Restructure the docs #21
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some other quick things, it would be good to add figures we have already:
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| | Barcode | multiseq_1 | htodemux_1 | ... | | ||
| |:---------: |:----------: |:----------: |:---: | | ||
| | ... | ... | ... | ... | | ||
| - `adata` folder: stores Anndata object with filtered scRNA-seq read counts and assignment of each deconvolution method if `params.generate_anndata` is `True`. Details see section "scverse compatibility" above. |
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Does the equivalent not exist for mudata?
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still in Mariana' branch, not merged yet. But i can add in the doc now
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| ```bash | ||
| sh test_data/download_data.sh | ||
| nextflow run main.nf |
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Maybe specify conda or docker here or something? Can you resemble a test profile like that the nf-core pipelines have?
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| Folder `data_output` with: | ||
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| - an Anndata object which contains the filtered scRNA-seq counts from `params.rna_matrix_filered` and the assignment of the best-matched method pair after donor matching |
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| ### Optinal output: scverse compatibility | ||
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| Folder `data_output` with: |
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didn't you say above that the folder is called adata?
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above? You mean probably in general.md right? In genetic or hashing deconvolution workflow, no matter which mode to use,AnnData object is saved in for example$mode/gene_demulti/genetic_summary/adata folder. And there should be also a folder for MuData equivalently. For the rescue mode if donor matching is wished, an extra AnnData object with matched donor identity is saved rescue/data_output folder together with MuData
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so here I only mentioned the additional adata output in the rescue mode compared with the genetic/hashing mode
| @@ -18,7 +20,7 @@ tar -xzvf refdata-cellranger-hg19-3.0.0.tar.gz | |||
| # Download common variants | |||
| wget --load-cookies /tmp/cookies.txt "https://docs.google.com/uc?export=download&confirm=$(wget --quiet --save-cookies /tmp/cookies.txt --keep-session-cookies --no-check-certificate 'https://docs.google.com/uc?export=download&id=1lw4T6d7uXsm9dt39ZtEwpuB2VTY3wK1y' -O- | sed -rn 's/.*confirm=([0-9A-Za-z_]+).*/\1\n/p')&id=1lw4T6d7uXsm9dt39ZtEwpuB2VTY3wK1y" -O common_variants_hg19.vcf && rm -rf /tmp/cookies.txt | |||
| wget https://master.dl.sourceforge.net/project/cellsnp/SNPlist/genome1K.phase3.SNP_AF5e2.chr1toX.hg19.vcf.gz | |||
| gunzip genome1K.phase3.SNP_AF5e2.chr1toX.hg19.vcf.gz | |||
| #gunzip genome1K.phase3.SNP_AF5e2.chr1toX.hg19.vcf.gz | |||
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Because cellsnp can use the compressed file directly, dont need to unzip it. will delete the comment
The docs should now have the following structure: