Simplify adapter trimming
The trimming of the fastq files was simplified. Before, the contaminants list from FastQC was used to inform the adapter trimming by Cutadapt. Afterwards, sickle-trim was used in single end mode to trim low quality bases. Finally, the fastq reads that went out of sync due to the single ended trimming were synced back together.
However, in practice, the Illumina adapters which were used during sequencing are known, so there is no need to parse the output from FastQC to determine the adapter content. Further more, in practice the amount of adapter detected by FastQC (~10% towards the end of the read) was not enough to trigger the contaminants report so that in practice no adapters were removed at all.
In the current version, Cutadapt is executed to trim the default Illumina adapters. It also trims low quality bases (Phred < 20) which matches the default setting in Sickle-trim. Note that the algorithm that is used by Cutadapt is different from what is used by Sickle-trim.
See https://cutadapt.readthedocs.io/en/stable/algorithms.html#quality-trimming-algorithm for details on how quality trimming is implemented in Cutadapt