Installation and Setup

sc-VirusScan by installed by following the below mentioned steps.

  1. Clone the Git Repository using: git clone https://github.com/maxplanck-ie/sc-VirusScan.git

  2. Change the directory to sc-virus-scan: cd sc-VirusScan

  3. The dependecies of sc-VirusScan can be installed from the provided env.yaml by using conda/mamba

    mamba env create -f env.yaml -n sc-VirusScan

  4. sc-VirusScan requires CellRanger as part of dependencies which can be installed from here.

  5. Upon successfull installation of CellRanger, the CellRanger path needs to be updated in the config.yaml file accordingly

  6. Lastly, the config.yaml needs to be modified as per your system environment variables. More information about config.yaml along with its description can be found here.

Contents of config.yaml file

samplesheet : #Path to samplesheet file. More details about Samplesheet schema can be found below.
mode : #Pipeline mode to execute. (synapse | sra | local)
local_data_dir : #If local mode chosen, specify the directory path for the input files here.
kraken_db: #Path to Custom KrakenDB. More details can be found below.
cellranger: #Path of CellRanger Executable.
transcriptome : #Path to your human transcriptome required from CellRanger count
scripts_dir:  #Path to scripts directory present in base directory of the workflow

Description of config.yaml file

  1. samplesheet : The pipeline requires a samplesheet.tsv file to initiate the analysis. The samplesheet is a tab seperated file (TSV) acts as blueprint schema for analysis. Depending on the mode of pipeline, there are two reprensatative schema of samplesheet file. The provided samplesheet file will be then used to download the files from SRA database or Synapse AD Knowledge Portal and perform subsequent analysis on it.

    1. SRA mode (SRA): For running the pipeline in SRA mode, the user needs to provide a list of SRA Ids as shown in the example below. This file is further used to download the files from SRA database and perform analysis on it.

    Samples
SRR13419001
SRR13419002
SRR13419003
SRR13419004
SRR13419005

    1. Synapse mode (synapse): To execute the pipeline in synapse mode, user needs to generate the samplesheet.tsv with the help of synapse_fetch.py script present in the scripts directory of the repository. This scripts takes a Parent SynapseID as input and internally programmatically queries the Synapse Server to retreive all the associated Syanpse Ids for the raw FASTQ files under the provided parent SynapseID and returning a Tab-Sepated file consisting of SampleName, Read1 SynapseID, Read2 SynapseID as representated below. This obtained file is further used to download the files from Synapse AD Knowledge Portal and perform analysis on it.

    Samples        R1      R2
D17-8765_S1L1   syn18641014     syn18641249
D17-8765_S1L2   syn18641325     syn18641475
D17-8765_S1L3   syn18641515     syn18641599
D17-8765_S1L4   syn18641650     syn18641733
D17-8766_S2L1   syn18641776     syn18641855

    1. Local mode (local):To execute the pipeline in local mode (ie. files are pre-downloaded),user needs to specify the Sample names in samplesheet.tsv file. Along with this, user has to provide the path to the directory where the files are present in the config.yaml file under local_data_dir key.

  2. mode (SRA | synapse): Currently, sc-VirusScan accomodates two distinct modes depending on the source of input data: Sequence Read Archive (SRA) and Synapse AD Portal (synapse) for specifying input files for analysis. Depending on the input data type, the mode can be modified in the config.yaml file.

  3. kraken_db: As sc-VirusScan consists of viral screening module internally relying on Kraken2 for rapid taxonomic classification, it requires a KrakenDB in the backend. One can provide pre-built Kraken2 database available here or create a custom Kraken database based on analysis specificity. The path of downloaded Kraken2 database, needs to be assigned to krakendb key in config.yaml file.

  4. cellranger: Path of CellRanger executable. This can be located using by the command which cellranger.

5. transcriptome: The CellRanger count requires a Human reference transcriptome for scRNA-seq analysis module. This reference transcriptome can be either be manually built using Cellranger mkref as described here or can be downloaded pre-built from 10X Genomics avalaible here. Once the transcriptome is downloaded/built, specify its path in the config.yaml file corresponding to transcriptome key.

  1. scripts_dir: This path refers to the scripts directory present in the base directory of the workflow.

Important Note For Synapse Data Analysis mode

Before you can download a file from Synapse, you must determine whether you have access to it. Further information about Synapse Data Access can be found here.

In order to download and analyse data from Synapse Portal, user needs a .synpaseConfig file located in ~/.synapseConfig directory. This file contains individual Username and Access Token to allow access to Synapse programmatically (Automatically taken care by the pipeline) and download the relevant data based on the user input. More information on setting up the synapseConfig file can be found here.

Steps to setup .synapseConfig file

  1. Check in the home directory if .synapseConfig file exists.

  2. If not, download the config template from here

  3. Once downloaded, the user needs to update the fields of username and authtoken. An example is respresented below:

###########################
# Login Credentials       #
###########################

## Used for logging in to Synapse
## Alternatively, you can use rememberMe=True in synapseclient.login or login subcommand of the commandline client.
[authentication]
username = YOUR_SYNAPSE_USERNAME
authtoken = YOUR_SYNAPSE_AUTHENTICATION_TOKEN

  1. Authentication Token can be generated from your Synapse User Account. More information can be found here.

  2. After the changes mentioned above, the .synapseConfig file is ready to be used and can be utilized by sc-VirusScan automatically.