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https://github.com/MillironX/nf-core_modules.git
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added dragstr model to haplotypecaller
This commit is contained in:
Nicolas Vannieuwkerke
parent
5447395975
commit
e53d091a6d
5 changed files with 42 additions and 8 deletions
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@ -8,7 +8,7 @@ process GATK4_HAPLOTYPECALLER {
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'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
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input:
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tuple val(meta), path(input), path(input_index), path(intervals)
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tuple val(meta), path(input), path(input_index), path(intervals), path(dragstr_model)
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path fasta
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path fai
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path dict
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@ -28,6 +28,7 @@ process GATK4_HAPLOTYPECALLER {
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def prefix = task.ext.prefix ?: "${meta.id}"
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def dbsnp_command = dbsnp ? "--dbsnp $dbsnp" : ""
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def interval_command = intervals ? "--intervals $intervals" : ""
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def dragstr_command = dragstr_model ? "--dragstr-params-path $dragstr_model" : ""
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def avail_mem = 3
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if (!task.memory) {
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@ -42,6 +43,7 @@ process GATK4_HAPLOTYPECALLER {
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--reference $fasta \\
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$dbsnp_command \\
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$interval_command \\
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$dragstr_command \\
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--tmp-dir . \\
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$args
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@ -32,6 +32,10 @@ input:
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- intervals:
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type: file
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description: Bed file with the genomic regions included in the library (optional)
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- dragstr_model:
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type: file
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description: Text file containing the DragSTR model of the used BAM/CRAM file (optional)
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pattern: "*.txt"
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- fasta:
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type: file
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description: The reference fasta file
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@ -266,6 +266,8 @@ params {
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test_pileups_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test.pileups.table"
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test2_pileups_table = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test2.pileups.table"
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test_paired_end_sorted_dragstrmodel = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_paired_end_sorted_dragstrmodel.txt"
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test_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_genomicsdb.tar.gz"
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test_pon_genomicsdb_tar_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/test_pon_genomicsdb.tar.gz"
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@ -8,6 +8,7 @@ workflow test_gatk4_haplotypecaller {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
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[],
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[]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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@ -21,6 +22,7 @@ workflow test_gatk4_haplotypecaller_cram {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
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[],
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[]
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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@ -34,7 +36,8 @@ workflow test_gatk4_haplotypecaller_intervals_dbsnp {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
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file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
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[]
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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@ -45,3 +48,20 @@ workflow test_gatk4_haplotypecaller_intervals_dbsnp {
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GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict, sites, sites_tbi )
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}
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workflow test_gatk4_haplotypecaller_dragstr_model {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
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[],
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_dragstrmodel'], checkIfExists: true)
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
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sites = []
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sites_tbi = []
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GATK4_HAPLOTYPECALLER ( input, fasta, fai, dict, sites, sites_tbi )
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}
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@ -6,7 +6,6 @@
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files:
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- path: output/gatk4/test.vcf.gz
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- path: output/gatk4/test.vcf.gz.tbi
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- path: output/gatk4/versions.yml
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- name: gatk4 haplotypecaller test_gatk4_haplotypecaller_cram
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command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_cram -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
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@ -16,7 +15,6 @@
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files:
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- path: output/gatk4/test.vcf.gz
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- path: output/gatk4/test.vcf.gz.tbi
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- path: output/gatk4/versions.yml
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- name: gatk4 haplotypecaller test_gatk4_haplotypecaller_intervals_dbsnp
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command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_intervals_dbsnp -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
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@ -26,4 +24,12 @@
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files:
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- path: output/gatk4/test.vcf.gz
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- path: output/gatk4/test.vcf.gz.tbi
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- path: output/gatk4/versions.yml
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- name: gatk4 haplotypecaller test_gatk4_haplotypecaller_dragstr_model
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command: nextflow run ./tests/modules/gatk4/haplotypecaller -entry test_gatk4_haplotypecaller_dragstr_model -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/haplotypecaller/nextflow.config
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tags:
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- gatk4/haplotypecaller
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- gatk4
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files:
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- path: output/gatk4/test.vcf.gz
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- path: output/gatk4/test.vcf.gz.tbi
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