updated pangolin and dockerhub

[JD2112]

The purpose of the code changes are as follows:

What Added updated version of Pangolin v3.0.5 with constellations and scorpio support, #13

Why This changes complete the newest version of Pangolin and add the latest updates for the analysis pipeline.

How I made changes in the environment.yml files for both Illumina and Nanopore workflows and also made some updates (like python>=3.7) on the dependencies.

Testing I tested the pipeline on the local computer as well as on the NGP server, and it is working on both systems.

Standard test procedure

• [x] The self-test mentioned in the README finished successfully
• [x] Produced files contain expected values
• [x] The code has been reviewed by @octocat

This version is a:

• [ ] MAJOR - when you make incompatible API changes
• [x] MINOR - when you add functionality in a backwards compatible manner
• [ ] PATCH - when you make backwards compatible bug fixes or documentation/instructions

[JD2112]

1. changes singularity "process.container" at nextflow.config - containers can be called from local (works with NGP server), dockerhub (doesn't work with NGP server) or singularity library (works with NGP server)
2. added 'sge' process.executor at nextflow.config
3. Updated ENV LC_ALL C.UTF-8, ENV LANG C.UTF-8 in docker and singularity env files
4. update pangolin (v3.0.3), scorpio, constellation, python>=3.7, usher at env*.yml files - latest version needs all these updates to run pangolin.

[JD2112]

@sylvinite created new pull request after changes.

[JD2112]

What

Added updated version of Pangolin v3.0.5 with constellations and scorpio support, #13

Why

This changes complete the newest version of Pangolin and add the latest updates for the analysis pipeline.

How

I made changes in the environment.yml files for both Illumina and Nanopore workflows and also made some updates (like python>=3.7) on the dependencies.

Testing

I tested the pipeline on the local computer as well as on the NGP server, and it is working on both systems.