Read QC, fastp trimming and read qc


Name (Type)

ch_reads (file)

Structure: [ val(meta), path (reads) ]
Groovy Map containing sample information
e.g. [ id:‘test’, single_end

], List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively. If you wish to run interleaved paired-end data, supply as single-end data
but with --interleaved_in in your modules.conf’s ext.args for the module.

ch_adapter_fasta (file)

Structure: path(adapter_fasta)
File in FASTA format containing possible adapters to remove.

val_save_trimmed_fail (boolean)

Structure: val(save_trimmed_fail)
Specify true to save files that failed to pass trimming thresholds ending in \*.fail.fastq.gz

val_save_merged (boolean)

Structure: val(save_merged)
Specify true to save all merged reads to the a file ending in \*.merged.fastq.gz

val_skip_fastqc (boolean)

Structure: val(skip_fastqc)
skip the fastqc process if true

val_skip_fastp (boolean)

Structure: val(skip_fastp)
skip the fastp process if true


Name (Type)

meta (value)

Groovy Map containing sample information e.g. [ id:‘test’, single_end


reads (file)

Structure: [ val(meta), path(reads) ]
The trimmed/modified/unmerged fastq reads

trim_json (file)

Structure: [ val(meta), path(trim_json) ]
Results in JSON format

trim_html (file)

Structure: [ val(meta), path(trim_html) ]
Results in HTML format

trim_log (file)

Structure: [ val(meta), path(trim_log) ]
fastq log file

trim_reads_fail (file)

Structure: [ val(meta), path(trim_reads_fail) ]
Reads the failed the preprocessing

trim_reads_merged (file)

Structure: [ val(meta), path(trim_reads_merged) ]
Reads that were successfully merged

fastqc_raw_html (file)

Structure: [ val(meta), path(fastqc_raw_html) ]
Raw fastQC report

fastqc_raw_zip (file)

Structure: [ val(meta), path(fastqc_raw_zip) ]
Raw fastQC report archive

fastqc_trim_html (file)

Structure: [ val(meta), path(fastqc_trim_html) ]
Trimmed fastQC report

fastqc_trim_zip (file)

Structure: [ val(meta), path(fastqc_trim_zip) ]
Trimmed fastQC report archive

versions (file)

File containing software versions