Merge pull request #17 from J-81/update_DPPD_7101-F

Update DPPD 7101-F

RNAseq/Pipeline_GL-DPPD-7101_Versions/GL-DPPD-7101-F.md

@@ -121,15 +121,15 @@ The DESeq2 Normalization and DGE step, [step 9](#9-normalize-read-counts-perform
 |DESeq2|1.34|[https://bioconductor.org/packages/release/bioc/html/DESeq2.html](https://bioconductor.org/packages/release/bioc/html/DESeq2.html)|
 |tximport|1.27.1|[https://github.com/mikelove/tximport](https://github.com/mikelove/tximport)|
 |tidyverse|1.3.1|[https://www.tidyverse.org](https://www.tidyverse.org)|
-|dp_tools|1.1.8|[https://github.com/J-81/dp_tools](https://github.com/J-81/dp_tools)|
-|singularity|3.9|[https://sylabs.io/](https://sylabs.io/)|
 |stringr|1.4.1|[https://github.com/tidyverse/stringr](https://github.com/tidyverse/stringr)|
+|dp_tools|1.1.8|[https://github.com/J-81/dp_tools](https://github.com/J-81/dp_tools)|
 |pandas|1.5.0|[https://github.com/pandas-dev/pandas](https://github.com/pandas-dev/pandas)|
 |seaborn|0.12.0|[https://seaborn.pydata.org/](https://seaborn.pydata.org/)|
 |matplotlib|3.6.0|[https://matplotlib.org/stable](https://matplotlib.org/stable)|
 |jupyter notebook|6.4.12|[https://jupyter-notebook.readthedocs.io/](https://jupyter-notebook.readthedocs.io/)|
 |numpy|1.23.3|[https://numpy.org/](https://numpy.org/)|
 |scipy|1.9.1|[https://scipy.org/](https://scipy.org/)|
+|singularity|3.9|[https://sylabs.io/](https://sylabs.io/)|
 
 ---
 
@@ -1097,7 +1097,7 @@ compare_csv_from_runsheet <- function(runsheet_path) {
 
 ### Load metadata from runsheet csv file ###
 
-compare_csv <- compare_csv_from_runsheet(params$runsheet_path)
+compare_csv <- compare_csv_from_runsheet(runsheet_path)
 
 
 ### Create data frame containing all samples and respective factors ###
@@ -1934,9 +1934,10 @@ import matplotlib.pyplot as plt
 # Get and unzip ISA.zip to extract metadata.
 
 accession = 'GLDS-NNN' # Replace Ns with GLDS number
-isaPath = 'path/to/GLDS-NNN-ISA.zip' # Replace with path to ISA archive file
-zip_file_object = zipfile.ZipFile(isaPath, "r")
-list_of_ISA_files = zip_file_object.namelist() 
+isaPath = '/path/to/GLDS-NNN_metadata_GLDS-NNN-ISA.zip' # Replace with path to ISA archive file
+zip_file_object =  zipfile.ZipFile(isaPath, "r")
+list_of_ISA_files = zip_file_object.namelist()
+UnnormalizedCountsPath = '/path/to/GLDS-NNN_rna_seq_RSEM_Unnormalized_Counts.csv'
 
 # Print contents of ISA zip file to view file order
 list_of_ISA_files
@@ -1973,7 +1974,7 @@ assay_table.head(n=3)
 
 # Get raw counts table
 
-raw_counts_table = pd.read_csv('/path/to/RSEM_Unnormalized_Counts.csv', index_col=0) 
+raw_counts_table = pd.read_csv(UnnormalizedCountsPath, index_col=0) 
 raw_counts_table.index.rename('Gene_ID', inplace=True)
 print(raw_counts_table.head(n=3))
 

RNAseq/Workflow_Documentation/NF_RCP-F/README.md

@@ -272,4 +272,3 @@ Standard Nextflow resource usage logs are also produced as follows:
      - Resource_Usage/execution_trace_{timestamp}.txt (an execution tracing file that contains information about each process executed in the workflow, including: submission time, start time, completion time, cpu and memory used, machine-readable output)
 
 <br>
-