Description of the bug
The '--trimmer fastp' option mentioned in the "Outputs" section of the docs is not recognised:
[main] WARN nextflow.validation.SchemaValidator - The following invalid input values have been detected:
* --trimmer: fastp
* --extra_fastp_args: --trim_front1 1 --trim_front2 1
I guessed that '--extra_fastp_args' would be appropriate based on the nf-core/rnaseq trimming options syntax, but accept it may not be valid. In any case, '--trimmer fastp' should be valid according to the docs.
Aaron.
Command used and terminal output
nextflow run nf-core/rnasplice \
-r 1.0.4 \
-w /tmp/nextflow \
-profile singularity \
--input $SAMPLESHEET \
--fasta $REF_GENOME \
--gtf $REF_ANNOT \
--gencode true \
--outdir $OUT_DIR \
--contrasts $CONTRASTS \
--multiqc_title $PROJECT_ID \
--trimmer fastp --extra_fastp_args '--trim_front1 1 --trim_front2 1' \
--save_trimmed true \
--miso_genes "ENSG00000004961.15, ENSG00000005302.19, ENSG00000147403.18"Relevant files
nextflow.log
System information
- Nextflow version: 25.04.6
- Hardware: HPC
- Executor: slurm
- Container engine: Singularity
- OS: Rocky Linux v9.2
- nf-core/rnasplice v1.0.4
Description of the bug
The '--trimmer fastp' option mentioned in the "Outputs" section of the docs is not recognised:
I guessed that '--extra_fastp_args' would be appropriate based on the nf-core/rnaseq trimming options syntax, but accept it may not be valid. In any case, '--trimmer fastp' should be valid according to the docs.
Aaron.
Command used and terminal output
Relevant files
nextflow.log
System information