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Catching up to main
… default, not a flag just in the if (TRUE) block
letaylor
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letaylor
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@grenkoca one small comment and requested change.
After that, I think we should merge. @henryjtaylor what do you think?
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@letaylor good idea-- added into the above commit. |
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@henryjtaylor as soon as you give this the OK, I'll merge |
henryjtaylor
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henryjtaylor
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@grenkoca This looks great! Could you make those quick changes I flagged?
The other quick thing, since this is a public repo, could you squash your commits to a single one, and just add a quick descriptor in the commit message?
| help = "Filter to remove genes with fewer cp10k/counts | ||
| averages. See option `--filter_type`" | ||
| ), | ||
| optparse::make_option(c("-x", "--filter_type"), |
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Can you do 'get_filter_phenotype'? Just to make it a bit more verbose
| optparse::make_option(c("-x", "--filter_type"), | ||
| type = "character", | ||
| default = 1, | ||
| help = "Either 'counts' or 'cp10k'" |
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can you go ahead and add logcp10?
main.nf
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| #!/usr/bin/env nextflow | ||
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| nextflow.preview.dsl = 2 | ||
| nextflow.enable.dsl=2 |
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when did they add this one? We're currently using v20.10.0.5430 -- if it's beyond that, we should add something to the README
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Not sure, but I'm on 22.04.3 and getting this error:
N E X T F L O W ~ version 22.04.3
Preview nextflow mode 'preview' is not supported anymore -- Please use `nextflow.enable.dsl=2` instead
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Update: I found this blog post from July 2020 stating that nextflow.enable.dsl is available in v20.07.1, but also:
Note that the previous
nextflow.previewdirective is still available, however, when using the above declaration the use of the final syntax is enforced.
It's quitting the pipeline on later versions of Nextflow. See below for a fix to check the version and use the appropriate command
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@henryjtaylor @letaylor
This is my custom branch I was using for the T2D KO work. Here are the changes I made, feel free to keep/discard what you want:
cp10k_filterwith flags forfilter_typeandfilter_thresholdif (TRUE)block. I was going to remove it after I worked out the real issue, but figured it might be useful if we ever need to run DGE on something with a small range in input values. (i.e. fixes this issue)nextflow.preview.dsl = 2tonextflow.enable.dsl=2due to deprication