Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]
input{:bash}
:file
FASTA/FASTQ containing reads (can be gzipped), or sorted BAM files of reads mapped to a reference.
If supplying PE fasta for multiple samples, should be in the order “sample1_1, sample1_2, sample2_1, sample2_2…”.
*.{fa,fq,fa.gz,fq.gz,bam}
meta2{:bash}
:map
Groovy Map containing reference information
e.g. [ id:'sample1', single_end:false ]
reference{:bash}
:file
Reference FASTA file to map reads to, or minimap2/strobealign index. Not required if using BAM input.
*.{fasta,fasta.gz,mmi,sti}
bam_input{:bash}
:boolean
True if input is bam files
interleaved{:bash}
:boolean
True if input is interleaved fastq file
Output
name:type
description
pattern
coverage{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]
*.depths.{txt}
*.depth.txt{:bash}
:map
Groovy Map containing sample information
e.g. [ id:'sample1', single_end:false ]
*.depths.{txt}
versions{:bash}
versions.yml{:bash}
:file
File containing software versions
versions.yml
Tools
coverm
GPL v3
CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications
