Converting Galaxy wf to Nextflow wf #1
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anilthanki
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Oct 28, 2024
main.nf
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| for i in $sample | ||
| do | ||
| scanpy-neighbors \ | ||
| --n-neighbors \$i \ | ||
| --method 'umap' \ | ||
| --metric 'euclidean' \ | ||
| --random-state '0' \ | ||
| --use-rep $pca_param \ | ||
| --n-pcs '50' \ | ||
| --input-format 'anndata' \ | ||
| $anndata \ | ||
| --show-obj stdout \ | ||
| --output-format anndata \ | ||
| 'neighbours\$i.h5ad' | ||
| done |
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This works but not parallelization compatible.. needs some work here
@pmb59 can you help
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anilthanki
commented
Oct 31, 2024
| """ | ||
| scanpy-filter-cells --gene-name 'gene_symbols' \ | ||
| --param 'c:n_counts' 750.0 1000000000.0 \ | ||
| --param 'c:pct_counts_mito' 0.0 0.35 \ |
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Suggested change
| --param 'c:pct_counts_mito' 0.0 0.35 \ | |
| --param 'c:pct_counts_mito' 0.0 0.35 \ | |
| --category 'c:predicted_doublet' 'False' \ |
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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:
Optional