search

nf-core / ampliseq

Amplicon sequencing analysis workflow using DADA2 and QIIME2
https://nf-co.re/ampliseq
MIT License
188 stars 119 forks source link

Cutadapt with "-u" instead of "fw/rv_primer seq" #744

Closed ilwookkim closed 6 months ago

ilwookkim commented 6 months ago

Description of the bug

Hi all,

I'm new in the 16s rRNA seq field. Our lab used Zymo 16s primer V3-V4 but they refused to provide primer sequence. They only provide length of primer. FW: 16, RV: 24 Therefore I would like to try to trim this seq by using "-u 16 -U 24" as in https://github.com/nf-core/ampliseq/issues/743

I created cutadpater.config as below: process { withName: CUTADAPT_BASIC { ext.args = { [ "--minimum-length 1 -u 16 -U 24", "-O ${params.cutadapt_min_overlap}", "-e ${params.cutadapt_max_error_rate}", params.pacbio ? "--rc -g ${meta.fw_primer}...${meta.rv_primer_revcomp}" : params.iontorrent ? "--rc -g ${meta.fw_primer}...${meta.rv_primer_revcomp}" : params.single_end ? "-g ${meta.fw_primer}" : "-g ${meta.fw_primer} -G ${meta.rv_primer}", params.retain_untrimmed ? '' : "--discard-untrimmed" ].join(' ').trim() } } }

But it returns following message.

Incompatible parameters: `--FW_primer` and `--RV_primer` are required for primer trimming. If primer trimming is not needed, use `--skip_cutadapt`.

Could you help me to solve the problem? Thanks a lot. Best,

Command used and terminal output

nextflow run nf-core/ampliseq -r 2.9.0 -profile singularity -resume -params-file ./nf-params.json -c ./cutadapt.config

Relevant files

No response

System information

N E X T F L O W ~ version 23.10.0 Hardware : Virtual Linux server Container engine: Singularity OS: RHEL8 Version of nf-core/ampliseq: 2.9.0

d4straub commented 6 months ago

Hi there,

this is no bug because you are modifying the pipeline behavior in a way that doesnt work. Thats my mistake. I close here in favor of #743 and write there possible solutions.