Trimbam

[replikation]

• additional output for porecov (bam file with primers still attached)

[replikation]

@hoelzer please check if everything is alright via slurm /singularity

[hoelzer]

# test w/ singularity and slurm
nextflow run replikation/poreCov -r trimbam --fastq_pass fastq_pass/ --samples samplesheet.csv --output results_trimbam --cachedir singularity --update --krakendb GRCh38.p13_SC2_2021-02-08.tar.gz --primerV V4 -profile slurm,singularity -w work_trimbam

# test w/ singularity on local
nextflow run replikation/poreCov -r trimbam --fastq_pass fastq_pass/ --samples samplesheet.csv --output results_trimbam --cachedir singularity/poreCov/ --update --krakendb kraken2/GRCh38.p13_SC2_2021-02-08.tar.gz --primerV V4.1 -profile local,singularity -w work_trimbam --cores 8 --max_cores 32

Worked and looks good!

Did not test basecalling... but the change should not affect much?