Feature/add outrider #78

lonnekevanbrussel · 2024-03-06T15:54:51Z

Outrider script for RNA seq pipeline in main.nf (main.yml) and outrider.R

…nf at NexflowModules

…parameter in functions main and save_output

…d choose accordingly

…ionMask, fitting, pvalue and zscore calculation to run outrider

…th in ext.prefix

…ate filtering for exon level and ratio fpkm

BasMonkey

Nice work!

Some minor remarks:

Some files are missing a newline at the end of the file. Why it's important? See https://stackoverflow.com/a/729795
Try to be consistent with the indentation across your files / code
See individual files for the remarks per line

BasMonkey · 2024-08-19T11:30:38Z

Fraser/1.99.3/environment.yml

+  - bioconda
+  - defaults
+dependencies:
+  - bioconda::fastqc=0.12.1


Missing newline at the end of this file, see https://stackoverflow.com/a/729795

BasMonkey · 2024-08-19T11:31:47Z

Fraser/1.99.3/fraser.R

+  sampleTable$pairedEnd <- TRUE
+
+  message(date(), ": sampleTable")
+  print(sampleTable)


Try to avoid print statements, since they might get lost in the stdout. If you want to save / view the data of a variable, write it to a logfile instead

BasMonkey · 2024-08-19T11:32:03Z

Fraser/1.99.3/fraser.R

+  # create FRASER object
+  settings <- FraserDataSet(colData=sampleTable, workingDir="./FRASER_output")
+  message(date(), ": settings...")
+  print(settings)


Same goes for this print statement

BasMonkey · 2024-08-19T11:32:57Z

Fraser/1.99.3/fraser.R

+  print(dim(assays(fds)$rawCountsJ))
+  print(dim(assays(fds)$rawCountsSS))


Same goes for these print statements aswell

BasMonkey · 2024-08-19T11:33:08Z

Fraser/1.99.3/fraser.R

+  print(dim(assays(fds)$rawCountsJ)) 
+  print(dim(assays(fds)$rawCountsSS))


And for these

BasMonkey · 2024-08-19T11:41:28Z

Outrider/1.20.0/outrider.R

+}
+
+
+main(args$query, args$ref, args$output_path, args$pref)


Missing newline at the end of this file

BasMonkey · 2024-08-19T11:42:19Z

Outrider/1.20.0/outrider.R

This is one of the two files that uses two spaces as indentation (instead of four). Try to be consistent throughout your code

BasMonkey · 2024-08-19T11:44:40Z

Fraser/1.99.3/fraser.R

+  fraser_res <- results(fraser_ds, all=TRUE)
+  #res <- results(fds, psiType=psiTypes, aggregate=TRUE, collapse=FALSE, all=TRUE)
+  message(date(), ": result...")
+  print(fraser_res)


Try to avoid print statements, since they might get lost in the stdout. If you want to save / view the data of a variable, write it to a logfile instead

BasMonkey · 2024-08-19T11:45:54Z

Fraser/1.99.3/fraser.R

This is one of the two files that uses two spaces as indentation (instead of four). Try to be consistent throughout your code

BasMonkey · 2024-08-19T11:51:47Z

Outrider/1.20.0/outrider.R

+filter_expression <- function(ods, query, prefix){
+  if(grepl("gene", prefix)){
+    ##FOR GENE LEVEL
+    ods <- filterExpression(ods, fpkmCutoff = 1, minCounts = FALSE, filterGenes = FALSE, gtfFile="/hpc/diaggen/data/databases/gencode/gencode.v44.primary_assembly.basic.annotation.gtf")


It may be better to fill this path as a parameter or via a config file. The path may change and to include that change a new release of the software must be made. (or worse: this line gets overlooked at all)

ellendejong · 2025-04-18T08:04:30Z

Outrider/1.20.0/Dockerfile

@@ -0,0 +1,19 @@
+################## BASE IMAGE ######################
+FROM --platform=linux/amd64 quay.io/biocontainers/bioconductor-outrider:1.18.1--r43hf17093f_0


The base image is using version 1.18.1--r43hf17093f_0. Folder name Outrider/1.20.0/ doesnot match.

ellendejong and others added 28 commits November 2, 2023 08:04

Add gitignore

8e9fe02

custom script to run outrider, not working yet.

156c79e

Dockerfile outrider for additional R packages

369cf70

changes NextflowModules to test and run pipeline

0e46a46

changed links to NextflowModules

a01ca9b

added nextflow.config

e095750

added conf folder witth config files

8918ddc

added main.nf and yml in outrider

5a9e228

edit outrider main.nf

6dc82eb

Delete all test files

03407c4

outrider.R with default output dir and correct R script call in main.…

fac6d0e

…nf at NexflowModules

Edit path to outrider dir

388de35

Outrider main.nf added tag meta.id and param feature exon/gene

fdaaa3b

outrider.R added argument feature to use in output tsv file, also as …

fdb3a80

…parameter in functions main and save_output

Added changes for feature and output in meta.yml file

808c148

Outrider main.nf changed input feature, input refset gene and exon an…

af534ae

…d choose accordingly

Added filtering, findEncodingDim, controlForConfounders, sampleExclus…

cefbef6

…ionMask, fitting, pvalue and zscore calculation to run outrider

versions.yml error

abae593

full result, no exclusion mask and fit

22b3d9a

Changes regarding separate outrider processes on GENE & EXON level wi…

8648706

…th in ext.prefix

Outrider.R additions to generate input files for EMC app. Added separ…

2acf151

…ate filtering for exon level and ratio fpkm

forgot }

ccf831f

filter_expression as a separate function in outrider.R

dd36ce0

chx->CHX in outrider.R

3e59c78

fraser module added for aberrant splicing

5d596e5

Instructions for Exon ratio code (un)commenting

12c1e1c

added returns for readability, CHX->chx

931a159

Fraser edits for readability and logging

0c330de

BasMonkey requested changes Aug 19, 2024

View reviewed changes

Newline, enter and genome_gtf passed as argument

21dab56

lonnekevanbrussel added 2 commits August 26, 2024 16:38

input format

84a34b1

working file now with gtf file as argument

b36dbb9

ellendejong requested changes Apr 18, 2025

View reviewed changes

		print(dim(assays(fds)$rawCountsJ))
		print(dim(assays(fds)$rawCountsSS))

		}


		main(args$query, args$ref, args$output_path, args$pref) No newline at end of file

		@@ -0,0 +1,19 @@
		################## BASE IMAGE ######################
		FROM --platform=linux/amd64 quay.io/biocontainers/bioconductor-outrider:1.18.1--r43hf17093f_0

Feature/add outrider #78

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lonnekevanbrussel commented Mar 6, 2024

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