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Merged
merged 65 commits into from
Sep 28, 2022
Merged

A new, improved Acanthophis #1

merged 65 commits into from
Sep 28, 2022

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@kdm9
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@kdm9 kdm9 commented Sep 22, 2022 •
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  • Full support for DPW2 pipeline
  • Hologenomics pipeline
    • Kraken2
    • Kaiju
    • Centrifuge
    • Megahit assembly of unmapped reads
  • Unify log and data paths
  • Cloud profiles via DPW2 work To be added later
  • New config
  • New rl2s.tsv
  • Fix bug in khmer, and get kwip working again
  • fastqc Pre & post
  • multiqc
  • qualimap
  • QCtype
  • theta_prior
  • Define regions based on coverage not size

kdm9 added 30 commits September 15, 2022 14:16
@kdm9
copy rules files to workingdir, use local rules
191f410 
Rather than those rules under $PYTHONPATH/acanthophis/.../rules/*.rules
@kdm9
Version 2 rules draft
7a978ce
@kdm9
functioning version 2, still some bits missing
26e98ce
@kdm9
remove symlink to rules
8a13ef3
@kdm9
Update demo
e7d98df
@kdm9
Fix up template for acanthophis init
08c3e2b
@kdm9
generate correct rl2s
7517116
@kdm9
nuke unused metadata
8b8b4b1
@kdm9
fix indexing rules
62ada56
@kdm9
try caching inputs
9481b67
@kdm9
fix align actually
8914e9f
@kdm9
fix cache
e16b419
@kdm9
Use viral kraken db
1d5b6b6
@kdm9
Don't track example dir files
5c0ff1d
@kdm9
No kraken reads by default
b084c8c
@kdm9
Fix up conda envs from template vs example
cba8ddb
@kdm9
Slightly improved docs in readme
0b2b43d
@kdm9
Fix remote providers
8aa104a
@kdm9
msprime still broken in conda, revert
46f9f70
@kdm9
Nuke duplicated kwip settings from config
aba45ab
@kdm9
Larger merge rule size
aa77971
@kdm9
Generate unmapped reads in default rules
92ef431
@kdm9
Fix rule order for new kraken rules
c5d5866
@kdm9
example: move krakendb build to snakefile
4b4a225
@kdm9
Capture stderr and stdout in logs
ef33d0d
@kdm9
extract_unmapped: don't use CASSAVA header option
d54fbe1
@kdm9
example: fix krakendb download
491ef56
@kdm9
Fix kraken db path
311fc93
@kdm9
kaiju
9fc5666
@kdm9
use all_ prefix to target rules
a0ba5be
@kdm9 kdm9 changed the title Version 0.3.0 A new, improved Acanthophis Sep 22, 2022
kdm9 added 24 commits September 22, 2022 22:18
@kdm9
Fix up all license headers
85ba91e
@kdm9
Add multiqc
dc4489d
@kdm9
Add changes from holopipe dir
eee176d
@kdm9
Fix split pair rules
8a4a57d
@kdm9
Helps if you give it an input file
0a23f05
@kdm9
init: Add warning about overwriting files
5e569a5
@kdm9
unify alignment paths
e100a5e
@kdm9
Add multiqc for samtools stats and fastqc
d48ea84
@kdm9
Full multiqc setup
ece3e76
@kdm9
put kraken multiqc in multiqc dir
4ca8589
@kdm9
remove unused rule files
e1eaded
@kdm9
Fix theta prior specification
0b5c4d1
@kdm9
Implement qctype in tests
51185a1
@kdm9
touch up test scripts
3bfa115
@kdm9
Various fixes
f6e25c8
@kdm9
nuke output in test script
b9a0cbe
@kdm9
bump cache to try fixing CI
595fef6
@kdm9
ci: cat log files on failure
c6620e1
@kdm9
Add nextera oligos
5a9e737
@kdm9
tests: Fix kaiju db creation
4e4d272
@kdm9
Cache keyed by test files
b03fbb3
@kdm9
Compress taxon id per-read outputs
2de9542
@kdm9
Auto-set regions based on coverage
945c2c8
@kdm9
ci: key cache by only the gen snakemake
63c10f4
@kdm9 kdm9 merged commit b003183 into main Sep 28, 2022
@kdm9 kdm9 deleted the copy-rules branch September 28, 2022 11:30
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2 participants

@kdm9