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nf-core / sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
https://nf-co.re/sarek
MIT License
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Output files are getting overwritten when sample ids are not unique #1393

Open famosab opened 5 months ago

famosab commented 5 months ago

Description of the bug

When the "sampleID" in the samplesheet is not unique, only the output files for the final patient are kept. For example the following samplesheet would only keep the outout of the patient called 10perc.

patient,status,sample,lane,bam
5perc,0,normal,lane_1,imgag-benchmark/NA12877_21.bam
5perc,1,tumor,lane_1,imgag-benchmark/NA12878x3_23_NA12877_21_5.bam
10perc,0,normal,lane_1,imgag-benchmark/NA12877_21.bam
10perc,1,tumor,lane_1,imgag-benchmark/NA12878x3_23_NA12877_21_10.bam

When the samplesheet is altered, all output is kept:

patient,status,sample,lane,bam
5perc,0,normal_5perc,lane_1,imgag-benchmark/NA12877_21.bam
5perc,1,tumor_5perc,lane_1,imgag-benchmark/NA12878x3_23_NA12877_21_5.bam
10perc,0,normal_10perc,lane_1,imgag-benchmark/NA12877_21.bam
10perc,1,tumor_10perc,lane_1,imgag-benchmark/NA12878x3_23_NA12877_21_10.bam

The sarek runs throws no errors just the files are missing in the end.

Command used and terminal output

nextflow run nf-core/sarek -r 3.4.0 -profile cfc -work-dir work-bm -params-file params.json

Relevant files

params.json:

{
    "input": "/sfs/9/ws/paifb01-pm4onco/imgag-benchmark/benchmark_samplesheet.csv",
    "outdir": "/sfs/9/ws/paifb01-pm4onco/imgag-benchmark/results",
    "tools": "mutect2,strelka,manta,vep",
    "save_output_as_bam": true,
    "only_paired_variant_calling": true,
    "email": "famke.baeuerle@qbic.uni-tuebingen.de"
}

System information

asp8200 commented 5 months ago

Thanks for reporting this, @famosab. I feel like this situation should have been covered by plugin nf-validation. The version of nf-validation is not fixed in Sarek v3.4 (it will be in future versions). Which version of nf-validation was used in your run of Sarek?

FriederikeHanssen commented 5 months ago

I think it is the fact we only check for uniqueness with lane https://github.com/nf-core/sarek/blob/6aeac929c924ba382baa42a0fe969b4e0e753ca9/assets/schema_input.json#L48 but not individually.

asp8200 commented 5 months ago

I think it is the fact we only check for uniqueness with lane

https://github.com/nf-core/sarek/blob/6aeac929c924ba382baa42a0fe969b4e0e753ca9/assets/schema_input.json#L48

but not individually.

You reckon that we should also require that the sample is unique?

FriederikeHanssen commented 5 months ago

no, because you can have the same sample split over multiple lanes. I think we need to prevent overwriting. I suspect it is overwritten on the mapping level @famosab? Can you send treeof the offending output?

famosab commented 5 months ago

Here is the complete tree with all folders: tree.txt

And here is the part without the work folder:

.
|-- params.json
|-- results
|   |-- annotation
|   |   |-- manta
|   |   |   `-- tumor_vs_normal
|   |   |       |-- tumor_vs_normal.manta.diploid_sv_VEP.ann.vcf.gz
|   |   |       |-- tumor_vs_normal.manta.diploid_sv_VEP.ann.vcf.gz.tbi
|   |   |       |-- tumor_vs_normal.manta.somatic_sv_VEP.ann.vcf.gz
|   |   |       `-- tumor_vs_normal.manta.somatic_sv_VEP.ann.vcf.gz.tbi
|   |   |-- mutect2
|   |   |   `-- tumor_vs_normal
|   |   |       |-- tumor_vs_normal.mutect2.filtered_VEP.ann.vcf.gz
|   |   |       `-- tumor_vs_normal.mutect2.filtered_VEP.ann.vcf.gz.tbi
|   |   `-- strelka
|   |       `-- tumor_vs_normal
|   |           |-- tumor_vs_normal.strelka.somatic_indels_VEP.ann.vcf.gz
|   |           |-- tumor_vs_normal.strelka.somatic_indels_VEP.ann.vcf.gz.tbi
|   |           |-- tumor_vs_normal.strelka.somatic_snvs_VEP.ann.vcf.gz
|   |           `-- tumor_vs_normal.strelka.somatic_snvs_VEP.ann.vcf.gz.tbi
|   |-- csv
|   |   |-- markduplicates.csv
|   |   |-- markduplicates_no_table.csv
|   |   |-- recalibrated.csv
|   |   `-- variantcalled.csv
|   |-- multiqc
|   |   |-- multiqc_data
|   |   |   |-- gatk_base_recalibrator.txt
|   |   |   |-- mosdepth_cov_dist.txt
|   |   |   |-- mosdepth_cumcov_dist.txt
|   |   |   |-- mosdepth_perchrom.txt
|   |   |   |-- mqc_bcftools_stats_depth_1.txt
|   |   |   |-- mqc_bcftools_stats_indel-lengths_1.txt
|   |   |   |-- mqc_bcftools-stats-subtypes_1.txt
|   |   |   |-- mqc_bcftools_stats_vqc_Count_Indels.txt
|   |   |   |-- mqc_bcftools_stats_vqc_Count_SNP.txt
|   |   |   |-- mqc_bcftools_stats_vqc_Count_Transitions.txt
|   |   |   |-- mqc_bcftools_stats_vqc_Count_Transversions.txt
|   |   |   |-- mqc_consequences_all__plot_Coding_consequences.txt
|   |   |   |-- mqc_consequences_all__plot_Consequences_all_.txt
|   |   |   |-- mqc_consequences_all__plot_Consequences_most_severe_.txt
|   |   |   |-- mqc_fastqc_adapter_content_plot_1.txt
|   |   |   |-- mqc_fastqc_per_base_n_content_plot_1.txt
|   |   |   |-- mqc_fastqc_per_base_sequence_quality_plot_1.txt
|   |   |   |-- mqc_fastqc_per_sequence_gc_content_plot_Counts.txt
|   |   |   |-- mqc_fastqc_per_sequence_gc_content_plot_Percentages.txt
|   |   |   |-- mqc_fastqc_per_sequence_quality_scores_plot_1.txt
|   |   |   |-- mqc_fastqc_sequence_counts_plot_1.txt
|   |   |   |-- mqc_fastqc_sequence_duplication_levels_plot_1.txt
|   |   |   |-- mqc_fastqc_sequence_length_distribution_plot_1.txt
|   |   |   |-- mqc_gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt
|   |   |   |-- mqc_gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.txt
|   |   |   |-- mqc_mosdepth-coverage-dist-id_1.txt
|   |   |   |-- mqc_mosdepth-coverage-per-contig_1.txt
|   |   |   |-- mqc_mosdepth-cumcoverage-dist-id_1.txt
|   |   |   |-- mqc_mosdepth-xy-coverage-plot_1.txt
|   |   |   |-- mqc_picard_deduplication_1.txt
|   |   |   |-- mqc_polyphen_summary_plot_1.txt
|   |   |   |-- mqc_position_in_protein_plot_1.txt
|   |   |   |-- mqc_samtools_alignment_plot_1.txt
|   |   |   |-- mqc_sift_summary_plot_1.txt
|   |   |   |-- mqc_variant_classes_plot_1.txt
|   |   |   |-- mqc_variants_by_chromosome_plot_1.txt
|   |   |   |-- mqc_vcftools_tstv_by_count_1.txt
|   |   |   |-- mqc_vcftools_tstv_by_qual_1.yaml
|   |   |   |-- multiqc_bcftools_stats.txt
|   |   |   |-- multiqc_citations.txt
|   |   |   |-- multiqc_data.json
|   |   |   |-- multiqc_fastqc.txt
|   |   |   |-- multiqc_general_stats.txt
|   |   |   |-- multiqc.log
|   |   |   |-- multiqc_picard_dups.txt
|   |   |   |-- multiqc_samtools_stats.txt
|   |   |   |-- multiqc_software_versions.txt
|   |   |   |-- multiqc_sources.txt
|   |   |   |-- picard_histogram_1.txt
|   |   |   |-- picard_histogram_2.txt
|   |   |   |-- picard_histogram.txt
|   |   |   |-- vcftools_tstv_by_count.txt
|   |   |   |-- vcftools_tstv_by_qual.yaml
|   |   |   `-- vep.txt
|   |   |-- multiqc_plots
|   |   |   |-- pdf
|   |   |   |   |-- mqc_bcftools_stats_depth_1.pdf
|   |   |   |   |-- mqc_bcftools_stats_indel-lengths_1.pdf
|   |   |   |   |-- mqc_bcftools-stats-subtypes_1_pc.pdf
|   |   |   |   |-- mqc_bcftools-stats-subtypes_1.pdf
|   |   |   |   |-- mqc_bcftools_stats_vqc_Count_Indels.pdf
|   |   |   |   |-- mqc_bcftools_stats_vqc_Count_SNP.pdf
|   |   |   |   |-- mqc_bcftools_stats_vqc_Count_Transitions.pdf
|   |   |   |   |-- mqc_bcftools_stats_vqc_Count_Transversions.pdf
|   |   |   |   |-- mqc_consequences_all__plot_Coding_consequences_pc.pdf
|   |   |   |   |-- mqc_consequences_all__plot_Coding_consequences.pdf
|   |   |   |   |-- mqc_consequences_all__plot_Consequences_all__pc.pdf
|   |   |   |   |-- mqc_consequences_all__plot_Consequences_all_.pdf
|   |   |   |   |-- mqc_consequences_all__plot_Consequences_most_severe__pc.pdf
|   |   |   |   |-- mqc_consequences_all__plot_Consequences_most_severe_.pdf
|   |   |   |   |-- mqc_fastqc_adapter_content_plot_1.pdf
|   |   |   |   |-- mqc_fastqc_per_base_n_content_plot_1.pdf
|   |   |   |   |-- mqc_fastqc_per_base_sequence_quality_plot_1.pdf
|   |   |   |   |-- mqc_fastqc_per_sequence_gc_content_plot_Counts.pdf
|   |   |   |   |-- mqc_fastqc_per_sequence_gc_content_plot_Percentages.pdf
|   |   |   |   |-- mqc_fastqc_per_sequence_quality_scores_plot_1.pdf
|   |   |   |   |-- mqc_fastqc_sequence_counts_plot_1_pc.pdf
|   |   |   |   |-- mqc_fastqc_sequence_counts_plot_1.pdf
|   |   |   |   |-- mqc_fastqc_sequence_duplication_levels_plot_1.pdf
|   |   |   |   |-- mqc_fastqc_sequence_length_distribution_plot_1.pdf
|   |   |   |   |-- mqc_gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.pdf
|   |   |   |   |-- mqc_gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.pdf
|   |   |   |   |-- mqc_mosdepth-coverage-dist-id_1.pdf
|   |   |   |   |-- mqc_mosdepth-coverage-per-contig_1.pdf
|   |   |   |   |-- mqc_mosdepth-cumcoverage-dist-id_1.pdf
|   |   |   |   |-- mqc_mosdepth-xy-coverage-plot_1_pc.pdf
|   |   |   |   |-- mqc_mosdepth-xy-coverage-plot_1.pdf
|   |   |   |   |-- mqc_picard_deduplication_1_pc.pdf
|   |   |   |   |-- mqc_picard_deduplication_1.pdf
|   |   |   |   |-- mqc_polyphen_summary_plot_1_pc.pdf
|   |   |   |   |-- mqc_polyphen_summary_plot_1.pdf
|   |   |   |   |-- mqc_position_in_protein_plot_1_pc.pdf
|   |   |   |   |-- mqc_position_in_protein_plot_1.pdf
|   |   |   |   |-- mqc_samtools_alignment_plot_1_pc.pdf
|   |   |   |   |-- mqc_samtools_alignment_plot_1.pdf
|   |   |   |   |-- mqc_sift_summary_plot_1_pc.pdf
|   |   |   |   |-- mqc_sift_summary_plot_1.pdf
|   |   |   |   |-- mqc_variant_classes_plot_1_pc.pdf
|   |   |   |   |-- mqc_variant_classes_plot_1.pdf
|   |   |   |   |-- mqc_variants_by_chromosome_plot_1_pc.pdf
|   |   |   |   |-- mqc_variants_by_chromosome_plot_1.pdf
|   |   |   |   |-- mqc_vcftools_tstv_by_count_1.pdf
|   |   |   |   `-- mqc_vcftools_tstv_by_qual_1.pdf
|   |   |   |-- png
|   |   |   |   |-- mqc_bcftools_stats_depth_1.png
|   |   |   |   |-- mqc_bcftools_stats_indel-lengths_1.png
|   |   |   |   |-- mqc_bcftools-stats-subtypes_1_pc.png
|   |   |   |   |-- mqc_bcftools-stats-subtypes_1.png
|   |   |   |   |-- mqc_bcftools_stats_vqc_Count_Indels.png
|   |   |   |   |-- mqc_bcftools_stats_vqc_Count_SNP.png
|   |   |   |   |-- mqc_bcftools_stats_vqc_Count_Transitions.png
|   |   |   |   |-- mqc_bcftools_stats_vqc_Count_Transversions.png
|   |   |   |   |-- mqc_consequences_all__plot_Coding_consequences_pc.png
|   |   |   |   |-- mqc_consequences_all__plot_Coding_consequences.png
|   |   |   |   |-- mqc_consequences_all__plot_Consequences_all__pc.png
|   |   |   |   |-- mqc_consequences_all__plot_Consequences_all_.png
|   |   |   |   |-- mqc_consequences_all__plot_Consequences_most_severe__pc.png
|   |   |   |   |-- mqc_consequences_all__plot_Consequences_most_severe_.png
|   |   |   |   |-- mqc_fastqc_adapter_content_plot_1.png
|   |   |   |   |-- mqc_fastqc_per_base_n_content_plot_1.png
|   |   |   |   |-- mqc_fastqc_per_base_sequence_quality_plot_1.png
|   |   |   |   |-- mqc_fastqc_per_sequence_gc_content_plot_Counts.png
|   |   |   |   |-- mqc_fastqc_per_sequence_gc_content_plot_Percentages.png
|   |   |   |   |-- mqc_fastqc_per_sequence_quality_scores_plot_1.png
|   |   |   |   |-- mqc_fastqc_sequence_counts_plot_1_pc.png
|   |   |   |   |-- mqc_fastqc_sequence_counts_plot_1.png
|   |   |   |   |-- mqc_fastqc_sequence_duplication_levels_plot_1.png
|   |   |   |   |-- mqc_fastqc_sequence_length_distribution_plot_1.png
|   |   |   |   |-- mqc_gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.png
|   |   |   |   |-- mqc_gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.png
|   |   |   |   |-- mqc_mosdepth-coverage-dist-id_1.png
|   |   |   |   |-- mqc_mosdepth-coverage-per-contig_1.png
|   |   |   |   |-- mqc_mosdepth-cumcoverage-dist-id_1.png
|   |   |   |   |-- mqc_mosdepth-xy-coverage-plot_1_pc.png
|   |   |   |   |-- mqc_mosdepth-xy-coverage-plot_1.png
|   |   |   |   |-- mqc_picard_deduplication_1_pc.png
|   |   |   |   |-- mqc_picard_deduplication_1.png
|   |   |   |   |-- mqc_polyphen_summary_plot_1_pc.png
|   |   |   |   |-- mqc_polyphen_summary_plot_1.png
|   |   |   |   |-- mqc_position_in_protein_plot_1_pc.png
|   |   |   |   |-- mqc_position_in_protein_plot_1.png
|   |   |   |   |-- mqc_samtools_alignment_plot_1_pc.png
|   |   |   |   |-- mqc_samtools_alignment_plot_1.png
|   |   |   |   |-- mqc_sift_summary_plot_1_pc.png
|   |   |   |   |-- mqc_sift_summary_plot_1.png
|   |   |   |   |-- mqc_variant_classes_plot_1_pc.png
|   |   |   |   |-- mqc_variant_classes_plot_1.png
|   |   |   |   |-- mqc_variants_by_chromosome_plot_1_pc.png
|   |   |   |   |-- mqc_variants_by_chromosome_plot_1.png
|   |   |   |   |-- mqc_vcftools_tstv_by_count_1.png
|   |   |   |   `-- mqc_vcftools_tstv_by_qual_1.png
|   |   |   `-- svg
|   |   |       |-- mqc_bcftools_stats_depth_1.svg
|   |   |       |-- mqc_bcftools_stats_indel-lengths_1.svg
|   |   |       |-- mqc_bcftools-stats-subtypes_1_pc.svg
|   |   |       |-- mqc_bcftools-stats-subtypes_1.svg
|   |   |       |-- mqc_bcftools_stats_vqc_Count_Indels.svg
|   |   |       |-- mqc_bcftools_stats_vqc_Count_SNP.svg
|   |   |       |-- mqc_bcftools_stats_vqc_Count_Transitions.svg
|   |   |       |-- mqc_bcftools_stats_vqc_Count_Transversions.svg
|   |   |       |-- mqc_consequences_all__plot_Coding_consequences_pc.svg
|   |   |       |-- mqc_consequences_all__plot_Coding_consequences.svg
|   |   |       |-- mqc_consequences_all__plot_Consequences_all__pc.svg
|   |   |       |-- mqc_consequences_all__plot_Consequences_all_.svg
|   |   |       |-- mqc_consequences_all__plot_Consequences_most_severe__pc.svg
|   |   |       |-- mqc_consequences_all__plot_Consequences_most_severe_.svg
|   |   |       |-- mqc_fastqc_adapter_content_plot_1.svg
|   |   |       |-- mqc_fastqc_per_base_n_content_plot_1.svg
|   |   |       |-- mqc_fastqc_per_base_sequence_quality_plot_1.svg
|   |   |       |-- mqc_fastqc_per_sequence_gc_content_plot_Counts.svg
|   |   |       |-- mqc_fastqc_per_sequence_gc_content_plot_Percentages.svg
|   |   |       |-- mqc_fastqc_per_sequence_quality_scores_plot_1.svg
|   |   |       |-- mqc_fastqc_sequence_counts_plot_1_pc.svg
|   |   |       |-- mqc_fastqc_sequence_counts_plot_1.svg
|   |   |       |-- mqc_fastqc_sequence_duplication_levels_plot_1.svg
|   |   |       |-- mqc_fastqc_sequence_length_distribution_plot_1.svg
|   |   |       |-- mqc_gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.svg
|   |   |       |-- mqc_gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.svg
|   |   |       |-- mqc_mosdepth-coverage-dist-id_1.svg
|   |   |       |-- mqc_mosdepth-coverage-per-contig_1.svg
|   |   |       |-- mqc_mosdepth-cumcoverage-dist-id_1.svg
|   |   |       |-- mqc_mosdepth-xy-coverage-plot_1_pc.svg
|   |   |       |-- mqc_mosdepth-xy-coverage-plot_1.svg
|   |   |       |-- mqc_picard_deduplication_1_pc.svg
|   |   |       |-- mqc_picard_deduplication_1.svg
|   |   |       |-- mqc_polyphen_summary_plot_1_pc.svg
|   |   |       |-- mqc_polyphen_summary_plot_1.svg
|   |   |       |-- mqc_position_in_protein_plot_1_pc.svg
|   |   |       |-- mqc_position_in_protein_plot_1.svg
|   |   |       |-- mqc_samtools_alignment_plot_1_pc.svg
|   |   |       |-- mqc_samtools_alignment_plot_1.svg
|   |   |       |-- mqc_sift_summary_plot_1_pc.svg
|   |   |       |-- mqc_sift_summary_plot_1.svg
|   |   |       |-- mqc_variant_classes_plot_1_pc.svg
|   |   |       |-- mqc_variant_classes_plot_1.svg
|   |   |       |-- mqc_variants_by_chromosome_plot_1_pc.svg
|   |   |       |-- mqc_variants_by_chromosome_plot_1.svg
|   |   |       |-- mqc_vcftools_tstv_by_count_1.svg
|   |   |       `-- mqc_vcftools_tstv_by_qual_1.svg
|   |   `-- multiqc_report.html
|   |-- pipeline_info
|   |   |-- execution_report_2024-02-07_14-16-12.html
|   |   |-- execution_timeline_2024-02-07_14-16-12.html
|   |   |-- execution_trace_2024-02-07_14-16-12.txt
|   |   |-- manifest_2024-02-07_14-16-12.bco.json
|   |   |-- params_2024-02-07_16-08-40.json
|   |   |-- pipeline_dag_2024-02-07_14-16-12.html
|   |   |-- pipeline_report.html
|   |   |-- pipeline_report.txt
|   |   |-- software_versions_mqc.yml
|   |   `-- software_versions.yml
|   |-- preprocessing
|   |   |-- fastp
|   |   |   |-- normal
|   |   |   `-- tumor
|   |   |-- markduplicates
|   |   |   |-- normal
|   |   |   |   |-- normal.md.bam
|   |   |   |   `-- normal.md.bam.bai
|   |   |   `-- tumor
|   |   |       |-- tumor.md.bam
|   |   |       `-- tumor.md.bam.bai
|   |   |-- recalibrated
|   |   |   |-- normal
|   |   |   |   |-- normal.recal.bam
|   |   |   |   `-- normal.recal.bam.bai
|   |   |   `-- tumor
|   |   |       |-- tumor.recal.bam
|   |   |       `-- tumor.recal.bam.bai
|   |   `-- recal_table
|   |       |-- normal
|   |       |   `-- normal.recal.table
|   |       `-- tumor
|   |           `-- tumor.recal.table
|   |-- reference
|   |   `-- intervals
|   |-- reports
|   |   |-- bcftools
|   |   |   |-- manta
|   |   |   |   `-- tumor_vs_normal
|   |   |   |       |-- tumor_vs_normal.manta.diploid_sv.bcftools_stats.txt
|   |   |   |       `-- tumor_vs_normal.manta.somatic_sv.bcftools_stats.txt
|   |   |   |-- mutect2
|   |   |   |   `-- tumor_vs_normal
|   |   |   |       `-- tumor_vs_normal.mutect2.filtered.bcftools_stats.txt
|   |   |   `-- strelka
|   |   |       `-- tumor_vs_normal
|   |   |           |-- tumor_vs_normal.strelka.somatic_indels.bcftools_stats.txt
|   |   |           `-- tumor_vs_normal.strelka.somatic_snvs.bcftools_stats.txt
|   |   |-- EnsemblVEP
|   |   |   |-- manta
|   |   |   |   `-- tumor_vs_normal
|   |   |   |       |-- tumor_vs_normal.manta.diploid_sv_VEP.ann.summary.html
|   |   |   |       `-- tumor_vs_normal.manta.somatic_sv_VEP.ann.summary.html
|   |   |   |-- mutect2
|   |   |   |   `-- tumor_vs_normal
|   |   |   |       `-- tumor_vs_normal.mutect2.filtered_VEP.ann.summary.html
|   |   |   `-- strelka
|   |   |       `-- tumor_vs_normal
|   |   |           |-- tumor_vs_normal.strelka.somatic_indels_VEP.ann.summary.html
|   |   |           `-- tumor_vs_normal.strelka.somatic_snvs_VEP.ann.summary.html
|   |   |-- fastp
|   |   |   |-- normal
|   |   |   |   |-- normal-lane_1.fastp.html
|   |   |   |   |-- normal-lane_1.fastp.json
|   |   |   |   `-- normal-lane_1.fastp.log
|   |   |   `-- tumor
|   |   |       |-- tumor-lane_1.fastp.html
|   |   |       |-- tumor-lane_1.fastp.json
|   |   |       `-- tumor-lane_1.fastp.log
|   |   |-- fastqc
|   |   |   |-- normal-lane_1
|   |   |   |   |-- normal-lane_1_1_fastqc.html
|   |   |   |   |-- normal-lane_1_1_fastqc.zip
|   |   |   |   |-- normal-lane_1_2_fastqc.html
|   |   |   |   `-- normal-lane_1_2_fastqc.zip
|   |   |   `-- tumor-lane_1
|   |   |       |-- tumor-lane_1_1_fastqc.html
|   |   |       |-- tumor-lane_1_1_fastqc.zip
|   |   |       |-- tumor-lane_1_2_fastqc.html
|   |   |       `-- tumor-lane_1_2_fastqc.zip
|   |   |-- markduplicates
|   |   |   |-- normal
|   |   |   |   `-- normal.md.cram.metrics
|   |   |   `-- tumor
|   |   |       `-- tumor.md.cram.metrics
|   |   |-- mosdepth
|   |   |   |-- normal
|   |   |   |   |-- normal.md.mosdepth.global.dist.txt
|   |   |   |   |-- normal.md.mosdepth.region.dist.txt
|   |   |   |   |-- normal.md.mosdepth.summary.txt
|   |   |   |   |-- normal.md.regions.bed.gz
|   |   |   |   |-- normal.md.regions.bed.gz.csi
|   |   |   |   |-- normal.recal.mosdepth.global.dist.txt
|   |   |   |   |-- normal.recal.mosdepth.region.dist.txt
|   |   |   |   |-- normal.recal.mosdepth.summary.txt
|   |   |   |   |-- normal.recal.regions.bed.gz
|   |   |   |   `-- normal.recal.regions.bed.gz.csi
|   |   |   `-- tumor
|   |   |       |-- tumor.md.mosdepth.global.dist.txt
|   |   |       |-- tumor.md.mosdepth.region.dist.txt
|   |   |       |-- tumor.md.mosdepth.summary.txt
|   |   |       |-- tumor.md.regions.bed.gz
|   |   |       |-- tumor.md.regions.bed.gz.csi
|   |   |       |-- tumor.recal.mosdepth.global.dist.txt
|   |   |       |-- tumor.recal.mosdepth.region.dist.txt
|   |   |       |-- tumor.recal.mosdepth.summary.txt
|   |   |       |-- tumor.recal.regions.bed.gz
|   |   |       `-- tumor.recal.regions.bed.gz.csi
|   |   |-- samtools
|   |   |   |-- normal
|   |   |   |   |-- normal.md.cram.stats
|   |   |   |   `-- normal.recal.cram.stats
|   |   |   `-- tumor
|   |   |       |-- tumor.md.cram.stats
|   |   |       `-- tumor.recal.cram.stats
|   |   `-- vcftools
|   |       |-- manta
|   |       |   `-- tumor_vs_normal
|   |       |       |-- tumor_vs_normal.manta.diploid_sv.FILTER.summary
|   |       |       |-- tumor_vs_normal.manta.diploid_sv.TsTv.count
|   |       |       |-- tumor_vs_normal.manta.diploid_sv.TsTv.qual
|   |       |       |-- tumor_vs_normal.manta.somatic_sv.FILTER.summary
|   |       |       |-- tumor_vs_normal.manta.somatic_sv.TsTv.count
|   |       |       `-- tumor_vs_normal.manta.somatic_sv.TsTv.qual
|   |       |-- mutect2
|   |       |   `-- tumor_vs_normal
|   |       |       |-- tumor_vs_normal.mutect2.filtered.FILTER.summary
|   |       |       |-- tumor_vs_normal.mutect2.filtered.TsTv.count
|   |       |       `-- tumor_vs_normal.mutect2.filtered.TsTv.qual
|   |       `-- strelka
|   |           `-- tumor_vs_normal
|   |               |-- tumor_vs_normal.strelka.somatic_indels.FILTER.summary
|   |               |-- tumor_vs_normal.strelka.somatic_indels.TsTv.count
|   |               |-- tumor_vs_normal.strelka.somatic_indels.TsTv.qual
|   |               |-- tumor_vs_normal.strelka.somatic_snvs.FILTER.summary
|   |               |-- tumor_vs_normal.strelka.somatic_snvs.TsTv.count
|   |               `-- tumor_vs_normal.strelka.somatic_snvs.TsTv.qual
|   |-- tabix
|   |   |-- wgs_calling_regions_noseconds.hg38.bed.gz
|   |   `-- wgs_calling_regions_noseconds.hg38.bed.gz.tbi
|   `-- variant_calling
|       |-- manta
|       |   `-- tumor_vs_normal
|       |       |-- tumor_vs_normal.manta.diploid_sv.vcf.gz
|       |       |-- tumor_vs_normal.manta.diploid_sv.vcf.gz.tbi
|       |       |-- tumor_vs_normal.manta.somatic_sv.vcf.gz
|       |       `-- tumor_vs_normal.manta.somatic_sv.vcf.gz.tbi
|       |-- mutect2
|       |   |-- normal
|       |   |   `-- normal.mutect2.pileups.table
|       |   |-- tumor
|       |   |   `-- tumor.mutect2.pileups.table
|       |   `-- tumor_vs_normal
|       |       |-- tumor_vs_normal.mutect2.artifactprior.tar.gz
|       |       |-- tumor_vs_normal.mutect2.contamination.table
|       |       |-- tumor_vs_normal.mutect2.filtered.vcf.gz
|       |       |-- tumor_vs_normal.mutect2.filtered.vcf.gz.filteringStats.tsv
|       |       |-- tumor_vs_normal.mutect2.filtered.vcf.gz.tbi
|       |       |-- tumor_vs_normal.mutect2.segmentation.table
|       |       |-- tumor_vs_normal.mutect2.vcf.gz
|       |       |-- tumor_vs_normal.mutect2.vcf.gz.stats
|       |       `-- tumor_vs_normal.mutect2.vcf.gz.tbi
|       `-- strelka
|           `-- tumor_vs_normal
|               |-- tumor_vs_normal.strelka.somatic_indels.vcf.gz
|               |-- tumor_vs_normal.strelka.somatic_indels.vcf.gz.tbi
|               |-- tumor_vs_normal.strelka.somatic_snvs.vcf.gz
|               `-- tumor_vs_normal.strelka.somatic_snvs.vcf.gz.tbi
|-- samplesheet.csv
|-- tree.txt