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lhqing / cemba_data

Mapping pipeline for snmC-seq based technologies.
https://hq-1.gitbook.io/mc/
MIT License
15 stars 7 forks source link

Update mc.Snakefile #10

Closed jksr closed 3 years ago

jksr commented 3 years ago

If trimming is interrupted for any reason, the error message will be written to .trimmed.stats.tsv, which will fool the snakemake to proceed with all downstreaming rules. Added a buffer step to make it more robust.

Same modification should be done for mct and m3c accordingly.

lhqing commented 3 years ago

Can you explain why this is necessary? If trimming is interrupted, it means some issue needs user attention?

jksr commented 3 years ago

occasionally, I come into this error when the snakemake proceeds to the rule "summary" Traceback (most recent call last): ...... raise KeyError(key) from err KeyError: 'in_reads'

which means cutadapt step has problem but somehow not detected. probably it still returns 0. No idea what happened, but rerun this step usually fix it.

jksr commented 3 years ago

No. if something wrong happens but returns 0, this step will not fix it... you can discard this change

jksr commented 3 years ago

I will write a checking step and create a pull request later.

lhqing commented 3 years ago

OK, thanks! Close for now.