Software used in the reports module
general_json_report
Convert input files to JSON for the general report.
Rule
rule general_json_report:
input:
files=[f'{filedef["input"]}' for filedef in general_report["files"]],
output_files=config.get("general_report", {}),
output:
json="reports/general_json_report/{sample}_{type}.general.json",
params:
sample="{sample}_{type}",
pipeline_version=pipeline_version,
pipeline_name=pipeline_name,
tc=get_tc_general_report,
units=units,
reference_genome=config.get("reference", {}).get("fasta", ""),
log:
"reports/general_json_report/{sample}_{type}.general_report.log",
benchmark:
repeat(
"reports/general_json_report/{sample}_{type}.output.benchmark.tsv",
config.get("general_json_report", {}).get("benchmark_repeats", 1),
)
threads: config.get("general_json_report", {}).get("threads", config["default_resources"]["threads"])
resources:
mem_mb=config.get("general_json_report", {}).get("mem_mb", config["default_resources"]["mem_mb"]),
mem_per_cpu=config.get("general_json_report", {}).get("mem_per_cpu", config["default_resources"]["mem_per_cpu"]),
partition=config.get("general_json_report", {}).get("partition", config["default_resources"]["partition"]),
threads=config.get("general_json_report", {}).get("threads", config["default_resources"]["threads"]),
time=config.get("general_json_report", {}).get("time", config["default_resources"]["time"]),
container:
config.get("general_json_report", {}).get("container", config["default_container"])
message:
"{rule}: generate general html report from json config"
script:
"../scripts/general_json_report.py"
| Rule parameters |
Key |
Value |
Description |
| input |
files |
[f'{filedef["input"]}' for filedef in general_report["files"]] |
Files that should be compiled into JSON.
|
| output_files |
config.get("general_report", {}) |
Path to yaml file with definitions of the input files.
|
| output |
json |
"reports/general_json_report/{sample}_{type}.general.json" |
JSON file with data to be presented in the general report.
|
Configuration
Resources settings (resources.yaml)
| Key |
Type |
Description |
| mem_mb |
integer |
max memory in MB to be available |
| mem_per_cpu |
integer |
memory in MB used per cpu |
| partition |
string |
partition to use on cluster |
| threads |
integer |
number of threads to be available |
| time |
string |
max execution time |
general_html_report
Generate a general HTML report for a sample.
Rule
rule general_html_report:
input:
config_schema=workflow.source_path("../schemas/general_html_report_json.schema.yaml"),
html_template=workflow.source_path("../templates/general_html_report/index.html"),
json="reports/general_json_report/{sample}_{type}.general.json",
css_files=[
workflow.source_path("../templates/general_html_report/style.css"),
workflow.source_path("../templates/assets/css/datatables.min.css"),
],
js_files=[workflow.source_path("../templates/assets/js/datatables.min.js")],
additional_json={},
output:
html="reports/general_html_report/{sample}_{type}.general_report.html",
params:
final_directory_depth=config.get("general_html_report", {}).get("final_directory_depth", 1),
multiqc_config=config.get("general_html_report", {}).get("multiqc_config", ""),
units=units,
extra=config.get("general_html_report", {}).get("extra", ""),
log:
"reports/general_html_report/{sample}_{type}.general_report.log",
benchmark:
repeat(
"reports/general_html_report/{sample}_{type}.output.benchmark.tsv",
config.get("general_html_report", {}).get("benchmark_repeats", 1),
)
threads: config.get("general_html_report", {}).get("threads", config["default_resources"]["threads"])
resources:
mem_mb=config.get("general_html_report", {}).get("mem_mb", config["default_resources"]["mem_mb"]),
mem_per_cpu=config.get("general_html_report", {}).get("mem_per_cpu", config["default_resources"]["mem_per_cpu"]),
partition=config.get("general_html_report", {}).get("partition", config["default_resources"]["partition"]),
threads=config.get("general_html_report", {}).get("threads", config["default_resources"]["threads"]),
time=config.get("general_html_report", {}).get("time", config["default_resources"]["time"]),
container:
config.get("general_html_report", {}).get("container", config["default_container"])
message:
"{rule}: generate general html report from json config {input.json}"
script:
"../scripts/general_html_report.py"
| Rule parameters |
Key |
Value |
Description |
| input |
config_schema |
workflow.source_path("../schemas/general_html_report_json.schema.yaml") |
Validation schema for the JSON input.
|
| html_template |
workflow.source_path("../templates/general_html_report/index.html") |
HTML template that the report should be based on.
|
| json |
"reports/general_json_report/{sample}_{type}.general.json" |
JSON that should be rendered in the report as produced by general_json_report.
|
| css_files |
[ workflow.source_path("../templates/general_html_report/style.css"), workflow.source_path("../templates/assets/css/datatables.min.css"), ] |
CSS files that should be included in the template.
|
| additional_json |
{} |
Additional JSON that should be included in the report.
|
| output |
html |
"reports/general_html_report/{sample}_{type}.general_report.html" |
Interactive HTML report for a sample.
|
Configuration
Software settings (config.yaml)
| Key |
Type |
Description |
| final_directory_depth |
integer |
How deep in the final results directory the report will be. This will be used to correctly resolve relative paths in the JSON config. For example, if the report is located in the directory results/reports, the depth would be 2.
|
| multiqc_config |
string |
Path to multiqc config file in cases where you have custom content in the multiqc report or if you want to hide certain general statistics columns in the general report that are also hidden in the multiqc report.
|
| benchmark_repeats |
integer |
set number of times benchmark should be repeated |
| container |
string |
name or path to docker/singularity container |
| extra |
string |
parameters that should be forwarded |
Resources settings (resources.yaml)
| Key |
Type |
Description |
| mem_mb |
integer |
max memory in MB to be available |
| mem_per_cpu |
integer |
memory in MB used per cpu |
| partition |
string |
partition to use on cluster |
| threads |
integer |
number of threads to be available |
| time |
string |
max execution time |
cnv_html_report
Generate an HTML report for CNVs.
Rule
rule cnv_html_report:
input:
json="reports/cnv_html_report/{sample}_{type}.{tc_method}.merged.json",
html_template=workflow.source_path("../templates/cnv_html_report/index.html"),
js_files=[
workflow.source_path("../templates/assets/js/d3.v7.min.js"),
workflow.source_path("../templates/cnv_html_report/01-chromosome-plot.js"),
workflow.source_path("../templates/cnv_html_report/02-genome-plot.js"),
workflow.source_path("../templates/cnv_html_report/03-results-table.js"),
workflow.source_path("../templates/cnv_html_report/04-window-summary.js"),
workflow.source_path("../templates/cnv_html_report/05-main.js"),
],
css_files=[
workflow.source_path("../templates/assets/css/icons.css"),
workflow.source_path("../templates/cnv_html_report/style.css"),
],
tc_file=get_tc_file,
extra_table_files=[t["path"] for t in config.get("cnv_html_report", {}).get("extra_tables", [])],
output:
html=temp("reports/cnv_html_report/{sample}_{type}.{tc_method}.cnv_report.html"),
params:
include_table=config.get("cnv_html_report", {}).get("show_table", True),
extra_tables=config.get("cnv_html_report", {}).get("extra_tables", []),
tc=get_tc,
tc_method=lambda wildcards: wildcards.tc_method,
include_cytobands=config.get("cnv_html_report", {}).get("cytobands", False),
log:
"reports/cnv_html_report/{sample}_{type}.{tc_method}.cnv_report.html.log",
benchmark:
repeat(
"reports/cnv_html_report/{sample}_{type}.{tc_method}.cnv_report.html.benchmark.tsv",
config.get("cnv_html_report", {}).get("benchmark_repeats", 1),
)
threads: config.get("cnv_html_report", {}).get("threads", config["default_resources"]["threads"])
resources:
mem_mb=config.get("cnv_html_report", {}).get("mem_mb", config["default_resources"]["mem_mb"]),
mem_per_cpu=config.get("cnv_html_report", {}).get("mem_per_cpu", config["default_resources"]["mem_per_cpu"]),
partition=config.get("cnv_html_report", {}).get("partition", config["default_resources"]["partition"]),
threads=config.get("cnv_html_report", {}).get("threads", config["default_resources"]["threads"]),
time=config.get("cnv_html_report", {}).get("time", config["default_resources"]["time"]),
container:
config.get("cnv_html_report", {}).get("container", config["default_container"])
message:
"{rule}: Compile a CNV HTML report for {wildcards.sample}_{wildcards.type}"
script:
"../scripts/cnv_html_report.py"
| Rule parameters |
Key |
Value |
Description |
| input |
json |
"reports/cnv_html_report/{sample}_{type}.{tc_method}.merged.json" |
Merged JSON file with CNV calls and other sample information.
|
| html_template |
workflow.source_path("../templates/cnv_html_report/index.html") |
Path to the html template
|
| js_files |
[ workflow.source_path("../templates/assets/js/d3.v7.min.js"), workflow.source_path("../templates/cnv_html_report/01-chromosome-plot.js"), workflow.source_path("../templates/cnv_html_report/02-genome-plot.js"), workflow.source_path("../templates/cnv_html_report/03-results-table.js"), workflow.source_path("../templates/cnv_html_report/04-window-summary.js"), workflow.source_path("../templates/cnv_html_report/05-main.js"), ] |
List of javascript files that should be included in the report. The order of the files is significant. If you have dependencies between the files, you need to supply the dependencies before the script(s) that depends on them.
|
| css_files |
[ workflow.source_path("../templates/assets/css/icons.css"), workflow.source_path("../templates/cnv_html_report/style.css"), ] |
List of css files that should be included in the report. Files are included in the order given.
|
| tc_file |
get_tc_file |
Path to a text file containing the tumor cell content estimated by the method tc_method.
|
| output |
html |
"reports/cnv_html_report/{sample}_{type}.{tc_method}.cnv_report.html" |
Interactive HTML report for CNVs.
|
Configuration
Software settings (config.yaml)
| Key |
Type |
Description |
| benchmark_repeats |
integer |
set number of times benchmark should be repeated |
| container |
string |
name or path to docker/singularity container |
| cytobands |
boolean |
Whether or not to add cytoband information to the plots and the CNV table.
|
| show_table |
boolean |
Whether or not to display a table of called CNVs in the report. If this is true, then the attributes filtered_cnv_vcfs and unfiltered_cnv_vcfs under merge_cnv_json are required.
|
| extra_tables |
array |
Additional tables that should be added to the report. The tables will be based on the columns of the TSV file listed, and column names are required and assumed to be present.
|
Resources settings (resources.yaml)
| Key |
Type |
Description |
| mem_mb |
integer |
max memory in MB to be available |
| mem_per_cpu |
integer |
memory in MB used per cpu |
| partition |
string |
partition to use on cluster |
| threads |
integer |
number of threads to be available |
| time |
string |
max execution time |
cnv_json
Convert CNV results from a particular CNV caller to JSON that is compatible with the final report.
Rule
rule cnv_json:
input:
ratios=get_cnv_ratios,
segments=get_cnv_segments,
output:
json=temp("reports/cnv_html_report/{sample}_{type}.{caller}.{tc_method}.json"),
params:
skip_chromosomes=config.get("reference", {}).get("skip_chrs"),
log:
"reports/cnv_html_report/{sample}_{type}.{caller}.{tc_method}.json.log",
benchmark:
repeat(
"reports/cnv_html_report/{sample}_{type}.{caller}.{tc_method}.json.benchmark.tsv",
config.get("cnv_json", {}).get("benchmark_repeats", 1),
)
threads: config.get("cnv_json", {}).get("threads", config["default_resources"]["threads"])
resources:
mem_mb=config.get("cnv_json", {}).get("mem_mb", config["default_resources"]["mem_mb"]),
mem_per_cpu=config.get("cnv_json", {}).get("mem_per_cpu", config["default_resources"]["mem_per_cpu"]),
partition=config.get("cnv_json", {}).get("partition", config["default_resources"]["partition"]),
threads=config.get("cnv_json", {}).get("threads", config["default_resources"]["threads"]),
time=config.get("cnv_json", {}).get("time", config["default_resources"]["time"]),
container:
config.get("cnv_json", {}).get("container", config["default_container"])
message:
"{rule}: Create JSON representation for CNV results from {wildcards.caller} "
"for {wildcards.sample}_{wildcards.type}"
script:
"../scripts/cnv_json.py"
| Rule parameters |
Key |
Value |
Description |
| input |
ratios |
get_cnv_ratios |
Path to a file with log2 ratios for a specific caller. Determined by an input function that returns a path to the correct file based on which caller was used.
|
| segments |
get_cnv_segments |
Path to a file with CNV segments for a specific caller. Determined by an input function that returns a path to the correct file based on which caller was used.
|
| output |
json |
"reports/cnv_html_report/{sample}_{type}.{caller}.{tc_method}.json" |
A JSON representation of the CNV results from a specific caller.
|
Configuration
Software settings (config.yaml)
| Key |
Type |
Description |
| benchmark_repeats |
integer |
set number of times benchmark should be repeated |
| container |
string |
name or path to docker/singularity container |
Resources settings (resources.yaml)
| Key |
Type |
Description |
| mem_mb |
integer |
max memory in MB to be available |
| mem_per_cpu |
integer |
memory in MB used per cpu |
| partition |
string |
partition to use on cluster |
| threads |
integer |
number of threads to be available |
| time |
string |
max execution time |
merge_cnv_json
Merge JSON files from multiple CNV callers and add annotations and other sample specific data.
Rule
rule merge_cnv_json:
input:
json=get_json_for_merge_cnv_json,
fai=config.get("reference", {}).get("fai", ""),
annotation_bed=config.get("merge_cnv_json", {}).get("annotations", []),
germline_vcf=get_germline_vcf,
filtered_cnv_vcfs=get_filtered_cnv_vcf,
cnv_vcfs=get_unfiltered_cnv_vcf,
cytobands=config.get("merge_cnv_json", {}).get("cytobands", []),
output:
json=temp("reports/cnv_html_report/{sample}_{type}.{tc_method}.merged.json"),
params:
skip_chromosomes=config.get("reference", {}).get("skip_chrs", []),
cytobands=config.get("cnv_html_report", {}).get("cytobands", False),
log:
"reports/cnv_html_report/{sample}_{type}.{tc_method}.merged.json.log",
benchmark:
repeat(
"reports/cnv_html_report/{sample}_{type}.{tc_method}.merged.json.benchmark.tsv",
config.get("merge_cnv_json", {}).get("benchmark_repeats", 1),
)
threads: config.get("merge_cnv_json", {}).get("threads", config["default_resources"]["threads"])
resources:
mem_mb=config.get("merge_cnv_json", {}).get("mem_mb", config["default_resources"]["mem_mb"]),
mem_per_cpu=config.get("merge_cnv_json", {}).get("mem_per_cpu", config["default_resources"]["mem_per_cpu"]),
partition=config.get("merge_cnv_json", {}).get("partition", config["default_resources"]["partition"]),
threads=config.get("merge_cnv_json", {}).get("threads", config["default_resources"]["threads"]),
time=config.get("merge_cnv_json", {}).get("time", config["default_resources"]["time"]),
container:
config.get("merge_cnv_json", {}).get("container", config["default_container"])
message:
"{rule}: Merge CNV JSON data for {wildcards.sample}_{wildcards.type}"
script:
"../scripts/merge_cnv_json.py"
| Rule parameters |
Key |
Value |
Description |
| input |
json |
get_json_for_merge_cnv_json |
One or more JSON files containing CNV information, one file per caller. Supplied by input function that determines the paths based on the included callers, and the callers that should be included is determined by the svdb_merge config. The paths to the files are based on the cnv_sv module.
|
| fai |
config.get("reference", {}).get("fai", "") |
Reference genome FASTA index.
|
| annotation_bed |
config.get("merge_cnv_json", {}).get("annotations", []) |
Zero or more BED files with regions that should be annotated in the chromosome plot.
|
| germline_vcf |
get_germline_vcf |
Optional VCF file with germline variants. Supplied by input function that takes it from the config.
|
| filtered_cnv_vcfs |
get_filtered_cnv_vcf |
Zero or more VCF files containing filtered CNV calls that should be displayed in the results table. Supplied by input function that takes these from the config.
|
| cnv_vcfs |
get_unfiltered_cnv_vcf |
Zero or more VCF files containing unfiltered CNV calls that should be displayed in the results table. Supplied by input function that takes these from the config.
|
| cytobands |
config.get("merge_cnv_json", {}).get("cytobands", []) |
Optional path to a file with cytoband definitions. This file should conform to the UCSC schema for cytobands. See https://www.genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=map&hgta_track=cytoBand&hgta_table=cytoBand&hgta_doSchema=describe+table+schema
|
| output |
json |
"reports/cnv_html_report/{sample}_{type}.{tc_method}.merged.json" |
Merged JSON file with CNV calls and other sample information that is ready to be included in the final report.
|
Configuration
Software settings (config.yaml)
| Key |
Type |
Description |
| benchmark_repeats |
integer |
set number of times benchmark should be repeated |
| container |
string |
name or path to docker/singularity container |
| annotations |
array |
List of BED files with custom annotations.
|
| cytoband_config |
object |
Cytoband visualisation configuration.
|
| cytobands |
string |
Tab-separated file containing cytoband information. The file should have five columns: chromosome name, start position (0-based), end position (exclusive), name, and Giemsa stain result. The Giemsa stain results should match with the config under cnv_html_report.cytoband_config
|
| filtered_cnv_vcfs |
array |
VCF files containing filtered CNV calls that should be displayed in the results table. Will only have an effect if show_table is true, and if show_table is true, this attribute is required.
|
| germline_vcf |
string |
Path to a germline VCF file that will be used to display VAFs in the plots of the report. The path supports the wildcards sample and type wildcards.
|
| unfiltered_cnv_vcfs |
array |
VCF files containing unfiltered CNV calls that should be displayed in the results table. Will only have an effect if show_table is true, and if show_table is true, this attribute is required.
|
Resources settings (resources.yaml)
| Key |
Type |
Description |
| mem_mb |
integer |
max memory in MB to be available |
| mem_per_cpu |
integer |
memory in MB used per cpu |
| partition |
string |
partition to use on cluster |
| threads |
integer |
number of threads to be available |
| time |
string |
max execution time |
input / output files