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View Code? Open in Web Editor NEWsingle cell analysis and more pipeline
Home Page: https://christopherbarrington.github.io/scamp/
single cell analysis and more pipeline
Home Page: https://christopherbarrington.github.io/scamp/
like software versions yaml file it may be useful to explicitly record these parameters so they can be more-easily reported.
and same for stages
assumes an inputs
directory - could just use the absolute path
NXF_HOME
isn't clear - not everyone has it set
Unused values will invalidate the cache?
when merging gif files to create an index, the names should be checked for consistency
could
SEURAT:
8 weeks replicate 1:
be used to indicate that this should be run with all default parameters
Ambiguous method overloading for method java.util.LinkedHashMap#plus.
Cannot resolve which method to invoke for [null] due to overlapping prototypes between:
[interface java.util.Collection]
[interface java.util.Map]
each main.nf
file should have an accompanying meta.yaml file to include easy to access information on the modules inputs/outputs etc
try to avoid using conflicting keys
for example: https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/mem/meta.yml
method to download and format as granges, if not provided in an index
remove the \
in scripts so they are properly formatted in work directories
write a module (?) that will present the information produced/data analysed/processes/steps for a (sub)workflow.
these should be collectable into a single document/webpage
may be better to have this option in the module so that it can be set as false for multimodal assays where the barcodes are checked
formats differ between R and shell scripts. and versions files need deciding
completed workbook/webpage reports could be pushed to a (or multiple) GitHub repositories
maybe specified with:
github:
remotes:
- ChristopherBarrington/scamp-push-test:babs/docs
is it worth having multiple remotes? maybe would have a public/private version of reports to different remotes?
these should be in the analysis stanza groups either _default or in an analysis
should be tidier!
use --scamp-params param.yaml
for example so that --params.stuff
can also be used
an output could be a parameters yaml file with additional fields added - eg seurat path so that the pipeline can be restarted from here rather than the cache in the longer-term
reports just titled 'output'
once a seurat object is created the workflow should be the same independent of technology, so different quantification methods can use the same subworkflow
make an assay for ensembl and another for gene names
the make granges and biomart (for example) may be duplicated, can they be moved to a genome processing subworkflow?
cc.genes
?)should only be needed in one place
include hive datasets for the guess parameters script, need indexes etc
no asf label for it, sample sheet lists 'None'
wit #54
match up with asf lims
better organisation of the utilities functions module into directories (particularly for the bigger functions)
move script
blocks to templates/main.sh
to keep better organised and easier to read scripts
steal from nf-core!
write the module that uses an R script to create the initial (basic) Seurat object
these could be value channels instead of mapped?
validate parameters before running pipeline
Using js.build
instead to pass parameters:
https://discourse.gohugo.io/t/variables-inside-javascript/39086/3
currently uses two function calls but seems it could be streamlined
merge_process_emissions(make_object, ['opt', 'seurat'])
.map{merge_metadata_and_process_output(it)}
.dump(tag: 'seurat:prepare:cell_ranger:objects', pretty: true)
.set{objects}
could this be in the {scampr} onLoad
?
rather than one big master library "csv" make each file separately for each dataset. the library and feature type information is not in the dataset config.
processes should have their own environments, not expect software to be available for them
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