Update readme - Githubissues

NBISweden / pipelines-nextflow

A set of workflows written in Nextflow for Genome Annotation.

GNU General Public License v3.0

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Update readme #11

Closed mahesh-panchal closed 4 years ago

mahesh-panchal commented 4 years ago

Change log:

[x] Remove pipelines dir.
[x] Update README with profile and usage info.
[x] Replace AGAT with GAAS in Annotation preprocessing pipeline.
[x] Add uppmax profile.

mahesh-panchal commented 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.

mahesh-panchal commented 4 years ago

Made some more updates:

[x] Updated pipeline README's to follow same format.
[x] Checked pipeline parameters and removed redundant parameters.
[x] Included params.config template to copy rather than generate from grep.
[x] Make singularity as suggested software profile rather than conda for reproducibility.

LucileSol commented 4 years ago

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!

Juke34 commented 4 years ago

Must be replaced by gaas_fasta_statistics.pl

LucileSol commented 4 years ago

my bad, same problem command not found

Juke34 commented 4 years ago

Must use GAAS-v1.0.1

Juke34 commented 4 years ago

I checked the code is fine

mahesh-panchal commented 4 years ago

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

mahesh-panchal commented 4 years ago

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.

mahesh-panchal commented 4 years ago

OK. nextflow run -profile nbis,singularity,test AnnotationPreprocessing is resulting in an error by busco. Something for me to fix.

mahesh-panchal commented 4 years ago

Is it ok to merge?