Misconfiguration is causing Trimmomatic adapter trimming to be skipped when demuxing RNAseq data

[Nicklas Nordborg]

In our config file we have the following setting for the adapter trimming step:

ILLUMINACLIP:${TRIMMOMATIC_ADAPTERS}:2:30:12:1:true MINLEN:20

The ${TRIMMOMATIC_ADAPTERS} environment variable used to contain the path the a FASTA-file with the adapter sequences: /usr/local/packages/trimmomatic/0.32/adapters/TruSeq3-PE-2.fa but when we moved to the new cluster and Singularity containers the filename was lost from the variable and it was never noticed that it was missing. Trimmomatic doesn't fail but doens't do any adapter trimming either.

The configuration need to be updated to:

ILLUMINACLIP:${TRIMMOMATIC_ADAPTERS}/TruSeq3-PE-2.fa:2:30:12:1:true MINLEN:20

UPDATE Turned out that adding the file name was not enough since the TRIMMOMATIC_ADAPTERS variable is not set until we are inside the container and the configuration happens before that when the variable is empty. The configuration file need to use the full path:

/miniconda/share/trimmomatic-0.33-3/adapters/TruSeq3-PE-2.fa

[Nicklas Nordborg]

The configuration has been incorrect on the lorry server since at least 2022-12-15 (but not before 2022-11-30). It was fixed 2024-07-04. There are 417 MergedSequences affected (they all have ADAPTER_READS=0) and 18 SequencingRun items.

[Nicklas Nordborg]

In 7812:

Fixes #1609: Misconfiguration is causing Trimmomatic adapter trimming to be skipped when demuxing RNAseq data

[Nicklas Nordborg]

In 7815:

References #1609: Misconfiguration is causing Trimmomatic adapter trimming to be skipped when demuxing RNAseq data

The configuration was still not working, since the ${TRIMMOMATIC_ADAPTERS} variable is not available until we enter the container and the configuration happens before that so the value was empty.