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small text updates and combine script order summary
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@drneavin
drneavin committed Oct 18, 2021
1 parent 51054a2 commit 5d4aa31
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4 changes: 2 additions & 2 deletions docs/source/Demuxlet.rst
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Expand Up @@ -59,7 +59,7 @@ First we will need to identify the number of reads from each allele at each SNP

.. code-block:: bash
singularity exec Demuxafy.sif popscle dsc-pileup --sam $BAM --vcf $VCF --group-list $BARCODES --out $DEMUXLET_OUTDIR/popscle --sm-list $INDS
singularity exec Demuxafy.sif popscle dsc-pileup --sam $BAM --vcf $VCF --group-list $BARCODES --out $DEMUXLET_OUTDIR/pileup --sm-list $INDS
.. tab:: Without ``$INDS`` file

Expand All @@ -68,7 +68,7 @@ First we will need to identify the number of reads from each allele at each SNP

.. code-block:: bash
singularity exec Demuxafy.sif popscle dsc-pileup --sam $BAM --vcf $VCF --group-list $BARCODES --out $DEMUXLET_OUTDIR/popscle
singularity exec Demuxafy.sif popscle dsc-pileup --sam $BAM --vcf $VCF --group-list $BARCODES --out $DEMUXLET_OUTDIR/pileup
If the pileup is successfull, you will have these files in your ``$DEMUXLET_OUTDIR``:

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20 changes: 11 additions & 9 deletions docs/source/Installation.rst
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Expand Up @@ -2,8 +2,8 @@ Installation
==========================
Installation should be pretty painless (we hope).
We have provided all the softwares in a singularity image which provides continuity across different computing platforms (see `HPCNG Singluarity <https://singularity.hpcng.org/>`__ and `Sylabs io <https://sylabs.io/singularity/>`__ for more information on singularity images).
The only thing to note before you download this image is that the image is **~9Gb** so, depending on the internet speed, it will take **~20-30 min to download**.
The good news is that you should only need to do this once.
The only thing to note before you download this image is that the image is **~6.5Gb** so, depending on the internet speed, it will take **~15-30 min to download**.
The good news is that you should only need to do this once unless updates are made to the scripts or image.

Just download the singluarity image with:

Expand Down Expand Up @@ -55,9 +55,11 @@ If everything was downloaded correctly, that command should report:
| +---------------------------+-------------------------------+
| | ``scDblFinder`` | v1.6.0 |
| +---------------------------+-------------------------------+
| | ``scrublet`` | 0.2.3 |
| | ``scds`` | v1.9.1 |
| +---------------------------+-------------------------------+
| | ``solo`` | 1.0 |
| | ``scrublet`` | v0.2.3 |
| +---------------------------+-------------------------------+
| | ``solo`` | v1.0 |
+----------------------------+---------------------------+-------------------------------+
| Supporting Softwares | ``minimap2`` | v2.7-r654 |
| +---------------------------+-------------------------------+
Expand All @@ -81,23 +83,23 @@ If everything was downloaded correctly, that command should report:
| +---------------------------+-------------------------------+
| | ``vcfR`` | v1.12.0 |
| +---------------------------+-------------------------------+
| | ``Seurat`` | 4.0.4 |
| | ``Seurat`` | 4.0.5 |
| +---------------------------+-------------------------------+
| | ``SingleCellExperiment`` | v1.14.1 |
+----------------------------+---------------------------+-------------------------------+
| Python Supporting Packages | ``argparse`` | v1.4.0 |
| (Python v3.7.10) +---------------------------+-------------------------------+
| | ``numpy`` | v1.19.5 |
| (Python v3.7.2) +---------------------------+-------------------------------+
| | ``numpy`` | v1.20.3 |
| +---------------------------+-------------------------------+
| | ``matplotlib`` | v3.2.2 |
| +---------------------------+-------------------------------+
| | ``pandas`` | v1.1.5 |
| | ``pandas`` | v1.3.4 |
| +---------------------------+-------------------------------+
| | ``PyVCF`` | v0.6.8 |
| +---------------------------+-------------------------------+
| | ``scipy`` | v1.7.1 |
| +---------------------------+-------------------------------+
| | ``scvi-tools`` | v0.14.0 |
| | ``scvi-tools`` | v0.14.1 |
| +---------------------------+-------------------------------+
| | ``umap-learn`` | v0.5.1 |
+----------------------------+---------------------------+-------------------------------+
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1 change: 1 addition & 0 deletions docs/source/Souporcell.rst
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Expand Up @@ -101,6 +101,7 @@ If souporcell is successfull, you will have these files in your ``$SOUPORCELL_OU
├── retag.err
├── retagging.done
├── souporcell_minimap_tagged_sorted.bam
├── souporcell_minimap_tagged_sorted.bam.bai
├── troublet.done
├── variants.done
└── vartrix.done
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3 changes: 3 additions & 0 deletions scripts/Combine_Results.R
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Expand Up @@ -420,9 +420,12 @@ if (length(which(c(!is.null(args$demuxlet), !is.null(args$freemuxlet), !is.null(
}
print(columns)
demultiplex_combined_results_summary <- combined_results[,.(N=.N), by = c(columns)]
demultiplex_combined_results_summary <- demultiplex_combined_results_summary[order(-N)]
fwrite(demultiplex_combined_results_summary, paste0(tools::file_path_sans_ext(args$out),"_demultiplexing_summary.tsv"), sep = "\t", append = FALSE)

}
combined_results_summary <- combined_results_summary[order(-N)]

fwrite(combined_results_summary, paste0(tools::file_path_sans_ext(args$out),"_summary.tsv"), sep = "\t", append = FALSE)


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