-
-
 ### Tools
 
 You can include additional analysis in your pipeline  via the `tools` parameter. Currently, the pipeline supports 

modules.json

@@ -15,6 +15,11 @@
             "git_sha": "33ef773a7ea36e88323902f63662aa53c9b88988",
             "installed_by": ["modules"]
           },
+          "bcftools/view": {
+            "branch": "master",
+            "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+            "installed_by": ["modules"]
+          },
           "ensemblvep/vep": {
             "branch": "master",
             "git_sha": "6e3585d9ad20b41adc7d271009f8cb5e191ecab4",