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462c77e
add metabuli
xonq Feb 7, 2026
6bfeb34
major version update
xonq Feb 10, 2026
b90a85f
taxon id optional for read extraction
xonq Feb 10, 2026
98fb69a
develop standalone wf through to testing
xonq Feb 10, 2026
26cf153
fix miniwdl check discrepancies
xonq Feb 10, 2026
bf38c3c
update read1 select first
xonq Feb 10, 2026
6cf3b28
change inputs for trimming
xonq Feb 10, 2026
f21bbab
merge fastp_pe and fastp_se
xonq Feb 10, 2026
04b4762
call fastp correct
xonq Feb 10, 2026
e3f8e7c
select_first optional output
xonq Feb 10, 2026
7e4c410
Update fastp task parameters for congruence with trimmomatic, disable…
xonq Feb 10, 2026
e1fc4d8
trim adapters by default
xonq Feb 10, 2026
468a9a5
Use select_first for read2 input in fastp call
xonq Feb 10, 2026
93f4e7c
add testing data
xonq Feb 11, 2026
d649f15
send it v1.1
xonq Feb 11, 2026
7bff258
1.0
xonq Feb 11, 2026
a5614d1
read 2 optional input circumvention
xonq Feb 11, 2026
98fb3f0
setup for SE
xonq Feb 11, 2026
1cd6354
fix output harvesting for SE
xonq Feb 11, 2026
d1c3a73
bash syntax correction
xonq Feb 11, 2026
2773061
new input vals
xonq Feb 11, 2026
1418943
add seqmode input
xonq Feb 11, 2026
7acc48a
change input naming
xonq Feb 11, 2026
6bc7e76
fix fastp trim adapters
xonq Feb 11, 2026
4a5e528
call_trim default on, fix implicit propagation
xonq Feb 11, 2026
b6058d9
add metabuli and update versions
xonq Feb 11, 2026
74dd730
init metabuli wf
xonq Feb 11, 2026
77752c7
restrict to ONT input
xonq Feb 11, 2026
45548cd
update with exposed options for wf
xonq Feb 11, 2026
a8429b5
update with illumina explanation
xonq Feb 11, 2026
425fec8
update default taxdump
xonq Feb 11, 2026
7c21284
update implicit illumina
xonq Feb 11, 2026
1a94b3c
fix select_first
xonq Feb 11, 2026
c9864e3
update fastp discussion, set adapter trimming to on by default
xonq Feb 11, 2026
78db6d1
update scoring explanation
xonq Feb 11, 2026
778bbcc
add workflow
xonq Feb 11, 2026
036d61c
get it straight
xonq Feb 11, 2026
d4924a5
update formatting
xonq Feb 11, 2026
ebeed3e
update tables
xonq Feb 11, 2026
e47032c
use concordant fastp output naming
xonq Feb 11, 2026
c6c6bac
update outputs
xonq Feb 11, 2026
64f2fc5
update database name
xonq Feb 11, 2026
c7f017e
add optional taxon input
xonq Feb 11, 2026
b3eb8f2
add ete4
xonq Feb 11, 2026
517e221
add taxon standardization
xonq Feb 11, 2026
46eeef3
add taxon
xonq Feb 11, 2026
0cfa25f
integrate metabuli status
xonq Feb 11, 2026
b7c3a9d
fix metabuli status quotes
xonq Feb 11, 2026
c0481f9
no reads recovered, error
xonq Feb 11, 2026
e75b901
attempt to fix terra grep query
xonq Feb 11, 2026
fc92dab
update table
xonq Feb 11, 2026
92b69eb
update disk size for gtdb
xonq Feb 12, 2026
c6a3742
update to bbp compatible name
xonq Feb 12, 2026
c629bb4
update i/o docs
xonq Feb 12, 2026
eff6183
update descriptions for metabuli workflow variables in input and outp…
xonq Feb 12, 2026
7a37fd4
rm md5s
xonq Feb 12, 2026
33bafc0
burning md5s
xonq Feb 12, 2026
cf6a19e
add example metabuli report
xonq Feb 12, 2026
4cc50ce
revert to 100 GB until discussed
xonq Feb 12, 2026
656e029
use metabuli status correctly
xonq Feb 12, 2026
5ead490
fix read1 propagation based on metabuli
xonq Feb 12, 2026
11d797c
one b
xonq Feb 12, 2026
aa35947
query report, not classifications
xonq Feb 12, 2026
5e3c826
Push Metabuli diagram
cimendes Feb 13, 2026
6228f09
fix workflow type for metabuli
cimendes Feb 16, 2026
fcb0e30
add warning for database size and disk space
cimendes Feb 16, 2026
62bba46
fiz disk size input
cimendes Feb 16, 2026
1b356e7
reorder things for readability
cimendes Feb 16, 2026
a56dddc
update disk size to accomodate gtdb
xonq Feb 18, 2026
db2527f
add metabuli_db input requirement
xonq Feb 18, 2026
a694160
update testing files
xonq Feb 18, 2026
689ae32
update i/o
xonq Feb 18, 2026
0f36a08
update db path and add decompressed size
xonq Feb 18, 2026
303a483
update default and ram/disk size
xonq Feb 18, 2026
449aa0e
init fastplong offload porechop
xonq Feb 19, 2026
6056b26
comment inputs
xonq Feb 19, 2026
70fdd40
init
xonq Feb 19, 2026
fbc6998
update input names
xonq Feb 19, 2026
22c7ebb
add fastplong
xonq Feb 19, 2026
629e34c
correct input
xonq Feb 19, 2026
2365d2e
update i/o docs
xonq Feb 19, 2026
f6fe068
update id
xonq Feb 19, 2026
751fabb
add ont bacterial
xonq Feb 19, 2026
fbb2a10
update with fastplong
xonq Mar 2, 2026
580f23c
add info on database size
xonq Mar 2, 2026
01803ea
update max_ram usage
xonq Mar 4, 2026
2426976
allow taxon name input
xonq Mar 4, 2026
66e1378
use taxon name instead of ID for common hits
xonq Mar 4, 2026
c73eda7
explicitly declare name
xonq Mar 4, 2026
6e7d09b
add gtdb taxdump
xonq Mar 4, 2026
5ec65e1
float taxdump to front
xonq Mar 4, 2026
5e20542
Merge remote-tracking branch 'origin/main' into kzm-metabuli-dev
xonq Mar 4, 2026
372e1a0
change inputs.tsv
xonq Mar 4, 2026
6507d45
taxdump explanation
xonq Mar 4, 2026
4d44164
rm default for optional input
xonq Mar 5, 2026
493366c
Merge remote-tracking branch 'origin/main' into kzm-metabuli-dev
xonq Mar 5, 2026
7fd14a3
remove sc2
xonq Mar 13, 2026
54e0558
Merge remote-tracking branch 'origin/main' into kzm-metabuli-dev
xonq Mar 20, 2026
51f49f7
rm extra
xonq Mar 20, 2026
add9043
rm line
xonq Mar 20, 2026
29bf5b6
update io
xonq Mar 20, 2026
223aa4f
simplify percent_human and target_lineage acquisitions
xonq Mar 23, 2026
eaa3c1f
change to fastplong
xonq Mar 23, 2026
b8953a0
harden regex
xonq Mar 23, 2026
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update with fastplong
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xonq committed Mar 2, 2026
commit fbb2a1089722815c02f041d732f69d9b1760d3b0
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