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…nf at NexflowModules
…parameter in functions main and save_output
…d choose accordingly
…ionMask, fitting, pvalue and zscore calculation to run outrider
…ate filtering for exon level and ratio fpkm
BasMonkey
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BasMonkey
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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
Fraser/1.99.3/environment.yml
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| - bioconda | ||
| - defaults | ||
| dependencies: | ||
| - bioconda::fastqc=0.12.1 No newline at end of file |
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Missing newline at the end of this file, see https://stackoverflow.com/a/729795
Fraser/1.99.3/fraser.R
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| sampleTable$pairedEnd <- TRUE | ||
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| message(date(), ": sampleTable") | ||
| print(sampleTable) |
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Try to avoid print statements, since they might get lost in the stdout. If you want to save / view the data of a variable, write it to a logfile instead
Fraser/1.99.3/fraser.R
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| # create FRASER object | ||
| settings <- FraserDataSet(colData=sampleTable, workingDir="./FRASER_output") | ||
| message(date(), ": settings...") | ||
| print(settings) |
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Same goes for this print statement
Fraser/1.99.3/fraser.R
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| print(dim(assays(fds)$rawCountsJ)) | ||
| print(dim(assays(fds)$rawCountsSS)) |
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Same goes for these print statements aswell
Fraser/1.99.3/fraser.R
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| print(dim(assays(fds)$rawCountsJ)) | ||
| print(dim(assays(fds)$rawCountsSS)) |
Outrider/1.20.0/outrider.R
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| } | ||
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| main(args$query, args$ref, args$output_path, args$pref) No newline at end of file |
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Missing newline at the end of this file
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This is one of the two files that uses two spaces as indentation (instead of four). Try to be consistent throughout your code
Fraser/1.99.3/fraser.R
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| fraser_res <- results(fraser_ds, all=TRUE) | ||
| #res <- results(fds, psiType=psiTypes, aggregate=TRUE, collapse=FALSE, all=TRUE) | ||
| message(date(), ": result...") | ||
| print(fraser_res) |
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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
There was a problem hiding this comment.
This is one of the two files that uses two spaces as indentation (instead of four). Try to be consistent throughout your code
Outrider/1.20.0/outrider.R
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| 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") |
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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)
| @@ -0,0 +1,19 @@ | |||
| ################## BASE IMAGE ###################### | |||
| FROM --platform=linux/amd64 quay.io/biocontainers/bioconductor-outrider:1.18.1--r43hf17093f_0 | |||
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The base image is using version 1.18.1--r43hf17093f_0. Folder name Outrider/1.20.0/ doesnot match.
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Outrider script for RNA seq pipeline in main.nf (main.yml) and outrider.R