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rotary-genomics / rotary

Assembly/annotation workflow for Nanopore-based microbial genome data containing circular DNA elements
BSD 3-Clause "New" or "Revised" License
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Misc changes #102

Closed LeeBergstrand closed 9 months ago

LeeBergstrand commented 9 months ago

Add various requested changes to dev suggested during the pull request https://github.com/rotary-genomics/rotary/pull/94

LeeBergstrand commented 9 months ago

@jmtsuji POLCA leaves an entire folder full of output files not specified in the rule output. I'm considering having it delete its entire folder using temp. See: https://github.com/rotary-genomics/rotary/issues/92

LeeBergstrand commented 9 months ago

@jmtsuji POLCA leaves an entire folder full of output files not specified in the rule output. I'm considering having it delete its entire folder using temp. See: #92

For example I'm find the following files in the polca directory: 

lrwxrwxrwx 1 lbergstrand lbergstrand   39 Dec 15 15:48 blam_polca.fasta -> blam_polypolish.fasta.PolcaCorrected.fa
-rw-rw-r-- 1 lbergstrand lbergstrand  18K Nov 14 02:01 blam_polypolish.fasta.alignSorted.bam.bai
-rw-rw-r-- 1 lbergstrand lbergstrand   48 Nov 14 02:01 blam_polypolish.fasta.batches
-rw-rw-r-- 1 lbergstrand lbergstrand   12 Nov 14 02:00 blam_polypolish.fasta.bwa.amb
-rw-rw-r-- 1 lbergstrand lbergstrand   43 Nov 14 02:00 blam_polypolish.fasta.bwa.ann
-rw-rw-r-- 1 lbergstrand lbergstrand 5.5M Nov 14 02:00 blam_polypolish.fasta.bwa.bwt
-rw-rw-r-- 1 lbergstrand lbergstrand 1.4M Nov 14 02:00 blam_polypolish.fasta.bwa.pac
-rw-rw-r-- 1 lbergstrand lbergstrand 2.8M Nov 14 02:00 blam_polypolish.fasta.bwa.sa
-rw-rw-r-- 1 lbergstrand lbergstrand    0 Nov 14 02:01 blam_polypolish.fasta.fix.success
-rw-rw-r-- 1 lbergstrand lbergstrand    0 Nov 14 02:00 blam_polypolish.fasta.index.success
-rw-rw-r-- 1 lbergstrand lbergstrand    0 Nov 14 02:01 blam_polypolish.fasta.map.success
-rw-rw-r-- 1 lbergstrand lbergstrand    9 Nov 14 02:01 blam_polypolish.fasta.names
-rw-rw-r-- 1 lbergstrand lbergstrand 5.5M Nov 14 02:01 blam_polypolish.fasta.PolcaCorrected.fa
-rw-rw-r-- 1 lbergstrand lbergstrand  123 Nov 14 02:01 blam_polypolish.fasta.report
-rw-rw-r-- 1 lbergstrand lbergstrand    0 Nov 14 02:01 blam_polypolish.fasta.report.success
-rw-rw-r-- 1 lbergstrand lbergstrand    0 Nov 14 02:01 blam_polypolish.fasta.sort.success
-rw-rw-r-- 1 lbergstrand lbergstrand  18K Nov 14 02:01 blam_polypolish.fasta.vcf
-rw-rw-r-- 1 lbergstrand lbergstrand    0 Nov 14 02:01 blam_polypolish.fasta.vc.success
jmtsuji commented 9 months ago

P.S. Let's continue to discuss POLCA in #100 -- agreed we should think on this more.