Novoalign command reset

[syansanofi]

Issue
Novoalign version 4 has new tune features that are sets of parameters specifically tested against data from individual sequencers such as Novaseq, Hiseq...etc. These features are available in --tune. Defaults without tuning has been updated as well.

Approach
Remove all aligner parameters and replace with tune. The tune parameter is optional so by default, command should have no --tune.

https://github.com/epam/fonda/blob/9322c5f7ddf34e7c4068b788c52c8599337f4202/src/main/resources/templates/novoalign_sort_tool_template.txt#L2

should become something similar to the following:

[(${novoalignSortFields.novoalign})] -c [(${novoalignSortFields.numThreads})] -d [(${novoalignSortFields.novoindex})] -o SAM $[(${novoalignSortFields.rg})] -f [# th:if = "${fastq2 != null}"][(${fastq1})] [(${fastq2})][/][# th:unless = "${fastq2 != null}"][(${fastq1})][/] [# th:if = "${novoalignSortFields.tune != null}"]--tune [(${novoalignSortFields.tune})] [/]| [(${novoalignSortFields.samtools})] view -bS -|[(${novoalignSortFields.samtools})] sort - [(${novoalignSortFields.tmpBam})]

For integration purposes, here are the --tune options and what other parameters are set to for each one. Column headers denote the option string.

	Default	V3-Defaults	HiSeqX	HiSeq	NextSeq	NOVASEQ	BGISEQ500	MGISEQ2000	IONTorrent-1	IONTorrent-2
-g	40	40	40	40	40	40	40	40	95	100
-x	2	6	20	1	1	1	1	1	2	3
--matchreward	4		4	4	4	4	4	4	2	2
--softclip	50,30	0,0	50,30	45,30	50,30	45,30	45,30	50,30	100,50	100,25
-H	5	2	7	17	22	17	17	12	5	5
-t	0,3	16,4.5	0,2.0	0,2.5	0,2.0	0,2.5	0,3.5	0,1.5	0,3.0	0,3.0
--hlimit	8	off	9	9	8	8	8	8	7	7
-v	150	70	150	150	150	150	150	150	150	150
-r	Random	None	Random	Random	Random	Random	Random	Random	Random	Random
--pechimera	on	off	on	on	on	on	on	on
-u	8	0	8	8	8	8	8	8	8	8
-o	SAM	Native
--tag LB	Off	On
--trim3hp					AG
-k									-k	-k

Source: http://www.novocraft.com/downloads/V4.00.Pre-20190805/NovoalignVersion4.pdf

[kamyshova]

@syansanofi Hi Shu, Do I understand correctly that the --amplicons argument should also be removed from the template along with other parameters?

[syansanofi]

@syansanofi Hi Shu, Do I understand correctly that the --amplicons argument should also be removed from the template along with other parameters?

Yes! We can remove it