Closed mahesh-panchal closed 4 years ago
I don't think there is any reason to keep these repos with the same folder structure, and that folder is just unnecessary keystrokes. Currently I see this repository as a repository for Nextflow Annotation pipelines. The bpipe repository is simply now an archive. I don't believe anyone is using it anymore. I don't see anyone contributing workflows to this repository outside of the Annotation scope here. They will most likely be separated into other repositories. This is better from an organisational stand point because then one doesn't download everything every time. As a result, I don't think that the number of pipelines will get too large either.
In terms of the swap to DLS2 and using modules, at the moment the workflows simply don't need a more elaborate folder structure. In the long term it may also be beneficial to use the nf-core/modules rather than recreate our own. The best case is that we make this repo mature enough to become a nf-core annotation pipeline.
Made some more updates:
grep
.if I do :
conda activate /active/me/work/conda/gaas-f0acbc7203062da92
and then
gaas_fasta_statisticsAndPlot.pl
it says gaas_fasta_statisticsAndPlot.pl: command not found
there is a problem with the GAAS package, I think!
Must be replaced by gaas_fasta_statistics.pl
my bad, same problem command not found
Must use GAAS-v1.0.1
I checked the code is fine
I cannot pull the GAAS docker container from biocontainers (conda).
singularity pull quay.io/biocontainers/gaas:1.0.1--pl526r35_0
FATAL: While pulling library image: image quay.io/biocontainers/gaas:1.0.1--pl526r35_0 (amd64) does not exist in the library
I cannot pull the GAAS docker container from biocontainers (conda).
singularity pull quay.io/biocontainers/gaas:1.0.1--pl526r35_0 FATAL: While pulling library image: image quay.io/biocontainers/gaas:1.0.1--pl526r35_0 (amd64) does not exist in the library
Never mind. I forgot the docker://
prefix.
OK.
nextflow run -profile nbis,singularity,test AnnotationPreprocessing
is resulting in an error by busco
. Something for me to fix.
Is it ok to merge?
Change log:
uppmax
profile.