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https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 02:58:17 +00:00
adjust cnvkit/batch for germline mode
This commit is contained in:
SusiJo
parent
0708f343de
commit
f6953b5147
4 changed files with 104 additions and 25 deletions
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@ -28,34 +28,48 @@ process CNVKIT_BATCH {
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script:
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def args = task.ext.args ?: ''
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// execute samtools only when cram files are input, cnvkit runs natively on bam but is prohibitively slow
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// input pair is assumed to have same extension if both exist
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def is_cram = tumor.Extension == "cram" ? true : false
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def tumor_out = is_cram ? tumor.BaseName + ".bam" : "${tumor}"
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def tumor_exists = tumor ? true : false
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def normal_exists = normal ? true : false
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// execute samtools only when cram files are input, cnvkit runs natively on bam but is prohibitively slow
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def tumor_cram = tumor_exists && tumor.Extension == "cram" ? true : false
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def normal_cram = normal_exists && normal.Extension == "cram" ? true : false
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def tumor_out = tumor_cram ? tumor.BaseName + ".bam" : "${tumor}"
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// do not run samtools on normal samples in tumor_only mode
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def normal_exists = normal ? true: false
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// tumor_only mode does not need fasta & target
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// instead it requires a pre-computed reference.cnn which is built from fasta & target
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def (normal_out, normal_args, fasta_args) = ["", "", ""]
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if (normal_exists){
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def normal_prefix = normal.BaseName
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normal_out = is_cram ? "${normal_prefix}" + ".bam" : "${normal}"
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normal_args = normal_prefix ? "--normal $normal_out" : ""
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normal_out = normal_cram ? "${normal_prefix}" + ".bam" : "${normal}"
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fasta_args = fasta ? "--fasta $fasta" : ""
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// germline mode
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// normal samples must be input without a flag
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// requires flag --normal to be empty
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if(!tumor_exists){
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tumor_out = normal.BaseName + ".bam"
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normal_args = "--normal "
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}
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// somatic mode
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else {
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normal_args = normal_prefix ? "--normal $normal_out" : ""
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}
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}
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def target_args = targets ? "--targets $targets" : ""
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def reference_args = reference ? "--reference $reference" : ""
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"""
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if $is_cram; then
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if $tumor_cram; then
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samtools view -T $fasta $tumor -@ $task.cpus -o $tumor_out
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if $normal_exists; then
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samtools view -T $fasta $normal -@ $task.cpus -o $normal_out
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fi
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fi
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if $normal_cram; then
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samtools view -T $fasta $normal -@ $task.cpus -o $normal_out
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fi
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cnvkit.py \\
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batch \\
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@ -23,6 +23,8 @@ params {
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test_bed12 = "${test_data_dir}/genomics/sarscov2/genome/bed/test.bed12"
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baits_bed = "${test_data_dir}/genomics/sarscov2/genome/bed/baits.bed"
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reference_cnn = "${test_data_dir}/genomics/sarscov2/genome/cnn/reference.cnn"
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kraken2 = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2"
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kraken2_tar_gz = "${test_data_dir}/genomics/sarscov2/genome/db/kraken2.tar.gz"
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@ -145,6 +147,7 @@ params {
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genome_21_multi_interval_bed_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz"
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genome_21_multi_interval_bed_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz.tbi"
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genome_21_chromosomes_dir = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz"
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genome_21_reference_cnn = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/reference_chr21.cnn"
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dbsnp_146_hg38_elsites = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.elsites"
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dbsnp_146_hg38_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz"
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@ -414,9 +417,6 @@ params {
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'txt' {
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hello = "${test_data_dir}/generic/txt/hello.txt"
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}
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'cnn' {
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reference = "${test_data_dir}/generic/cnn/reference.cnn"
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}
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'cooler'{
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test_pairix_pair_gz = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz"
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test_pairix_pair_gz_px2 = "${test_data_dir}/genomics/homo_sapiens/cooler/cload/hg19/hg19.GM12878-MboI.pairs.subsample.blksrt.txt.gz.px2"
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@ -5,6 +5,7 @@ nextflow.enable.dsl = 2
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include { CNVKIT_BATCH as CNVKIT_HYBRID } from '../../../../modules/cnvkit/batch/main.nf'
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include { CNVKIT_BATCH as CNVKIT_WGS } from '../../../../modules/cnvkit/batch/main.nf'
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include { CNVKIT_BATCH as CNVKIT_TUMORONLY } from '../../../../modules/cnvkit/batch/main.nf'
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include { CNVKIT_BATCH as CNVKIT_GERMLINE } from '../../../../modules/cnvkit/batch/main.nf'
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workflow test_cnvkit_hybrid {
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@ -47,10 +48,10 @@ workflow test_cnvkit_tumoronly {
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input = [
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[ id:'test'], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true),
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[]
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]
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reference = file(params.test_data['generic']['cnn']['reference'], checkIfExists: true)
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reference = file(params.test_data['homo_sapiens']['genome']['genome_21_reference_cnn'], checkIfExists: true)
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CNVKIT_TUMORONLY ( input, [], [], reference )
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}
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@ -59,11 +60,24 @@ workflow test_cnvkit_tumoronly_cram {
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input = [
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[ id:'test'], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], 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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reference = file(params.test_data['generic']['cnn']['reference'], checkIfExists: true)
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reference = file(params.test_data['homo_sapiens']['genome']['genome_21_reference_cnn'], checkIfExists: true)
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CNVKIT_TUMORONLY ( input, fasta, [], reference )
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}
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workflow test_cnvkit_germline_cram {
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input = [
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[ id:'test'], // meta map
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[],
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file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true)
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
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targets = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
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CNVKIT_GERMLINE ( input, fasta, targets, [])
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}
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@ -92,9 +92,22 @@
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- cnvkit
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- cnvkit/batch
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files:
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- path: output/cnvkit/reference.antitarget-tmp.bed
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- path: output/cnvkit/reference.target-tmp.bed
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md5sum: 26d25ff2d6c45b6d92169b3559c6acdb
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- path: output/cnvkit/reference_chr21.antitarget-tmp.bed
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md5sum: 3d4d20f9f23b39970865d29ef239d20b
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- path: output/cnvkit/reference_chr21.target-tmp.bed
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md5sum: 657b25dbda8516624efa8cb2cf3716ca
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- path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
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md5sum: 067115082c4af4b64d58c0dc3a3642e4
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- path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
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md5sum: f6adc75a0a86b7a921eca1b79a394cb0
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- path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
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md5sum: f7caeca04aba28b125ce26b511f42afb
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- path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
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md5sum: d9bdb71ce807051369577ee7f807a40c
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- path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
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md5sum: 2b56aac606ba6183d018b30ca58afcec
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- path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
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md5sum: e6d0190c1c37ce6e41f76ca5b24ccca3
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- name: cnvkit batch test_cnvkit_tumoronly_cram
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command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly_cram -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
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@ -102,6 +115,44 @@
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- cnvkit
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- cnvkit/batch
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files:
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- path: output/cnvkit/reference.antitarget-tmp.bed
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- path: output/cnvkit/reference.target-tmp.bed
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md5sum: 26d25ff2d6c45b6d92169b3559c6acdb
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- path: output/cnvkit/reference_chr21.antitarget-tmp.bed
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md5sum: 3d4d20f9f23b39970865d29ef239d20b
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- path: output/cnvkit/reference_chr21.target-tmp.bed
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md5sum: 657b25dbda8516624efa8cb2cf3716ca
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- path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
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md5sum: 067115082c4af4b64d58c0dc3a3642e4
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- path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
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md5sum: f6adc75a0a86b7a921eca1b79a394cb0
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- path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
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md5sum: f7caeca04aba28b125ce26b511f42afb
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- path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
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md5sum: d9bdb71ce807051369577ee7f807a40c
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- path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
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md5sum: 2b56aac606ba6183d018b30ca58afcec
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- path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
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md5sum: e6d0190c1c37ce6e41f76ca5b24ccca3
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- name: cnvkit batch test_cnvkit_germline_cram
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command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_germline_cram -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
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tags:
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- cnvkit
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- cnvkit/batch
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files:
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- path: output/cnvkit/multi_intervals.antitarget.bed
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md5sum: 3d4d20f9f23b39970865d29ef239d20b
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- path: output/cnvkit/multi_intervals.target.bed
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md5sum: 86d30493bb2e619a93f4ebc2923d29f3
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- path: output/cnvkit/reference.cnn
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md5sum: a09ee4be5dda1cf0f68073bdb3aad8ec
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- path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
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md5sum: 067115082c4af4b64d58c0dc3a3642e4
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- path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
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md5sum: 68b62b75cd91b2ffe5633686fb943490
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- path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
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md5sum: df196edd72613c59186f4d87df3dc4a4
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- path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
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md5sum: 3b4fc0cc73be78f978cfe2422470753e
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- path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
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md5sum: 4e67451dbcb6601fc3fa5dd7e570f1d4
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- path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
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md5sum: b4a49faf170e436ec32dcc21ccc3ce8f
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