Facets: snp-pileup¶
FacetsSnpPileup
· 2 contributors · 3 versions
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Quickstart¶
from janis_bioinformatics.tools.facets.snp_pileup.versions import FacetsSnpPileup_0_5_14_1 wf = WorkflowBuilder("myworkflow") wf.step( "facetssnppileup_step", FacetsSnpPileup_0_5_14_1( vcf_file=None, normal=None, tumour=None, ) ) wf.output("out", source=facetssnppileup_step.out)
OR
- Install Janis
- Ensure Janis is configured to work with Docker or Singularity.
- Ensure all reference files are available:
Note
More information about these inputs are available below.
- Generate user input files for FacetsSnpPileup:
# user inputs
janis inputs FacetsSnpPileup > inputs.yaml
inputs.yaml
normal: normal.bam
tumour: tumour.bam
vcf_file: vcf_file.vcf
- Run FacetsSnpPileup with:
janis run [...run options] \
--inputs inputs.yaml \
FacetsSnpPileup
Information¶
ID: | FacetsSnpPileup |
---|---|
URL: | https://github.com/vanallenlab/facets |
Versions: | 0.5.14.1, 0.5.14-2, 0.5.14 |
Container: | vanallenlab/facets:v0.5.14.1 |
Authors: | mumbler, evanwehi |
Citations: | Ronglai Shen, Venkatraman E. Seshan; FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing, Nucleic Acids Research, Volume 44, Issue 16, 19 September 2016, Pages e131, |
DOI: | https://doi.org/10.1093/nar/gkw520 |
Created: | 2019-12-16 |
Updated: | 2019-12-16 |
Outputs¶
name | type | documentation |
---|---|---|
out | File |
Additional configuration (inputs)¶
name | type | prefix | position | documentation |
---|---|---|---|---|
vcf_file | VCF | 18 | ||
normal | IndexedBam | 20 | ||
tumour | IndexedBam | 21 | ||
count_orphans | Optional<Boolean> | –count-orphans | 2 | Do not discard anomalous read pairs |
ignore_overlaps | Optional<Boolean> | –ignore-overlaps | 4 | Disable read-pair overlap detection. |
max_depth | Optional<Integer> | –maxdepth= | 6 | Sets the maximum depth. Default is 4000. |
min_map_quality | Optional<Integer> | –min-map-quality= | 8 | Sets the minimum threshold for mapping quality. Default is 0. |
min_base_quality | Optional<Integer> | –min-base-quality= | 10 | Sets the minimum threshold for base quality. Default is 0. |
min_read_counts | Optional<String> | –min-read-counts= | 12 | Comma separated list of minimum read counts for a position to be output. Default is 0. |
gzip | Optional<Boolean> | –gzip | 14 | Compresses the output file with BGZF. |
pseudo_snps | Optional<String> | –pseudo-snps= | 16 | Every MULTIPLE positions, if there is no SNP,insert a blank record with the total count at theposition. |
output_filename | Optional<Filename> | 19 |
Workflow Description Language¶
version development
task FacetsSnpPileup {
input {
Int? runtime_cpu
Int? runtime_memory
Int? runtime_seconds
Int? runtime_disks
Boolean? count_orphans
Boolean? ignore_overlaps
Int? max_depth
Int? min_map_quality
Int? min_base_quality
String? min_read_counts
Boolean? gzip
String? pseudo_snps
File vcf_file
String? output_filename
File normal
File normal_bai
File tumour
File tumour_bai
}
command <<<
set -e
LD_LIBRARY_PATH=/opt/conda/lib /snp-pileup \
~{if (defined(count_orphans) && select_first([count_orphans])) then "--count-orphans" else ""} \
~{if (defined(ignore_overlaps) && select_first([ignore_overlaps])) then "--ignore-overlaps" else ""} \
~{if defined(max_depth) then ("--maxdepth=" + max_depth) else ''} \
~{if defined(min_map_quality) then ("--min-map-quality=" + min_map_quality) else ''} \
~{if defined(min_base_quality) then ("--min-base-quality=" + min_base_quality) else ''} \
~{if defined(min_read_counts) then ("--min-read-counts='" + min_read_counts + "'") else ""} \
~{if (defined(gzip) && select_first([gzip])) then "--gzip" else ""} \
~{if defined(pseudo_snps) then ("--pseudo-snps='" + pseudo_snps + "'") else ""} \
'~{vcf_file}' \
'~{select_first([output_filename, "generated.csv.gz"])}' \
'~{normal}' \
'~{tumour}'
>>>
runtime {
cpu: select_first([runtime_cpu, 1])
disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
docker: "vanallenlab/facets:v0.5.14.1"
duration: select_first([runtime_seconds, 86400])
memory: "~{select_first([runtime_memory, 4])}G"
preemptible: 2
}
output {
File out = select_first([output_filename, "generated.csv.gz"])
}
}
Common Workflow Language¶
#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: 'Facets: snp-pileup'
doc: ''
requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
dockerPull: vanallenlab/facets:v0.5.14.1
inputs:
- id: count_orphans
label: count_orphans
doc: Do not discard anomalous read pairs
type:
- boolean
- 'null'
inputBinding:
prefix: --count-orphans
position: 2
- id: ignore_overlaps
label: ignore_overlaps
doc: Disable read-pair overlap detection.
type:
- boolean
- 'null'
inputBinding:
prefix: --ignore-overlaps
position: 4
- id: max_depth
label: max_depth
doc: Sets the maximum depth. Default is 4000.
type:
- int
- 'null'
inputBinding:
prefix: --maxdepth=
position: 6
separate: false
- id: min_map_quality
label: min_map_quality
doc: Sets the minimum threshold for mapping quality. Default is 0.
type:
- int
- 'null'
inputBinding:
prefix: --min-map-quality=
position: 8
separate: false
- id: min_base_quality
label: min_base_quality
doc: Sets the minimum threshold for base quality. Default is 0.
type:
- int
- 'null'
inputBinding:
prefix: --min-base-quality=
position: 10
separate: false
- id: min_read_counts
label: min_read_counts
doc: |-
Comma separated list of minimum read counts for a position to be output. Default is 0.
type:
- string
- 'null'
inputBinding:
prefix: --min-read-counts=
position: 12
separate: false
- id: gzip
label: gzip
doc: Compresses the output file with BGZF.
type:
- boolean
- 'null'
inputBinding:
prefix: --gzip
position: 14
- id: pseudo_snps
label: pseudo_snps
doc: |-
Every MULTIPLE positions, if there is no SNP,insert a blank record with the total count at theposition.
type:
- string
- 'null'
inputBinding:
prefix: --pseudo-snps=
position: 16
separate: false
- id: vcf_file
label: vcf_file
type: File
inputBinding:
position: 18
- id: output_filename
label: output_filename
type:
- string
- 'null'
default: generated.csv.gz
inputBinding:
position: 19
- id: normal
label: normal
type: File
secondaryFiles:
- pattern: .bai
inputBinding:
position: 20
- id: tumour
label: tumour
type: File
secondaryFiles:
- pattern: .bai
inputBinding:
position: 21
outputs:
- id: out
label: out
type: File
outputBinding:
glob: generated.csv.gz
loadContents: false
stdout: _stdout
stderr: _stderr
baseCommand:
- LD_LIBRARY_PATH=/opt/conda/lib /snp-pileup
arguments: []
hints:
- class: ToolTimeLimit
timelimit: |-
$([inputs.runtime_seconds, 86400].filter(function (inner) { return inner != null })[0])
id: FacetsSnpPileup