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Converting Galaxy wf to Nextflow wf #1

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Converting Galaxy wf to Nextflow wf #1

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@anilthanki anilthanki commented Oct 25, 2024 •
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Creating a Nextflow wf from existing Galaxy plate workflow and Galaxy Droplet workflow

Required Scanpy-script v1.1.6

To Do:

  • Create a working workflow for plate
  • Test on smaller plate dataset
  • Create a working wf Droplet workflow
  • Test on smaller droplet dataset
  • Modify the scxa-control-wf submission submitTertiaryWorkflow.sh to submit DSL 2 workflow

Optional

  • Merge both workflow if feasable
  • adopt nf-core standards, if possible

@anilthanki anilthanki self-assigned this Oct 25, 2024
@anilthanki anilthanki marked this pull request as draft October 25, 2024 14:14
@pmb59 pmb59 mentioned this pull request Oct 25, 2024
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pmb59 and others added 20 commits October 25, 2024 15:47
@pmb59
add nextflow.config for Slurm
f87d49b
@anilthanki
Update main.nf - moving input channels to workflow
7169e98
@anilthanki
Update main.nf - deleting redundant input channels
b7de140
@anilthanki
Update main.nf - adds wf step for mergeGeneFile
aab1b63
@anilthanki
Update main.nf - adds workflow step for scanpy-read-10x
681aeb5
@anilthanki
Update main.nf - fixing typo
4cec90b
@anilthanki
Update main.nf - fixes input file names, process mergeGeneFiles and s…
9842c6a 
…canpy_read_10x
@anilthanki
removes duplicated process and renames a file
c23bb3a
@anilthanki
populate scanpy_filter_cells process
2b039d0
@anilthanki
replaes anndata file name with var
32731d0
@anilthanki
Populate scanpy_filter_genes process
9de5090
@anilthanki
Adds missing quote
772d841
@anilthanki
Populate normalise_data process
f8ae27e
@anilthanki
Populate normalise_data_internal process
c02a8c4
@anilthanki
Populate find_variable_genes process
813c7ac
@anilthanki
Populate run_PCA process
418610e
@anilthanki
Populate harmony_batch process
e3e74b0
@anilthanki
Populate neighbours process
9a23c62
@anilthanki
Applies batch_varibale
e5e82e3
@anilthanki
Populate neighbours_for_umap process
458a7b4
anilthanki
anilthanki commented Oct 28, 2024
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anilthanki
anilthanki commented Dec 3, 2024
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pmb59
pmb59 reviewed Dec 12, 2024
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@anilthanki @pmb59 @irisdianauy