commit 31/05/2021 10:47:08

README.md

@@ -27,9 +27,9 @@ These are the steps to install perSVade. If you are running it in the BSC (inter
 
 Download the perSVade source code from one of the releases and decompress. For example:
 
-`wget https://github.com/Gabaldonlab/perSVade/archive/v0.9.tar.gz`
+`wget https://github.com/Gabaldonlab/perSVade/archive/0.10.tar.gz`
 
-`tar -xvf v0.9.tar.gz; rm v0.9.tar.gz`
+`tar -xvf 0.10.tar.gz; rm 0.10.tar.gz`
 
 This already contains all the scripts to run the pipeline. Note that the created file (for example `perSVade-v0.9`) will be referred as `<perSVade_dir>`
 
@@ -88,11 +88,11 @@ If you are working from any cluster that has access to the BSC /gpfs filesystem
 
 `source /gpfs/projects/bsc40/mschikora/anaconda3/etc/profile.d/conda.sh`  # activate the conda environment of mschikora
 
-`conda activate perSVade_v0.9_env` # activate the environment of perSVade version 0.9. You can change the version
+`conda activate perSVade_v0.10_env` # activate the environment of perSVade version 0.10. You can change the version
 
 You can next run perSVade from the releases folder (these are stable versions of the pipeline). For example:
 
-`python /gpfs/projects/bsc40/mschikora/scripts/perSVade/releases/perSVade-0.9/scripts/perSVade.py -r <path to the reference genome (fasta)> -o <output_directory> -p <ploidy, 1 or 2> -f1 <forward_reads.fastq.gz> -f2 <reverse_reads.fastq.gz> `
+`python /gpfs/projects/bsc40/mschikora/scripts/perSVade/releases/perSVade-0.10/scripts/perSVade.py -r <path to the reference genome (fasta)> -o <output_directory> -p <ploidy, 1 or 2> -f1 <forward_reads.fastq.gz> -f2 <reverse_reads.fastq.gz> `
 
 IMPORTANT NOTE: The activation of the perSVade conda environment works well from version 0.7 on. This means that you can activate from the login of MN or interactive nodes. However, the activation of older versions (v0.4 and below) is costly, and it overloads the login nodes. If you want to use an old version of perSVade, always activate it on an interactive node (i.e.: `salloc`). In addition, you can't run the perSVade pipeline from a login, because it takes too many resources. You can submit perSVade as a job or run from an interactive session with `salloc -n 1 --time=02:00:00 -c 48 --qos debug`.
 

scripts/sv_functions.py

@@ -8069,8 +8069,6 @@ def keep_relevant_filters_lists_inparallel(filterName_to_filtersList, df_gridss,
     filterChanging_to_filtersDict = dict(zip(filter_changing_list, filters_dict_list))
     filterChanging_to_breakpoints = dict(zip(filter_changing_list, bp_tuples_list))
 
-    print(filterChanging_to_breakpoints)
-
     # get those filters that change the df
     if type_filtering=="keeping_all_filters_that_change":
 

scripts/varcall_cnv_pipeline.py

@@ -152,9 +152,9 @@
 ############### CNV #################
 #####################################
 
-if opt.skip_cnv_analysis is False or opt.gff is None:
+if opt.skip_cnv_analysis is False and opt.gff is not None:
 
-    print("Starting CNV per gene analysis")
+    print("Starting CNV per gene analysis. This step only runs if -gff is specified.")
 
     # make a folder for the CNV anlysis
     cnv_outdir = "%s/CNV_results"%opt.outdir
@@ -190,7 +190,7 @@
 
     # In Laia's script, she calculates coverage as the median reads per gene (cov per gene) / mean of the cov per gene across all genes
 
-print("CNV analysis finished")
+print("per gene CNV analysis finished")
 
 
 #####################################