diff --git a/docs/source/Demuxlet.rst b/docs/source/Demuxlet.rst
index c8da517..dc371aa 100644
--- a/docs/source/Demuxlet.rst
+++ b/docs/source/Demuxlet.rst
@@ -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
@@ -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``:
diff --git a/docs/source/Installation.rst b/docs/source/Installation.rst
index c65e0ab..41b226e 100644
--- a/docs/source/Installation.rst
+++ b/docs/source/Installation.rst
@@ -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 `__ and `Sylabs io `__ 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:
@@ -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 |
| +---------------------------+-------------------------------+
@@ -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 |
+----------------------------+---------------------------+-------------------------------+
diff --git a/docs/source/Souporcell.rst b/docs/source/Souporcell.rst
index 3bf2101..d5eb94f 100644
--- a/docs/source/Souporcell.rst
+++ b/docs/source/Souporcell.rst
@@ -101,6 +101,7 @@ If souporcell is successfull, you will have these files in your ``$SOUPORCELL_OU
├── retag.err
├── retagging.done
├── souporcell_minimap_tagged_sorted.bam
+ ├── souporcell_minimap_tagged_sorted.bam.bai
├── troublet.done
├── variants.done
└── vartrix.done
diff --git a/scripts/Combine_Results.R b/scripts/Combine_Results.R
index 9fb0873..ff628e5 100644
--- a/scripts/Combine_Results.R
+++ b/scripts/Combine_Results.R
@@ -420,9 +420,12 @@ if (length(which(c(!is.null(args$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)