Workflow: Single-Cell Preprocessing Pipeline
Devel version of Single-Cell Preprocessing Pipeline ===================================================
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
ID | Type | Title | Doc |
---|---|---|---|
alias | String | Experiment short name/Alias | |
threads | Integer (Optional) | Number of threads |
Number of threads for those steps that support multithreading |
fastq_file_1 | File [FASTQ] | FASTQ file 1 (optionally compressed) |
FASTQ file 1 (optionally compressed) |
fastq_file_2 | File [FASTQ] | FASTQ file 2 (optionally compressed) |
FASTQ file 2 (optionally compressed) |
memory_limit | String (Optional) | Maximum memory used |
Maximum memory used |
sc_technology | https://w3id.org/cwl/view/git/09267e79fd867aa68a219c69e6db7d8e2e877be2/workflows/single-cell-preprocess.cwl#sc_technology/sc_technology | Single-cell technology used |
Single-cell technology used |
workflow_type | https://w3id.org/cwl/view/git/09267e79fd867aa68a219c69e6db7d8e2e877be2/workflows/single-cell-preprocess.cwl#workflow_type/workflow_type (Optional) | Workflow type |
Type of workflow. Use lamanno to calculate RNA velocity based on La Manno et al. 2018 logic. Use nucleus to calculate RNA velocity on single-nucleus RNA-seq reads. Default: standard |
genome_fasta_file | File [FASTA] | Reference genome FASTA file |
Reference genome FASTA file that includes all chromosomes |
annotation_gtf_file | File [GTF] | GTF annotation file |
GTF annotation file that includes refGene and mitochondrial DNA annotations |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
extract_fastq_1 |
../tools/extract-fastq.cwl
(CommandLineTool)
|
Tool to decompress input FASTQ file(s). 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_2 |
../tools/extract-fastq.cwl
(CommandLineTool)
|
Tool to decompress input FASTQ file(s). 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 |
|
prepare_indices |
../tools/kb-ref.cwl
(CommandLineTool)
|
Builds a kallisto index, transcript-to-gene mapping and cDNA/mismatch FASTA files.
If workflow_type is lamanno or nucleus tool will produce additional three
outputs:
- intron FASTA file
- cDNA transcripts-to-capture TSV file
- intron transcripts-to-capture TSV file
Otherwise the correspondent outputs will be null. |
|
collect_statistics |
single-cell-preprocess.cwl#collect_statistics/4f83b677-3b75-4da5-acb6-a2828a4d6ad0
(CommandLineTool)
|
||
compress_counts_folder |
../tools/tar-compress.cwl
(CommandLineTool)
|
Compresses input directory to tar.gz |
|
generate_counts_matrix |
../tools/kb-count.cwl
(CommandLineTool)
|
Uses kallisto to pseudoalign reads and bustools to quantify the data. |
|
run_fastqc_for_fastq_1 |
../tools/fastqc.cwl
(CommandLineTool)
|
Tool runs FastQC from Babraham Bioinformatics |
|
run_fastqc_for_fastq_2 |
../tools/fastqc.cwl
(CommandLineTool)
|
Tool runs FastQC from Babraham Bioinformatics |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
whitelist_file | File | Whitelisted barcodes |
Whitelisted barcodes that correspond to the used single-cell technology |
ec_mapping_file | File | Mapping equivalence classes to transcripts |
Mapping equivalence classes to transcripts generated by kallisto bus |
transcripts_file | File | Transcript names |
Transcript names file generated by kallisto bus |
kallisto_bus_report | File | Pseudoalignment report |
Pseudoalignment report generated by kallisto bus |
not_sorted_bus_file | File | Not sorted BUS file |
Not sorted BUS file generated by kallisto bus |
collected_statistics | File | Collected statistics in Markdown format |
Collected statistics in Markdown format |
fastqc_report_fastq_1 | File | FastqQC report for FASTQ file 1 |
FastqQC report for FASTQ file 1 |
fastqc_report_fastq_2 | File | FastqQC report for FASTQ file 2 |
FastqQC report for FASTQ file 2 |
bustools_inspect_report | File | Report summarizing BUS file content |
Report summarizing BUS file content generated by bustools inspect |
counts_unfiltered_folder | File | Compressed folder with count matrix files |
Compressed folder with count matrix files generated by bustools count |
corrected_sorted_bus_file | File | Sorted BUS file with corrected barcodes |
Sorted BUS file with corrected barcodes generated by bustools correct |
prepare_indices_stderr_log | File | stderr log generated by kb ref |
stderr log generated by kb ref |
prepare_indices_stdout_log | File | stdout log generated by kb ref |
stdout log generated by kb ref |
generate_counts_matrix_stderr_log | File | stderr log generated by kb count |
stderr log generated by kb count |
generate_counts_matrix_stdout_log | File | stdout log generated by kb count |
stdout log generated by kb count |
https://w3id.org/cwl/view/git/09267e79fd867aa68a219c69e6db7d8e2e877be2/workflows/single-cell-preprocess.cwl