Workflow: BD Rhapsody™ WTA Analysis Pipeline
Fetched 2024-11-27 08:25:34 GMT
Verified with cwltool version 3.1.20230201224320
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 | |
| Seq_Run | String (Optional) | ||
| Run_Name | String (Optional) | Run Name |
This is a name for output files, for example Experiment1_Metrics_Summary.csv. Default if left empty is to name run based on a library. Any non-alpha numeric characters will be changed to a hyphen. |
| Use_DBEC | Boolean (Optional) | ||
| AbSeq_UMI | Integer (Optional) | ||
| 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) | Sample Tag Names |
Specify the Sample Tag number followed by - (hyphen) and a sample name to appear in the output files. For example: 4-Ramos. Should be alpha numeric, with + - and _ allowed. Any special characters: &, (), [], {}, <>, ?, | will be corrected to underscores. |
| Extra_Seqs | File (Optional) | ||
| Barcode_Num | Integer (Optional) | ||
| VDJ_Version | https://w3id.org/cwl/view/git/c8d75785fd6accf3b47d1f9ee056675611e22e61/wf.cwl#main/VDJ_Version/VDJ_Version (Optional) | VDJ Species Version |
The VDJ species and chain types. This option should only be set for VDJ experiment. |
| Generate_Bam | Boolean (Optional) | Generate Bam Output |
By default, a Bam file that is comprised of reads from all the input libraries is generated. However, this can consume a lot of compute and disk resources. By setting this field to false, the Bam is no longer created. |
| MinChunkSize | Integer (Optional) | ||
| 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. |
| Read_Filter_Off | Boolean (Optional) | ||
| Target_analysis | Boolean (Optional) | ||
| 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 | |
| VDJ_JGene_Evalue | Float (Optional) | e-value threshold for J gene |
The e-value threshold for J gene call by IgBlast/PyIR, default is set as 0.001 |
| VDJ_VGene_Evalue | Float (Optional) | e-value threshold for V gene |
The e-value threshold for V gene call by IgBlast/PyIR, default is set as 0.001 |
| NumRecordsPerSplit | Long (Optional) | ||
| Putative_Cell_Call | https://w3id.org/cwl/view/git/c8d75785fd6accf3b47d1f9ee056675611e22e61/wf.cwl#main/Putative_Cell_Call/Putative_Cell_Call (Optional) | Putative Cell Calling |
Specify the data to be used for putative cell calling. mRNA is the default selected option. |
| Sample_Tags_Version | https://w3id.org/cwl/view/git/c8d75785fd6accf3b47d1f9ee056675611e22e61/wf.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. |
| Exclude_Intronic_Reads | Boolean (Optional) | Exclude Intronic Reads |
By default, reads aligned to exons and introns are considered and represented in molecule counts. Including intronic reads may increase sensitivity, resulting in an increase in molecule counts and the number of genes per cell for both cellular and nuclei samples. Intronic reads may indicate unspliced mRNAs and are also useful, for example, in the study of nuclei and RNA velocity. When set to true, intronic reads will be excluded. |
| Supplemental_Reference | File[] (Optional) | Supplemental Reference | |
| Transcriptome_Annotation | File | Transcriptome Annotation |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| AlignR2 |
wf.cwl#AlignR2.cwl
(CommandLineTool)
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| Metrics |
wf.cwl#Metrics.cwl
(CommandLineTool)
|
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| Version |
wf.cwl#Version.cwl
(CommandLineTool)
|
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| AddtoBam |
wf.cwl#AddtoBam.cwl
(CommandLineTool)
|
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| IndexBAM |
wf.cwl#IndexBAM.cwl
(CommandLineTool)
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| MergeBAM |
wf.cwl#MergeBAM.cwl
(CommandLineTool)
|
||
| AnnotateR1 |
wf.cwl#AnnotateR1.cwl
(CommandLineTool)
|
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| AnnotateR2 |
wf.cwl#AnnotateR2.cwl
(CommandLineTool)
|
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| BundleLogs |
wf.cwl#BundleLogs.cwl
(ExpressionTool)
|
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| Start_Time |
a615493dba82c34c61e316741baca0d2
(ExpressionTool)
|
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| CheckFastqs |
wf.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. |
|
| Bam_Settings |
wf.cwl#BamSettings.cwl
(ExpressionTool)
|
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| GetDataTable |
wf.cwl#GetDataTable.cwl
(CommandLineTool)
|
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| VDJ_Settings |
wf.cwl#VDJ_Settings.cwl
(ExpressionTool)
|
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| AnnotateReads |
wf.cwl#AnnotateReads.cwl
(CommandLineTool)
|
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| Name_Settings |
wf.cwl#NameSettings.cwl
(ExpressionTool)
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| PairReadFiles |
wf.cwl#PairReadFiles.cwl
(ExpressionTool)
|
PairReadFiles takes an array of split files and pairs them, such that an R1 file is transferred to the QualityFilter with its corresponding R2 file. The original FASTQ files are paired in CheckFastqs and then split and sub-sampled in SplitAndSubsample. The pairing information is taken from CheckFastqs. |
|
| CheckReference |
wf.cwl#CheckReference.cwl
(CommandLineTool)
|
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| MergeMultiplex |
48704625cc45f4bceb403f3fc8656b6f
(ExpressionTool)
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| AnnotateMolecules |
wf.cwl#AnnotateMolecules.cwl
(CommandLineTool)
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| Internal_Settings |
wf.cwl#InternalSettings.cwl
(ExpressionTool)
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| Metadata_Settings |
wf.cwl#Metadata.cwl
(CommandLineTool)
|
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| SplitAndSubsample |
wf.cwl#SplitAndSubsample.cwl
(Workflow)
|
SplitAndSubsample splits, subsamples and formats read files to be deposited in QualityFilter. |
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| QualityFilterOuter |
wf.cwl#QualityFilterOuter.cwl
(Workflow)
|
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| Subsample_Settings |
wf.cwl#SubsampleSettings.cwl
(ExpressionTool)
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| VDJ_Compile_Results |
wf.cwl#VDJ_Compile_Results.cwl
(CommandLineTool)
|
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| Dense_to_Sparse_File |
wf.cwl#DensetoSparseFile.cwl
(CommandLineTool)
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| VDJ_Analyze_Reads_IG |
wf.cwl#VDJ_Analyze_Reads_IG.cwl
(Workflow)
|
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| Multiplexing_Settings |
wf.cwl#MultiplexingSettings.cwl
(ExpressionTool)
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| Uncompress_Datatables |
wf.cwl#UncompressDatatables.cwl
(Workflow)
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| VDJ_Analyze_Reads_TCR |
wf.cwl#VDJ_Analyze_Reads_TCR.cwl
(Workflow)
|
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| Intronic_Reads_Settings |
wf.cwl#IntronicReadsSettings.cwl
(ExpressionTool)
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| Dense_to_Sparse_Datatable |
wf.cwl#DensetoSparse.cwl
(CommandLineTool)
|
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| Putative_Cell_Calling_Settings |
wf.cwl#PutativeCellSettings.cwl
(ExpressionTool)
|
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| Dense_to_Sparse_Datatable_Unfiltered |
wf.cwl#DensetoSparse.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| Bam | File (Optional) | BAM File | |
| Logs | Directory | Pipeline Logs | |
| Bam_Index | File (Optional) | BAM Index | |
| Multiplex | File[] (Optional) | ||
| Data_Tables | File[] (Optional) | Data Tables | |
| vdjMetricsCsv | File (Optional) | vdjMetricsCsv | |
| Expression_Data | File (Optional) | Expression Matrix | |
| Metrics_Summary | File | Metrics Summary | |
| Bioproduct_Stats | File (Optional) | Bioproduct Statistics | |
| vdjCellsDatatable | File (Optional) | vdjCellsDatatable | |
| Dim_Reduction_Coord | File (Optional) | Dimensionality Reduction Coordinates | |
| Visual_Metrics_html | File (Optional) | Pipeline Report HTML | |
| Putative_Cells_Origin | File (Optional) | Putative Cells Origin | |
| Data_Tables_Unfiltered | File[] (Optional) | Unfiltered Data Tables | |
| vdjDominantContigsAIRR | File (Optional) | vdjDominantContigsAIRR | |
| vdjUnfilteredContigsAIRR | File (Optional) | vdjUnfilteredContigsAIRR | |
| Expression_Data_Unfiltered | File (Optional) | Unfiltered Expression Matrix | |
| vdjCellsDatatableUncorrected | File (Optional) | vdjCellsDatatableUncorrected | |
| Protein_Aggregates_Experimental | File (Optional) | Protein Aggregates (Experimental) | |
| Immune_Cell_Classification(Experimental) | File (Optional) | Immune Cell Classification (Experimental) |
https://w3id.org/cwl/view/git/c8d75785fd6accf3b47d1f9ee056675611e22e61/wf.cwl?part=main
