flowcraft.templates.skesa module¶
Purpose¶
This module is intended execute Skesa on paired-end FastQ files.
Expected input¶
The following variables are expected whether using NextFlow or the
main()
executor.
sample_id
: Sample Identification string.- e.g.:
'SampleA'
- e.g.:
fastq_pair
: Pair of FastQ file paths.- e.g.:
'SampleA_1.fastq.gz SampleA_2.fastq.gz'
- e.g.:
clear
: If ‘true’, remove the input fastq files at the end of the- component run, IF THE FILES ARE IN THE WORK DIRECTORY
Generated output¶
${sample_id}_*.assembly.fasta
: Main output of skesawith the assembly- e.g.:
sample_1_skesa.fasta
- e.g.:
clear
: If ‘true’, remove the input fastq files at the end of the- component run, IF THE FILES ARE IN THE WORK DIRECTORY