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