From 881c6612b31e74efbb854b85d4e5328e300e7c2e Mon Sep 17 00:00:00 2001 From: Thomas Weber <thomas.weber@embl.de> Date: Wed, 18 May 2022 16:56:50 +0200 Subject: [PATCH] Update README.md --- README.md | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index c8686aa..626707e 100644 --- a/README.md +++ b/README.md @@ -252,7 +252,7 @@ Pass additional args to singularity. `-B` stands for binding point between the h **â„¹ï¸ Note** Currently, the binding command needs to correspond to the mounting point of your system (i.e: "/tmp:/tmp"). -On seneca for example (EMBL), use "/g:/g" +On seneca for example (EMBL), use `"/g:/g"` if you are working on `/g/korbel[2]` or `"/scratch:/scratch"` if you plan to work on `scratch`. --- @@ -262,7 +262,6 @@ Obviously, all other snakemake CLI options can also be used. #### MosaiCatcher arguments -!# TODO : simplified pipeline image MosaiCatcher currently supports three different modes of execution : `count`, `segmentation` and `mosaiclassifier`. - `count` (selected by default) will only performs `Mosaic count` binning and count reads for each bin produced @@ -274,7 +273,7 @@ To select your mode of execution, use the following argument `--config mode=[cou For each of these modes, you can *enable* or *disable* the plots generation by using `--config plot=[True|False]` -### 📊 5. Generate report Optional] +### 📊 5. Generate report [Optional] Optionally, you can also MosaiCatcher rules that produce plots @@ -292,7 +291,8 @@ snakemake \ ## 📆 Roadmap -- [x] Zenodo automatic download of external files + indexes (1.2.1) +- [x] Zenodo automatic download of external files + indexes ([1.2.1](https://git.embl.de/tweber/mosaicatcher-update/-/tags/1.2.1)) +- [x] Multiple samples in the parent folder ([1.2.2](https://git.embl.de/tweber/mosaicatcher-update/-/tags/1.2.2)) - [ ] Change of reference genome (currently only GRCh38) - [ ] Plotting options (enable/disable segmentation back colors) - [ ] Full singularity image with preinstalled conda envs @@ -305,6 +305,7 @@ snakemake \ - Do not change the structure of your input folder after running the pipeline, first execution will build a config dataframe file (`workflow/config/config.tsv`) that contains the list of cells and the associated paths - Do not change the list of chromosomes after a first execution (i.e: first execution using `count` mode on `chr21`, second execution using `segmentation` mode on all chromosomes) +- Pipeline is unstable on **male** samples (LCL sample for example) for the moment due to the impossibility to run strandphaser (only one haplotype for the X chrom) ## 📕 References -- GitLab