2.1.3: fixes

grimbough · Jul 6, 2023 · 7239154 · 7239154
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diff --git a/docs/output.md b/docs/output.md
@@ -1,85 +1,9 @@
-# Outputs (ongoing)
+# Outputs
 
 This document describes the final outputs produced by the pipeline. Most of the plots are taken from report generated from the [full-sized test dataset](https://sandbox.zenodo.org/record/1074721) for the pipeline.
 
 The files listed below will be created in the selected results directory (`output_location` parameter). All paths are relative to the top-level results directory.
 
-## Directory structure (example for `<SAMPLE>`=_RPE-BM510_)
-
-```bash
-<DATA_LOCATION>/<SAMPLE>
-|-- alfred
-|   |-- Celln.tsv.gz
-|   `-- Celln.json.gz
-|-- bam
-|   |-- Cell1.sort.mdup.bam
-|   |-- Cell2.sort.mdup.bam
-|   `-- Celln.sort.mdup.bam
-|-- cell_selection
-|   |-- labels_raw.tsv
-|   `-- labels.tsv
-|-- config
-|   |-- chroms_to_exclude.txt
-|   `-- single_paired_end_detection.txt
-|-- counts
-|   `-- RPE-BM510
-|       `-- counts-per-cell
-|-- fastq
-|   |-- Cell1.1.fastq.gz
-|   |-- Cell1.2.fastq.gz
-|   |-- Cell2.1.fastq.gz
-|   `-- Cell2.2.fastq.gz
-|-- haplotag
-|   |-- bam
-|   |   `-- RPE-BM510
-|   |-- bed
-|   `-- table
-|       `-- RPE-BM510
-|           `-- by-cell
-|-- log
-|   |-- ...
-|   `-- ...
-|-- merged_bam
-|   `-- merged_bam.bam
-|-- mosaiclassifier
-|   |-- haplotag_likelihoods
-|   |-- postprocessing
-|   |   |-- filter
-|   |   |   `-- RPE-BM510
-|   |   |-- group-table
-|   |   |   `-- RPE-BM510
-|   |   `-- merge
-|   |       `-- RPE-BM510
-|   |-- sv_calls
-|   |   `-- RPE-BM510
-|   `-- sv_probabilities
-|       `-- RPE-BM510
-|-- plots
-|   `-- RPE-BM510
-|       |-- counts
-|       |-- final_results
-|       |-- sv_calls
-|       |-- sv_clustering
-|       `-- sv_consistency
-|-- segmentation
-|   `-- RPE-BM510
-|       `-- segmentation-per-cell
-|-- snv_genotyping
-|   `-- RPE-BM510
-|-- stats
-|   `-- RPE-BM510
-`-- strandphaser
-    |-- phased-snvs
-    |-- RPE-BM510
-    |   `-- StrandPhaseR_analysis.chr21
-    |       |-- browserFiles
-    |       |-- data
-    |       |-- Phased
-    |       |-- SingleCellHaps
-    |       `-- VCFfiles
-    `-- R_setup
-```
-
 ## Plots folder
 
 ### Mosaic count - reads density across bins
@@ -208,7 +132,6 @@ By using these heatmaps, the user can easily identify subclones based on the SV
 
 ---
 
-
 File path: `<OUTPUT_FOLDER>/<SAMPLE>/stats/stats-merged.tsv`
 
 Report category: `Stats`

diff --git a/docs/parameters.md b/docs/parameters.md
@@ -33,8 +33,9 @@ All these arguments can be specified in two ways:
 | ---------------------------------------- | --------------------------------------------------------------------------------------------------- | ------- | ------------ |
 | `multistep_normalisation_analysis`       | Allow to perform multistep normalisation including GC correction for visualization (Marco Cosenza). | False   | False        |
 | `multistep_normalisation_for_SV_calling` | Allow to use multistep normalisation count file during SV calling (Marco Cosenza).                  | False   | False        |
-| `arbigent`                               | Enable ArbiGent mode of execution to genotype SV based on arbitrary segments                        | False   | True         |
-| `scNOVA`                                 | Enable scNOVA mode of execution to compute Nucleosome Occupancy (NO) of detected SV                 | False   | True         |
+| `hgsvc_based_normalized_counts`          | Use HGSVC based normalisation .                                                                     | True    | False        |
+| `arbigent`                               | Enable ArbiGent mode of execution to genotype SV based on arbitrary segments                        | False   | False        |
+| `scNOVA`                                 | Enable scNOVA mode of execution to compute Nucleosome Occupancy (NO) of detected SV                 | False   | False        |
 
 ### External files
 
@@ -66,10 +67,12 @@ All these arguments can be specified in two ways:
 
 ### EMBL specific options
 
-| Parameter              | Comment                                                                                               | Default |
-| ---------------------- | ----------------------------------------------------------------------------------------------------- | ------- |
-| `genecore`             | Enable/disable genecore mode to give as input the genecore shared folder in /g/korbel/shared/genecore | False   |
-| `genecore_date_folder` | Specify folder to be processed                                                                        |         |
+| Parameter                 | Comment                                                                                               | Default                                     |
+| ------------------------- | ----------------------------------------------------------------------------------------------------- | ------------------------------------------- |
+| `genecore`                | Enable/disable genecore mode to give as input the genecore shared folder in /g/korbel/shared/genecore | False                                       |
+| `genecore_date_folder`    | Specify folder to be processed                                                                        |                                             |
+| `genecore_prefix`         | Specify genecore prefix folder                                                                        | /g/korbel/STOCKS/Data/Assay/sequencing/2023 |
+| `genecore_regex_elements` | Specify genecore regex element to be used to distinguish sample from well number                      | PE20                                        |
 
 If `genecore` and `genecore_date_folder` are correctly specified, each plate will be processed independently by creating a specific folder in the `data_location` folder.
 

diff --git a/docs/usage.md b/docs/usage.md
@@ -61,7 +61,7 @@ snakemake \
 
 **ℹ️ Note for 🇪🇺 EMBL users**
 
-- You can load already installed snakemake modusl on the HPC (by connecting to login01 & login02) using the following `module load snakemake/7.14.0-foss-2022a`
+- You can load already installed snakemake modules on the HPC (by connecting to login01 & login02) using the following `module load snakemake/7.14.0-foss-2022a`
 - Use the following command for singularity-args parameter: `--singularity-args "-B /g:/g -B /scratch:/scratch"`
 
 ---

diff --git a/workflow/rules/external_data.smk b/workflow/rules/external_data.smk
@@ -147,11 +147,31 @@ rule download_scnova_data:
             keep_local=True,
         ),
     output:
+        "workflow/data/scNOVA/utils/bin_chr_length.bed",
+        "workflow/data/scNOVA/utils/bin_Genebody_all.bed ",
+        "workflow/data/scNOVA/utils/bin_Genes_for_CNN_num_sort_ann_sort_GC_ensemble.txt",
+        "workflow/data/scNOVA/utils/bin_Genes_for_CNN_num_sort.txt",
         "workflow/data/scNOVA/utils/bin_Genes_for_CNN_reshape_annot.txt",
+        "workflow/data/scNOVA/utils/bin_Genes_for_CNN_sort.txt.corrected ",
+        "workflow/data/scNOVA/utils/Deeptool_Genes_for_CNN_merge_sort_lab_final.txt",
+        "workflow/data/scNOVA/utils/Features_reshape_CpG_orientation_impute.txt",
+        "workflow/data/scNOVA/utils/Features_reshape_CpG_orientation.txt",
+        "workflow/data/scNOVA/utils/Features_reshape_GC_orientation_impute.txt",
+        "workflow/data/scNOVA/utils/Features_reshape_GC_orientation.txt",
+        "workflow/data/scNOVA/utils/Features_reshape_RT_orientation.txt",
+        "workflow/data/scNOVA/utils/Features_reshape_size_orientation.txt",
+        "workflow/data/scNOVA/utils/FPKM_sort_LCL_RPE_19770_renamed.txt",
+        "workflow/data/scNOVA/utils/regions_all_hg38_v2_resize_2kb_sort_num_sort_for_chromVAR.bed",
+        "workflow/data/scNOVA/utils/regions_all_hg38_v2_resize_2kb_sort.bed ",
+        "workflow/data/scNOVA/utils/Strand_seq_matrix_Genebody_for_SCDE.txt",
+        "workflow/data/scNOVA/utils/Strand_seq_matrix_Genebody_for_SVM.txt",
+        "workflow/data/scNOVA/utils/Strand_seq_matrix_TES_for_SVM.txt",
+        "workflow/data/scNOVA/utils/Strand_seq_matrix_TSS_for_SVM.txt",
     log:
         touch("log/config/dl_arbigent_mappability_track.ok"),
     conda:
         "../envs/scNOVA/scNOVA_DL.yaml"
+    container: None
     shell:
         """
         directory="workflow/data/ref_genomes/"