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Update ICA, Terra handling to remove launchdir from module #149

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slsevilla opened this issue Mar 31, 2024 · 1 comment
Closed

Update ICA, Terra handling to remove launchdir from module #149

slsevilla opened this issue Mar 31, 2024 · 1 comment

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@slsevilla
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slsevilla commented Mar 31, 2024 •
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Description

Currently the ICA handling of scripts is written as variables with the launchDir being called directly in the module. This is affecting the ability for the output of these modules to cache correctly (relating to #129).

Also adding Terra to this type of refactoring

Solution

  • Rewrite module as a def
  • Create param for path so that launchDir is only called in the config
@slsevilla slsevilla mentioned this issue Mar 31, 2024
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slsevilla added a commit to slsevilla/phoenix that referenced this issue Mar 31, 2024
@slsevilla
refactor: ica handling CDCgov#149
4e8df4c
slsevilla added a commit to slsevilla/phoenix that referenced this issue Mar 31, 2024
@slsevilla
refactor: updating new ica handling CDCgov#149
5ad96ba
slsevilla added a commit to slsevilla/phoenix that referenced this issue Mar 31, 2024
@slsevilla
refactor: handling errors, ica handling, filtering CDCgov#147 CDCgov#149
f131ab6
slsevilla added a commit to slsevilla/phoenix that referenced this issue Mar 31, 2024
@slsevilla
refactor: ica handling, filtering CDCgov#147 CDCgov#149
3c87d90
slsevilla added a commit to slsevilla/phoenix that referenced this issue Mar 31, 2024
@slsevilla
refactor: ica handling, filtering CDCgov#147 CDCgov#149
25a2ca6
slsevilla added a commit to slsevilla/phoenix that referenced this issue Apr 1, 2024
@slsevilla
refactor: fastqc ica handling, filtering CDCgov#147 CDCgov#149
1a6fa53
slsevilla added a commit to slsevilla/phoenix that referenced this issue Apr 1, 2024
@slsevilla
refactor: krakenbh handle ica and terra CDCgov#149
10c7bdc
slsevilla added a commit to slsevilla/phoenix that referenced this issue Apr 1, 2024
@slsevilla
refactor: kraken subwf and modules for ica, reorg wf calls CDCgov#149
606e6e5
slsevilla added a commit to slsevilla/phoenix that referenced this issue Apr 3, 2024
@slsevilla
refactor: spades for ica CDCgov#149
e2c3145
slsevilla added a commit to slsevilla/phoenix that referenced this issue Apr 3, 2024
@slsevilla
refactor: spades wf modules for ica CDCgov#149
05343da
slsevilla added a commit to slsevilla/phoenix that referenced this issue Apr 3, 2024
@slsevilla
refactor: rename_headers for ica CDCgov#149
66e8f46
slsevilla added a commit to slsevilla/phoenix that referenced this issue Apr 3, 2024
@slsevilla
refactor: ica, output file handling CDCgov#149
f72f42a
@slsevilla slsevilla changed the title Update ICA handling to remove launchdir from module Update ICA, Terra handling to remove launchdir from module Apr 3, 2024
slsevilla added a commit to slsevilla/phoenix that referenced this issue Apr 4, 2024
@slsevilla
refactor: scaffolds samplesshet ica CDCgov#149
c22897c
slsevilla added a commit to slsevilla/phoenix that referenced this issue Apr 4, 2024
@slsevilla
refactor: kraken2 makereport, top mash hits ica CDCgov#149
ef6339b
slsevilla added a commit to slsevilla/phoenix that referenced this issue Apr 4, 2024
@slsevilla
refactor: phoenix wf filtering, ica CDCgov#147 CDCgov#149
5ab72ca
slsevilla added a commit to slsevilla/phoenix that referenced this issue Apr 4, 2024
@slsevilla
refactor: determine taxaID, fast ani ica CDCgov#149
fd2463a
slsevilla added a commit to slsevilla/phoenix that referenced this issue Apr 4, 2024
@slsevilla
refactor: mlst ica CDCgov#149
b056478
slsevilla added a commit to slsevilla/phoenix that referenced this issue Apr 4, 2024
@slsevilla
refactor: mlst, amrfinder for terra, ica CDCgov#149
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slsevilla added a commit to slsevilla/phoenix that referenced this issue Apr 4, 2024
@slsevilla
refactor: summary lines ica CDCgov#149
2700945
slsevilla added a commit to slsevilla/phoenix that referenced this issue Apr 4, 2024
@slsevilla
refactor: summary lines ica CDCgov#149
bb780f3
slsevilla added a commit to slsevilla/phoenix that referenced this issue Apr 4, 2024
@slsevilla
refactor: griphin ica CDCgov#149
28f9029
@jvhagey
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jvhagey commented Jun 13, 2024

addressed with a17b58f will be in v2.2.0 when its released.

@jvhagey jvhagey closed this as completed Jun 13, 2024
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Refactor pipeline filtering, create params flags for tools slsevilla/phoenix
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