(Most latest nextflow script on top - Earliest scripts go bottom)
This Nextflow pipeline does
- FastQC
- Trims adapters and quality filtering on Illumina reads
- Runs short read Spades assembly
$ time nextflow minipipeline-sr3.nf
N E X T F L O W ~ version 21.04.3
Launching `minipipeline-sr3.nf` [determined_bose] - revision: 73d0117dc7
executor > local (12)
[c6/02f475] process > fastqc (null) [100%] 6 of 6 ✔
[80/8823d3] process > bbduk (N16003_DDMS210004241-1a_HFMWLDSX2_L2) [100%] 3 of 3 ✔
[09/8692af] process > spades (N16003_DDMS210004241-1a_HFMWLDSX2_L2) [100%] 3 of 3 ✔
Completed at: 16-Aug-2021 16:04:23
Duration : 2h 42m 50s
CPU hours : 7.2
Succeeded : 12
real 162m52.445s
user 434m33.407s
sys 7m49.247s
The first version of the nextflow script take a single fasta file
- counts the number of sequences in a fasta file
- calculates the genome size of fasta
$ time nextflow toyPipeline1.nf
N E X T F L O W ~ version 21.04.3
Launching `toyPipeline1.nf` [silly_montalcini] - revision: a2aeb90791
executor > local (3)
[85/bd7b64] process > newSeqFile [100%] 1 of 1 ✔
[83/13c256] process > count [100%] 1 of 1 ✔
[61/070271] process > calculate [100%] 1 of 1 ✔
3
5281967
real 0m3.757s
user 0m6.669s
sys 0m1.052s