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Update rnasum input parameters #480

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Apr 5, 2024
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2 changes: 1 addition & 1 deletion config/project.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -473,7 +473,7 @@ projects:
- name: 0.5.0
path: 0.5.0/rnasum__0.5.0.cwl
ica_workflow_version_name: 0.5.0
modification_time: 2024-04-04T02:32:11UTC
modification_time: 2024-04-05T00:48:41UTC
run_instances: []
- name: samtools-stats
path: samtools-stats
Expand Down
2 changes: 1 addition & 1 deletion config/tool.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -453,7 +453,7 @@ tools:
md5sum: 8b05e1c40c2ff0befb56df0b31560c04
- name: 0.5.0
path: 0.5.0/rnasum__0.5.0.cwl
md5sum: 796c913d5ca9630fe96eae4dc4b93308
md5sum: 81ecc826d2909bc215249864b2ff3422
categories: []
- name: samtools-stats
path: samtools-stats
Expand Down
97 changes: 45 additions & 52 deletions tools/rnasum/0.5.0/rnasum__0.5.0.cwl
Original file line number Diff line number Diff line change
Expand Up @@ -39,18 +39,6 @@ hints:

baseCommand: [ "rnasum.R" ]

arguments:
- position: -5
valueFrom: "--batch_rm"
- position: -4
valueFrom: "--filter"
- position: -3
valueFrom: "--log"
- position: -2
valueFrom: "--save_tables"
- position: -1
valueFrom: "--pcgr_splice_vars"

inputs:
# Input folders
dragen_wts_dir:
Expand All @@ -60,6 +48,13 @@ inputs:
type: Directory?
inputBinding:
prefix: "--dragen_wts_dir"
dragen_mapping_metrics:
label: dragen fusions
doc: |
Location of the mapping metrics from Dragen RNA-seq pipeline
type: File?
inputBinding:
prefix: "--dragen_mapping_metrics"
dragen_fusions:
label: dragen fusions
doc: |
Expand Down Expand Up @@ -95,7 +90,7 @@ inputs:
type: File?
inputBinding:
prefix: "--arriba_tsv"
umccrise_directory:
umccrise:
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Thanks for changing this :-)

label: umccrise directory
doc: |
The umccrise output directory
Expand Down Expand Up @@ -185,13 +180,6 @@ inputs:
type: int?
inputBinding:
prefix: "--pcgr_tier"
pcgr_splice_vars:
label: pcgr splice vars
doc: |
Include non-coding splice region variants reported in PCGR.
type: boolean?
inputBinding:
prefix: "--pcgr_splice_vars"
cn_loss:
label: cn loss
default: 5
Expand All @@ -208,20 +196,6 @@ inputs:
type: int?
inputBinding:
prefix: "--cn_gain"
clinical_info:
label: clinical info
doc: |
xslx file with clinical information.
type: File?
inputBinding:
prefix: "--clinical_info"
clinical_id:
label: clinical id
doc: |
ID required to match sample with the subject clinical information (specified in flag --clinical_info).
type: string?
inputBinding:
prefix: "--clinical_id"
subject_id:
label: subject id
doc: |
Expand Down Expand Up @@ -260,50 +234,69 @@ inputs:
type: int?
inputBinding:
prefix: "--top_genes"
hide_code_btn:
label: hide code btn
doc: |
Hide the "Code" button allowing to show/hide code chunks in the final HTML report.
type: boolean?
inputBinding:
prefix: "--hide_code_btn"
grch_version:
label: grch version
doc: |
Human reference genome version used for genes annotation.
type: int?
inputBinding:
prefix: "--grch_version"
dataset:
label: dataset
label: dataset
default: "PANCAN"
doc: |
Reference dataset selection from https://github.com/umccr/RNAsum/blob/master/TCGA_projects_summary.md
type: string
inputBinding:
prefix: "--dataset"
batch_rm:
label: batch rm
default: TRUE
doc: |
Remove batch-associated effects between datasets. Available options are: "TRUE" (default) and "FALSE"
type: boolean?
inputBinding:
prefix: "--batch_rm"
filter:
label: filter
default: TRUE
doc: |
Filtering out low expressed genes. Available options are: "TRUE" (default) and "FALSE"
type: boolean?
inputBinding:
prefix: "--filter"
log:
label: log
default: TRUE
doc: |
Log (base 2) transform data before normalisation. Available options are: "TRUE" (default) and "FALSE"
type: boolean?
inputBinding:
prefix: "--log"
save_tables:
label: save tables
default: TRUE
doc: |
save tables
Save interactive summary tables as HTML. Available options are: "TRUE" (default) and "FALSE"
type: boolean?
inputBinding:
prefix: "--save_tables"
pcgr_splice_vars:
label: PCGR splice vars
default: TRUE
doc: |
Include non-coding splice region variants reported in PCGR. Available options are: "TRUE" (default) and "FALSE"
type: boolean?
inputBinding:
prefix: "--pcgr_splice_vars"

outputs:
rnasum_output_directory:
label: RNAsum output directory
doc: Output directory containing all outputs of the RNAsum run
type: Directory
outputBinding:
glob: "$(inputs.report_directory)"
glob: "$(inputs.report_dir)"
rnasum_html:
label: rnasum html
doc: |
The HTML report output of RNAsum
type: File
outputBinding:
glob: "$(inputs.report_directory)/$(inputs.sample_name).RNAseq_report.html"
glob: "$(inputs.report_dir)/$(inputs.sample_name).RNAseq_report.html"

successCodes:
- 0
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