fasta_clean_fcs

Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies

contamination screeningcleaningassembliesfasta

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

Description

Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies

Input

name

description

pattern

`ch_fasta`

Channel containing the assembly to screen. The meta map must carry the
taxonomy ID of the expected organism, e.g. [ id:‘test’, taxid:‘id’ ].

Structure: [ val(meta), path(fasta) ]

*.{fasta,fa}

`database`

Directory containing the FCS-GX database.

Structure: [ path(database) ]

`ramdisk_path`

Path to RAM disk for improved performance (optional)

Output

name

description

pattern

`fcsadaptor_cleaned_assembly`

Cleaned assembly in fasta format, alongside the taxonomy ID it was screened
against. Falls back to the unmodified input assembly when FCS-adaptor found
nothing to clean.

Structure: [ val(meta), val(taxid), path(fasta) ]

*.cleaned_sequences.fa.gz

`fcsadaptor_report`

Report of identified adaptors.

Structure: [ val(meta), path(report) ]

*.fcs_adaptor_report.txt

`fcsadaptor_log`

FCS-adaptor log file.

Structure: [ val(meta), path(log) ]

*.fcs_adaptor.log

`fcsadaptor_pipeline_args`

Run arguments.

Structure: [ val(meta), path(pipeline_args) ]

*.pipeline_args.yaml

`fcsadaptor_skipped_trims`

Skipped trim information.

Structure: [ val(meta), path(skipped_trims) ]

*.skipped_trims.jsonl

`fcsgx_report`

Report containing the contig identifier and recommended action (EXCLUDE, TRIM, FIX, REVIEW).

Structure: [ val(meta), path(report) ]

*.fcs_gx_report.txt

`fcsgx_taxonomy_report`

Report containing the contig identifier and mapped contaminant species.

Structure: [ val(meta), path(taxonomy_report) ]

*.taxonomy.rpt

`fcsgx_log`

FCS-GX log file.

Structure: [ val(meta), path(summary) ]

*.summary.txt

`fcsgx_hits`

Intermediate FCS-GX alignments.

Structure: [ val(meta), path(hits) ]

*.hits.tsv.gz