Trimming parameters not used

[misiti-1864309]

Description of the bug

The pipeline docs specify --clip_r1 as a parameter for the trimming step, however it is ignored

Command used and terminal output

nextflow run nf-core/rnasplice -r dev -profile docker --input samplesheet.csv --contrasts contrastsheet.csv --outdir results_nfcore --clip_r1 5 --genome GRCh37

The bug occurs in both latest release and dev branch.
The pipeline runs normally but read 1 is not trimmed at the 5' end as specified

Relevant files

No response

System information

Nextflow version 24.10.4
Hardware: Desktop
Executor: local
Container engine: Docker
OS: Ubunyu
Version of nf-core/rnasplice: 1.0.4 and dev

[ajeffs]

I have the same issue with 1.0.4: pipeline completes successfully, but trimming parameters are ignored.

The input fastq's are from Illumina Stranded mRNA libs, so have a "T" at cycle 1 of both R1 and R2 - the "T" remains after trimming:

nextflow run nf-core/rnasplice \
    -r 1.0.4 \
    -w $WORK_DIR \
    -profile singularity \
    --input $SAMPLESHEET \
    --fasta $REF_GENOME \
    --gtf $REF_ANNOT \
    --gencode true \
    --outdir $OUT_DIR \
    --contrasts $CONTRASTS \
    --multiqc_title $PROJECT_ID \
    --clip_r1 1 \
    --clip_r2 1

Nextflow.log shows that the parameters should have been passed to trimgalore:

Read trimming options
  clip_r1               : 1
  clip_r2               : 1

The trimming reports do not indicate that anything other than adapter trimming was performed.

I've also found that the option to use fastp is also ignored, i.e., "--trimmer fastp", and trimgalore runs instead; I'll submit that as a separate ticket.

All the best!

Aaron.