merge devel into master

[Lioscro]

General

• [DEPRECATION] Support for split indices (with the -n option) will be deprecated in the next major release. It is now recommended to use --include-attribute and --exclude-attribute options, similar to Cellranger's mkref options (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references), to kb ref to reduce index size and memory usage.

ref

• A remote URL may be provided as the fasta (genomic FASTA) and/or gtf (gene annotation GTF) arguments. Support from ngs_tools 1.5.13.
• GTF is now allowed to have 0-length segments (https://github.com/pachterlab/kallisto/issues/340).

count

• [DEPRECATION] Technology SMARTSEQ is now deprecated. All future uses should use BULK, SMARTSEQ2 or SMARTSEQ3.
• Genes that do not have a gene name will now have their gene IDs in the gene_name column (or the adata.var_names if --gene-names is used).
• Support for --workflow lamanno for -x BULK and -x SMARTSEQ2 technologies.

[codecov-commenter]

Codecov Report

Merging #159 (1d7b285) into master (4f5e2cd) will decrease coverage by 0.19%. The diff coverage is 82.85%.

@@            Coverage Diff             @@
##           master     #159      +/-   ##
==========================================
- Coverage   97.17%   96.98%   -0.20%     
==========================================
  Files          14       14              
  Lines        1630     1626       -4     
==========================================
- Hits         1584     1577       -7     
- Misses         46       49       +3     

Impacted Files	Coverage Δ
kb_python/config.py	95.60% <ø> (ø)
kb_python/count.py	94.71% <76.00%> (-0.59%)	:arrow_down:
kb_python/utils.py	98.42% <100.00%> (+0.04%)	:arrow_up:

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