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GATB / gatb-minia-pipeline

GATB Minia assembly pipeline
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create a system link to the contigs of the latest k iteration #18

Closed Krannich479 closed 4 years ago

Krannich479 commented 4 years ago

I had a hard time to automatically pass the results of minia, i.e. the final contigs, to further programs. If parameter -k is not specified (I favor not to do) I can hardly estimate the highest k and therefore don't know the name of the final contig file. I added a simple one-liner to create a system link, just like it's done for the scaffolds. The execution is independent of the success of the scaffolding (avoiding issue #15 ). The link follows the syntax of the remaining files.

Krannich479 commented 4 years ago

And I added a parameter flag to the parser "--no-scaffolding" to skip the scaffolding in the end.

rchikhi commented 4 years ago

Finally got around to merging your PR Thomas, thanks! (and also made some other minor changes in gatb-pipeline to improve installation experience in modern systems)