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Merging template updates #128

Merged
merged 57 commits into from
Dec 17, 2024
Merged

Merging template updates #128

merged 57 commits into from
Dec 17, 2024

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zachary-foster
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Zachary Foster and others added 30 commits October 30, 2024 17:01
reduce fastp RAM usage
87c3420
reduced FASTQC's RAM usage
9b51026
@cahuparo
Update schema_input.json
8d4355c
raise ref_min_ani default
a4082c2
Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance int…
caa1716 
…o dev
decrease RAM usage of FASTERQDUMP
7b77363
@cahuparo
handling warnings for biosamples without read data
d79aca8
@cahuparo
Merge branch 'dev' of https://github.com/grunwaldlab/pathogensurveill…
bb3adf7 
…ance into dev
disable use of swap RAM for all processes
77633d0
Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance int…
b79f390 
…o dev
adapt core gene subsetting code to busco gene subsetting
60f12ef
adapt main report code to changes in busco tree
5b51c98
change resource use of assemblies based on predicted kingdom
07d100c
fix duplicated references in busco bug
fcdba0d
trying to fix bug when using only exclusive references
61e5a15
fixed bug when using only exclusive references
edadbff
fix bug when only a single row/column is provided as input
9c07403
fix bug caused by both single and paired end reads asscoaited with nc…
cf87fe0 
…bi accession; resolved nf-core#110
@cahuparo
update spades
8ac3fee
@cahuparo
Merge branch 'dev' of https://github.com/grunwaldlab/pathogensurveill…
0cca7cd 
…ance into dev
@cahuparo
increase ram scaling for fastp
f93fb0d
@cahuparo
update spades conda env
0b3f215
@cahuparo
Merge branch 'dev' of https://github.com/grunwaldlab/pathogensurveill…
0e3b808 
…ance into dev
add new parameters to control which references are considered
791822a
Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance int…
ce7f3ef 
…o dev
fix new parameters for filtering references from NCBI
fd67a13
force error when looking up assembly metadata fails
7119931
@cahuparo
Merge branch 'dev' of https://github.com/grunwaldlab/pathogensurveill…
3a66438 
…ance into dev
trying to make reference downloading more robust
0ec282a
@cahuparo
remove maxErros for all modules
7ff1177
cahuparo and others added 27 commits November 8, 2024 11:51
@cahuparo
Merge branch 'dev' of https://github.com/grunwaldlab/pathogensurveill…
fb15d42 
…ance into dev
improve selection of downloaded references
9821502
added new test samples
5c9d6fc
force error when find_assemblies does not work
16a4a19
adjust process resources usage
89700ff
fix mising mafft resource requirements
1146d9e
adjust number of references considered
cc3dcad
increase min number of genes required for phylogenies
0518807
moslty automated modules updates
40a8513
more updated to modules
eb7a362
@grunwald
typo
4305869
@grunwald
test
a16c55d
@masudermann
add Logan's test dataset
02e36c0
@masudermann
Add Logan's test dataset to test folder
029a9fc
@masudermann
add conf info for new test dataset
d6c04ec
lots of changes to make udated modules work
1d9d82a
Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance int…
8a9cc78 
…o dev
@logankblair
Singularity supposrt for cqls profile
0a2ce42
@logankblair
Update find_assemblies.nf
008c30f
updated json parser to rcppsimdjson
31721a2
Merge branch 'dev' of github.com:grunwaldlab/pathogensurveillance int…
683f972 
…o dev
fix bug when ref metadata is in sample metadata but no ref_id is supp…
b5c73fd 
…lied
undo fix that caused bug in multiline FASTA formats
4a1918b
fix linting issue
715b144
add new test profile with small genome/data
528f12e
@nf-core-bot
Template update for nf-core/tools version 3.1.0
903bebe
update from TEMPLATE
f489573
@zachary-foster zachary-foster merged commit ee2764e into nf-core:dev Dec 17, 2024
1 of 5 checks passed
@zachary-foster zachary-foster deleted the merging_template_updates branch December 17, 2024 19:00
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6 participants
@zachary-foster @cahuparo @grunwald @masudermann @logankblair @nf-core-bot