AVITI manifest improvements

[kedhammar]

For AVITI manifest generation: make PhiX manifest variant, fix udf typo, remove unused func, clarify var names

[chuan-wang]

Hi @kedhammar, there is one more thing for us to fix. For the following cases index 2 need to be converted to the reverse complementary form:

(1) All inhouse-prepared libraries
(2) User submitted libraries with special indexes that match with TENX_DUAL_PAT or SMARTSEQ_PAT.

Please refer to the codes for MiSeq as example.

[chuan-wang]

Changes required.

[kedhammar]

Changes required.

How's this @chuan-wang? Not tested.

2bc45ad

[chuan-wang]

``> > Changes required.

How's this @chuan-wang? Not tested.

2bc45ad

Hi, the logic should be the opposite:

# Special cases to reverse-complement index2
if not user_library or (
    user_library
    and (
        TENX_DUAL_PAT.findall(lims_label)
        or SMARTSEQ_PAT.findall(lims_label)
    )
):
    logging.info(f"Reverse-complementing index2 of {sample.name}.")
    row["Index2"] = revcomp(row["Index2"])

[kedhammar]

``> > Changes required.

How's this @chuan-wang? Not tested.
2bc45ad

Hi, the logic should be the opposite:

# Special cases to reverse-complement index2
if not user_library or (
    user_library
    and (
        TENX_DUAL_PAT.findall(lims_label)
        or SMARTSEQ_PAT.findall(lims_label)
    )
):
    logging.info(f"Reverse-complementing index2 of {sample.name}.")
    row["Index2"] = revcomp(row["Index2"])

Oop, that's right 👀

ab77d5e