From 00330520752dac634c4350955b86380f6b199e1c Mon Sep 17 00:00:00 2001
From: scorreard <solenne.correard@gmail.com>
Date: Fri, 17 Jun 2022 20:07:33 -0700
Subject: [PATCH] SGP-376 - small updates

---
 modules/Hail_variant_QC.nf         | 2 +-
 modules/Hail_variant_QC.py         | 2 +-
 modules/annotation_table_merged.nf | 2 +-
 nextflow.config                    | 4 ++--
 4 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/modules/Hail_variant_QC.nf b/modules/Hail_variant_QC.nf
index 27351d0..8ee5e87 100644
--- a/modules/Hail_variant_QC.nf
+++ b/modules/Hail_variant_QC.nf
@@ -12,7 +12,7 @@ process Hail_variant_QC {
 
         publishDir "$params.outdir_ind/${assembly}/${batch}/${run}/QC/Aggregated/Hail/Variants/", mode: 'copy', pattern : '*.html'
         publishDir "$params.outdir_ind/${assembly}/${batch}/${run}/vcf_post_hail/", mode: 'copy', pattern : '*filtered_samples_variants.vcf.bgz*'
-        publishDir "$params.outdir_pop/${assembly}/${run}/${var_type}/Vcf_pre_annotation/", mode: 'copy', pattern : 'SNV_filtered_frequ_*'
+        publishDir "$params.outdir_pop/${assembly}/${run}/SNV/Vcf_pre_annotation/", mode: 'copy', pattern : 'SNV_filtered_frequ_*'
 
 	input :
 	file vcf_sample_filtered
diff --git a/modules/Hail_variant_QC.py b/modules/Hail_variant_QC.py
index 8dd9011..2c069ac 100644
--- a/modules/Hail_variant_QC.py
+++ b/modules/Hail_variant_QC.py
@@ -317,7 +317,7 @@ def report_stats():
 # Calculate the variants frequency per sex
 # 
 
-SNV_mt_var_filtered_sex = SNV_mt_var_filteredi_tot.annotate_cols(**sex_table[SNV_mt_var_filtered_tot.s])
+SNV_mt_var_filtered_sex = SNV_mt_var_filtered_tot.annotate_cols(**sex_table[SNV_mt_var_filtered_tot.s])
 SNV_mt_var_filtered_XX = SNV_mt_var_filtered_sex.filter_cols(SNV_mt_var_filtered_sex.sex == 'XX')
 SNV_mt_var_filtered_XX = hl.variant_qc(SNV_mt_var_filtered_XX)
 SNV_mt_var_filtered_XX = SNV_mt_var_filtered_XX.annotate_rows(
diff --git a/modules/annotation_table_merged.nf b/modules/annotation_table_merged.nf
index 10b48f2..40ad22d 100644
--- a/modules/annotation_table_merged.nf
+++ b/modules/annotation_table_merged.nf
@@ -11,7 +11,7 @@
 process annotation_table_merged {
 	tag "${chr}"
 
-        publishDir "$params.outdir_pop/${assembly}/${run}/${var_type}/VEP_annotation/", mode: 'copy', pattern : '*_annotation_table_merged.*'
+        publishDir "$params.outdir_pop/${assembly}/${run}/${var_type}/VEP_annotation/", mode: 'copy', pattern : '*_annotation_table_merged*'
 	publishDir "$params.outdir_pop/${assembly}/${run}/QC/${var_type}/${vcf.simpleName}/", mode: 'copy', pattern : '*_VEP_stats*'
 
         input :
diff --git a/nextflow.config b/nextflow.config
index 04c9850..1674e6d 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -145,8 +145,8 @@ process {
 
 // 32GB, 4 cpus
           withName: 'annotation_table_merged' {
-                memory = 60.GB
-                cpus = 12
+                memory = 120.GB
+                cpus = 20
         }
 
 // 20GB, 8 cpus