mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
Merge branch 'master' into new-module-gatk4/CalibrateDragstrModel
This commit is contained in:
nvnieuwk
GitHub
commit
4b430e8ece
5 changed files with 293 additions and 63 deletions
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@ -10,6 +10,7 @@ process CNVKIT_BATCH {
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input:
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tuple val(meta), path(tumor), path(normal)
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path fasta
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path fasta_fai
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path targets
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path reference
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@ -28,35 +29,69 @@ 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" : "${tumor}"
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def tumor_exists = tumor ? true : false
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def normal_exists = normal ? true : false
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// execute samtools only when cram files are input, cnvkit runs natively on bam but is prohibitively slow
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def tumor_cram = tumor_exists && tumor.Extension == "cram" ? true : false
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def normal_cram = normal_exists && normal.Extension == "cram" ? true : false
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def tumor_bam = tumor_exists && tumor.Extension == "bam" ? true : false
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def normal_bam = normal_exists && normal.Extension == "bam" ? true : false
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def tumor_out = tumor_cram ? tumor.BaseName + ".bam" : "${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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def fai_reference = fasta_fai ? "--fai-reference ${fasta_fai}" : ""
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if (normal_exists){
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def normal_prefix = normal.BaseName
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normal_out = is_cram ? "${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_prefix}" + ".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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// somatic_mode cram_input
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if (tumor_cram && normal_cram){
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"""
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if $is_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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samtools view -T $fasta $fai_reference $tumor -@ $task.cpus -o $tumor_out
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samtools view -T $fasta $fai_reference $normal -@ $task.cpus -o $normal_out
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cnvkit.py \\
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batch \\
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$tumor_out \\
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$normal_args \\
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$fasta_args \\
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$reference_args \\
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$target_args \\
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--processes $task.cpus \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
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END_VERSIONS
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"""
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}
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// somatic_mode bam_input
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else if (tumor_bam && normal_bam){
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"""
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cnvkit.py \\
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batch \\
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$tumor_out \\
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@ -72,4 +107,89 @@ process CNVKIT_BATCH {
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cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
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END_VERSIONS
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"""
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}
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// tumor_only_mode cram_input
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else if(tumor_cram && !normal_exists){
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"""
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samtools view -T $fasta $fai_reference $tumor -@ $task.cpus -o $tumor_out
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cnvkit.py \\
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batch \\
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$tumor_out \\
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$normal_args \\
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$fasta_args \\
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$reference_args \\
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$target_args \\
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--processes $task.cpus \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
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END_VERSIONS
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"""
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}
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// tumor_only bam_input
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else if(tumor_bam && !normal_exists){
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"""
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cnvkit.py \\
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batch \\
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$tumor_out \\
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$normal_args \\
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$fasta_args \\
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$reference_args \\
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$target_args \\
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--processes $task.cpus \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
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END_VERSIONS
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"""
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}
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// germline mode cram_input
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// normal_args must be --normal []
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else if (normal_cram && !tumor_exists){
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"""
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samtools view -T $fasta $fai_reference $normal -@ $task.cpus -o $tumor_out
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cnvkit.py \\
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batch \\
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$tumor_out \\
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$normal_args \\
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$fasta_args \\
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$reference_args \\
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$target_args \\
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--processes $task.cpus \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
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END_VERSIONS
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"""
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}
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// germline mode bam_input
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else if (normal_bam && !tumor_exists){
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"""
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cnvkit.py \\
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batch \\
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$tumor_out \\
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$normal_args \\
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$fasta_args \\
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$reference_args \\
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$target_args \\
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--processes $task.cpus \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g")
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END_VERSIONS
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"""
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}
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}
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@ -29,6 +29,10 @@ input:
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type: file
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description: |
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Input reference genome fasta file (only needed for cram_input and/or when normal_samples are provided)
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- fasta_fai:
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type: file
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description: |
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Input reference genome fasta index (optional, but recommended for cram_input)
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- targetfile:
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type: file
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description: |
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@ -23,6 +23,8 @@ params {
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test_bed12 = "${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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@ -147,6 +149,7 @@ 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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@ -416,9 +419,6 @@ 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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@ -5,8 +5,9 @@ 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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workflow test_cnvkit_hybrid_somatic {
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input = [
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[ id:'test' ], // meta map
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@ -16,10 +17,10 @@ workflow test_cnvkit_hybrid {
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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targets = file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true)
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CNVKIT_HYBRID ( input, fasta, targets, [] )
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CNVKIT_HYBRID ( input, fasta, [], targets, [] )
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}
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workflow test_cnvkit_wgs {
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workflow test_cnvkit_wgs_somatic {
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input = [
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[ id:'test'], // meta map
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@ -28,10 +29,10 @@ workflow test_cnvkit_wgs {
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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CNVKIT_WGS ( input, fasta, [], [] )
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CNVKIT_WGS ( input, fasta, [], [], [] )
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}
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workflow test_cnvkit_cram {
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workflow test_cnvkit_cram_wgs_somatic {
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input = [
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[ id:'test'], // meta map
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@ -39,31 +40,60 @@ workflow test_cnvkit_cram {
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], 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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fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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CNVKIT_WGS ( input, fasta, [], [] )
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CNVKIT_WGS ( input, fasta, fasta_fai, [], [] )
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}
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workflow test_cnvkit_tumoronly {
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workflow test_cnvkit_tumoronly_hybrid_bam {
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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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CNVKIT_TUMORONLY ( input, [], [], [], reference )
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}
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workflow test_cnvkit_tumoronly_cram {
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workflow test_cnvkit_tumoronly_hybrid_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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CNVKIT_TUMORONLY ( input, fasta, [], [], reference )
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}
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workflow test_cnvkit_germline_hybrid_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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fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], 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, fasta_fai, targets, [])
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}
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workflow test_cnvkit_germline_hybrid_bam {
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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_bam'], 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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|
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CNVKIT_GERMLINE ( input, fasta, [], targets, [])
|
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}
|
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|
|
|
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|
|
@ -1,5 +1,5 @@
|
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- name: cnvkit batch test_cnvkit_hybrid
|
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command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_hybrid -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
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- name: cnvkit batch test_cnvkit_hybrid_somatic
|
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command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_hybrid_somatic -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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|
|
@ -26,8 +26,8 @@
|
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- path: output/cnvkit/test.single_end.sorted.targetcoverage.cnn
|
||||
md5sum: aa8a018b1d4d1e688c9f9f6ae01bf4d7
|
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|
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- name: cnvkit batch test_cnvkit_wgs
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command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_wgs -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
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- name: cnvkit batch test_cnvkit_wgs_somatic
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command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_wgs_somatic -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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|
|
@ -56,8 +56,8 @@
|
|||
- path: output/cnvkit/test2.paired_end.sorted.targetcoverage.cnn
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||||
md5sum: 6ae6b3fce7299eedca6133d911c38fe1
|
||||
|
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- name: cnvkit batch test_cnvkit_cram
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command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_cram -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
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- name: cnvkit batch test_cnvkit_cram_wgs_somatic
|
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command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_cram_wgs_somatic -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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|
|
@ -86,22 +86,98 @@
|
|||
- path: output/cnvkit/test2.paired_end.sorted.targetcoverage.cnn
|
||||
md5sum: 6ae6b3fce7299eedca6133d911c38fe1
|
||||
|
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- name: cnvkit batch test_cnvkit_tumoronly
|
||||
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
|
||||
- name: cnvkit batch test_cnvkit_tumoronly_hybrid_bam
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command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly_hybrid_bam -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
|
||||
tags:
|
||||
- cnvkit
|
||||
- cnvkit/batch
|
||||
files:
|
||||
- path: output/cnvkit/reference.antitarget-tmp.bed
|
||||
- path: output/cnvkit/reference.target-tmp.bed
|
||||
md5sum: 26d25ff2d6c45b6d92169b3559c6acdb
|
||||
- path: output/cnvkit/reference_chr21.antitarget-tmp.bed
|
||||
md5sum: 3d4d20f9f23b39970865d29ef239d20b
|
||||
- path: output/cnvkit/reference_chr21.target-tmp.bed
|
||||
md5sum: 657b25dbda8516624efa8cb2cf3716ca
|
||||
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
|
||||
md5sum: 067115082c4af4b64d58c0dc3a3642e4
|
||||
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
|
||||
md5sum: f6adc75a0a86b7a921eca1b79a394cb0
|
||||
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
|
||||
md5sum: f7caeca04aba28b125ce26b511f42afb
|
||||
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
|
||||
md5sum: d9bdb71ce807051369577ee7f807a40c
|
||||
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
|
||||
md5sum: 2b56aac606ba6183d018b30ca58afcec
|
||||
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
|
||||
md5sum: e6d0190c1c37ce6e41f76ca5b24ccca3
|
||||
|
||||
- name: cnvkit batch test_cnvkit_tumoronly_cram
|
||||
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly_cram -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
|
||||
- name: cnvkit batch test_cnvkit_tumoronly_hybrid_cram
|
||||
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_tumoronly_hybrid_cram -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
|
||||
tags:
|
||||
- cnvkit
|
||||
- cnvkit/batch
|
||||
files:
|
||||
- path: output/cnvkit/reference.antitarget-tmp.bed
|
||||
- path: output/cnvkit/reference.target-tmp.bed
|
||||
md5sum: 26d25ff2d6c45b6d92169b3559c6acdb
|
||||
- path: output/cnvkit/reference_chr21.antitarget-tmp.bed
|
||||
md5sum: 3d4d20f9f23b39970865d29ef239d20b
|
||||
- path: output/cnvkit/reference_chr21.target-tmp.bed
|
||||
md5sum: 657b25dbda8516624efa8cb2cf3716ca
|
||||
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
|
||||
md5sum: 067115082c4af4b64d58c0dc3a3642e4
|
||||
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
|
||||
md5sum: f6adc75a0a86b7a921eca1b79a394cb0
|
||||
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
|
||||
md5sum: f7caeca04aba28b125ce26b511f42afb
|
||||
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
|
||||
md5sum: d9bdb71ce807051369577ee7f807a40c
|
||||
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
|
||||
md5sum: 2b56aac606ba6183d018b30ca58afcec
|
||||
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
|
||||
md5sum: e6d0190c1c37ce6e41f76ca5b24ccca3
|
||||
|
||||
- name: cnvkit batch test_cnvkit_germline_hybrid_cram
|
||||
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_germline_hybrid_cram -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
|
||||
tags:
|
||||
- cnvkit
|
||||
- cnvkit/batch
|
||||
files:
|
||||
- path: output/cnvkit/multi_intervals.antitarget.bed
|
||||
md5sum: 3d4d20f9f23b39970865d29ef239d20b
|
||||
- path: output/cnvkit/multi_intervals.target.bed
|
||||
md5sum: 86d30493bb2e619a93f4ebc2923d29f3
|
||||
- path: output/cnvkit/reference.cnn
|
||||
md5sum: a09ee4be5dda1cf0f68073bdb3aad8ec
|
||||
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
|
||||
md5sum: 067115082c4af4b64d58c0dc3a3642e4
|
||||
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
|
||||
md5sum: 68b62b75cd91b2ffe5633686fb943490
|
||||
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
|
||||
md5sum: df196edd72613c59186f4d87df3dc4a4
|
||||
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
|
||||
md5sum: 3b4fc0cc73be78f978cfe2422470753e
|
||||
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
|
||||
md5sum: 4e67451dbcb6601fc3fa5dd7e570f1d4
|
||||
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
|
||||
md5sum: b4a49faf170e436ec32dcc21ccc3ce8f
|
||||
|
||||
- name: cnvkit batch test_cnvkit_germline_hybrid_bam
|
||||
command: nextflow run ./tests/modules/cnvkit/batch -entry test_cnvkit_germline_hybrid_bam -c ./tests/config/nextflow.config -c ./tests/modules/cnvkit/batch/nextflow.config
|
||||
tags:
|
||||
- cnvkit
|
||||
- cnvkit/batch
|
||||
files:
|
||||
- path: output/cnvkit/multi_intervals.antitarget.bed
|
||||
md5sum: 3d4d20f9f23b39970865d29ef239d20b
|
||||
- path: output/cnvkit/multi_intervals.target.bed
|
||||
md5sum: 86d30493bb2e619a93f4ebc2923d29f3
|
||||
- path: output/cnvkit/reference.cnn
|
||||
md5sum: a09ee4be5dda1cf0f68073bdb3aad8ec
|
||||
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn
|
||||
md5sum: 067115082c4af4b64d58c0dc3a3642e4
|
||||
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.bintest.cns
|
||||
md5sum: 68b62b75cd91b2ffe5633686fb943490
|
||||
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.call.cns
|
||||
md5sum: df196edd72613c59186f4d87df3dc4a4
|
||||
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.cnr
|
||||
md5sum: 3b4fc0cc73be78f978cfe2422470753e
|
||||
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.cns
|
||||
md5sum: 4e67451dbcb6601fc3fa5dd7e570f1d4
|
||||
- path: output/cnvkit/test2.paired_end.recalibrated.sorted.targetcoverage.cnn
|
||||
md5sum: b4a49faf170e436ec32dcc21ccc3ce8f
|
||||
|
|
|
|||
Loading…
Reference in a new issue