When using fastp as trimmer and "save_trimmed=true", the command of fastp includes "-m --mergedout XXX.merged.fastq.gz". This mode performs a stringent overlap analysis by default and changes output files, as mentioned in the documentation of fastp (https://github.com/OpenGene/fastp). This is inconsistent with the design of trimming modules and downstream modules.
This bug can be traced to line 175 in the "subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf". The parameter "save_trimmed" was passed into the FASTQ_FASTQC_UMITOOLS_FASTP workflow as "save_merged".
if (trimmer == 'fastp') { FASTQ_FASTQC_UMITOOLS_FASTP ( ch_filtered_reads, skip_fastqc, with_umi, skip_umi_extract, umi_discard_read, skip_trimming, [], save_trimmed, save_trimmed, min_trimmed_reads )
In "subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf"
workflow FASTQ_FASTQC_UMITOOLS_FASTP { take: reads // channel: [ val(meta), [ reads ] ] skip_fastqc // boolean: true/false with_umi // boolean: true/false skip_umi_extract // boolean: true/false umi_discard_read // integer: 0, 1 or 2 skip_trimming // boolean: true/false adapter_fasta // file: adapter.fasta save_trimmed_fail // boolean: true/false save_merged // boolean: true/false min_trimmed_reads // integer: > 0
In "/modules/nf-core/fastp/main.nf"
def merge_fastq = save_merged ? "-m --merged_out ${prefix}.merged.fastq.gz" : ''
Description of the bug
When using fastp as trimmer and "save_trimmed=true", the command of fastp includes "-m --mergedout XXX.merged.fastq.gz". This mode performs a stringent overlap analysis by default and changes output files, as mentioned in the documentation of fastp (https://github.com/OpenGene/fastp). This is inconsistent with the design of trimming modules and downstream modules.
This bug can be traced to line 175 in the "subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf". The parameter "save_trimmed" was passed into the FASTQ_FASTQC_UMITOOLS_FASTP workflow as "save_merged".
if (trimmer == 'fastp') { FASTQ_FASTQC_UMITOOLS_FASTP ( ch_filtered_reads, skip_fastqc, with_umi, skip_umi_extract, umi_discard_read, skip_trimming, [], save_trimmed, save_trimmed, min_trimmed_reads )In "subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf"workflow FASTQ_FASTQC_UMITOOLS_FASTP { take: reads // channel: [ val(meta), [ reads ] ] skip_fastqc // boolean: true/false with_umi // boolean: true/false skip_umi_extract // boolean: true/false umi_discard_read // integer: 0, 1 or 2 skip_trimming // boolean: true/false adapter_fasta // file: adapter.fasta save_trimmed_fail // boolean: true/false save_merged // boolean: true/false min_trimmed_reads // integer: > 0In "/modules/nf-core/fastp/main.nf"def merge_fastq = save_merged ? "-m --merged_out ${prefix}.merged.fastq.gz" : ''Command used and terminal output
Relevant files
XXX.fastp.json "command": "fastp --in1 XXX_1.fastq.gz --in2 XXX_2.fastq.gz --out1 XXX_1.fastp.fastq.gz --out2 XXX_2.fastp.fastq.gz --json XXX.fastp.json --html XXX.fastp.html --unpaired1 XXX_1.fail.fastq.gz --unpaired2 XXX_2.fail.fastq.gz -m --merged_out XXX.merged.fastq.gz --thread 6 --detect_adapter_for_pe [extra_star_align_args]"
System information
No response