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connor-lab / ncov2019-artic-nf

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019
GNU Affero General Public License v3.0
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adding -f Mark reads as QCFAIL instead of excluding them to trim. #70

Open FredDodd6 opened 4 years ago

dkj commented 4 years ago

We're on hold with this as it still removes records that we would like to retain (but mark as QCFAIL) for reanalysis.

m-bull commented 4 years ago

Good compromise might be to put it behind an option? Code written then, just need to update profile as required later?

dkj commented 4 years ago

@m-bull (sorry for the late reply) - I think the code will have to change to accommodate further change required in ivar...

m-bull commented 4 years ago

No probs @dkj. I'm waiting on this too, so anticipating some tweaks pretty soon.

gkarthik commented 4 years ago

Hello all, with https://github.com/andersen-lab/ivar/commit/29cf79d73a4c0828bdbacf15ff8b12c3b181f896 (resolving https://github.com/andersen-lab/ivar/issues/73), in cases where the insert size is smaller than the read length, the read is treated an unpaired and both forward and reverse primers are trimmed off.