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Update salmon transcriptome index generation

Merged Update salmon transcriptome index generation
new_salmon_index into master
2 unresolved threads
Merged BIOPZ-Bak Maciej requested to merge new_salmon_index into master
2 unresolved threads
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tests/test_integration_workflow/expected_output.files
+ 3
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results/kallisto_indexes/homo_sapiens/kallisto.idx
results/salmon_indexes/homo_sapiens/salmon.idx/versionInfo.json
results/salmon_indexes/homo_sapiens/salmon.idx/duplicate_clusters.tsv
results/salmon_indexes/homo_sapiens/salmon.idx/info.json
results/salmon_indexes/homo_sapiens/31/salmon.idx/versionInfo.json
results/salmon_indexes/homo_sapiens/31/salmon.idx/duplicate_clusters.tsv
results/salmon_indexes/homo_sapiens/31/salmon.idx/info.json
results/star_indexes/homo_sapiens/75/STAR_index/chrLength.txt
results/star_indexes/homo_sapiens/75/STAR_index/chrNameLength.txt
results/star_indexes/homo_sapiens/75/STAR_index/chrName.txt