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First of all I'd like to congratulate you to this great effort to present meta-data in a standardized way !
As I'm writing a script to read sdrf files into R for using this information (with my CRAN-…
wraff updated
3 years ago
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## Bug report
### Expected behavior and actual behavior
Expect that files updated/ added to a directory will trigger watchPath() and downstream operations regardless of the machine from which t…
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## DatabaseSearchEngines
Including the following processes: process search_engine_msgf, process search_engine_comet and index_peptides (starting from 2.7.1, indexing is done internally per default…
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In the "dev" version of the pipeline on "nf-core", this information on the "Usage" page (https://nf-co.re/proteomicslfq/dev/usage) is outdated:
> The typical command for running the pipeline is as …
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The Label-free and TMT example URLs do not work (https://github.com/bigbio/proteomics-metadata-standard/blob/master/annotated-projects/PXD008934/sdrf.tsv and https://raw.githubusercontent.com/bigbio/p…
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We need to review https://ebi-ait.github.io/hca-ebi-wrangler-central/SOPs/hca_to_scea_tools_SOP.html and make sure that the whole process can be run without previous knowledge of the tools.
Identif…
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**Wrangler responsible for this dataset/lab:**
Primary: Ami
Secondary: Enrique
**Description of the task:**
GSE116222: EpithelialDiversityHealthInflammation
https://docs.google.com/spre…
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**Describe the bug**
Running the hca_to_scea script produces the following error:
`script.py: error: the following arguments are required: -study`
even though the -study argument is included.
**To …
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Whenever we trigger the GEO importer for bulk RNA-seq experiments, the freshly converted MAGE-TAB file (with name E-GEOD-xxx.idf.txt) gets copied to the $ATLAS_PROD/GEO_import/GEOD/E-GEOD-xxx/ folder …
anjaf updated
3 years ago