build: upgrade tool versions

[uniqueg]

Description

• Upgraded most tools to latest versions in Conda environments in workflow/envs
• Upgraded Docker containers accordingly
• Upgrade Ubuntu Docker images from Focal Fossa to Jammy Jellyfish
• Use sra-tools and pigz images from BioContainers (now all images except Ubuntu-based ones are from BioContainers)

Fixes #154

Type of change

• Maintenance

Conventional Commits guidelines

• I made sure the PR title follows the
  https://www.conventionalcommits.org/en/v1.0.0/

Checklist:

• My code changes follow the style of this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing tests pass locally with my changes
• I have updated the project's documentation

[uniqueg]

Expecting this to fail, of course - at the very least the expected outputs have to be updated. The main questions for now are (a) whether the tests run through at all and (b) whether the results are compatible.

[uniqueg]

In all tests, we currently get an error in rule create_kallisto_index. Will restore the old version of kallisto and see if the error goes away

[uniqueg]

The problem with kallisto index likely stems from this release that introduced a new and improved kallisto index:
https://github.com/pachterlab/kallisto/releases/tag/v0.50.0

I have now set the version to the last version before the offending version (0.50.0), so now it's 0.48.0, up from 0.46.2 that we previously used. With that all test workflows run through. As expected, the tests still fail, as many of the outputs changed (different MD5 sums).

Now, the question is whether they change in a way that we believe is worse than before. Do we have any way of assessing the testing quantitatively? How have we previously done this when upgrading tools (I'm sure this is not the first time)? Just ran a pipeline on one or more known samples and checked if the results look roughly the same and, if so, just upgraded? Because I think I would like to do that here as well. What do you think @mkatsanto?

@balajtimate As discussed, I rolled back the changes to the HTSinfer Docker image from this PR, so that it'll still pull the latest image from the Zavolab registry after merging. We can put in a separate PR for that when the image is fixed on BioContainers.

[uniqueg]

Actually, looking at the 57 files whose MD5 sum changed, it's not too bad at all:

• 56 are related to FastQC, so they have no downstream dependencies, e.g., on alignments, quantification etc.
• 1 is a file with version info (expected to change)

So I think the question about still getting compatible outputs doesn't arise.

Here's a list of the files whose MD5 check failed (renamed and grouped to make them easier to read/process):

fastqc/fq1/single/fastqc_data.txt
fastqc/fq1/single/fastqc.fo
fastqc/fq1/single/Images/adapter_content.png
fastqc/fq1/single/Images/duplication_levels.png
fastqc/fq1/single/Images/per_base_n_content.png
fastqc/fq1/single/Images/per_base_sequence_content.png
fastqc/fq1/single/Images/per_sequence_gc_content.png
fastqc/fq1/single/Images/per_sequence_quality.png
fastqc/fq1/single/Images/sequence_length_distribution.png
fastqc/fq1/paired/fastqc_data.txt
fastqc/fq1/paired/fastqc.fo
fastqc/fq1/paired/Images/adapter_content.png
fastqc/fq1/paired/Images/duplication_levels.png
fastqc/fq1/paired/Images/per_base_n_content.png
fastqc/fq1/paired/Images/per_base_sequence_content.png
fastqc/fq1/paired/Images/per_sequence_gc_content.png
fastqc/fq1/paired/Images/per_sequence_quality.png
fastqc/fq1/paired/Images/sequence_length_distribution.png
fastqc/fq2/paired/fastqc_data.txt
fastqc/fq2/paired/fastqc.fo
fastqc/fq2/paired/Images/adapter_content.png
fastqc/fq2/paired/Images/duplication_levels.png
fastqc/fq2/paired/Images/per_base_n_content.png
fastqc/fq2/paired/Images/per_base_sequence_content.png
fastqc/fq2/paired/Images/per_sequence_gc_content.png
fastqc/fq2/paired/Images/per_sequence_quality.png
fastqc/fq2/paired/Images/sequence_length_distribution.png
fastqc_trimmed/fq1/single/fastqc_data.txt
fastqc_trimmed/fq1/single/fastqc.fo
fastqc_trimmed/fq1/single/Images/adapter_content.png
fastqc_trimmed/fq1/single/Images/duplication_levels.png
fastqc_trimmed/fq1/single/Images/per_base_n_content.png
fastqc_trimmed/fq1/single/Images/per_base_sequence_content.png
fastqc_trimmed/fq1/single/Images/per_sequence_gc_content.png
fastqc_trimmed/fq1/single/Images/per_sequence_quality.png
fastqc_trimmed/fq1/single/Images/sequence_length_distribution.png
fastqc_trimmed/fq1/paired/fastqc_data.txt
fastqc_trimmed/fq1/paired/fastqc.fo
fastqc_trimmed/fq1/paired/Images/adapter_content.png
fastqc_trimmed/fq1/paired/Images/duplication_levels.png
fastqc_trimmed/fq1/paired/Images/per_base_n_content.png
fastqc_trimmed/fq1/paired/Images/per_base_sequence_content.png
fastqc_trimmed/fq1/paired/Images/per_sequence_gc_content.png
fastqc_trimmed/fq1/paired/Images/per_sequence_quality.png
fastqc_trimmed/fq1/paired/Images/sequence_length_distribution.png
fastqc_trimmed/fq2/paired/fastqc_data.txt
fastqc_trimmed/fq2/paired/fastqc.fo
fastqc_trimmed/fq2/paired/Images/adapter_content.png
fastqc_trimmed/fq2/paired/Images/duplication_levels.png
fastqc_trimmed/fq2/paired/Images/per_base_n_content.png
fastqc_trimmed/fq2/paired/Images/per_base_sequence_content.png
fastqc_trimmed/fq2/paired/Images/per_sequence_gc_content.png
fastqc_trimmed/fq2/paired/Images/per_sequence_quality.png
fastqc_trimmed/fq2/paired/Images/sequence_length_distribution.png
multiqc_summary/multiqc_data/multiqc_fastqc_fastqc_raw.txt
multiqc_summary/multiqc_data/multiqc_fastqc_fastqc_trimmed.txt
salmon_indexes/homo_sapiens/31/salmon.idx/versionInfo.json