docs: adding missing information regarding the FAI input now required in protein mode and automatically generated in genome mode

Adds the synteny coverage to the synteny report and closes the associated issue.

fix: specifiying diamond package version for conda since the current one failed to create the diamond DB

feat: adding the synteny coverage at the chromosome and genome scale. For that, a new input was introduced, the .fai to obtain chromosome sizes. It is generated for a genome input, but needs to be given for a protein input.

feat: adding the synteny coverage at the chromosome and genome scale. For that, a new input was introduced, the .fai to obtain chromosome sizes. It is generated for a genome input, but needs to be given for a protein input.

fix: testing new builds for orthofinder 2.5.5 since orthofinder 3.0.1b1 does not work with the example_data

Resolve "Use bioconda to run MCScanX"

Closes #32

See merge request !2

Ha Trang Phung authored 2 months ago and Baptiste Imbert committed 2 months ago

Closes #32.

fix: intra-species syntenic blocks comparing the same chromosome (e.g. Mt04&Mt04) were not properly dealed with.

bug: the statistics were incorrect. The species concerned for the block size was not mentioned so the values were wrong. Furthermore, the sd for the block gene count was missing.

feat: adding a new module of descriptive statistics for MCScanX collinearity file (number of blocks inter/intra, their length, gene content, etc.

fix: adding a global maxForks since some servers have a fork limit which result in errors such as 'OpenBLAS blas_thread_init'