Dupradar #154
Dupradar #154
Conversation
This reverts commit 38f586b.
src/dupradar/config.vsh.yaml
Outdated
| - name: Output | ||
| arguments: | ||
| - name: --output_dupmatrix | ||
| type: file | ||
| direction: output | ||
| description: path to output file (txt) of duplicate tag counts | ||
| example: dup_matrix.txt | ||
| - name: --output_dup_intercept_mqc | ||
| type: file | ||
| direction: output | ||
| description: path to output file (txt) of multiqc intercept value DupRadar | ||
| example: dup_intercept_mqc.txt | ||
| - name: --output_duprate_exp_boxplot | ||
| type: file | ||
| direction: output | ||
| default: duprate_exp_boxplot.pdf | ||
| description: | | ||
| Path to output file (pdf) of distribution of expression box plot | ||
| - name: --output_duprate_exp_densplot | ||
| type: file | ||
| direction: output | ||
| description: | | ||
| Path to output file (pdf) of 2D density scatter plot of duplicate tag counts | ||
| example: duprate_exp_densityplot.pdf | ||
| - name: --output_duprate_exp_denscurve_mqc | ||
| type: file | ||
| direction: output | ||
| description: | | ||
| Path to output file (pdf) of density curve of gene duplication multiqc | ||
| example: duprate_exp_density_curve_mqc.txt | ||
| - name: --output_expression_histogram | ||
| type: file | ||
| direction: output | ||
| description: | | ||
| Path to output file (pdf) of distribution of RPK values per gene histogram | ||
| example: expression_hist.pdf | ||
| - name: --output_intercept_slope | ||
| type: file | ||
| direction: output | ||
| description: output file (txt) with progression of duplication rate values | ||
| example: intercept_slope.txt |
There was a problem hiding this comment.
None of these are required: true.
src/dupradar/script.sh
Outdated
| mv "$par_id"_dupMatrix.txt $par_output_dupmatrix | ||
| mv "$par_id"_dup_intercept_mqc.txt $par_output_dup_intercept_mqc | ||
| mv "$par_id"_duprateExpBoxplot.pdf $par_output_duprate_exp_boxplot | ||
| mv "$par_id"_duprateExpDens.pdf $par_output_duprate_exp_densplot | ||
| mv "$par_id"_duprateExpDensCurve_mqc.txt $par_output_duprate_exp_denscurve_mqc | ||
| mv "$par_id"_expressionHist.pdf $par_output_expression_histogram | ||
| mv "$par_id"_intercept_slope.txt $par_output_intercept_slope |
There was a problem hiding this comment.
This expects all output files to be generated/present which is in contrast with the required: false of those parameters.
There was a problem hiding this comment.
Right, I will keep the default names from the original tool if they are not specified.
src/dupradar/test.sh
Outdated
There was a problem hiding this comment.
Please provide a test scenario where not all output parameters have been provided.
src/dupradar/config.vsh.yaml
Outdated
| required: true | ||
| description: Path to GTF annotation file. | ||
| - name: --paired | ||
| type: boolean |
There was a problem hiding this comment.
Shouldn't this be type: boolean_true?
| argument_groups: | ||
| - name: Input | ||
| arguments: | ||
| - name: --id |
There was a problem hiding this comment.
What if this parameter is not set?
src/dupradar/dupradar.r
Outdated
| input_bam <- args[1] | ||
| output_prefix <- args[2] | ||
| annotation_gtf <- args[3] | ||
| stranded <- as.numeric(args[4]) | ||
| paired_end <- ifelse(args[5] == "true", TRUE, FALSE) | ||
| threads <- as.numeric(args[6]) |
There was a problem hiding this comment.
I wonder if it makes more sense to combine script.sh and dupradar.r and directly call the R script instead of using the wrapper. But that would force us to change the dupradar.r code itself. What do you think?
There was a problem hiding this comment.
That could be good, it's pretty straightforward and I think it would simplify the component, I'll get on that.
|
I only made suggestions for individual lines of code, but they should be applied to the whole script |
Right, my bad! lmk if I missed anything now |
Description
Add DupRadar component
Checklist before requesting a review
I have performed a self-review of my code
Conforms to the Contributing guidelines
Proposed changes are described in the CHANGELOG.md
I have tested my code with
viash ns test --parallel -q <name or namespace>Check the correct box. Does this PR contain: