Workflow: Single-cell RNA-Seq Alignment

Fetched 2025-01-16 17:30:10 GMT

Single-cell RNA-Seq Alignment Runs Cell Ranger Count to quantify gene expression from a single-cell RNA-Seq library.

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Inputs

ID Type Title Doc
threads Integer (Optional)

Number of threads for those steps that support multithreading

expect_cells Integer (Optional)

Expected number of recovered cells

memory_limit Integer (Optional)

Maximum memory used (GB). The same will be applied to virtual memory

fastq_file_r1 File

FASTQ file R1 (optionally compressed)

fastq_file_r2 File

FASTQ file R2 (optionally compressed)

indices_folder Directory

Cell Ranger reference genome indices folder

include_introns Boolean (Optional)

Count reads mapping to intronic regions. This may improve sensitivity for samples with a significant amount of pre-mRNA molecules, such as nuclei.

force_expect_cells Boolean (Optional)

Force pipeline to use the expected number of recovered cell. The value provided in expect_cells will be sent to Cell Ranger Count as --force-cells. The latter will bypass the cell detection algorithm. Use this if the number of cells estimated by Cell Ranger is not consistent with the barcode rank plot.

Steps

ID Runs Label Doc
count_gene_expr
../tools/cellranger-count.cwl (CommandLineTool)
Cell Ranger Count Gene Expression

Cell Ranger Count Gene Expression

Quantifies gene expression from a single-cell RNA-Seq library.

Input parameters for Feature Barcode, Targeted Gene Expression and CRISPR-specific analyses are not implemented, therefore the correspondent outputs are also excluded.

Parameters set by default: --disable-ui - no need in any UI when running in Docker container --id - can be hardcoded as we rename input files anyway --fastqs - points to the current directory, because input FASTQ files are staged there

Why do we need to rename input files? Refer to the \"My FASTQs are not named like any of the above examples\" section of https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/fastq-input
extract_fastq_r1
../tools/extract-fastq.cwl (CommandLineTool)
Extract FASTQ

Extract FASTQ

Extracts bzip2-/gzip-/zip-compressed FASTQ file. If several FASTQ files are provided, they will be concatenated in the order that corresponds to files in input. Bash script's logic: - disable case sensitive glob check - check if root name of input file already include '.fastq' or '.fq' extension. If yes, set DEFAULT_EXT to \"\", otherwise use '.fastq' - check file type, decompress if needed - return 1, if file type is not recognized This script also works of input file doesn't have any extension at all.
extract_fastq_r2
../tools/extract-fastq.cwl (CommandLineTool)
Extract FASTQ

Extract FASTQ

Extracts bzip2-/gzip-/zip-compressed FASTQ file. If several FASTQ files are provided, they will be concatenated in the order that corresponds to files in input. Bash script's logic: - disable case sensitive glob check - check if root name of input file already include '.fastq' or '.fq' extension. If yes, set DEFAULT_EXT to \"\", otherwise use '.fastq' - check file type, decompress if needed - return 1, if file type is not recognized This script also works of input file doesn't have any extension at all.
cellbrowser_build
../tools/cellbrowser-build-cellranger.cwl (CommandLineTool)
Cell Ranger Count/Aggregate to UCSC Cell Browser

Cell Ranger Count/Aggregate to UCSC Cell Browser

Exports clustering results from Cell Ranger Count Gene Expression and Cell Ranger Aggregate experiments into compatible with UCSC Cell Browser format.
compress_html_data_folder
../tools/tar-compress.cwl (CommandLineTool)
TAR compress

TAR compress

Creates compressed TAR file from a folder
compress_raw_feature_bc_matrices_folder
../tools/tar-compress.cwl (CommandLineTool)
TAR compress

TAR compress

Creates compressed TAR file from a folder
compress_secondary_analysis_report_folder
../tools/tar-compress.cwl (CommandLineTool)
TAR compress

TAR compress

Creates compressed TAR file from a folder
compress_filtered_feature_bc_matrix_folder
../tools/tar-compress.cwl (CommandLineTool)
TAR compress

TAR compress

Creates compressed TAR file from a folder

Outputs

ID Type Label Doc
molecule_info_h5 File

Molecule-level information used by cellranger aggr to aggregate samples into larger datasets

web_summary_report File

Run summary metrics and charts in HTML format

loupe_browser_track File

Loupe Browser visualization and analysis file

metrics_summary_report File

Run summary metrics in CSV format

possorted_genome_bam_bai File

Indexed reads aligned to the genome and transcriptome annotated with barcode information

count_gene_expr_stderr_log File

stderr log generated by cellranger count

count_gene_expr_stdout_log File

stdout log generated by cellranger count

raw_feature_bc_matrices_h5 File

Unfiltered feature-barcode matrices containing all barcodes in HDF5 format

compressed_html_data_folder File

Compressed folder with UCSC Cellbrowser formatted results

filtered_feature_bc_matrix_h5 File

Filtered feature-barcode matrices containing only cellular barcodes in HDF5 format

raw_feature_bc_matrices_folder File

Compressed folder with unfiltered feature-barcode matrices containing all barcodes in MEX format

secondary_analysis_report_folder File

Compressed folder with secondary analysis results including dimensionality reduction, cell clustering, and differential expression

filtered_feature_bc_matrix_folder File

Compressed folder with filtered feature-barcode matrices containing only cellular barcodes in MEX format

html json turtle jsonld rdfxml svg png dot zip ro yaml raw
Permalink: https://w3id.org/cwl/view/git/8614e5d20f5e81dce537216bd340cdbc1067bbc7/workflows/sc-rna-align-wf.cwl