FAQ¶

Pipeline initialisation¶

Workflow defines configfile config_chip.yml but it is not present or accessible.¶

This error occurs when the pipeline is run without a config file present in the working directory. Ensure that seqnado-config has been run before starting the pipeline and that you are in the new directory created by seqnado-config.

Follow the Configuration Guide instructions to create a config file.

Singularity configuration¶

Workflow Error¶

Failed to pull singularity image from library://asmith151/seqnado/seqnado_pipeline:latest:
FATAL: Unable to get library client configuration:
remote has no library client (see https://apptainer.org/docs/user/latest/endpoint.html#no-default-remote)

Fix:

re-run seqnado init: See the Initialisation Guide

or

apptainer remote add --no-login SylabsCloud cloud.sylabs.io  
apptainer remote use SylabsCloud

Optional configuration¶

Can I merge multiple samples into a single sample?¶

Yes, you can merge multiple samples into a single sample to generate merged bigWig files and consensus peaks. To do this, you need to create a design file that specifies the samples to be merged. The design file should have a column named "merge" that specifies the samples to be merged e.g.:

sample	r1	r2	merge
sample-control-rep1	/path/to/sample-control-rep1_R1.fastq.gz	/path/to/sample-control-rep1_R2.fastq.gz	control
sample-control-rep2	/path/to/sample-control-rep2_R1.fastq.gz	/path/to/sample-control-rep2_R2.fastq.gz	control
sample-control-rep3	/path/to/sample-control-rep3_R1.fastq.gz	/path/to/sample-control-rep3_R2.fastq.gz	control
sample-treated-rep1	/path/to/sample-treated-rep1_R1.fastq.gz	/path/to/sample-treated-rep1_R2.fastq.gz	treated
sample-treated-rep2	/path/to/sample-treated-rep2_R1.fastq.gz	/path/to/sample-treated-rep2_R2.fastq.gz	treated
sample-treated-rep3	/path/to/sample-treated-rep3_R1.fastq.gz	/path/to/sample-treated-rep3_R2.fastq.gz	treated