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--- a/studies/Bulk_segregant_analysis/isa.study.xlsx
+++ b/studies/Bulk_segregant_analysis/isa.study.xlsx
--- a/studies/additional_data/README.md
+++ b/studies/additional_data/README.md
--- a/studies/additional_data/isa.study.xlsx
+++ b/studies/additional_data/isa.study.xlsx
--- a/studies/additional_data/protocols/.gitkeep
+++ b/studies/additional_data/protocols/.gitkeep
--- a/studies/additional_data/resources/.gitkeep
+++ b/studies/additional_data/resources/.gitkeep
--- a/studies/additional_data/resources/color_pathway_genes.bed
+++ b/studies/additional_data/resources/color_pathway_genes.bed
--- a/studies/additional_data/resources/color_pathway_genes.csv
+++ b/studies/additional_data/resources/color_pathway_genes.csv
--- a/studies/additional_data/resources/reference_genomes/Ahypochondriacus/assembly/Ahypochondriacus_459_v2.0.softmasked.nospace.underscore.fa
+++ b/studies/additional_data/resources/reference_genomes/Ahypochondriacus/assembly/Ahypochondriacus_459_v2.0.softmasked.nospace.underscore.fa
--- a/studies/additional_data/resources/reference_genomes/Ahypochondriacus/assembly/Ahypochondriacus_459_v2.0.softmasked.nospace.underscore.fa.fai
+++ b/studies/additional_data/resources/reference_genomes/Ahypochondriacus/assembly/Ahypochondriacus_459_v2.0.softmasked.nospace.underscore.fa.fai
--- a/studies/hairy_root_transformation/README.md
+++ b/studies/hairy_root_transformation/README.md
--- a/studies/hairy_root_transformation/isa.study.xlsx
+++ b/studies/hairy_root_transformation/isa.study.xlsx
--- a/studies/hairy_root_transformation/protocols/.gitkeep
+++ b/studies/hairy_root_transformation/protocols/.gitkeep
--- a/studies/hairy_root_transformation/protocols/Detailed protocol for amaranth hairy root transformation modified from Lota et al_v1.pdf
+++ b/studies/hairy_root_transformation/protocols/Detailed protocol for amaranth hairy root transformation modified from Lota et al_v1.pdf
--- a/studies/hairy_root_transformation/resources/.gitkeep
+++ b/studies/hairy_root_transformation/resources/.gitkeep
--- a/studies/isoform_sequencing/isa.study.xlsx
+++ b/studies/isoform_sequencing/isa.study.xlsx
--- a/studies/leek_epidermis_bombardment/README.md
+++ b/studies/leek_epidermis_bombardment/README.md
--- a/studies/leek_epidermis_bombardment/isa.study.xlsx
+++ b/studies/leek_epidermis_bombardment/isa.study.xlsx
--- a/studies/leek_epidermis_bombardment/protocols/.gitkeep
+++ b/studies/leek_epidermis_bombardment/protocols/.gitkeep
--- a/studies/leek_epidermis_bombardment/protocols/Leek_epidermis_bombardment_Pietsch.pdf
+++ b/studies/leek_epidermis_bombardment/protocols/Leek_epidermis_bombardment_Pietsch.pdf
--- a/studies/leek_epidermis_bombardment/resources/.gitkeep
+++ b/studies/leek_epidermis_bombardment/resources/.gitkeep
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