Merge pull request #50 from friendsofstrandseq/dev

2.2.2: IGV genome browsing, scTRIP multiplot & fixes

.gitignore

@@ -215,3 +215,7 @@ workflow/data/arbigent/scTRIP_segmentation.bed
 .tests/data_CHR17/RPE-BM510/bam/*.bam.sort
 .tests/external_data/chr17.fa.log
 LOGS_DEV/
+
+# scTRIP multiplot
+workflow/scripts/plotting/scTRIP_multiplot/scTRIPmultiplot
+workflow/config/scTRIP_multiplot.ok

.pre-commit-config.yaml

@@ -9,13 +9,13 @@ repos:
         #    id: no-commit-to-branch
     repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v3.4.0
-  - hooks:
-      - id: snakefmt
-    repo: https://github.com/snakemake/snakefmt
-    rev: 0.4.0
-  - hooks:
-      - id: commitizen
-        stages:
-          - commit-msg
-    repo: https://github.com/commitizen-tools/commitizen
-    rev: v2.17.12
+  # - hooks:
+  #     - id: snakefmt
+  #   repo: https://github.com/snakemake/snakefmt
+  #   rev: 0.4.0
+  # - hooks:
+  #     - id: commitizen
+  #       stages:
+  #         - commit-msg
+  #   repo: https://github.com/commitizen-tools/commitizen
+  #   rev: v2.17.12

.tests/config/simple_config.yaml

@@ -3,10 +3,10 @@
 # --------------------------------------------------------
 
 # MosaiCatcher version
-version: 2.2.1
+version: 2.2.2
 
 # Ashleys-QC pipeline version
-ashleys_pipeline_version: 2.2.1
+ashleys_pipeline_version: 2.2.2
 
 # Email for notifications about the pipeline's status
 email: ""
@@ -157,6 +157,11 @@ additional_sce_cutoff: 20000000
 # SCE min distance
 sce_min_distance: 500000
 
+# --------------------------------------------------------
+# Downstream modules configuration - genome browsing
+# --------------------------------------------------------
+genome_browsing_files_generation: False
+
 # --------------------------------------------------------
 # Downstream modules configuration - ArbiGent
 # --------------------------------------------------------
@@ -211,6 +216,14 @@ plottype_clustering:
   - "position"
   - "chromosome"
 
+scTRIP_multiplot: False
+
+# --------------------------------------------------------
+# StrandScape
+# --------------------------------------------------------
+
+use_strandscape_labels: False
+
 # --------------------------------------------------------
 # Internal Parameters
 # --------------------------------------------------------

README.md

@@ -22,7 +22,7 @@ the workflow goes through the following steps:
 
 |                    ![summary](docs/images/figure_pipeline.png)                     |
 | :--------------------------------------------------------------------------------: |
-|                         _MosaiCatcher snakemake pipeline_                          |
+|           _MosaiCatcher snakemake pipeline and visualisations examples_            |
 | _[ashleys-qc-pipeline](https://github.com/friendsofstrandseq/ashleys-qc-pipeline)_ |
 
 # 📘 Documentation
@@ -49,6 +49,7 @@ the workflow goes through the following steps:
 - [x] Version synchronisation between ashleys-qc-pipeline and mosaicatcher-pipeline ([1.8.3](https://github.com/friendsofstrandseq/mosaicatcher-pipeline/releases/tag/1.8.3))
 - [x] Report captions update ([1.8.5](https://github.com/friendsofstrandseq/mosaicatcher-pipeline/releases/tag/1.8.5))
 - [x] Clustering plot (heatmap) & SV calls plot update ([1.8.6](https://github.com/friendsofstrandseq/mosaicatcher-pipeline/releases/tag/1.8.6))
+- [x] [`ashleys_pipeline_only` parameter](/docs/usage.md#usage): using mosaicatcher-pipeline, trigger ashleys-qc-pipeline only and will stop after the generation of the counts, ashleys predictions & plots to allow the user manual reviewing/selection of the cells to be processed ([2.2.0](https://github.com/friendsofstrandseq/mosaicatcher-pipeline/releases/tag/2.2.0))
 - [ ] Plotting options (enable/disable segmentation back colors)
 
 ## Bioinformatic-related features
@@ -59,15 +60,20 @@ the workflow goes through the following steps:
 - [x] Ploidy detection at the segment and the chromosome level: used to bypass StrandPhaseR if more than half of a chromosome is haploid ([1.7.0](https://github.com/friendsofstrandseq/mosaicatcher-pipeline/releases/tag/1.7.0))
 - [x] inpub_bam_legacy mode (bam/selected folders) ([1.8.4](https://github.com/friendsofstrandseq/mosaicatcher-pipeline/releases/tag/1.8.4))
 - [x] Blacklist regions files for T2T & hg19 ([1.8.5](https://github.com/friendsofstrandseq/mosaicatcher-pipeline/releases/tag/1.8.5))
-- [x] ArbiGent integration: Strand-Seq based genotyper to study SV containly at least 500bp of uniquely mappable sequence ([1.9.0](https://github.com/friendsofstrandseq/mosaicatcher-pipeline/releases/tag/1.9.0))
-- [x] scNOVA integration: Strand-Seq Single-Cell Nucleosome Occupancy and genetic Variation Analysis ([1.9.2](https://github.com/friendsofstrandseq/mosaicatcher-pipeline/releases/tag/1.9.2))
+- [x] [ArbiGent](/docs/usage.md#arbigent-mode-of-execution) integration: Strand-Seq based genotyper to study SV containly at least 500bp of uniquely mappable sequence ([1.9.0](https://github.com/friendsofstrandseq/mosaicatcher-pipeline/releases/tag/1.9.0))
+- [x] [scNOVA](/docs/usage.md#scnova-mode-of-execution) integration: Strand-Seq Single-Cell Nucleosome Occupancy and genetic Variation Analysis ([1.9.2](https://github.com/friendsofstrandseq/mosaicatcher-pipeline/releases/tag/1.9.2))
+- [x] [`multistep_normalisation` and `multistep_normalisation_for_SV_calling` parameters](/docs/usage.md#multistep-normalisation) to replace GC analysis module (library size normalisation, GC correction, Variance Stabilising Transformation) ([2.1.1](https://github.com/friendsofstrandseq/mosaicatcher-pipeline/releases/tag/2.1.1))
+- [x] Strand-Seq processing based on mm10 assembly ([2.1.2](https://github.com/friendsofstrandseq/mosaicatcher-pipeline/releases/tag/2.1.2))
+- [x] UCSC ready to use file generation including counts & SV calls ([2.1.2](https://github.com/friendsofstrandseq/mosaicatcher-pipeline/releases/tag/2.1.2))
+- [x] `blacklist_regions` parameter: ([2.2.0](https://github.com/friendsofstrandseq/mosaicatcher-pipeline/releases/tag/2.2.0))
+- [x] IGV ready to use XML session generation: ([2.2.2](https://github.com/friendsofstrandseq/mosaicatcher-pipeline/releases/tag/2.2.2))
 - [ ] Pooled samples
 
 ## Small issues to fix
 
-- [ ] Move pysam / SM tag comparison script to snakemake rule
 - [x] replace `input_bam_location` by `data_location` (harmonization with [ashleys-qc-pipeline](https://github.com/friendsofstrandseq/ashleys-qc-pipeline.git))
 - [x] List of commands available through list_commands parameter ([1.8.6](https://github.com/friendsofstrandseq/mosaicatcher-pipeline/releases/tag/1.8.6)
+- [x] Move pysam / SM tag comparison script to snakemake rule ([2.2.0](https://github.com/friendsofstrandseq/mosaicatcher-pipeline/releases/tag/2.2.0))
 
 # 🛑 Troubleshooting & Current limitations
 
@@ -103,3 +109,5 @@ the workflow goes through the following steps:
 > ArbiGent publication: Porubsky, David, Wolfram Höps, Hufsah Ashraf, PingHsun Hsieh, Bernardo Rodriguez-Martin, Feyza Yilmaz, Jana Ebler, et al. 2022. “Recurrent Inversion Polymorphisms in Humans Associate with Genetic Instability and Genomic Disorders.” Cell 185 (11): 1986-2005.e26. https://doi.org/10.1016/j.cell.2022.04.017.
 
 > scNOVA publication: Jeong, Hyobin, Karen Grimes, Kerstin K. Rauwolf, Peter-Martin Bruch, Tobias Rausch, Patrick Hasenfeld, Eva Benito, et al. 2022. “Functional Analysis of Structural Variants in Single Cells Using Strand-Seq.” Nature Biotechnology, November, 1–13. https://doi.org/10.1038/s41587-022-01551-4.
+
+> scNOVA publication: Jeong, Hyobin, Karen Grimes, Kerstin K. Rauwolf, Peter-Martin Bruch, Tobias Rausch, Patrick Hasenfeld, Eva Benito, et al. 2022. “Functional Analysis of Structural Variants in Single Cells Using Strand-Seq.” Nature Biotechnology, November, 1–13. https://doi.org/10.1038/s41587-022-01551-4.