Add iSeq retrieval - Githubissues

Clinical-Genomics / demultiplexing

To keep scripts associated with execution of the Illumina demultiplexing pipeline

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Add iSeq retrieval #80

Closed ingkebil closed 5 years ago

ingkebil commented 5 years ago

This PR solves the retrieval of the iSeq samplesheet.

How to test?

bash update-demux-stage.sh isheet on clinical-preproc stage.
run: demux sheet fetch -a iseq --pad --indexlength 10 $flowcell with $flowcell BPC29611-2526 or BPC29611-3324 (see comment below)

Expected outcome The fecth command will print the samplesheet to stdout. The samplesheet should contain an index and index2 column. index should end with AT and index2 should start with AC.

This is minor version bump: extending and not modifying public API.

@emiliaol can you provide a FC id?

[x] Code reviewed by @ingkebil
[x] Tested by @patrikgrenfeldt and @emiliaol
[x] Deploy signature @ingkebil

emiliaol commented 5 years ago

BPA73008-1225 BPA73008-1825 BPC29611-2526 BPC29611-3324

There you go. 4 of them! But I think only the last two are useful as we may not have created the others in LIMS

ingkebil commented 5 years ago

Thanks!

patrikgrenfeldt commented 5 years ago

@ingkebil is it possible to create a test for this? What about having a test for iSeq in tests/utils/test_samplesheet.py?

ingkebil commented 5 years ago

Hi Patrik, yeas please add a unit test for this, wkr, kenny

ingkebil commented 5 years ago

In case it wasn't clear, I handed over this work to you on Wednesday ;)

patrikgrenfeldt commented 5 years ago

Configuration: Command: Output: Expected outcome?

[x] The fecth command will print the samplesheet to stdout.
[x] The samplesheet should contain an index and index2 column.
👎 index should end with AT and index2 should start with AC.

patrikgrenfeldt commented 5 years ago

Command: Output: Expected outcome?

[x] The fecth command will print the samplesheet to stdout.
[x] The samplesheet should contain an index and index2 column.
[x] index should end with AT and index2 should start with AC.

patrikgrenfeldt commented 5 years ago

Headers should be:

[x] Sample_ID | Sample_Name | Sample_Plate | Description | I7_Index_ID | index | I5_Index_ID | index2 | Manifest | GenomeFolder | Sample_Project | Sample_Well data should be like
[x] ACC5726A1 | ACC5726A1 | | ACC5726A1 | | TATCGCACAT | | ACCTTAGTGT | | | 881352 | 👍

patrikgrenfeldt commented 5 years ago

@ingkebil this has been tested OK on the iSeq machine, ready for merge and deploy?

ingkebil commented 5 years ago

Awesome! Merge and deploy :moneybag:

ingkebil commented 5 years ago

I'll merge and bump. Not sure where this needs to be deployed?

emiliaol commented 5 years ago

It would be nice to have on both hasta and thalamus