fastq_trim_fastp_fastqc

Read QC, fastp trimming and read qc

qcquality_controladapterstrimmingfastq

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/fastq_trim_fastp_fastqc

Description

Read QC, fastp trimming and read qc

Input

name:type

description

pattern

`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

Output

name:type

description

pattern

`meta :string`

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

versions.yml