Matthieu Muffato

Uninstall

9

Fixes #601 The problem was that the `Module` object was too tightly bound to the registry. All we need a light-weight object that can provide `container_dir` and `module_dir`. I've made...

shpc uninstall and tool versions

1

**Describe the bug** `shpc uninstall $tool` actually only deletes the latest tag of that tool, not the other tags, while letting the user think all tags are deleted. `shpc uninstall...

Reinstallation mode

12

Closes #501 Hi @vsoch . Working my way through #501. It's not as straightforward as I though it would be ! This is a draft pull-request. So far I've expanded...

Support accessing remote registries via ssh

7

(extension of #585 ) Note: the URL has to be given as `ssh://[user@]host.xz[:port]/path/to/repo.git` rather than the shorter version `[user@]host.xz:path/to/repo.git`. Comments: 1. The shpc code was sometimes using `https://` to test...

Hiya, I've got the feeling that `chrU1` is a typo, and it should have been `chrU`. The change was made in [#117](https://github.com/open2c/pairtools/pull/117/files#diff-52ac73f774be95a098068c3b942c2c575e43ec45ad3b0848131313336cc8b750R25). Best, Matthieu

Misc. minor dev

1

## Use case A collection of minor changes I have locally: bugfixes and new features ## Description 1. bugfix: avoid Perl's warning about undefined values. 2. New SQL view similar...

Test init_pipeline outside of the test process and drop the (partial) database if the initialisation fails

3

## Use case 1. `init_pipeline` was the last script tested in the test process itself. A long time ago, I thought it would simplify testing, but I gradually realised it's...

### Description of feature We use Busco to assess the completeness & fragmentation of an assembly. The main parameter is a lineage name, that needs to be phylogenetically relevant to...

### Description of the bug The `genome_note_template.docx` provided in the pipeline has inconsistent naming of some variables. For instance, the scaffold N50 is indicated with both `SCAFF_N50` (in the text)...

### Description of the bug On the public_dev branch, the input fasta is called `GCA_946965045.1.fasta.gz` and the Hi-C CRAM file `GCA_946965045.1.unmasked.hic.uoEpiScrs1.subsampled.cram`, but the assembly parameter is set to `GCA_946965045.2`. After...