Workflow: BD Rhapsody™ WTA Analysis Pipeline
Fetched 2024-04-30 00:43:40 GMT
Verified with cwltool version 3.1.20221201130942
The BD Rhapsody™ WTA Analysis Pipeline is used to create sequencing libraries from single cell transcriptomes without having to specify a targeted panel. After sequencing, the analysis pipeline takes the FASTQ files, a reference genome file and a transcriptome annotation file for gene alignment. The pipeline generates molecular counts per cell, read counts per cell, metrics, and an alignment file.
- Selected
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- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| Reads | File[] | Reads | |
| Subsample | Float (Optional) | Subsample Reads |
Any number of reads >1 or a fraction between 0 < n < 1 to indicate the percentage of reads to subsample. |
| Tag_Names | String[] (Optional) | Tag Names |
Specify the Sample Tag number followed by - (hyphen) and a sample name to appear in the output files. For example: 4-Ramos. Do not use the special characters: &, (), [], {}, <>, ?, | |
| Subsample_Tags | Float (Optional) | Subsample Sample Tags |
Any number of reads > 1 or a fraction between 0 < n < 1 to indicate the percentage of tag reads to subsample. |
| Subsample_seed | Integer (Optional) | Subsample Seed |
For use when replicating a previous subsampling run only. Obtain the seed generated from the log file for the SplitFastQ node. |
| AbSeq_Reference | File[] (Optional) | AbSeq Reference | |
| Basic_Algo_Only | Boolean (Optional) | Disable Refined Putative Cell Calling |
Determine putative cells using only the basic algorithm (minimum second derivative along the cumulative reads curve). The refined algorithm attempts to remove false positives and recover false negatives, but may not be ideal for certain complex mixtures of cell types. Does not apply if Exact Cell Count is set. |
| Exact_Cell_Count | Integer (Optional) | Exact Cell Count |
Set a specific number (>=1) of cells as putative, based on those with the highest error-corrected read count |
| Reference_Genome | File | Reference Genome | |
| Sample_Tags_Version | https://w3id.org/cwl/view/git/b9ec66d82bc04934fbe9f9088ae7e802d72c4a4e/v1.8/rhapsody_wta_1.8.cwl#main/Sample_Tags_Version/Sample_Tags_Version (Optional) | Sample Tags Version |
The sample multiplexing kit version. This option should only be set for a multiplexed experiment. |
| Transcriptome_Annotation | File | Transcriptome Annotation |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| Metrics |
rhapsody_wta_1.8.cwl#Metrics.cwl
(CommandLineTool)
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| AddtoBam |
rhapsody_wta_1.8.cwl#AddtoBam.cwl
(CommandLineTool)
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| IndexBAM |
rhapsody_wta_1.8.cwl#IndexBAM.cwl
(CommandLineTool)
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| MergeBAM |
rhapsody_wta_1.8.cwl#MergeBAM.cwl
(CommandLineTool)
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| AnnotateR1 |
rhapsody_wta_1.8.cwl#AnnotateR1.cwl
(CommandLineTool)
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| AnnotateR2 |
rhapsody_wta_1.8.cwl#AnnotateR2.cwl
(CommandLineTool)
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| BundleLogs |
rhapsody_wta_1.8.cwl#BundleLogs.cwl
(ExpressionTool)
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| CheckFastqs |
rhapsody_wta_1.8.cwl#CheckFastqs.cwl
(CommandLineTool)
|
CheckFastqs does several quality control routines including: (1) ensuring that read pair file names are formatted correctly and contain a read pair mate; (2) disambiguating the \"Subsample Reads\" input and; (3) if not provided, generating a subsampling seed that the downstream instances can use. |
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| GetDataTable |
rhapsody_wta_1.8.cwl#GetDataTable.cwl
(CommandLineTool)
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| AnnotateReads |
rhapsody_wta_1.8.cwl#AnnotateReads.cwl
(CommandLineTool)
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| PairReadFiles |
rhapsody_wta_1.8.cwl#PairReadFiles.cwl
(ExpressionTool)
|
PairReadsFiles takes an array of split files and pairs them, such that an R1 file is transferred to a QualityFilter with its corresponding R2 file. Each file should be formatted as illumina outputs it from basespace: e.g. sample_L001_R1_001.fastq.gz. After being split, that sample file would be an array files named sample_L001_R1_001-00.fastq, sample_L001_R1_001-01.fastq, etc |
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| QualityFilter |
rhapsody_wta_1.8.cwl#QualityFilter.cwl
(CommandLineTool)
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| CheckReference |
rhapsody_wta_1.8.cwl#CheckReference.cwl
(CommandLineTool)
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| AnnotateMolecules |
rhapsody_wta_1.8.cwl#AnnotateMolecules.cwl
(CommandLineTool)
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| Internal_Settings |
rhapsody_wta_1.8.cwl#InternalSettings.cwl
(ExpressionTool)
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| SplitAndSubsample |
rhapsody_wta_1.8.cwl#SplitAndSubsample.cwl
(Workflow)
|
SplitAndSubsample splits, subsamples and formats read files to be deposited in QualityFilter. |
|
| FilteredDataTables |
rhapsody_wta_1.8.cwl#FilteredDataTables.cwl
(ExpressionTool)
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| Subsample_Settings |
rhapsody_wta_1.8.cwl#SubsampleSettings.cwl
(ExpressionTool)
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| Sparse_to_Dense_File |
rhapsody_wta_1.8.cwl#SparsetoDenseFile.cwl
(CommandLineTool)
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| Multiplexing_Settings |
rhapsody_wta_1.8.cwl#MultiplexingSettings.cwl
(ExpressionTool)
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| Uncompress_Datatables | |||
| Sparse_to_Dense_Datatable |
rhapsody_wta_1.8.cwl#SparsetoDense.cwl
(CommandLineTool)
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| Putative_Cell_Calling_Settings |
rhapsody_wta_1.8.cwl#PutativeCellSettings.cwl
(ExpressionTool)
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| Sparse_to_Dense_Datatable_Unfiltered |
rhapsody_wta_1.8.cwl#SparsetoDense.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| Logs | Directory | Pipeline Logs | |
| Bam_Index | File | Bam Index | |
| Final_Bam | File | Final BAM File | |
| Multiplex | File[] (Optional) | ||
| Data_Tables | File[] (Optional) | Data Tables | |
| Expression_Data | File (Optional) | Expression Matrix | |
| Metrics_Summary | File | Metrics Summary | |
| Cell_Label_Filter | File[] (Optional) | Cell Label Filter | |
| UMI_Adjusted_Stats | File (Optional) | UMI Adjusted Statistics | |
| Putative_Cells_Origin | File (Optional) | Putative Cells Origin | |
| Data_Tables_Unfiltered | File[] (Optional) | Unfiltered Data Tables | |
| Expression_Data_Unfiltered | File (Optional) | Unfiltered Expression Matrix |
https://w3id.org/cwl/view/git/b9ec66d82bc04934fbe9f9088ae7e802d72c4a4e/v1.8/rhapsody_wta_1.8.cwl?part=main
