Workflow: scRNA-seq pipeline using Salmon and Alevin
Fetched 2023-01-04 09:23:22 GMT
Verified with cwltool version 3.1.20221201130942
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source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| threads | Integer | Number of threads for Salmon | |
| fastq_dir | Directory | Directory containing FASTQ files |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| fastqc |
steps/fastqc.cwl
(CommandLineTool)
|
Runs fastQC on each fastq file in fastq directory | |
| salmon |
steps/salmon.cwl
(CommandLineTool)
|
Run Salmon Alevin tool on FASTQ input | |
| qc_checks |
steps/qc.cwl
(CommandLineTool)
|
Compute QC measures | |
| cluster_diffexpr |
steps/cluster-diffexpr.cwl
(CommandLineTool)
|
Compute differentially expressed genes between each cluster and the rest | |
| filter_normalize |
steps/filter-normalize.cwl
(CommandLineTool)
|
Filtering and normalization | |
| alevin_to_anndata |
steps/alevin-to-anndata.cwl
(CommandLineTool)
|
Convert Alevin sparse output to anndata.AnnData object, save as h5ad | |
| dim_reduce_cluster |
steps/dim-reduction-clustering.cwl
(CommandLineTool)
|
Dimensionality reduction and clustering |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| umap_pdf | File | UMAP dimensionality reduction plot | |
| qc_results | File | Quality control metrics | |
| count_matrix | File | Count matrix from Alevin | |
| report_files | File[] | HTML reports with embedded graphs | |
| zipped_files | File[] | Individual graph files and additional data files containing the raw data from which plots were drawn. | |
| cluster_marker_genes | File | Cluster marker genes | |
| dim_reduced_clustered | File | Dimensionality reduced and clustered data | |
| marker_gene_plot_logreg | File | Cluster marker genes, logreg method | |
| marker_gene_plot_t_test | File | Cluster marker genes, t-test |
Permalink:
https://w3id.org/cwl/view/git/c01ba083d8467df40f3b87a86712a3965111d90e/pipeline.cwl
