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MVP #13

Closed
wants to merge 21 commits into from
Closed

MVP #13

wants to merge 21 commits into from

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evanroyrees
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@evanroyrees evanroyrees commented Feb 9, 2022 •
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TODO:

  • Subworkflow for coverage calculations #7
  • Create working database input channels
  • Finish implementation of taxon-profilers
  • Finish implementation of binners
  • Create collected results channel for benchmarking binners
  • Create collected results channel for benchmarking taxon-profilers
  • Samplesheet inputs
  • Implement BENCHMARK_BINNING module
  • Implement BENCHMARK_TAXON_PROFILING module
  • Decide on what to do with FASTQC, MULTIQC modules from nf-core template
  • Update relevant nextflow_schema.json sections for appropriate input parameters
  • Update conf/modules.config for implemented modules

evanroyrees and others added 20 commits January 27, 2022 15:04
@evanroyrees
🎨 WIP samplesheet digest
b54f3e8
@evanroyrees
🎨 merge main into module-confs
9f554ab
@evanroyrees
🎨 WIP for sample inputs
c043503
@evanroyrees
🎨🍏 WIP for issue-#5 and issue-#7
ed2ccd4
@evanroyrees
🎨🍏 unsaved changes in mmseqs2.nf (WIP)
2074f30
@evanroyrees
📝🍏 Add comment for mmseqs2.nf (WIP)
2005715
@evanroyrees
🎨🍏 WIP for adding mmseqs2 module
19dab21
@chasemc
escape bash for nextflow
88c597f
@chasemc
remove nfcore v1 saveas
dae047f
@chasemc
add downloaders for kraken dbs and fix publishdir/storedir
110c784
@chasemc
fix includes
c8f72f6
@chasemc
fix includes
74bab48
@chasemc
fix includes
f2b79ef
@chasemc
add kraken downloads
2ef82f4
@chasemc
add kraken downloads and fix schema
375c4d5
@chasemc
update test config
0d1f3f3
@chasemc
comment out no-nworking
e5cd4a8
@chasemc
pr suggesstions
f9c651d
@chasemc
Merge pull request #12 from KwanLab/kraken_download
18eb59d 
some updates to download kraken db
@Sidduppal
WIP
8fe10c4 
Add subdirectories for local modules with multiple processes
Implement autometa-coverage process
Add benchmarking process
@chasemc
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chasemc commented Feb 9, 2022

Is this ready to review or the checklist needs to get done first?

@evanroyrees
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No, this is still a work in progress. Since the main branch is also a WIP we could merge whenever.

Just placing this here to get some of these knocked off the checklist

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@chasemc chasemc Awaiting requested review from chasemc

@Sidduppal Sidduppal Awaiting requested review from Sidduppal

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@evanroyrees @chasemc @Sidduppal