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Unverified Commit b85258ad authored by Laurent Modolo's avatar Laurent Modolo
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SNP_calling.nf: cleanup gatk code

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src/SNP_calling.config
+ 0
− 15
View file @ b85258ad
......@@ -45,21 +45,6 @@ profiles {
withName: vcf_to_csv_norm {
container = "gatk:4.0.8.1"
}
withName: HaplotypeCaller {
container = "gatk:4.0.8.1"
}
withName: GetPileupSummaries {
container = "gatk:4.0.8.1"
}
withName: CalculateContamination {
container = "gatk:4.0.8.1"
}
withName: CollectSequencingArtifactMetrics {
container = "gatk:4.0.8.1"
}
withName: filter_SNP {
container = "gatk:4.0.8.1"
}
}
}
sge {
......
src/SNP_calling.nf
+ 4
− 165
View file @ b85258ad
......@@ -296,46 +296,29 @@ final_indexed_bam_files_norm = index_bam_files_norm
final_indexed_bam_files_tumor = index_bam_files_tumor
.filter{ "tumor_sample" == it[0] }
final_bam_files_norm.into{
haplotypecaller_bam_files_norm;
final_bam_files_norm.set{
samtools_SNP_bam_files_norm
}
final_bam_files_tumor.into{
haplotypecaller_bam_files_tumor;
final_bam_files_tumor.set{
samtools_SNP_bam_files_tumor;
artifact_bam_files_tumor;
pileup_bam_files_tumor
}
final_indexed_bam_files_norm.into{
haplo_index_bam_files_norm;
final_indexed_bam_files_norm.set{
samtools_SNP_index_bam_files_norm
}
final_indexed_bam_files_tumor.into{
haplo_index_bam_files_tumor;
final_indexed_bam_files_tumor.set{
samtools_SNP_index_bam_files_tumor;
artifact_index_bam_files_tumor;
pileup_index_bam_files_tumor
}
final_fasta_file.into{
haplo_fasta_file;
samtools_SNP_fasta_file_tumor;
samtools_SNP_fasta_file_norm;
artifact_fasta_file;
filter_fasta_file
}
indexed2_fasta_file.into{
haplo_indexed2_fasta_file;
samtools_SNP_indexed2_fasta_file_tumor;
samtools_SNP_indexed2_fasta_file_norm;
artifact_indexed2_fasta_file;
filter_indexed2_fasta_file
}
indexed3_fasta_file.into{
haplo_indexed3_fasta_file;
samtools_SNP_indexed3_fasta_file_tumor;
samtools_SNP_indexed3_fasta_file_norm;
artifact_indexed3_fasta_file;
filter_indexed3_fasta_file
}
process samtools_SNP_tumor {
......@@ -432,147 +415,3 @@ gatk VariantsToTable -V ${file_id_norm}_filtered.vcf \
"""
}
/*
process HaplotypeCaller {
tag "$file_id_norm"
cpus 10
publishDir "results/SNP/vcf/", mode: 'copy'
input:
set file_id_norm, file(bam_norm) from haplotypecaller_bam_files_norm
set file_ididx_norm, file(bamidx_norm) from haplo_index_bam_files_norm
set file_id_tumor, file(bam_tumor) from haplotypecaller_bam_files_tumor
set file_ididx_tumor, file(bamidx_tumor) from haplo_index_bam_files_tumor
set genome_id, file(fasta) from haplo_fasta_file
set genome2_idx, file(fasta2idx) from haplo_indexed2_fasta_file
set genome3_idx, file(fasta3idx) from haplo_indexed3_fasta_file
output:
set file_id_norm, "*.vcf" into vcf_files
set file_id_norm, "*.vcf.idx" into index_vcf_files
set file_id_norm, "*.bam" into realigned_bams_files
file "*_mutect2_report.txt" into mutect2_report
script:
"""
gatk --java-options "-Xmx32G" Mutect2 --native-pair-hmm-threads ${task.cpus} -R ${fasta} \
-I ${bam_tumor} -tumor ${file_id_tumor} \
-I ${bam_norm} -normal ${file_id_norm} \
-O ${file_id_norm}_raw_calls.g.vcf \
-bamout ${file_id_norm}_realigned.bam 2> ${file_id_norm}_mutect2_report.txt
"""
}
vcf_files.into{
pileup_vcf_files;
filter_vcf_files
}
index_vcf_files.into{
pileup_index_vcf_files;
filter_index_vcf_files
}
process GetPileupSummaries {
tag "$file_id_norm"
cpus 1
publishDir "results/SNP/vcf/", mode: 'copy'
input:
set file_id_norm, file(vcf) from pileup_vcf_files
set fileidx_id_norm, file(vcfidx) from pileup_index_vcf_files
set file_id_tumor, file(bam_tumor) from pileup_bam_files_tumor
output:
set file_id_tumor, "*.table" into pileup_files
file "*_pileup_report.txt" into pileup_report
script:
"""
gatk --java-options "-Xmx32G" GetPileupSummaries \
-I ${bam_tumor} \
-V ${vcf} \
-O ${file_id_tumor}_pileup.table \
2> ${file_id_tumor}_pileup_report.txt
"""
}
process CalculateContamination {
tag "$file_id_tumor"
cpus 1
publishDir "results/SNP/vcf/", mode: 'copy'
input:
set file_id_tumor, file(pileup_table) from pileup_files
output:
set file_id_tumor, "*.table" into contamination_files
file "*_contamination_report.txt" into contamination_report
script:
"""
gatk --java-options "-Xmx32G" CalculateContamination \
-I ${pileup_table} \
-O $file_id_tumor}_contamination.table \
2> ${file_id_tumor}_contamination_report.txt
"""
}
*/
/*
process CollectSequencingArtifactMetrics {
tag "$file_id_tumor"
cpus 1
publishDir "results/SNP/vcf/", mode: 'copy'
input:
set file_id_tumor, file(bam_tumor) from artifact_bam_files_tumor
set genome_id, file(fasta) from artifact_fasta_file
set genome2_idx, file(fasta2idx) from artifact_indexed2_fasta_file
set genome3_idx, file(fasta3idx) from artifact_indexed3_fasta_file
output:
set file_id_tumor, "*_artifact.*" into artifact_files
file "*_artifact_report.txt" into artifact_report
script:
"""
gatk CollectSequencingArtifactMetrics \
-I ${bam_tumor} \
-O ${file_id_tumor}_artifact \
-R ${fasta} \
2> ${file_id_tumor}_artifact_report.txt
"""
}
process filter_SNP {
tag "$file_id_norm"
cpus 1
publishDir "results/SNP/vcf/", mode: 'copy'
input:
set file_id_norm, file(vcf) from filter_vcf_files
set fileidx_id_norm, file(vcfid) from filter_index_vcf_files
set genome_id, file(fasta) from filter_fasta_file
set genome2_idx, file(fasta2idx) from filter_indexed2_fasta_file
set genome3_idx, file(fasta3idx) from filter_indexed3_fasta_file
output:
set file_id_norm, "*.vcf" into vcf_files_filtered
file "*_filter_report.txt" into filter_report
script:
"""
gatk FilterMutectCalls \
-V ${vcf} \
-O ${file_id_norm}_filtered.vcf \
2> ${file_id_norm}_filter_report.txt
gatk SelectVariants \
-R ${fasta} \
--variant ${file_id_norm}_filtered.vcf \
--exclude-filtered \
-O ${file_id_norm}_filtered_pass.vcf \
2>> ${file_id_norm}_filter_report.txt
"""
}
*/
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