Add support for generating taxprofiler/funcscan input samplesheets for preprocessed FASTQs/FASTAs - #688

Draft

vagkaratzas wants to merge 19 commits into

nf-core:devfrom

vagkaratzas:samplsheet-for-taxprofiler

Commits on Oct 10, 2024

first draft push with TODOs
vagkaratzas
committed
2a48e7f
first attempt, files not yet being published in outdir
vagkaratzas
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3b80e0c
4 conditions for different short reads outdirs
vagkaratzas
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2bd8352
Add funcscan code
jasmezz
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a744175
Generate multiple samplesheets
jasmezz
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8672790
Update multi-samplesheet generation
jasmezz
committed
be91462

Commits on Oct 14, 2024

Update docs [skip ci]

jasmezz
and
jfy133
authored
e9df126

Commits on Oct 15, 2024

Added channelToSamplesheet function to subworkflow, added nf-test (not run yet)
vagkaratzas
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e441e76
Validate samplesheet generation parameters, null defaults,
vagkaratzas
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ddb9c96
nf-test updated (no snapshot yet)
vagkaratzas
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bf11fb3
Update function and minor tweaks
jfy133
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8724961
Merge branch 'dev' into samplsheet-for-taxprofiler
jfy133
authored
b354da9
Put the if/else within the function, not as an argument to the function
jfy133
committed
f6b9a99
Fix name of file,remove duplicated check
jfy133
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bec8347
Only check save_clipped_reads if taxprofiler in pipeline list
jfy133
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67958ec

Commits on Oct 16, 2024

Fix logic for generating taxprofiler paths; make new channel to pass correct assemblies files (Funcsan)
jfy133
committed
997674a

Commits on Oct 24, 2024

Merge remote-tracking branch 'upstream/dev' into samplsheet-for-taxprofiler
jfy133
committed
aa71298
Compelte template merge
jfy133
committed
0163690

Commits on Oct 27, 2024

Merge branch 'dev' into samplsheet-for-taxprofiler
jfy133
authored
535747c