flowcraft.templates.spades module¶
Purpose¶
This module is intended execute Spades 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 Spades kmers. Can be either'auto'
,'default'
or a user provided list.- e.g.:
'auto'
or'default'
or'55 77 99 113 127'
- e.g.:
opts
: List of options for spades execution.- The minimum number of reads to consider an edge in the de Bruijn graph during the assembly.
- e.g.:
'5'
- e.g.:
- Minimum contigs k-mer coverage.
- e.g.:
['2' '2']
- 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.fasta
: Main output of spades with the assembly- e.g.:
contigs.fasta
- e.g.:
spades_status
: Stores the status of the spades run. If it was successfully executed, it stores'pass'
. Otherwise, it stores theSTDERR
message.- e.g.:
'pass'
- e.g.:
Code documentation¶
-
flowcraft.templates.spades.
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 Spades.