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…kflow Create rnasum v1.1.0 pipeline
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workflows/rnasum-pipeline/1.1.0/rnasum-pipeline__1.1.0.cwl
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,294 @@ | ||
| cwlVersion: v1.1 | ||
| class: Workflow | ||
|
|
||
| # Extensions | ||
| $namespaces: | ||
| s: https://schema.org/ | ||
| $schemas: | ||
| - https://schema.org/version/latest/schemaorg-current-http.rdf | ||
|
|
||
| # Metadata | ||
| s:author: | ||
| class: s:Person | ||
| s:name: Alexis Lucattini | ||
| s:email: [email protected] | ||
| s:identifier: https://orcid.org/0000-0001-9754-647X | ||
|
|
||
| # ID/Docs | ||
| id: rnasum-pipeline--1.1.0 | ||
| label: rnasum-pipeline v(1.1.0) | ||
| doc: | | ||
| Documentation for rnasum-pipeline v1.1.0 | ||
|
|
||
| requirements: | ||
| InlineJavascriptRequirement: {} | ||
| ScatterFeatureRequirement: {} | ||
| MultipleInputFeatureRequirement: {} | ||
| StepInputExpressionRequirement: {} | ||
|
|
||
| inputs: | ||
| # Input folders | ||
| dragen_wts_dir: | ||
| label: dragen transcriptome directory | ||
| doc: | | ||
| Location of the results from Dragen RNA-seq pipeline | ||
| type: Directory? | ||
| dragen_mapping_metrics: | ||
| label: dragen mapping metrics | ||
| doc: | | ||
| Location of the mapping metrics from Dragen RNA-seq pipeline | ||
| type: File? | ||
| dragen_fusions: | ||
| label: dragen fusions | ||
| doc: | | ||
| Location of the fusion output from Dragen RNA-seq pipeline | ||
| type: File? | ||
| salmon: | ||
| label: salmom | ||
| doc: | | ||
| Location of the quantification output from salmon | ||
| type: File? | ||
| arriba_dir: | ||
| label: arriba directory | ||
| doc: | | ||
| Location of the arriba outputs directory | ||
| type: Directory? | ||
| arriba_pdf: | ||
| label: arriba pdf | ||
| doc: | | ||
| Location of the pdf output from arriba | ||
| type: File? | ||
| arriba_tsv: | ||
| label: arriba tsv | ||
| doc: | | ||
| Location of the tsv output from arriba | ||
| type: File? | ||
| umccrise: | ||
| label: umccrise directory | ||
| doc: | | ||
| The umccrise output directory | ||
| type: Directory? | ||
| manta_tsv: | ||
| label: manta tsv | ||
| doc: | | ||
| Location of the tsv output from manta | ||
| type: File? | ||
| report_dir: | ||
| label: report dir | ||
| doc: | | ||
| Desired location for the outputs | ||
| type: string | ||
| # Additional inputs | ||
| sample_name: | ||
| label: sample name | ||
| doc: | | ||
| Desired sample name to be presented in the report | ||
| type: string | ||
| transform: | ||
| label: transform | ||
| default: "CPM" | ||
| doc: | | ||
| Transformation method to be used when converting read counts | ||
| type: string? | ||
| norm: | ||
| label: norm | ||
| default: "TMM" | ||
| doc: | | ||
| Normalisation method | ||
| type: string? | ||
| scaling: | ||
| label: scaling | ||
| default: "gene-wise" | ||
| doc: | | ||
| Apply "gene-wise" (default) or "group-wise" data scaling | ||
| type: string? | ||
| drugs: | ||
| label: drugs | ||
| doc: | | ||
| Include drug matching section in the report. | ||
| type: boolean? | ||
| immunogram: | ||
| label: immunogram | ||
| doc: | | ||
| Include drug matching section in the report. | ||
| type: boolean? | ||
| pcgr_tiers_tsv: | ||
| label: pcgr tiers tsv | ||
| doc: | | ||
| Location of the tsv output from pcgr | ||
| type: File? | ||
| purple_gene_tsv: | ||
| label: purple gene tsv | ||
| doc: | | ||
| Location of the tsv output from purple | ||
| type: File? | ||
| pcgr_tier: | ||
| label: pcgr tier | ||
| default: 4 | ||
| doc: | | ||
| Tier threshold for reporting variants reported in PCGR. | ||
| type: int? | ||
| cn_loss: | ||
| label: cn loss | ||
| default: 5 | ||
| doc: | | ||
| CN threshold value to classify genes within lost regions. | ||
| type: int? | ||
| cn_gain: | ||
| label: cn gain | ||
| default: 95 | ||
| doc: | | ||
| CN threshold value to classify genes within gained regions. | ||
| type: int? | ||
| subject_id: | ||
| label: subject id | ||
| doc: | | ||
| Subject ID. If umccrise output is specified (flag --umccrise) then Subject ID | ||
| is extracted from there and used to overwrite this argument. | ||
| type: string? | ||
| sample_source: | ||
| label: sample source | ||
| doc: | | ||
| Source of investigated sample (e.g. fresh frozen tissue, organoid). | ||
| This information is for annotation purposes only | ||
| type: string? | ||
| dataset_name_incl: | ||
| label: dataset name incl | ||
| doc: | | ||
| Include dataset in the report and sample name. | ||
| type: boolean? | ||
| project: | ||
| label: project | ||
| doc: | | ||
| Project name. This information is for annotation purposes only | ||
| type: string? | ||
| top_genes: | ||
| label: top genes | ||
| default: 5 | ||
| doc: | | ||
| The number of top ranked genes to be presented. | ||
| type: int? | ||
| dataset: | ||
| label: dataset | ||
| default: "PANCAN" | ||
| doc: | | ||
| Reference dataset selection from https://github.com/umccr/RNAsum/blob/master/TCGA_projects_summary.md | ||
| type: string | ||
| batch_rm: | ||
| label: batch rm | ||
| default: TRUE | ||
| doc: | | ||
| Remove batch-associated effects between datasets. Available options are: "TRUE" (default) and "FALSE" | ||
| type: boolean? | ||
| filter: | ||
| label: filter | ||
| default: TRUE | ||
| doc: | | ||
| Filtering out low expressed genes. Available options are: "TRUE" (default) and "FALSE" | ||
| type: boolean? | ||
| log: | ||
| label: log | ||
| default: TRUE | ||
| doc: | | ||
| Log (base 2) transform data before normalisation. Available options are: "TRUE" (default) and "FALSE" | ||
| type: boolean? | ||
| save_tables: | ||
| label: save tables | ||
| default: TRUE | ||
| doc: | | ||
| Save interactive summary tables as HTML. Available options are: "TRUE" (default) and "FALSE" | ||
| type: boolean? | ||
| 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? | ||
|
|
||
| steps: | ||
| run_rnasum_step: | ||
| label: run rnasum step | ||
| doc: | | ||
| Run the rnasum pipeline | ||
| in: | ||
| dragen_wts_dir: | ||
| source: dragen_wts_dir | ||
| dragen_mapping_metrics: | ||
| source: dragen_mapping_metrics | ||
| dragen_fusions: | ||
| source: dragen_fusions | ||
| salmon: | ||
| source: salmon | ||
| arriba_dir: | ||
| source: arriba_dir | ||
| arriba_pdf: | ||
| source: arriba_pdf | ||
| arriba_tsv: | ||
| source: arriba_tsv | ||
| umccrise: | ||
| source: umccrise | ||
| manta_tsv: | ||
| source: manta_tsv | ||
| report_dir: | ||
| source: report_dir | ||
| sample_name: | ||
| source: sample_name | ||
| transform: | ||
| source: transform | ||
| norm: | ||
| source: norm | ||
| scaling: | ||
| source: scaling | ||
| drugs: | ||
| source: drugs | ||
| immunogram: | ||
| source: immunogram | ||
| pcgr_tiers_tsv: | ||
| source: pcgr_tiers_tsv | ||
| purple_gene_tsv: | ||
| source: purple_gene_tsv | ||
| pcgr_tier: | ||
| source: pcgr_tier | ||
| cn_loss: | ||
| source: cn_loss | ||
| cn_gain: | ||
| source: cn_gain | ||
| subject_id: | ||
| source: subject_id | ||
| sample_source: | ||
| source: sample_source | ||
| dataset_name_incl: | ||
| source: dataset_name_incl | ||
| project: | ||
| source: project | ||
| top_genes: | ||
| source: top_genes | ||
| dataset: | ||
| source: dataset | ||
| batch_rm: | ||
| source: batch_rm | ||
| filter: | ||
| source: filter | ||
| log: | ||
| source: log | ||
| save_tables: | ||
| source: save_tables | ||
| pcgr_splice_vars: | ||
| source: pcgr_splice_vars | ||
| out: | ||
| - id: rnasum_output_directory | ||
| - id: rnasum_html | ||
| run: ../../../tools/rnasum/1.1.0/rnasum__1.1.0.cwl | ||
|
|
||
| outputs: | ||
| rnasum_output_directory: | ||
| label: RNAsum output directory | ||
| doc: Output directory containing all outputs of the RNAsum run | ||
| type: Directory | ||
| outputSource: run_rnasum_step/rnasum_output_directory | ||
| rnasum_html: | ||
| label: rnasum html | ||
| doc: | | ||
| The HTML report output of RNAsum | ||
| type: File | ||
| outputSource: run_rnasum_step/rnasum_html |