smrnaseq

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Description of the bug

I'm wondering if the protocol option is well interpreted for the adapter trimming.
If I use --protocol illumina or --protocol qiaseq, there is no difference in the fastp command which is always run with ;

fastp \
    --in1 XXX.fastq.gz \
    --out1  XXX.fastp.fastq.gz \
    --thread 6 \
    --json XXX.fastp.json \
    --html XXX.fastp.html \
    --adapter_fasta known_adapters.fa \
     \
    -l 17 --max_len1 100 --adapter_sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCA \
    2> >(tee XXXX.fastp.log >&2)

I do not think that it has a strong impact on the results, because all adapter sequences are available in the known_adapters.fa file, but based on the code ;

code: subworkflows/local/utils_nfcore_smrnaseq_pipeline/main.nf

def formatProtocol(params,log) {

    switch(params.protocol){
        case 'illumina':
            params.putIfAbsent("clip_r1", 0);
            params.putIfAbsent("three_prime_clip_r1",0);
            params.putIfAbsent("three_prime_adapter", "TGGAATTCTCGGGTGCCAAGG");
            break
        case 'nextflex':
            params.putIfAbsent("clip_r1", 4);
            params.putIfAbsent("three_prime_clip_r1", 4);
            params.putIfAbsent("three_prime_adapter", "TGGAATTCTCGGGTGCCAAGG");
            break
	case 'qiaseq':
            params.putIfAbsent("clip_r1",0);
            params.putIfAbsent("three_prime_clip_r1",0);
            params.putIfAbsent("three_prime_adapter","AACTGTAGGCACCATCAAT");
            break
        case 'cats':
            params.putIfAbsent("clip_r1",3);
            params.putIfAbsent("three_prime_clip_r1", 0);
            params.putIfAbsent("three_prime_adapter", "AAAAAAAA");
            break
        case 'custom':
            params.putIfAbsent("clip_r1", params.clip_r1)
            params.putIfAbsent("three_prime_clip_r1", params.three_prime_clip_r1)
        default:
            log.warn "Please make sure to specify all required clipping and trimming parameters, otherwise only adapter detection will be performed."
        }

        log.warn "Running with Protocol ${params.protocol}"
        log.warn "Therefore using Adapter: ${params.three_prime_adapter}"
        log.warn "Clipping ${params.clip_r1} bases from R1"
        log.warn "And clipping ${params.three_prime_clip_r1} bases from 3' end"
    }

and conf/modules.config

    withName: '.*:FASTQ_FASTQC_UMITOOLS_FASTP:FASTP' {
        ext.args = [ "",
            params.trim_fastq                           ? "" : "--disable_adapter_trimming",
            params.clip_r1 > 0                          ? "--trim_front1 ${params.clip_r1}" : "", // Remove bp from the 5' end of read 1.                                                                                                                              
            params.three_prime_clip_r1 > 0              ? "--trim_tail1 ${params.three_prime_clip_r1}" : "", // Remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed.                                                                 
            params.fastp_min_length > 0                 ? "-l ${params.fastp_min_length}" : "",
            params.fastp_max_length > 0                 ? "--max_len1 ${params.fastp_max_length}" : "",
            params.three_prime_adapter == "auto-detect" ?  "" : "--adapter_sequence ${params.three_prime_adapter}"
        ].join(" ").trim()
}

I would expect the parameter --adapter_sequence to be updated according to the ${params.three_prime_adapter} which is itself defined based on the protocol ?

Command used and terminal output

Apps/nextflow-23.10.1/nextflow run smrnaseq-2.3.1 \
  --input ${PROJ_DIR}/data/samplesheet.csv \
  --protocol 'illumina' \
  --mirtrace_species 'rno' \
  --genome 'Rnor_6.0' \
  --outdir ${PROJ_DIR}/results \
  -w ${PROJ_DIR}/results/work \
  -profile singularity \
  -c ${PROJ_DIR}/curie.config \
  -resume "

Relevant files

No response

System information

nextflow-23.10.1 smrnaseq-2.3.1