Initial setup for element aviti

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 45.50409% with 400 lines in your changes missing coverage. Please review.

Project coverage is 29.52%. Comparing base (6390b97) to head (81ea936). Report is 233 commits behind head on master.

Files with missing lines	Patch %	Lines
taca/element/Element_Runs.py	46.51%	315 Missing :warning:
taca/analysis/analysis_element.py	44.44%	60 Missing :warning:
taca/utils/statusdb.py	27.27%	16 Missing :warning:
taca/analysis/cli.py	0.00%	9 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## master #432 +/- ## ========================================== + Coverage 26.57% 29.52% +2.95% ========================================== Files 28 31 +3 Lines 3959 4691 +732 ========================================== + Hits 1052 1385 +333 - Misses 2907 3306 +399 ```

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[chuan-wang]

@kedhammar One more missing puzzle: for 10X 8-mer single indexes (e.g. SI-NA-A1) it is usually required that index 1 sequences shall be written as a separate FastQ file (I1). In this case we need the additional option I1Fastq,TRUE

[kedhammar]

@kedhammar One more missing puzzle: for 10X 8-mer single indexes (e.g. SI-NA-A1) it is usually required that index 1 sequences shall be written as a separate FastQ file (I1). In this case we need the additional option I1Fastq,TRUE

After discussion: We can have the LIMS EPP write the name of the index set as an additional sample column in the master manifest, which TACA can use to discern this special case.

[chuan-wang]

@kedhammar One more missing puzzle: for 10X 8-mer single indexes (e.g. SI-NA-A1) it is usually required that index 1 sequences shall be written as a separate FastQ file (I1). In this case we need the additional option I1Fastq,TRUE

After discussion: We can have the LIMS EPP write the name of the index set as an additional sample column in the master manifest, which TACA can use to discern this special case.

Could we add an optional and generalized column in the master RunManifest called Addtional_options, and put the option I1Fastq,TRUE in that column? With this solution we can handle other special cases if they come up in the future without changing TACA.

[kedhammar]

@kedhammar One more missing puzzle: for 10X 8-mer single indexes (e.g. SI-NA-A1) it is usually required that index 1 sequences shall be written as a separate FastQ file (I1). In this case we need the additional option I1Fastq,TRUE

After discussion: We can have the LIMS EPP write the name of the index set as an additional sample column in the master manifest, which TACA can use to discern this special case.

Could we add an optional and generalized column in the master RunManifest called Addtional_options, and put the option I1Fastq,TRUE in that column? With this solution we can handle other special cases if they come up in the future without changing TACA.

How's this?

https://github.com/SciLifeLab/scilifelab_epps/pull/372 https://github.com/ssjunnebo/TACA/pull/17

[chuan-wang]

@kedhammar One more missing puzzle: for 10X 8-mer single indexes (e.g. SI-NA-A1) it is usually required that index 1 sequences shall be written as a separate FastQ file (I1). In this case we need the additional option I1Fastq,TRUE

After discussion: We can have the LIMS EPP write the name of the index set as an additional sample column in the master manifest, which TACA can use to discern this special case.

Could we add an optional and generalized column in the master RunManifest called Addtional_options, and put the option I1Fastq,TRUE in that column? With this solution we can handle other special cases if they come up in the future without changing TACA.

How's this?

SciLifeLab/scilifelab_epps#372 ssjunnebo#17

Looks good! Thanks!