Seqfu
note
Manipulate FASTA/FASTQ files.
Supported commands:
stats
:
seqfu stats
Input files
seqfu stats
can generated reports in multiple formats, see https://telatin.github.io/seqfu2/tools/stats.html. Only TSVs with headers (default seqfu stats
output) are currently detected and parsed by MultiQC.
note
seqfu stats
has a --multiqc
option that generates a _mqc.txt
file can be used with MuliQC as custom content. This is different from this module which enables additional features.
Configuration
Sample names are automatically extracted from the "File" columns by default. If you only have one sample per file and prefer to use the filename as the sample name instead, you can set the global use_filename_as_sample_name
option to true
or list seqfu
under it.
File search patterns
seqfu/stats:
contents: "File\t#Seq\tTotal bp\tAvg\tN50\tN75\tN90\tauN\tMin\tMax"
num_lines: 1