Snakemake Report

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Workflow

Click the nodes to obtain details about each step.

Circle calls

Statistics

If the workflow has been executed in cluster/cloud, runtimes include the waiting time in the queue.

Configuration

File Code

calling:
  samples: config/samples.tsv
  units: config/units.tsv

  reference:
#     name: "grch38_with_plasmid_replacements"
#     path: "resources/grch38_with_plasmid_replacements.fasta"
    name: "grch38_with_alk_myc_plasmids"
    path: "resources/grch38_with_alk_myc_plasmids.fasta"

  min_read_depth: 2
  min_split_reads: 5
  max_paths_per_component: 15
  max_deletion_length: 10000

  # TODO: actually use these settings
  filter:
    fdr-control:
      threshold: 0.05
      local: true
      events:
        circular:
          varlociraptor:
            - present

Rule properties
Input files
Jobs	2
results/calling/tables/{group}.sorted.csv resources/grch38_with_alk_myc_plasmids.fasta
Output files
results/calling/tables/{group}.sorted.annotated.csv
Conda software stack
pandas >=1.3.4 pandarallel >=1.5.4 dinopy >=2.2.0

Rule properties
Input files
Jobs	2
results/calling/tables/{group}.tsv
Output files
results/calling/tables/{group}.sorted.csv
Conda software stack
pandas >=1.3.4 pandarallel >=1.5.4 dinopy >=2.2.0

Jobs 2

Input files

results/calling/calls/filtered/{group}.bcf

Output files

results/calling/tables/{group}.tsv

Conda software stack

vembrane =0.7
bcftools =1.12

Code

1	`vembrane table {params.extra} '{params.expression}' {input.vcf} > {output.tsv}`

Jobs 2

Input files

results/calling/calls/annotated/{group}.bcf

Output files

results/calling/calls/filtered/{group}.bcf
results/calling/calls/filtered/{group}.at_least_one_exon.bcf

Conda software stack

vembrane =0.7
bcftools =1.12

Code

1
2
3

        vembrane filter '{params.filter_expression}' {input} -O bcf > {output.by_exons} 2> {log}
        varlociraptor filter-calls control-fdr {params.mode} --events PRESENT --var BND --fdr {params.fdr} {output.by_exons} | varlociraptor decode-phred | bcftools sort -m 4G -Ob > {output.calls} 2>> {log}

Jobs 2

Input files

results/calling/calls/pre_annotated/{sample}.bcf
results/calling/calls/pre_annotated/{sample}.bcf.csi
results/calling/candidates/{sample}.sorted.bcf
results/calling/candidates/{sample}.sorted.bcf.csi

Output files

results/calling/calls/annotated/{sample,[a-zA-Z_0-9-]+}.bcf

Conda software stack

bcftools =1.12

Code

1 2	`bcftools annotate --annotations {input.candidates_with_annotation} --columns {params.columns} --output-type b --output {output.variants} {input.variants}`

Rule properties
Input files
Jobs	2
resources/gencode.v38.annotation.sorted.gff3.gz results/calling/calls/merged/{sample}.bcf
Output files
results/calling/calls/pre_annotated/{sample,[a-zA-Z_0-9-]+}.bcf
Conda software stack
bcftools =1.13 pysam gff3sort

Jobs 1

Input files

resources/gencode.v38.annotation.gff3.gz

Output files

resources/gencode.v38.annotation.sorted.gff3.gz
resources/gencode.v38.annotation.sorted.gff3.gz.tbi
resources/gencode.v38.annotation.sorted.gff3.gz.csi

Conda software stack

bcftools =1.13
pysam
gff3sort

Code

        gff3sort.pl <(pigz -dc {input}) | bgzip -@ {threads} -c > {output.gff} 2> {log}
        tabix {output.gff} 2>> {log}
        tabix --csi {output.gff} 2>> {log}

Rule properties
Input files
Jobs	2
results/calling/calls/initial_sorted/{group}.1-of-12.bcf results/calling/calls/initial_sorted/{group}.2-of-12.bcf results/calling/calls/initial_sorted/{group}.3-of-12.bcf results/calling/calls/initial_sorted/{group}.4-of-12.bcf results/calling/calls/initial_sorted/{group}.5-of-12.bcf results/calling/calls/initial_sorted/{group}.6-of-12.bcf results/calling/calls/initial_sorted/{group}.7-of-12.bcf results/calling/calls/initial_sorted/{group}.8-of-12.bcf results/calling/calls/initial_sorted/{group}.9-of-12.bcf results/calling/calls/initial_sorted/{group}.10-of-12.bcf results/calling/calls/initial_sorted/{group}.11-of-12.bcf results/calling/calls/initial_sorted/{group}.12-of-12.bcf results/calling/calls/initial_sorted/{group}.1-of-12.bcf.csi results/calling/calls/initial_sorted/{group}.2-of-12.bcf.csi results/calling/calls/initial_sorted/{group}.3-of-12.bcf.csi results/calling/calls/initial_sorted/{group}.4-of-12.bcf.csi results/calling/calls/initial_sorted/{group}.5-of-12.bcf.csi results/calling/calls/initial_sorted/{group}.6-of-12.bcf.csi results/calling/calls/initial_sorted/{group}.7-of-12.bcf.csi results/calling/calls/initial_sorted/{group}.8-of-12.bcf.csi results/calling/calls/initial_sorted/{group}.9-of-12.bcf.csi results/calling/calls/initial_sorted/{group}.10-of-12.bcf.csi results/calling/calls/initial_sorted/{group}.11-of-12.bcf.csi results/calling/calls/initial_sorted/{group}.12-of-12.bcf.csi
Output files
results/calling/calls/merged/{group}.bcf
Conda software stack
bcftools =1.12 snakemake-wrapper-utils ==0.2.0

Rule properties
Input files
Jobs	24
results/calling/calls/initial/{group}.{scatteritem}.bcf
Output files
results/calling/calls/initial_sorted/{group}.{scatteritem,\d+-of-\d+}.bcf
Conda software stack
bcftools ==1.11

Jobs 24

Input files

Output files

results/calling/calls/initial/{group}.{scatteritem,\d+-of-\d+}.bcf

Code

1	`varlociraptor call variants generic --obs {params.obs} --scenario {input.scenario} > {output} 2> {log}`

Jobs 24

Input files

resources/grch38_with_alk_myc_plasmids.fasta
resources/grch38_with_alk_myc_plasmids.fasta.fai
results/calling/mapping/{sample}.bam
results/calling/mapping/{sample}.bam.bai

Output files

results/calling/calls/observations/{sample,[a-zA-Z_0-9-]+}.{scatteritem,\d+-of-\d+}.bcf

Code

1	`varlociraptor preprocess variants {input.ref} --candidates {input.candidates} --model {params.model} --max-depth 200 --bam {input.bam} --output {output} 2> {log}`

Jobs 2

Input files

results/calling/candidates/{sample}.sorted.bcf

Output files

results/calling/candidate-calls/{sample,[a-zA-Z_0-9-]+}.1-of-12.bcf
results/calling/candidate-calls/{sample,[a-zA-Z_0-9-]+}.2-of-12.bcf
results/calling/candidate-calls/{sample,[a-zA-Z_0-9-]+}.3-of-12.bcf
results/calling/candidate-calls/{sample,[a-zA-Z_0-9-]+}.4-of-12.bcf
results/calling/candidate-calls/{sample,[a-zA-Z_0-9-]+}.5-of-12.bcf
results/calling/candidate-calls/{sample,[a-zA-Z_0-9-]+}.6-of-12.bcf
results/calling/candidate-calls/{sample,[a-zA-Z_0-9-]+}.7-of-12.bcf
results/calling/candidate-calls/{sample,[a-zA-Z_0-9-]+}.8-of-12.bcf
results/calling/candidate-calls/{sample,[a-zA-Z_0-9-]+}.9-of-12.bcf
results/calling/candidate-calls/{sample,[a-zA-Z_0-9-]+}.10-of-12.bcf
results/calling/candidate-calls/{sample,[a-zA-Z_0-9-]+}.11-of-12.bcf
results/calling/candidate-calls/{sample,[a-zA-Z_0-9-]+}.12-of-12.bcf

Code

1	`rbt vcf-split {input} {output}`

Rule properties
Input files
Jobs	2
results/calling/candidates/{sample}.bcf
Output files
results/calling/candidates/{sample,[a-zA-Z_0-9-]+}.sorted.bcf
Conda software stack
bcftools ==1.11

Jobs 2

Input files

results/calling/mapping/{sample}.bam
results/calling/mapping/{sample}.bam.bai
resources/grch38_with_alk_myc_plasmids.fasta

Output files

results/calling/candidates/{sample,[a-zA-Z_0-9-]+}.bcf
results/calling/graphs/{sample,[a-zA-Z_0-9-]+}.graph
results/calling/graphs/{sample,[a-zA-Z_0-9-]+}

Code

cyrcular        graph        breakends        {input.bam}        --reference {input.ref}        --min-read-depth {params.min_read_depth}        --min-split-reads {params.min_split_reads}        --max-paths-per-component {params.max_paths_per_component}        --max-deletion-length {params.max_deletion_length}        -t 8        --output {output.bnds}        --graph {output.graph}        --dot {output.dot}        2> {log}

Rule properties
Input files
Jobs	2
results/calling/index/grch38_with_alk_myc_plasmids.mmi
Output files
results/calling/mapping/{sample,[a-zA-Z_0-9-]+}.bam
Conda software stack
minimap2 ==2.17 samtools ==1.12

Rule properties
Input files
Jobs	1
resources/grch38_with_alk_myc_plasmids.fasta
Output files
results/calling/index/grch38_with_alk_myc_plasmids.mmi
Conda software stack
minimap2 ==2.17

Rule properties
Input files
Jobs	2

Output files
results/calling/merged/{sample,[a-zA-Z_0-9-]+}_{read,single\|R1\|R2}.fastq.gz

Rule properties
Input files
Jobs	2
results/calling/mapping/{sample}.bam
Output files
results/calling/mapping/{sample,[a-zA-Z_0-9-]+}.bam.bai
Conda software stack
samtools ==1.10

Rule properties
Input files
Jobs	28
{prefix}.bcf
Output files
{prefix}.bcf.csi
Conda software stack
bcftools =1.11

Jobs 2

Input files

results/calling/mapping/{sample}.bam
results/calling/mapping/{sample}.bam.bai
results/calling/graphs/{sample}.graph

Output files

results/calling/coverage_graphs/{sample,[a-zA-Z_0-9-]+}

Code

1	`cyrcular graph plot {input.bam} --graph {input.graph} --output {output.plots} 2> {log}`

Jobs 2

Input files

results/calling/tables/{group}.sorted.annotated.csv
results/calling/coverage_graphs/{group}

Output files

results/calling/report/tables/{group}

Code

        mkdir -p {output}/qc_plots
        for f in {input.plots}/*.html; do ( cp "$f" {output}/qc_plots/ ); done
        rbt csv-report {input.csv} {output} {params.extra} &> {log}