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:type

description

pattern

`meta :map`

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

`assembly :file`

assembly fasta file

*.{fasta,fa}

Output

name:type

description

pattern

`meta :map`

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

`versions :file`

File containing software versions

versions.yml

`fcsadaptor_cleaned_assembly :file`

Cleaned assembly in fasta format

*.{cleaned_sequences.fa.gz}

`fcsadaptor_report :file`

Report of identified adaptors

*.{fcs_adaptor_report.txt}

`fcsadaptor_log :file`

Log file

*.{fcs_adaptor.log}

`fcsadaptor_pipeline_args :file`

Run arguments

*.{pipeline_args.yaml}

`fcsadaptor_skipped_trims :file`

Skipped trim information

*.{skipped_trims.jsonl}

`fcs_gx_report :file`

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

*.fcs_gx_report.txt

`fcsgx_taxonomy_report :file`

Report containing the contig identifier and mapped contaminant species

*.taxonomy.rpt

fasta_clean_fcs

Description

Input

`meta :map`

`assembly :file`

Output

`meta :map`

`versions :file`

`fcsadaptor_cleaned_assembly :file`

`fcsadaptor_report :file`

`fcsadaptor_log :file`

`fcsadaptor_pipeline_args :file`

`fcsadaptor_skipped_trims :file`

`fcs_gx_report :file`

`fcsgx_taxonomy_report :file`

included modules and subworkflows

maintainer

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