Fix @RG tag in sam/bam file output

[syansanofi]

Issue 1
Currently FONDA does not discriminate between lanes of a single sample. All lanes receive identical @RG ID: tags

Approach
Since alignment are done on a per lane basis for DNA based workflows (eg DNACapVar_Fastq), add lane number to read group. This would align more to standard practice (link)

Example
sample_manifest.txt

parameterType	shortName	Parameter1	Parameter2
fastqFile	SampleA	SampleA_S1_L001_R1_001.fastq.gz	SampleA_S1_L001_R2_001.fastq.gz
fastqFile	SampleA	SampleA_S2_L002_R1_001.fastq.gz	SampleA_S2_L002_R2_001.fastq.gz

The @RG ID: tag would be:

parameterType
fastqFile
fastqFile

I would rather the lane numbers are iterated and appended onto the sample name:

SampleA+L001

rather than pulled out of the longest common substring of the sample's reads. This will make the lane numbering consecutive and easier to enforce because there will be no dependency on sample name prefixes.

Please let me know if this is clear.

Issue 2
All workflows should get the LB tag instead of only amplicon seq. Rationale follows previous, to align with current best practice.

fonda/src/main/java/com/epam/fonda/tools/impl/BwaSort.java

Lines 108 to 110 in 4a651ca

	.equals(configuration.getGlobalConfig().getPipelineInfo().getWorkflow())
	? String.format("\"@RG\\tID:%s\\tSM:%s\\tLB:%s\\tPL:Illumina\"", sampleName, sampleName, sampleName)
	: String.format("\"@RG\\tID:%s\\tSM:%s\\tLB:DNA\\tPL:Illumina\"", sampleName, sampleName);

fonda/src/main/java/com/epam/fonda/tools/impl/NovoalignSort.java

Lines 117 to 119 in 4a651ca

	return isDnaAmpliconWorkflow(configuration)
	? String.format("\'@RG\\tID:%s\\tSM:%s\\tLB:%s\\tPL:Illumina\'", sampleName, sampleName, sampleName)
	: String.format("\'@RG\\tID:%s\\tSM:%s\\tLB:DNA\\tPL:Illumina\'", sampleName, sampleName);

Approach
Remove this check, use @RG\\tID:%s\\tSM:%s\\tLB:%s\\tPL:Illumina for all workflows.