diff --git a/config/Aquifer/config.fast5.yaml b/config/aquifer/config.fast5.yaml
similarity index 100%
rename from config/Aquifer/config.fast5.yaml
rename to config/aquifer/config.fast5.yaml
diff --git a/config/Aquifer/config.yaml b/config/aquifer/config.yaml
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rename to config/aquifer/config.yaml
diff --git a/config/Aquifer/sbatch.fast5.sh b/config/aquifer/sbatch.fast5.sh
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diff --git a/config/Aquifer/sbatch.sh b/config/aquifer/sbatch.sh
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rename from config/Aquifer/sbatch.sh
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diff --git a/config/Aquifer/slurm.fast5.yaml b/config/aquifer/slurm.fast5.yaml
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rename from config/Aquifer/slurm.fast5.yaml
rename to config/aquifer/slurm.fast5.yaml
diff --git a/config/Aquifer/slurm.yaml b/config/aquifer/slurm.yaml
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diff --git a/config/GDB/config.fast5.yaml b/config/gdb/config.fast5.yaml
similarity index 100%
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diff --git a/config/GDB/config.yaml b/config/gdb/config.yaml
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diff --git a/config/GDB/sbatch.fast5.sh b/config/gdb/sbatch.fast5.sh
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diff --git a/config/GDB/sbatch.sh b/config/gdb/sbatch.sh
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diff --git a/config/GDB/slurm.fast5.yaml b/config/gdb/slurm.fast5.yaml
similarity index 100%
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diff --git a/config/GDB/slurm.yaml b/config/gdb/slurm.yaml
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diff --git a/config/Rumen/config.fast5.yaml b/config/rumen/config.fast5.yaml
similarity index 100%
rename from config/Rumen/config.fast5.yaml
rename to config/rumen/config.fast5.yaml
diff --git a/config/Rumen/config.yaml b/config/rumen/config.yaml
similarity index 100%
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rename to config/rumen/config.yaml
diff --git a/config/Rumen/sbatch.fast5.sh b/config/rumen/sbatch.fast5.sh
similarity index 100%
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diff --git a/config/Rumen/sbatch.sh b/config/rumen/sbatch.sh
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diff --git a/config/Rumen/slurm.fast5.yaml b/config/rumen/slurm.fast5.yaml
similarity index 100%
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diff --git a/config/Rumen/slurm.yaml b/config/rumen/slurm.yaml
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diff --git a/config/Zymo/config.fast5.yaml b/config/zymo/config.fast5.yaml
similarity index 100%
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rename to config/zymo/config.fast5.yaml
diff --git a/config/Zymo/config.yaml b/config/zymo/config.yaml
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rename to config/zymo/config.yaml
diff --git a/config/Zymo/sbatch.fast5.sh b/config/zymo/sbatch.fast5.sh
similarity index 100%
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diff --git a/config/Zymo/sbatch.sh b/config/zymo/sbatch.sh
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diff --git a/config/Zymo/slurm.fast5.yaml b/config/zymo/slurm.fast5.yaml
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diff --git a/config/Zymo/slurm.yaml b/config/zymo/slurm.yaml
similarity index 100%
rename from config/Zymo/slurm.yaml
rename to config/zymo/slurm.yaml