API
solosis-cli
Command line utility for the Cellular Genetics programme at the Wellcome Sanger Institute
solosis-cli [OPTIONS] COMMAND [ARGS]...
Options
- --version
Show the version and exit.
alignment
Commands for running alignment tools.
solosis-cli alignment [OPTIONS] COMMAND [ARGS]...
cellranger-arc
Cell Ranger ARC aligns GEX & ATAC seq reads…
Cell Ranger ARC (2.0.2) Software suite designed for analysing & interpreting scRNA seq data, including multi-omics data.
solosis-cli alignment cellranger-arc [OPTIONS]
Options
- --libraries <libraries>
Path to a single libraries file
- --librariesfile <librariesfile>
Path to a CSV containing paths to multiple library files
- --create-bam
Generate BAM files for each library
- --version <version>
Cell Ranger ARC version to use (e.g., ‘2.0.2’)
cellranger-count
Cell Ranger aligns and analyses sc-RNA seq data…
Cell Ranger (7.2.0) performs sample demultiplexing, barcode processing, and gene counting for single-cell 3’ and 5’ RNA-seq data, as well as V(D)J transcript sequence assembly.
solosis-cli alignment cellranger-count [OPTIONS]
Options
- --sample <sample>
Sample ID (string)
- --samplefile <samplefile>
Path to a CSV or TSV file containing sample IDs
- --create-bam
Generate BAM files for each sample
- --version <version>
Cell Ranger version to use (e.g., ‘7.2.0’)
starsolo
STARsolo aligns single-cell RNA sequencing reads…
STARsolo (2.7.11b) Aligner processes scRNA seq data to generate GEX matrices & identify cell-specific transcripts.
solosis-cli alignment starsolo [OPTIONS]
Options
- --sample <sample>
Sample ID (string)
- --samplefile <samplefile>
Path to a CSV or TSV file containing sample IDs
filesystem
Commands for file and directory operations.
solosis-cli filesystem [OPTIONS] COMMAND [ARGS]...
disk-usage
Check disk usage for Team298 workspaces.
This command retrieves the disk usage for Team298 workspaces including NFS, Lustre, Warehouse & /archive/team298 irods storage systems.
solosis-cli filesystem disk-usage [OPTIONS]
filecount
Check filecounts for Team298 workspaces.
This command retrieves the filecounts for Team298 workspaces including NFS, Lustre, or warehouse storage systems.
solosis-cli filesystem filecount [OPTIONS]
irods
Commands for working with iRODS.
solosis-cli irods [OPTIONS] COMMAND [ARGS]...
iget-cellranger
Downloads cellranger outputs from iRODS…
solosis-cli irods iget-cellranger [OPTIONS]
Options
- --sample <sample>
Sample ID (string).
- --samplefile <samplefile>
Path to a CSV or TSV file containing sample IDs.
- --retainbam
Include the BAM file in the download. By default, it is excluded.
- --overwrite
Overwrite existing output directories
iget-fastqs
Downloads fastqs from iRODS…
Utilising NF-irods-to-fastq pipeline developed by Cellgeni. Pulled directly from Github repo- up-to-date.
solosis-cli irods iget-fastqs [OPTIONS]
Options
- --sample <sample>
Sample ID (string)
- --samplefile <samplefile>
Path to a CSV or TSV file containing sample IDs
ncl-bsu
Commands for Newcastle University BSU.
solosis-cli ncl-bsu [OPTIONS] COMMAND [ARGS]...
migrate
Placeholder
solosis-cli ncl-bsu migrate [OPTIONS]
sc-rna
Commands for single-cell RNA-seq workflows.
solosis-cli sc-rna [OPTIONS] COMMAND [ARGS]...
cellbender
Removes droplets & ambient RNA from scRNA-seq data…
Cellbender (0.3.0.) Removes droplets & ambient RNA from scRNA seq data.
solosis-cli sc-rna cellbender [OPTIONS]
Options
- --samplefile <samplefile>
Required Sample file text file
- --total_droplets_included <total_droplets_included>
Required total_droplets_included
merge-h5ad
Merges multiple h5ads objects…
Please run solosis-cli sc-rna scanpy –samplefile … command first.
Example: /lustre/scratch126/cellgen/team298/soft/bin/examples/irods_download.txt Input file should have 3 mandatory columns: 1st column: sanger_id, 2nd column: sample_name, LAST column: irods path
solosis-cli sc-rna merge-h5ad [OPTIONS]
Options
- --samplefile <samplefile>
Required Sample file text file
- --merged_filename <merged_filename>
Required Output file name: Eg. merged.h5ad
scanpy
Basic Scanpy workflow for scRNA-seq data, generates Jupyter Notebook …
Example: /lustre/scratch126/cellgen/team298/soft/bin/examples/irods_download.txt Input file should have 3 mandatory columns: 1st column: sanger_id, 2nd column: sample_name, LAST column: irods path
solosis-cli sc-rna scanpy [OPTIONS]
Options
- --samplefile <samplefile>
Required Sample file text file
- --sample_basedir <sample_basedir>
sample database folder