pandora2eager

Gather information from Pandora and format it for use with nf-core/eager.

Quickstart

To run pandora2eager.R you will need an input file containing a list of Pandora sequencing IDs you wish to include in your eager run. An example file with 5 sequencing IDs can be seen below.

$ cat input_seq_IDs_file.txt
ABC001.A0101.TF1.1
ABC001.A0101.SG1.1
ABC001.A0101.SG1.2
ABC001.A0102.TF1.1
ABC002.A0101.TF1.1

⚠️ These IDs are made-up and do not correspond to any valid entries in Pandora.

Running the pandora2eager Singularity container

At EVA, a container is available that takes care of all dependencies needed for running pandora2eager.R. You will find all past and current versions of the container and a required wrapper script for using it at /mnt/archgen/tools/pandora2eager/. Usage information for the wrapper script pandora2eager.sh is provided below:

Usage: pandora2eager.sh [OPTIONS] /path/to/input_seq_IDs_file.txt

Options:
	-f/--file_type		Specify the file type of the input files. Accepted values are: 'bam', 'fastq_pathogens'.
				Note: if this flag is not provided, raw fastq will be used to generate the table
	-r/--rename		Changes all dots (.) in the Library_ID field of the output to underscores (_).
				Some tools used in nf-core/eager will strip everything after the first dot (.)
				from the name of the input file, which can cause naming conflicts in rare cases.
	-d/--debug		Activate debug mode, it produces a file called: 'Debug_table.txt'.
	-s/--add_ss_suffix	Adds the suffix '_ss' to the Sample_ID and Library_ID field of the output for single-stranded libraries.
	-h/--help		Show usage information.
	-v/--version		Show version information.

When using the container, there is no need to provide a credentials file, as those are already included in the container.

Running without a container

pandora2eager.R uses the sidora.core R package. You can find installation instructions for sidora.core here.

Accessing Pandora requires the correct .credentials. Contact Stephan Schiffels, James Fellows Yates, or Clemens Schmid to obtain them. You also have to be in the institute's subnet.

You can get usage information and a descripition of optional arguments by running pandora2eager.R without specifying any arguments.

Usage: ./exec/pandora2eager.R [options] /path/to/input_seq_IDs_file.txt /path/to/pandora/.credentials


Options:
        -h, --help
                Show this help message and exit

        -r, --rename
                Changes all dots (.) in the Library_ID field of the output to underscores (_).
                        Some tools used in nf-core/eager will strip everything after the first dot (.)
                        from the name of the input file, which can cause naming conflicts in rare cases.


        -d, --debug
                Activate debug mode, it produces a file called: Debug_table.txt

        -f FILE_TYPE, --file_type=FILE_TYPE
                Specify the file type of the input files. Accepted values are: "bam", "fastq_pathogens". 
                        Note: if this flag is not provided, raw fastq will be used to generate the table

        -s, --add_ss_suffix
                Adds the suffix '_ss' to the Sample_ID and Library_ID field of the output for single-stranded libraries.

You can then run pandora2eager.R as shown below:

Rscript pandora2eager.R /path/to/input_seq_IDs_file.txt /path/to/pandora/.credentials

Including -r or --rename at the end of your command will change all dots in the Library_ID field of the output to underscores.

By default pandora2eager.R will output the raw fastq files. However, you can change this behaviour by adding the -f or --file_type flag and specifying the allowed options: bam or fastq_pathogens. The bam mode will produce a table containing as input for eager the ouput BAM file from the Autorun pipelines for Human. The fastq_pathogens mode will produce a table containing as input for eager the output fastq containing mapped reads to the multi-FASTA reference from the Pathogen prescreening pipelines.

Building the pandora2eager Singularity container

p2e_singularity.def contains build instructions for a singularity image containing all the dependencies for running pandora2eager.R installed. To build this container you can use the following instructions. You will need to provide a valid .credentials file yourself.

Linux

First use git clone to download this repository, then cd into the repository directory. Copy your valid .credentials file into the repository directory and run

singularity build pandora2eager.sif p2e_singularity.def

OSX

First use git clone to download this repository, then cd into the repository directory.
Copy your valid .credentials file into the repository directory.
With docker installed, run:

bash build_singularity_with_docker.sh