dlaehnemann
commented
1 year ago What I have just spotted is this:
--cores 8 nanIn the cutadapt-pe wrapper code, the place where nan appears is where usually an adapter sequence is inserted via whatever is specified in params: adapters=. In this workflow, this is pulled in from the units.tsv file (from a column called adapters):
So I guess that you either have not specified an adapter sequence (including the cutadapt adapter type specification flag) to cut for this particular unit, or your units.tsv has some more subtle formatting problem that messes up columns (a whitespace as a separator instead of a tab somewhere, for example).
And cutadapt then only recognizes the
aryazand
Hello,
When I set trimming to true in the config file, I get the following error
cutadapt: error: unrecognized arguments: pipe/cutadapt/1/lane1.fq1.fastq.gz pipe/cutadapt/1/lane1.fq2.fastq.gzIn looking through log files, it appears this error occurs with the following command (which is called by the cutadapt_pe recipe):
subprocess.CalledProcessError: Command 'set -euo pipefail; cutadapt --cores 8 nan -o results/trimmed/1_lane2_R1.fastq.gz -p results/trimmed/1_lane2_R2.fastq.gz pipe/cutadapt/1/lane2.fq1.fastq.gz pipe/cutadapt/1/lane2.fq2.fastq.gz > results/trimmed/1_lane2.paired.qc.txt 2> logs/cutadapt/1_lane2.log' returned non-zero exit status 2.I haven't been able to figure out why there is this "unrecognized arguments" error, since commands seems to look good to me. Any help with this would be appreciated!