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Adding meningotype #248

Merged
merged 71 commits into from
Jan 29, 2025
Merged

Adding meningotype #248

merged 71 commits into from
Jan 29, 2025

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erinyoung
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Still needs

  • test for meningotype
  • json converter

erinyoung added 30 commits January 7, 2025 17:02
@erinyoung
updated file structure
31c43d8
@erinyoung
moved subworkflows
08e8794
@erinyoung
moved files
fce1677
@erinyoung
added meningotype and updated amrfinder
4d9efb8
@erinyoung
added meningotype
af27c97
@erinyoung
moved workflow on complete
3d52fb1
@erinyoung
moved plus to args
1a70fa8
@erinyoung
fixed tee typo
8ef2750
@erinyoung
updated command for version 3
2b9e36f
@erinyoung
removed MASH_ERR
e39ba83
@erinyoung
combined fasta and fastq
b7ba3de
@erinyoung
fixed version
516c6db
@erinyoung
made path optional
0b1d6df
@erinyoung
fixed capitalization
5f5e4e8
@erinyoung
moved flags to args
337607e
@erinyoung
removed tmp directory
4c898d7
@erinyoung
changed file paths
9b06ac1
@erinyoung
removed extra line
a47e6fb
@erinyoung
removed jsonConvert function
ba321da
@erinyoung
simplified mash sketch
4922f7f
@erinyoung
quast works with just fasta files
67f0f68
@erinyoung
removed storeDir
294cac0
@erinyoung
fixed ch_reads_contigs
92adccb
@erinyoung
added tests for gc
b3203bc
@erinyoung
ignore versions
e191801
@erinyoung
removed TODO
a627e52
@erinyoung
added meta to emit
12e240c
@erinyoung
added genome sizes
893ee1f
@erinyoung
changed versions channels
4a338da
@erinyoung
added emit
4cb4309
erinyoung and others added 26 commits January 10, 2025 17:09
@erinyoung
added gbff channel
86e8737
@erinyoung
simplified path for core genome evaluation
3100131
@erinyoung
combined fasta and gff like prokka
6fbbbdf
@erinyoung
changed channel back to gff
86d20b0
moved to docker
0ef55e6
fixed file extension
c36be20
removed download sra
98f1f38
removed extra path
98dd869
added ena download for fastq files
c4df107
removed view
e326cd8
adding versions
dac65b3
fixed function name
9f00e5c
added writing to log
6c07173
link to reduce size
e83b3c6
rplaced download with ena
d9fbdcc
rplaced download with ena
915a390
added link for all tests
b54b329
added versions
3ae3b85
added versions
dc11ce3
adjusted filter
ac3cf98
removed gzip
38fc0d0
@erinyoung
chaged final file test
bda15a2
@erinyoung
removed figure creation
f025608
@erinyoung
removed link since it wasn't doing anything
fdd489d
added links and reduced size
93e84c4
added main
15961fb
@erinyoung erinyoung marked this pull request as ready for review January 29, 2025 16:50
@erinyoung erinyoung merged commit b718289 into main Jan 29, 2025
29 checks passed
@erinyoung erinyoung mentioned this pull request Jan 29, 2025
Closed
@erinyoung erinyoung deleted the adding_meningotype branch January 29, 2025 17:02
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@erinyoung