flowcraft.templates.megahit module¶
Purpose¶
This module is intended execute megahit 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.:
kmers
: Setting for megahit kmers. Can be either'auto'
,'default'
or a user provided list. All must be odd, in the range 15-255, increment <= 28- e.g.:
'auto'
or'default'
or'55 77 99 113 127'
- e.g.:
clear
: If ‘true’, remove the input fastq files at the end of thecomponent run, IF THE FILES ARE IN THE WORK DIRECTORY
Generated output¶
contigs.fa
: Main output of megahit with the assembly- e.g.:
contigs.fa
- e.g.:
megahit_status
: Stores the status of the megahit run. If it was successfully executed, it stores'pass'
. Otherwise, it stores theSTDERR
message.- e.g.:
'pass'
- e.g.:
Code documentation¶
-
flowcraft.templates.megahit.
set_kmers
(kmer_opt, max_read_len)[source]¶ Returns a kmer list based on the provided kmer option and max read len.
Parameters: - kmer_opt : str
The k-mer option. Can be either
'auto'
,'default'
or a sequence of space separated integers,'23, 45, 67'
.- max_read_len : int
The maximum read length of the current sample.
Returns: - kmers : list
List of k-mer values that will be provided to megahit.