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SGP-373 - Push in order to run 80 samples (fastq --> annotated vcf)
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scorreard committed Jun 17, 2022
1 parent 27635ac commit d78857a
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Showing 54 changed files with 1,208 additions and 1,028 deletions.
1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -16,6 +16,7 @@ report.html*
hail*
/archive
/vcf_to_try_hail
filtered_samples_sex.tsv

# Error and output files #
##########################
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16 changes: 7 additions & 9 deletions Nextflow_SNV_MT_211220.nf
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Expand Up @@ -22,12 +22,11 @@ if (params.help) {


// Include the other workflow that themselves includes the modules
include { ALN } from "./subworkflow/ALN"
include { QC_indiv } from "./subworkflow/QC_indiv"
include { Initialisation } from "./subworkflow/Initialisation"
include { Mapping } from "./subworkflow/Mapping"
include { SNV } from "./subworkflow/SNV"
include { MT } from "./subworkflow/MT"
include { SV } from "./subworkflow/SV"
include { Hail } from "./subworkflow/Hail"

workflow{
samples = Channel
Expand All @@ -40,10 +39,9 @@ workflow{
outdir_ind = file (params.outdir_ind)

main :
ALN()
QC_indiv(ALN.out.bam_sorted, ALN.out.bam_sorted_index)
SNV(ALN.out.bam_sorted, ALN.out.bam_sorted_index, QC_indiv.out.mosdepth_output)
MT(ALN.out.bam_sorted, ALN.out.bam_sorted_index, QC_indiv.out.mosdepth_output)
SV(ALN.out.bam_sorted, ALN.out.bam_sorted_index, SNV.out.sample_sex_file)
Hail(SNV.out.SNV_vcf, SNV.out.sample_sex_file)
// Initialisation()
Mapping()
SNV(Mapping.out.bam_sorted, Mapping.out.bam_sorted_index, Mapping.out.mosdepth_output)
MT(Mapping.out.bam_sorted, Mapping.out.bam_sorted_index, Mapping.out.mosdepth_output)
SV(Mapping.out.bam_sorted, Mapping.out.bam_sorted_index, SNV.out.sample_sex_file)
}
1 change: 1 addition & 0 deletions modules/GLnexus.nf
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Expand Up @@ -20,6 +20,7 @@ process GLnexus_cli {
"""
glnexus_cli \
--config DeepVariantWGS \
--mem-gbytes 128 \
--list ${list_gvcf} > DeepVariant_GLnexus_${run}.bcf
"""
}
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1 change: 1 addition & 0 deletions modules/Hail_sample_QC.nf
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Expand Up @@ -21,6 +21,7 @@ process Hail_sample_QC {
output :
path '*.html', emit : graph
path '*filtered_samples.vcf.bgz', emit : vcf_sample_filtered
path '*filtered_samples_sex.tsv', emit : filtered_sample_sex

conda '/home/BCRICWH.LAN/Solenne.Correard/miniconda3/envs/hail'

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