search

GATB / gatb-minia-pipeline

GATB Minia assembly pipeline
29 stars 8 forks source link

Bloocoo results used only once in the first minia iteration #10

Closed sletort closed 7 years ago

sletort commented 7 years ago

I added a function to save list_reads file, and used it on each iteration of minia. I placed the bloocoo results (as list_reads) in extra_reads on the first iteration. I added a test on blooco in minia iteration to prevent entry duplication when bloocoo is not used.

=> I'll proposed another pull request to have bloocoo on all iteration of minia. choose the one needed.

rchikhi commented 7 years ago

I'm not sure if this PR is correct. The extra_reads variable is here to input previous contigs to the next iteration (should have named it previous_contigs_given_as_input_again instead of extra_reads, if it was to be made more explicit). But in this PR, when bloocoo is used, the extra_reads seem to be misused to input reads.

sletort commented 7 years ago

No, ignore this one. (i'll try "close & comment").