Create single environment for bin python scripts.

[FedericaBrando]

This pull request includes updates to several Nextflow processes to standardize the container image used across the pipeline. The main change involves replacing various container images with a single unified container image.

steps:

• create docker recipe
• changed shebangs of python scripts
• changed container for each python process
• tested pipeline not failing
• checked results with current expected

Tests are on-going.

closes #225

[Copilot]

Copilot reviewed 55 out of 75 changed files in this pull request and generated no comments.

Files not reviewed (20)

• modules/local/annotatedepth/main.nf: Language not supported
• modules/local/bbgtools/oncodrive3d/preprocessing/main.nf: Language not supported
• modules/local/bbgtools/sitecomparison/main.nf: Language not supported
• modules/local/blacklistmuts/main.nf: Language not supported
• modules/local/combine_sbs/main.nf: Language not supported
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• modules/local/compute_trinucleotide/main.nf: Language not supported
• modules/local/computemutrate/main.nf: Language not supported
• modules/local/dna2protein/main.nf: Language not supported
• modules/local/dnds/preprocess/main.nf: Language not supported
• modules/local/expand_regions/main.nf: Language not supported
• modules/local/filterbed/main.nf: Language not supported
• modules/local/filtermaf/main.nf: Language not supported
• modules/local/group_genes/main.nf: Language not supported
• modules/local/indels/main.nf: Language not supported
• modules/local/mergemafs/main.nf: Language not supported
• modules/local/mutation_matrix/main.nf: Language not supported
• modules/local/mutations2sbs/main.nf: Language not supported
• modules/local/plot/omega/main.nf: Language not supported

[Copilot]

Copilot reviewed 57 out of 77 changed files in this pull request and generated no comments.

Files not reviewed (20)

• modules/local/annotatedepth/main.nf: Language not supported
• modules/local/bbgtools/oncodrive3d/plot_chimerax/main.nf: Language not supported
• modules/local/bbgtools/oncodrive3d/preprocessing/main.nf: Language not supported
• modules/local/bbgtools/sitecomparison/main.nf: Language not supported
• modules/local/blacklistmuts/main.nf: Language not supported
• modules/local/combine_sbs/main.nf: Language not supported
• modules/local/compute_mutability/main.nf: Language not supported
• modules/local/compute_profile/main.nf: Language not supported
• modules/local/compute_trinucleotide/main.nf: Language not supported
• modules/local/computemutrate/main.nf: Language not supported
• modules/local/dna2protein/main.nf: Language not supported
• modules/local/dnds/preprocess/main.nf: Language not supported
• modules/local/expand_regions/main.nf: Language not supported
• modules/local/filterbed/main.nf: Language not supported
• modules/local/filtermaf/main.nf: Language not supported
• modules/local/group_genes/main.nf: Language not supported
• modules/local/indels/main.nf: Language not supported
• modules/local/mergemafs/main.nf: Language not supported
• modules/local/mutation_matrix/main.nf: Language not supported
• modules/local/mutations2sbs/main.nf: Language not supported

[FedericaBrando]

Please give it a look!

[FerriolCalvet]

All looks good!
If the final test with Seqera works you can merge it!

I guess that in a way we could keep track of the scripts whose container have change and create a list of all the ones that require updating the input handling with click, but I guess this is also part of the code review and you may want to address it one file at a time instead of a batch update

[FerriolCalvet]

also you are combining the use of single and double quotes for the containers, but I don't really care.
I comment it just in case you have a preference and want to make it uniform.

[FedericaBrando]

also you are combining the use of single and double quotes for the containers, but I don't really care.
I comment it just in case you have a preference and want to make it uniform.

good catch, I'll fix it

I guess that in a way we could keep track of the scripts whose container have change and create a list of all the ones that require updating the input handling with click, but I guess this is also part of the code review and you may want to address it one file at a time instead of a batch update

better a one-by-one update! It would also impact the processes and how you declare the params for the scripts

[FerriolCalvet]

True, it is a bigger thing! Sounds like a good plan.
Whenever I update some script, if I do I will take this into account but doing it in a one-by-one manner makes total sense.