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kfdrc_combined_somatic_wgs_cnv_wf.cwl
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kfdrc_combined_somatic_wgs_cnv_wf.cwl
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class: Workflow
cwlVersion: v1.0
id: kfdrc_combined_somatic_wgs_cnv_wf
$namespaces:
sbg: 'https://sevenbridges.com'
inputs:
- id: annotation_file
type: File
doc: refFlat.txt file
'sbg:x': 296.890625
'sbg:y': 1165.5
- id: b_allele
type: File?
doc: >-
germline calls, needed for BAF. GATK HC VQSR input recommended. Tool
will prefilter for germline and pass if expression given
secondaryFiles:
- .tbi
'sbg:x': 0
'sbg:y': 1712
- id: capture_regions
type: File?
doc: 'If not WGS, provide this bed file'
'sbg:x': 296.890625
'sbg:y': 909.5
- id: cfree_sex
type:
- 'null'
- type: enum
symbols:
- XX
- XY
name: sex
doc: 'If known, XX for female, XY for male'
'sbg:x': 596.5790405273438
'sbg:y': 1268
- id: chr_len
type: File
doc: file with chromosome lengths
'sbg:x': 596.5790405273438
'sbg:y': 1161
- id: cnvkit_cnn_input
type: File?
doc: 'If running using an existing .cnn, supply here'
'sbg:x': 0
'sbg:y': 1605
- id: cnvkit_sex
type: string?
doc: 'If known, choices are m,y,male,Male,f,x,female,Female'
'sbg:x': 0
'sbg:y': 1498
- id: coeff_var
type: float?
doc: Coefficient of variation to set window size. Default 0.05 recommended
default: 0.05
'sbg:x': 596.5790405273438
'sbg:y': 793
- id: combined_exclude_expression
type: string?
doc: 'Filter expression if vcf has non-PASS combined calls, use as-needed'
'sbg:x': 0
'sbg:y': 1391
- id: combined_include_expression
type: string?
doc: 'Filter expression if vcf has non-PASS combined calls, use as-needed'
'sbg:x': 0
'sbg:y': 1284
- id: contamination_adjustment
type: boolean?
doc: TRUE or FALSE to have ControlFreec estimate normal contam
'sbg:x': 596.5790405273438
'sbg:y': 686
- id: indexed_reference_fasta
type: File
secondaryFiles:
- .fai
- ^.dict
'sbg:x': 0
'sbg:y': 1177
- id: input_normal_aligned
type: File
doc: normal BAM or CRAM
secondaryFiles:
- |
${
var dpath = self.location.replace(self.basename, "")
if(self.nameext == '.bam'){
return {"location": dpath+self.nameroot+".bai", "class": "File"}
}
else{
return {"location": dpath+self.basename+".crai", "class": "File"}
}
}
'sbg:x': 0
'sbg:y': 1070
- id: input_normal_name
type: string
'sbg:x': 0
'sbg:y': 963
- id: input_tumor_aligned
type: File
doc: tumor BAM or CRAM
secondaryFiles:
- |
${
var dpath = self.location.replace(self.basename, "")
if(self.nameext == '.bam'){
return {"location": dpath+self.nameroot+".bai", "class": "File"}
}
else{
return {"location": dpath+self.basename+".crai", "class": "File"}
}
}
'sbg:x': 0
'sbg:y': 856
- id: input_tumor_name
type: string
'sbg:x': 0
'sbg:y': 749
- id: mate_orientation_control
type:
- 'null'
- type: enum
symbols:
- '0'
- FR
- RF
- FF
name: mate_orientation_control
doc: >-
0 (for single ends), RF (Illumina mate-pairs), FR (Illumina paired-ends),
FF (SOLiD mate-pairs)
default: FR
'sbg:x': 0
'sbg:y': 642
- id: mate_orientation_sample
type:
- 'null'
- type: enum
symbols:
- '0'
- FR
- RF
- FF
name: mate_orientation_sample
doc: >-
0 (for single ends), RF (Illumina mate-pairs), FR (Illumina paired-ends),
FF (SOLiD mate-pairs)
default: FR
'sbg:x': 0
'sbg:y': 535
- id: min_theta2_frac
type: float?
doc: >-
Minimum fraction of genome with copy umber alterations. Default is 0.05,
recommend 0.01
default: 0.01
'sbg:x': 1018.6522216796875
'sbg:y': 355.5
- id: output_basename
type: string
'sbg:x': 1018.6522216796875
'sbg:y': 248.5
- id: paired_vcf
type: File
doc: Combined somatic and germline call file. VarDict input recommended.
'sbg:x': 0
'sbg:y': 428
- id: ploidy
type: 'int[]'
doc: Array of ploidy possibilities for ControlFreeC to try
'sbg:x': 0
'sbg:y': 321
- id: reference_fai
type: File
'sbg:x': 0
'sbg:y': 214
- id: threads
type: int?
doc: >-
For ControlFreeC. Recommend 16 max, as I/O gets saturated after that
losing any advantage.
default: 16
'sbg:x': 0
'sbg:y': 107
- id: wgs_mode
type: string?
doc: 'for WGS mode, input Y. leave blank for hybrid mode'
default: 'Y'
'sbg:x': 0
'sbg:y': 0
outputs:
- id: cnvkit_calls
outputSource:
- cnvkit/output_calls
type: File
'sbg:x': 1018.6522216796875
'sbg:y': 1463.5
- id: cnvkit_cnn_output
outputSource:
- cnvkit/output_cnn
type: File?
'sbg:x': 1018.6522216796875
'sbg:y': 1356.5
- id: cnvkit_cnr
outputSource:
- cnvkit/output_cnr
type: File
'sbg:x': 1018.6522216796875
'sbg:y': 1249.5
- id: cnvkit_gainloss
outputSource:
- cnvkit/output_gainloss
type: File
'sbg:x': 1018.6522216796875
'sbg:y': 979.5
- id: cnvkit_metrics
outputSource:
- cnvkit/output_metrics
type: File
'sbg:x': 1018.6522216796875
'sbg:y': 872.5
- id: cnvkit_seg
outputSource:
- cnvkit/output_seg
type: File
'sbg:x': 1018.6522216796875
'sbg:y': 765.5
- id: ctrlfreec_baf
outputSource:
- rename_outputs/ctrlfreec_baf
type: File
'sbg:x': 1979.84619140625
'sbg:y': 1149
- id: ctrlfreec_bam_ratio
outputSource:
- rename_outputs/ctrlfreec_bam_ratio
type: File
'sbg:x': 1979.84619140625
'sbg:y': 1042
- id: ctrlfreec_bam_seg
outputSource:
- convert_ratio_to_seg/ctrlfreec_ratio2seg
type: File
'sbg:x': 1979.84619140625
'sbg:y': 935
- id: ctrlfreec_config
outputSource:
- rename_outputs/ctrlfreec_config
type: File
'sbg:x': 1979.84619140625
'sbg:y': 828
- id: ctrlfreec_info
outputSource:
- rename_outputs/ctrlfreec_info
type: File
'sbg:x': 1979.84619140625
'sbg:y': 721
- id: ctrlfreec_pngs
outputSource:
- rename_outputs/ctrlfreec_pngs
type: 'File[]'
'sbg:x': 1979.84619140625
'sbg:y': 614
- id: ctrlfreec_pval
outputSource:
- rename_outputs/ctrlfreec_pval
type: File
'sbg:x': 1979.84619140625
'sbg:y': 507
- id: theta2_calls
outputSource:
- cnvkit_import_theta2/theta2_adjusted_cns
type: File
'sbg:x': 2335.287109375
'sbg:y': 1016.5
- id: theta2_seg
outputSource:
- cnvkit_import_theta2/theta2_adjusted_seg
type: File
'sbg:x': 2335.287109375
'sbg:y': 909.5
- id: theta2_subclonal_cns
outputSource:
- cnvkit_import_theta2/theta2_subclone_cns
type: 'File[]'
'sbg:x': 2335.287109375
'sbg:y': 802.5
- id: theta2_subclonal_results
outputSource:
- run_theta2/n3_graph
- run_theta2/n2_results
- run_theta2/best_results
type: 'File[]'
'sbg:x': 1979.84619140625
'sbg:y': 400
- id: theta2_subclone_seg
outputSource:
- cnvkit_import_theta2/theta2_subclone_seg
type: 'File[]'
'sbg:x': 2335.287109375
'sbg:y': 695.5
steps:
- id: bcftools_filter_combined_vcf
in:
- id: exclude_expression
source: combined_exclude_expression
- id: include_expression
source: combined_include_expression
- id: input_vcf
source: paired_vcf
- id: output_basename
source: output_basename
out:
- id: filtered_vcf
run:
class: CommandLineTool
cwlVersion: v1.0
id: bcftools_filter_vcf
baseCommand: []
inputs:
- id: exclude_expression
type: string?
- id: include_expression
type: string?
- id: input_vcf
type: File
- id: output_basename
type: string?
outputs:
- id: filtered_vcf
type: File
outputBinding:
glob: '*.vcf.gz'
secondaryFiles:
- .tbi
doc: >-
More generic tool to take in an include expression and optionally an
exclude expresssion to filter a vcf
arguments:
- position: 1
shellQuote: false
valueFrom: |-
${
var out_base = inputs.output_basename;
if (out_base == null){
out_base = inputs.input_vcf.nameroot + ".bcf_filtered"
}
var cmd = "bcftools view ";
if (inputs.include_expression != null){
cmd += "--include '" + inputs.include_expression + "' " + inputs.input_vcf.path;
if (inputs.exclude_expression != null){
cmd += " | bcftools view --exclude '" + inputs.exclude_expression + "' -O z > " + out_base + ".vcf.gz;";
} else {
cmd += " -O z > " + out_base + ".vcf.gz;";
}
} else if (inputs.include_expression == null && inputs.exclude_expression != null){
cmd += "--exclude '" + inputs.exclude_expression + "' " + inputs.input_vcf.path + " -O z > " + out_base + ".vcf.gz;";
} else if (inputs.include_expression == null && inputs.exclude_expression == null){
cmd = "cp " + inputs.input_vcf.path + " ./" + out_base + ".vcf.gz;";
}
cmd += "tabix " + out_base + ".vcf.gz;"
return cmd;
}
requirements:
- class: ShellCommandRequirement
- class: ResourceRequirement
ramMin: 1000
coresMin: 1
- class: DockerRequirement
dockerPull: 'kfdrc/bvcftools:latest'
- class: InlineJavascriptRequirement
'sbg:x': 296.890625
'sbg:y': 1037.5
- id: cnvkit
in:
- id: annotation_file
source: annotation_file
- id: b_allele_vcf
source: gatk_filter_germline/filtered_pass_vcf
- id: capture_regions
source: capture_regions
- id: cnvkit_cnn
source: cnvkit_cnn_input
- id: input_control
source: samtools_normal_cram2bam/bam_file
- id: input_sample
source: samtools_tumor_cram2bam/bam_file
- id: output_basename
source: output_basename
- id: reference
source: indexed_reference_fasta
- id: sex
source: cnvkit_sex
- id: threads
source: threads
- id: tumor_sample_name
source: input_tumor_name
- id: wgs_mode
source: wgs_mode
out:
- id: output_calls
- id: output_cnn
- id: output_cnr
- id: output_diagram
- id: output_gainloss
- id: output_metrics
- id: output_scatter
- id: output_seg
run:
class: CommandLineTool
cwlVersion: v1.0
id: cnvkit_batch
baseCommand: []
inputs:
- id: annotation_file
type: File?
doc: 'refFlat.txt file, needed if cnv kit cnn not already built'
- id: b_allele_vcf
type: File?
doc: 'b allele germline vcf, if available'
- id: capture_regions
type: File?
doc: target regions for WES
- id: cnvkit_cnn
type: File?
doc: 'If running using an existing .cnn, supply here'
- id: input_control
type: File?
doc: normal bam file
secondaryFiles:
- ^.bai
- id: input_sample
type: File
doc: tumor bam file
secondaryFiles:
- ^.bai
- id: output_basename
type: string
- id: reference
type: File?
doc: 'fasta file, needed if cnv kit cnn not already built'
secondaryFiles:
- .fai
- id: sex
type: string
doc: Set sample sex. CNVkit isn't always great at guessing it
- default: 16
id: threads
type: int?
- id: tumor_sample_name
type: string
- id: wgs_mode
type: string?
doc: 'for WGS mode, input Y. leave blank for hybrid mode'
outputs:
- id: output_calls
type: File
outputBinding:
glob: '*.call.cns'
- id: output_cnn
doc: >-
Output if starting from cnn scratch. Should not appear if an
existing .cnn was given as input.
type: File?
outputBinding:
glob: '*_reference.cnn'
- id: output_cnr
type: File
outputBinding:
glob: '*.cnr'
- id: output_diagram
type: File
outputBinding:
glob: '*.diagram.pdf'
- id: output_gainloss
type: File
outputBinding:
glob: '*.gainloss.txt'
- id: output_metrics
type: File
outputBinding:
glob: '*.metrics.txt'
- id: output_scatter
type: File
outputBinding:
glob: '*.scatter.pdf'
- id: output_seg
type: File
outputBinding:
glob: '*.seg'
arguments:
- position: 1
shellQuote: false
valueFrom: >-
ln -s $(inputs.input_sample.path) .; ln -s
$(inputs.input_sample.secondaryFiles[0].path)
./$(inputs.input_sample.basename).bai
${
var cmd = "";
if (inputs.input_control != null) {
cmd = "ln -s " + inputs.input_control.path + " .; ln -s " + inputs.input_control.secondaryFiles[0].path + " ./" + inputs.input_control.basename + ".bai"
}
return cmd;
}
cnvkit.py batch -p $(inputs.threads) ${
var cmd = "";
if (inputs.wgs_mode == 'Y') {
cmd = " -m wgs ";
}
return cmd;
} $(inputs.input_sample.path) ${
var cmd = "";
if (inputs.capture_regions != null) {
cmd = "--targets " + inputs.capture_regions.path;
}
return cmd;
} ${
if (inputs.cnv_kit_cnn == null){
var arg = "--output-reference " + inputs.output_basename + "_cnvkit_reference.cnn --fasta " + inputs.reference.path + " --annotate " + inputs.annotation_file.path;
if (inputs.input_control != null) {
arg += " --normal " + inputs.input_control.path;
}
}
else{
var arg = "--reference " + inputs.cnv_kit_cnn.path;
var msex = ['m','y','male','Male']
if (msex.indexOf(inputs.sex) >= 0){
arg += " --male-reference";
}
}
return arg;
} --diagram --scatter
cnvkit.py call $(inputs.input_sample.nameroot).cns ${
var arg = "";
if (inputs.b_allele_vcf != null){
arg = "--vcf " + inputs.b_allele_vcf.path;
}
return arg;
} ${
var arg = "--sample-sex " + inputs.sex;
var msex = ['m','y','male','Male']
if (msex.indexOf(inputs.sex) >= 0){
arg += " --male-reference";
}
return arg;
} -o $(inputs.output_basename).call.cns
ln -s $(inputs.output_basename).call.cns
$(inputs.tumor_sample_name).cns
cnvkit.py export seg $(inputs.tumor_sample_name).cns -o
$(inputs.output_basename).call.seg
rm $(inputs.tumor_sample_name).cns
cnvkit.py metrics $(inputs.input_sample.nameroot).cnr -s
$(inputs.input_sample.nameroot).cns -o
$(inputs.output_basename).metrics.txt
cnvkit.py gainloss $(inputs.input_sample.nameroot).cnr -o
$(inputs.output_basename).gainloss.txt
mv $(inputs.input_sample.nameroot).cnr $(inputs.output_basename).cnr
mv $(inputs.input_sample.nameroot)-diagram.pdf
$(inputs.output_basename).diagram.pdf
mv $(inputs.input_sample.nameroot)-scatter.pdf
$(inputs.output_basename).scatter.pdf
requirements:
- class: ShellCommandRequirement
- class: ResourceRequirement
ramMin: 32000
coresMin: $(inputs.threads)
- class: DockerRequirement
dockerPull: 'images.sbgenomics.com/milos_nikolic/cnvkit:0.9.3'
- class: InlineJavascriptRequirement
'sbg:x': 596.5790405273438
'sbg:y': 977
- id: cnvkit_export_theta2
in:
- id: normal_ID
source: input_normal_name
- id: paired_vcf
source: bcftools_filter_combined_vcf/filtered_vcf
- id: reference_cnn
source: cnvkit/output_cnn
- id: tumor_ID
source: input_tumor_name
- id: tumor_cns
source: cnvkit/output_calls
out:
- id: call_interval_count
- id: call_normal_snp
- id: call_tumor_snp
run:
class: CommandLineTool
cwlVersion: v1.0
id: cnvkit_export_theta2
baseCommand:
- cnvkit.py
- export
- theta
inputs:
- id: normal_ID
type: string
- id: paired_vcf
type: File
- id: reference_cnn
type: File
- id: tumor_ID
type: string
- id: tumor_cns
type: File
outputs:
- id: call_interval_count
type: File
outputBinding:
glob: '*.call.interval_count'
- id: call_normal_snp
type: File
outputBinding:
glob: '*.call.normal.snp_formatted.txt'
- id: call_tumor_snp
type: File
outputBinding:
glob: '*.call.tumor.snp_formatted.txt'
arguments:
- position: 1
shellQuote: false
valueFrom: >-
-r $(inputs.reference_cnn.path) -v $(inputs.paired_vcf.path) -i
$(inputs.tumor_ID) -n $(inputs.normal_ID) $(inputs.tumor_cns.path)
requirements:
- class: ShellCommandRequirement
- class: ResourceRequirement
ramMin: 16000
coresMin: 4
- class: DockerRequirement
dockerPull: 'images.sbgenomics.com/milos_nikolic/cnvkit:0.9.3'
- class: InlineJavascriptRequirement
'sbg:x': 1018.6522216796875
'sbg:y': 1114.5
- id: cnvkit_import_theta2
in:
- id: output_basename
source: output_basename
- id: theta2_best_results
source: run_theta2/best_results
- id: theta2_n2_results
source: run_theta2/n2_results
- id: tumor_cns
source: cnvkit/output_calls
- id: tumor_sample_name
source: input_tumor_name
out:
- id: theta2_adjusted_cns
- id: theta2_adjusted_seg
- id: theta2_subclone_cns
- id: theta2_subclone_seg
run:
class: CommandLineTool
cwlVersion: v1.0
id: cnvkit_import_theta2
baseCommand:
- cnvkit.py
- import-theta
inputs:
- id: output_basename
type: string
- id: theta2_best_results
type: File
- id: theta2_n2_results
type: File
- id: tumor_cns
type: File
- id: tumor_sample_name
type: string
outputs:
- id: theta2_adjusted_cns
type: File
outputBinding:
glob: '*.theta2.total.cns'
- id: theta2_adjusted_seg
type: File
outputBinding:
glob: '*.theta2.total.seg'
- id: theta2_subclone_cns
type: 'File[]'
outputBinding:
glob: '*.theta2.subclone*.cns'
- id: theta2_subclone_seg
type: 'File[]'
outputBinding:
glob: '*.theta2.subclone*.seg'
arguments:
- position: 1
shellQuote: false
valueFrom: >-
$(inputs.tumor_cns.path) $(inputs.theta2_n2_results.path) -d ./
mv $(inputs.output_basename).call-1.cns
$(inputs.output_basename).theta2.total.cns
ln -s $(inputs.output_basename).theta2.total.cns
$(inputs.tumor_sample_name).cns
cnvkit.py export seg $(inputs.tumor_sample_name).cns -o
$(inputs.output_basename).theta2.total.seg
rm $(inputs.tumor_sample_name).cns
cnvkit.py import-theta $(inputs.tumor_cns.path)
$(inputs.theta2_best_results.path) -d ./
mv $(inputs.output_basename).call-1.cns
$(inputs.output_basename).theta2.subclone1.cns
ln -s $(inputs.output_basename).theta2.subclone1.cns
$(inputs.tumor_sample_name).cns
cnvkit.py export seg $(inputs.tumor_sample_name).cns -o
$(inputs.output_basename).theta2.subclone1.seg
rm $(inputs.tumor_sample_name).cns
SC2=$(inputs.output_basename).call-2.cns;
if [ -f "$SC2" ]; then
mv $(inputs.output_basename).call-2.cns $(inputs.output_basename).theta2.subclone2.cns;
ln -s $(inputs.output_basename).theta2.subclone2.cns $(inputs.tumor_sample_name).cns;
cnvkit.py export seg $(inputs.tumor_sample_name).cns -o $(inputs.output_basename).theta2.subclone2.seg;
rm $(inputs.tumor_sample_name).cns;
else
echo "second subclone file not found. skipping!";
fi
requirements:
- class: ShellCommandRequirement
- class: ResourceRequirement
ramMin: 8000
coresMin: 4
- class: DockerRequirement
dockerPull: 'images.sbgenomics.com/milos_nikolic/cnvkit:0.9.3'
- class: InlineJavascriptRequirement
'sbg:x': 1979.84619140625
'sbg:y': 1284
- id: control_free_c
in:
- id: capture_regions
source: capture_regions
- id: chr_len
source: chr_len
- id: coeff_var
source: coeff_var
- id: contamination_adjustment
source: contamination_adjustment
- id: mate_file_control
source: samtools_normal_cram2bam/bam_file
- id: mate_file_sample
source: samtools_tumor_cram2bam/bam_file
- id: mate_orientation_control
source: mate_orientation_control
- id: mate_orientation_sample
source: mate_orientation_sample
- id: max_threads
source: threads
- id: mini_pileup_control
source: controlfreec_normal_mini_pileup/pileup
- id: mini_pileup_sample
source: controlfreec_tumor_mini_pileup/pileup
- id: ploidy
source:
- ploidy
- id: reference
source: indexed_reference_fasta
- id: sex
source: cfree_sex
- id: snp_file
source: gatk_filter_germline/filtered_pass_vcf
out:
- id: GC_profile
- id: cnvs
- id: cnvs_pvalue
- id: config_script
- id: control_cpn
- id: control_pileup
- id: info_txt
- id: pngs
- id: ratio
- id: ratio_BedGraph
- id: sample_BAF
- id: sample_cpn
- id: sample_pileup
run:
class: CommandLineTool
cwlVersion: v1.0
$namespaces:
sbg: 'https://sevenbridges.com'
id: brownm28/mb-controlfreec-troubleshoot/control-freec-11-6-sbg/0
baseCommand: []
inputs:
- 'sbg:category': General
id: GC_content_profile
type: File?
label: GC content profile
doc: GC-content profile for a given window-size.
'sbg:fileTypes': CNP
- 'sbg:category': General
'sbg:toolDefaultValue': 'FALSE'
id: bed_graph_output
type: boolean?
label: Bed Graph output
doc: >-
Set "BedGraphOutput=TRUE" if you want an additional output in
BedGraph format for the UCSC genome browser.
- 'sbg:category': General
'sbg:toolDefaultValue': '0.8'
id: break_point_threshold
type: float?
label: Break point threshold
doc: >-
Positive value of threshold for segmentation of normalized profiles.
The closer it is to zero, the more breakpoints will be called. Its
recommended value is between 0.1 and 1.2.
- 'sbg:category': General
'sbg:toolDefaultValue': '2'
id: break_point_type
type:
- 'null'
- type: enum
symbols:
- '0'
- '1'
- '2'
- '3'
- '4'
name: break_point_type
label: Break point type
doc: >-
Desired behavior in the ambiguous regions (poly-N or low mappability
regions between two different copy number values). 0: the "unknown"
region is attached to the "known" region on the right 1: make a
separate fragment of this “unknown” region and then attaches it to
the left or to the right region choosing the longer one 2: make a
separate fragment of this “unknown” region and then attaches it to
the left or to the right region but the “ploidy” copy number has a
priority 3: make a separate fragment of this “unknown” region and
then attaches it to the left or to the right region choosing the
longer one but this “known” region should make at least half-size of
the “unknown” region 4: make a separate fragment of this “unknown”
region and do not assign any copy number to this region at all
- 'sbg:category': Target
id: capture_regions
type: File?
label: Capture regions
doc: >-
Capture regions in .bed format; sorted .bed file should contain the
following colomns: chr 0-based start 1-based end.
'sbg:fileTypes': BED
- 'sbg:category': File Input
id: chr_len
type: File
label: Chromosomes length file
doc: Chromosome length file in a tab-delimited format.
'sbg:fileTypes': 'TXT, LEN, SIZES'
- 'sbg:toolDefaultValue': '0.05'
id: coeff_var
type: float?
label: Coefficient of variation
doc: Coefficient of variation to evaluate necessary window size.
- 'sbg:category': General
'sbg:toolDefaultValue': '0'
id: contamination
type: float?
label: Contamination
doc: >-
A priori known value of tumor sample contamiantion by normal cells.
Set "contaminationAdjustment=TRUE" to correct for the contamination.
- 'sbg:category': General
'sbg:toolDefaultValue': 'FALSE'
id: contamination_adjustment
type: boolean?
label: Contamination adjustment
doc: >-
Set TRUE to correct for contamination by normal cells. If
"contamination" is not provided, it will automatically evaluate the
level of contamination.
- 'sbg:category': General
'sbg:toolDefaultValue': >-
3&4 (GC-content based normalization, WGS) or 1
(control-read-count-based normalization, WES)
id: degree
type: float?
label: Degree
doc: Degree of polynomial.
- 'sbg:category': General
'sbg:toolDefaultValue': 'WGS: 0, WES: 1'
id: force_GC_content_normalization
type:
- 'null'
- type: enum
symbols:
- '0'
- '1'
- '2'
name: force_GC_content_normalization
label: Force GC content normalization
doc: >-
Set 1 or 2 to correct the Read Count (RC) for GC-content bias and
low mappability even when you have a control sample. 0: simply model
"sample RC ~ Control RC" 1: normalize the sample and the control RC
using GC-content and then calculate the ratio "Sample RC/contol RC"
2: model "sample RC ~ Control RC" bias, and then normalize for
GC-content.
- 'sbg:category': File Input
id: gem_mappability_file
type: File?
label: GEM mappability file
doc: Mappability file in GEM format.
'sbg:fileTypes': GEM
- 'sbg:category': Execution
'sbg:toolDefaultValue': '1 - with GC-content, 0 - with a control dataset'
id: intercept
type: float?
label: Intercept
doc: Intercept of polynomial.
- 'sbg:category': Control
id: mate_copynumber_file_control
type: File?
label: Mate copy number file control
doc: >-
Raw copy number profile for a given window-size (higher priority
than mateFile) (don't need to provide a mateFile if
mateCopyNumberFile is provided).
'sbg:fileTypes': CPN
- 'sbg:category': Sample
id: mate_copynumber_file_sample
type: File?
label: Mate copy number file sample
doc: >-
Raw copy number profile for a given window-size (higher priority
than mateFile) (don't need to provide a mateFile if
mateCopyNumberFile is provided).
'sbg:fileTypes': CPN
- 'sbg:category': Control
id: mate_file_control
type: File?
label: Mate file Control
doc: >-
Mapped reads (can be single end reads, mate-pairs or paired-end
reads).
'sbg:fileTypes': 'SAM, BAM, PILEUP, PILEUP.GZ'
- 'sbg:category': Sample
id: mate_file_sample
type: File?
label: Mate file Sample
doc: >-
Mapped reads (can be single end reads, mate-pairs or paired-end
reads).
'sbg:fileTypes': 'SAM, BAM, PILEUP, PILEUP.GZ'
- 'sbg:category': Control
id: mate_orientation_control
type:
- 'null'
- type: enum
symbols:
- '0'
- RF
- FR
- FF
name: mate_orientation_control
label: Mate orientation control
doc: >-
Format of reads (in mateFile). 0 (for single ends), RF (Illumina
mate-pairs), FR (Illumina paired-ends), FF (SOLiD mate-pairs).
- 'sbg:category': Sample
id: mate_orientation_sample
type:
- 'null'
- type: enum
symbols:
- '0'
- RF
- FR
- FF
name: mate_orientation_sample
label: Mate orientation sample
doc: >-
Format of reads (in mateFile). 0 (for single ends), RF (Illumina
mate-pairs), FR (Illumina paired-ends), FF (SOLiD mate-pairs).
- 'sbg:category': General
'sbg:toolDefaultValue': 0.55 (change only if you run Control-FREEC on a bacterial genome)
id: max_expected_GC
type: float?
label: Maximum expected GC
doc: >-