restored old report for demo

nf-core · Jan 19, 2024 · 89c6b30 · 89c6b30
1 parent f46a2c7
commit 89c6b30
Show file tree

Hide file tree

Showing 416 changed files with 918 additions and 895 deletions.
diff --git a/assets/main_report/index.qmd b/assets/main_report/index.qmd
diff --git a/assets/main_report/packages.bib b/assets/main_report/packages.bib
@@ -32,11 +32,20 @@ @Manual{R-base
   url = {https://www.R-project.org/},
 }
 
+@Manual{R-bookdown,
+  title = {bookdown: Authoring Books and Technical Documents with R Markdown},
+  author = {Yihui Xie},
+  year = {2023},
+  note = {R package version 0.36, 
+https://pkgs.rstudio.com/bookdown/},
+  url = {https://github.com/rstudio/bookdown},
+}
+
 @Manual{R-dplyr,
   title = {dplyr: A Grammar of Data Manipulation},
   author = {Hadley Wickham and Romain François and Lionel Henry and Kirill Müller and Davis Vaughan},
   year = {2023},
-  note = {R package version 1.1.3},
+  note = {R package version 1.1.4},
   url = {https://dplyr.tidyverse.org},
 }
 
@@ -78,7 +87,7 @@ @Manual{R-ggtree
   title = {ggtree: an R package for visualization of tree and annotation data},
   author = {Guangchuang Yu and Tommy Tsan-Yuk Lam and Shuangbin Xu},
   year = {2023},
-  note = {R package version 3.10.0},
+  note = {R package version 3.8.2},
   url = {https://bioconductor.org/packages/ggtree},
   doi = {10.18129/B9.bioc.ggtree},
 }
@@ -174,10 +183,10 @@ @Manual{R-plotly
 @Manual{R-poppr,
   title = {poppr: Genetic Analysis of Populations with Mixed Reproduction},
   author = {Zhian N. Kamvar and Javier F. Tabima and Jonah C. Brooks and David Folarin},
-  year = {2023},
   note = {R package version 2.9.4, 
 https://github.com/grunwaldlab/poppr/},
   url = {https://grunwaldlab.github.io/poppr/},
+  year = {2023},
 }
 
 @Manual{R-purrr,
@@ -208,8 +217,8 @@ @Manual{R-rmarkdown
 @Manual{R-stringr,
   title = {stringr: Simple, Consistent Wrappers for Common String Operations},
   author = {Hadley Wickham},
-  year = {2022},
-  note = {R package version 1.5.0, 
+  year = {2023},
+  note = {R package version 1.5.1, 
 https://github.com/tidyverse/stringr},
   url = {https://stringr.tidyverse.org},
 }
@@ -344,6 +353,16 @@ @Article{ape2019
   doi = {10.1093/bioinformatics/bty633},
 }
 
+@Book{bookdown2016,
+  title = {bookdown: Authoring Books and Technical Documents with {R} Markdown},
+  author = {Yihui Xie},
+  publisher = {Chapman and Hall/CRC},
+  address = {Boca Raton, Florida},
+  year = {2016},
+  isbn = {978-1138700109},
+  url = {https://bookdown.org/yihui/bookdown},
+}
+
 @Book{ggplot22016,
   author = {Hadley Wickham},
   title = {ggplot2: Elegant Graphics for Data Analysis},
@@ -365,7 +384,7 @@ @Book{ggtree2022a
 
 @Article{ggtree2022b,
   title = {Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data},
-  author = {Shuangbin Xu and Lin Li and Xiao Luo and Meijun Chen and Wenli Tang and Li Zhan and Zehan Dai and {Tommy T. Lam} and Yi Guan and Guangchuang Yu},
+  author = {Shuangbin Xu and Lin Li and Xiao Luo and Meijun Chen and Wenli Tang and Li Zhan and Zehan Dai and Tommy T. Lam and Yi Guan and Guangchuang Yu},
   year = {2022},
   journal = {iMeta},
   volume = {1},

diff --git a/assets/main_report_old/.gitignore → assets/main_report_new/.gitignore b/assets/main_report_old/.gitignore → assets/main_report_new/.gitignore
diff --git a/...ons/quarto-ext/fontawesome/_extension.yml → ...ons/quarto-ext/fontawesome/_extension.yml b/...ons/quarto-ext/fontawesome/_extension.yml → ...ons/quarto-ext/fontawesome/_extension.yml
diff --git a/...quarto-ext/fontawesome/assets/css/all.css → ...quarto-ext/fontawesome/assets/css/all.css b/...quarto-ext/fontawesome/assets/css/all.css → ...quarto-ext/fontawesome/assets/css/all.css
diff --git a/...fontawesome/assets/css/latex-fontsize.css → ...fontawesome/assets/css/latex-fontsize.css b/...fontawesome/assets/css/latex-fontsize.css → ...fontawesome/assets/css/latex-fontsize.css
diff --git a/...bfonts/FontAwesome6Brands-Regular-400.ttf → ...bfonts/FontAwesome6Brands-Regular-400.ttf b/...bfonts/FontAwesome6Brands-Regular-400.ttf → ...bfonts/FontAwesome6Brands-Regular-400.ttf
diff --git a/...onts/FontAwesome6Brands-Regular-400.woff2 → ...onts/FontAwesome6Brands-Regular-400.woff2 b/...onts/FontAwesome6Brands-Regular-400.woff2 → ...onts/FontAwesome6Brands-Regular-400.woff2
diff --git a/...webfonts/FontAwesome6Free-Regular-400.ttf → ...webfonts/FontAwesome6Free-Regular-400.ttf b/...webfonts/FontAwesome6Free-Regular-400.ttf → ...webfonts/FontAwesome6Free-Regular-400.ttf
diff --git a/...bfonts/FontAwesome6Free-Regular-400.woff2 → ...bfonts/FontAwesome6Free-Regular-400.woff2 b/...bfonts/FontAwesome6Free-Regular-400.woff2 → ...bfonts/FontAwesome6Free-Regular-400.woff2
diff --git a/...s/webfonts/FontAwesome6Free-Solid-900.ttf → ...s/webfonts/FontAwesome6Free-Solid-900.ttf b/...s/webfonts/FontAwesome6Free-Solid-900.ttf → ...s/webfonts/FontAwesome6Free-Solid-900.ttf
diff --git a/...webfonts/FontAwesome6Free-Solid-900.woff2 → ...webfonts/FontAwesome6Free-Solid-900.woff2 b/...webfonts/FontAwesome6Free-Solid-900.woff2 → ...webfonts/FontAwesome6Free-Solid-900.woff2
diff --git a/...awesome/assets/webfonts/fa-brands-400.ttf → ...awesome/assets/webfonts/fa-brands-400.ttf b/...awesome/assets/webfonts/fa-brands-400.ttf → ...awesome/assets/webfonts/fa-brands-400.ttf
diff --git a/...esome/assets/webfonts/fa-brands-400.woff2 → ...esome/assets/webfonts/fa-brands-400.woff2 b/...esome/assets/webfonts/fa-brands-400.woff2 → ...esome/assets/webfonts/fa-brands-400.woff2
diff --git a/...wesome/assets/webfonts/fa-regular-400.ttf → ...wesome/assets/webfonts/fa-regular-400.ttf b/...wesome/assets/webfonts/fa-regular-400.ttf → ...wesome/assets/webfonts/fa-regular-400.ttf
diff --git a/...some/assets/webfonts/fa-regular-400.woff2 → ...some/assets/webfonts/fa-regular-400.woff2 b/...some/assets/webfonts/fa-regular-400.woff2 → ...some/assets/webfonts/fa-regular-400.woff2
diff --git a/...tawesome/assets/webfonts/fa-solid-900.ttf → ...tawesome/assets/webfonts/fa-solid-900.ttf b/...tawesome/assets/webfonts/fa-solid-900.ttf → ...tawesome/assets/webfonts/fa-solid-900.ttf
diff --git a/...wesome/assets/webfonts/fa-solid-900.woff2 → ...wesome/assets/webfonts/fa-solid-900.woff2 b/...wesome/assets/webfonts/fa-solid-900.woff2 → ...wesome/assets/webfonts/fa-solid-900.woff2
diff --git a/...me/assets/webfonts/fa-v4compatibility.ttf → ...me/assets/webfonts/fa-v4compatibility.ttf b/...me/assets/webfonts/fa-v4compatibility.ttf → ...me/assets/webfonts/fa-v4compatibility.ttf
diff --git a/.../assets/webfonts/fa-v4compatibility.woff2 → .../assets/webfonts/fa-v4compatibility.woff2 b/.../assets/webfonts/fa-v4compatibility.woff2 → .../assets/webfonts/fa-v4compatibility.woff2
diff --git a/...ns/quarto-ext/fontawesome/fontawesome.lua → ...ns/quarto-ext/fontawesome/fontawesome.lua b/...ns/quarto-ext/fontawesome/fontawesome.lua → ...ns/quarto-ext/fontawesome/fontawesome.lua
diff --git a/...s/schochastics/academicons/_extension.yml → ...s/schochastics/academicons/_extension.yml b/...s/schochastics/academicons/_extension.yml → ...s/schochastics/academicons/_extension.yml
diff --git a/.../schochastics/academicons/academicons.lua → .../schochastics/academicons/academicons.lua b/.../schochastics/academicons/academicons.lua → .../schochastics/academicons/academicons.lua
diff --git a/...hochastics/academicons/assets/css/all.css → ...hochastics/academicons/assets/css/all.css b/...hochastics/academicons/assets/css/all.css → ...hochastics/academicons/assets/css/all.css
diff --git a/...ochastics/academicons/assets/css/size.css → ...ochastics/academicons/assets/css/size.css b/...ochastics/academicons/assets/css/size.css → ...ochastics/academicons/assets/css/size.css
diff --git a/...ademicons/assets/webfonts/academicons.eot → ...ademicons/assets/webfonts/academicons.eot b/...ademicons/assets/webfonts/academicons.eot → ...ademicons/assets/webfonts/academicons.eot
diff --git a/...ademicons/assets/webfonts/academicons.svg → ...ademicons/assets/webfonts/academicons.svg b/...ademicons/assets/webfonts/academicons.svg → ...ademicons/assets/webfonts/academicons.svg
diff --git a/...ademicons/assets/webfonts/academicons.ttf → ...ademicons/assets/webfonts/academicons.ttf b/...ademicons/assets/webfonts/academicons.ttf → ...ademicons/assets/webfonts/academicons.ttf
diff --git a/...demicons/assets/webfonts/academicons.woff → ...demicons/assets/webfonts/academicons.woff b/...demicons/assets/webfonts/academicons.woff → ...demicons/assets/webfonts/academicons.woff
diff --git a/...ons/shafayetShafee/bsicons/_extension.yml → ...ons/shafayetShafee/bsicons/_extension.yml b/...ons/shafayetShafee/bsicons/_extension.yml → ...ons/shafayetShafee/bsicons/_extension.yml
diff --git a/...shafayetShafee/bsicons/assets/css/all.css → ...shafayetShafee/bsicons/assets/css/all.css b/...shafayetShafee/bsicons/assets/css/all.css → ...shafayetShafee/bsicons/assets/css/all.css
diff --git a/...cons/assets/webfonts/bootstrap-icons.woff → ...cons/assets/webfonts/bootstrap-icons.woff b/...cons/assets/webfonts/bootstrap-icons.woff → ...cons/assets/webfonts/bootstrap-icons.woff
diff --git a/...ons/assets/webfonts/bootstrap-icons.woff2 → ...ons/assets/webfonts/bootstrap-icons.woff2 b/...ons/assets/webfonts/bootstrap-icons.woff2 → ...ons/assets/webfonts/bootstrap-icons.woff2
diff --git a/...nsions/shafayetShafee/bsicons/bsicons.lua → ...nsions/shafayetShafee/bsicons/bsicons.lua b/...nsions/shafayetShafee/bsicons/bsicons.lua → ...nsions/shafayetShafee/bsicons/bsicons.lua
diff --git a/assets/main_report_old/_quarto.yml → assets/main_report_new/_quarto.yml b/assets/main_report_old/_quarto.yml → assets/main_report_new/_quarto.yml
diff --git a/...rt_old/_test_data/1/inputs/ani_matrix.csv → ...rt_new/_test_data/1/inputs/ani_matrix.csv b/...rt_old/_test_data/1/inputs/ani_matrix.csv → ...rt_new/_test_data/1/inputs/ani_matrix.csv
diff --git a/...d/_test_data/1/inputs/core_phylo.treefile → ...w/_test_data/1/inputs/core_phylo.treefile b/...d/_test_data/1/inputs/core_phylo.treefile → ...w/_test_data/1/inputs/core_phylo.treefile
diff --git a/...port_old/_test_data/1/inputs/group_id.txt → ...port_new/_test_data/1/inputs/group_id.txt b/...port_old/_test_data/1/inputs/group_id.txt → ...port_new/_test_data/1/inputs/group_id.txt
diff --git a/...ata/mqc_fastqc_adapter_content_plot_1.txt → ...ata/mqc_fastqc_adapter_content_plot_1.txt b/...ata/mqc_fastqc_adapter_content_plot_1.txt → ...ata/mqc_fastqc_adapter_content_plot_1.txt
diff --git a/.../mqc_fastqc_per_base_n_content_plot_1.txt → .../mqc_fastqc_per_base_n_content_plot_1.txt b/.../mqc_fastqc_per_base_n_content_plot_1.txt → .../mqc_fastqc_per_base_n_content_plot_1.txt
diff --git a/...stqc_per_base_sequence_quality_plot_1.txt → ...stqc_per_base_sequence_quality_plot_1.txt b/...stqc_per_base_sequence_quality_plot_1.txt → ...stqc_per_base_sequence_quality_plot_1.txt
diff --git a/...c_per_sequence_gc_content_plot_Counts.txt → ...c_per_sequence_gc_content_plot_Counts.txt b/...c_per_sequence_gc_content_plot_Counts.txt → ...c_per_sequence_gc_content_plot_Counts.txt
diff --git a/..._sequence_gc_content_plot_Percentages.txt → ..._sequence_gc_content_plot_Percentages.txt b/..._sequence_gc_content_plot_Percentages.txt → ..._sequence_gc_content_plot_Percentages.txt
diff --git a/...qc_per_sequence_quality_scores_plot_1.txt → ...qc_per_sequence_quality_scores_plot_1.txt b/...qc_per_sequence_quality_scores_plot_1.txt → ...qc_per_sequence_quality_scores_plot_1.txt
diff --git a/...ata/mqc_fastqc_sequence_counts_plot_1.txt → ...ata/mqc_fastqc_sequence_counts_plot_1.txt b/...ata/mqc_fastqc_sequence_counts_plot_1.txt → ...ata/mqc_fastqc_sequence_counts_plot_1.txt
diff --git a/...qc_sequence_duplication_levels_plot_1.txt → ...qc_sequence_duplication_levels_plot_1.txt b/...qc_sequence_duplication_levels_plot_1.txt → ...qc_sequence_duplication_levels_plot_1.txt
diff --git a/...c_sequence_length_distribution_plot_1.txt → ...c_sequence_length_distribution_plot_1.txt b/...c_sequence_length_distribution_plot_1.txt → ...c_sequence_length_distribution_plot_1.txt
diff --git a/...1/inputs/multiqc/multiqc_data/multiqc.log → ...1/inputs/multiqc/multiqc_data/multiqc.log b/...1/inputs/multiqc/multiqc_data/multiqc.log → ...1/inputs/multiqc/multiqc_data/multiqc.log
diff --git a/...ultiqc/multiqc_data/multiqc_citations.txt → ...ultiqc/multiqc_data/multiqc_citations.txt b/...ultiqc/multiqc_data/multiqc_citations.txt → ...ultiqc/multiqc_data/multiqc_citations.txt
diff --git a/...ts/multiqc/multiqc_data/multiqc_data.json → ...ts/multiqc/multiqc_data/multiqc_data.json b/...ts/multiqc/multiqc_data/multiqc_data.json → ...ts/multiqc/multiqc_data/multiqc_data.json
diff --git a/...s/multiqc/multiqc_data/multiqc_fastqc.txt → ...s/multiqc/multiqc_data/multiqc_fastqc.txt b/...s/multiqc/multiqc_data/multiqc_fastqc.txt → ...s/multiqc/multiqc_data/multiqc_fastqc.txt
diff --git a/...qc/multiqc_data/multiqc_general_stats.txt → ...qc/multiqc_data/multiqc_general_stats.txt b/...qc/multiqc_data/multiqc_general_stats.txt → ...qc/multiqc_data/multiqc_general_stats.txt
diff --git a/.../multiqc/multiqc_data/multiqc_sources.txt → .../multiqc/multiqc_data/multiqc_sources.txt b/.../multiqc/multiqc_data/multiqc_sources.txt → .../multiqc/multiqc_data/multiqc_sources.txt
diff --git a/...pdf/mqc_fastqc_adapter_content_plot_1.pdf → ...pdf/mqc_fastqc_adapter_content_plot_1.pdf b/...pdf/mqc_fastqc_adapter_content_plot_1.pdf → ...pdf/mqc_fastqc_adapter_content_plot_1.pdf
diff --git a/.../mqc_fastqc_per_base_n_content_plot_1.pdf → .../mqc_fastqc_per_base_n_content_plot_1.pdf b/.../mqc_fastqc_per_base_n_content_plot_1.pdf → .../mqc_fastqc_per_base_n_content_plot_1.pdf
diff --git a/...stqc_per_base_sequence_quality_plot_1.pdf → ...stqc_per_base_sequence_quality_plot_1.pdf b/...stqc_per_base_sequence_quality_plot_1.pdf → ...stqc_per_base_sequence_quality_plot_1.pdf
diff --git a/...c_per_sequence_gc_content_plot_Counts.pdf → ...c_per_sequence_gc_content_plot_Counts.pdf b/...c_per_sequence_gc_content_plot_Counts.pdf → ...c_per_sequence_gc_content_plot_Counts.pdf
diff --git a/..._sequence_gc_content_plot_Percentages.pdf → ..._sequence_gc_content_plot_Percentages.pdf b/..._sequence_gc_content_plot_Percentages.pdf → ..._sequence_gc_content_plot_Percentages.pdf
diff --git a/...qc_per_sequence_quality_scores_plot_1.pdf → ...qc_per_sequence_quality_scores_plot_1.pdf b/...qc_per_sequence_quality_scores_plot_1.pdf → ...qc_per_sequence_quality_scores_plot_1.pdf
diff --git a/...pdf/mqc_fastqc_sequence_counts_plot_1.pdf → ...pdf/mqc_fastqc_sequence_counts_plot_1.pdf b/...pdf/mqc_fastqc_sequence_counts_plot_1.pdf → ...pdf/mqc_fastqc_sequence_counts_plot_1.pdf
diff --git a/.../mqc_fastqc_sequence_counts_plot_1_pc.pdf → .../mqc_fastqc_sequence_counts_plot_1_pc.pdf b/.../mqc_fastqc_sequence_counts_plot_1_pc.pdf → .../mqc_fastqc_sequence_counts_plot_1_pc.pdf
diff --git a/...qc_sequence_duplication_levels_plot_1.pdf → ...qc_sequence_duplication_levels_plot_1.pdf b/...qc_sequence_duplication_levels_plot_1.pdf → ...qc_sequence_duplication_levels_plot_1.pdf
diff --git a/...c_sequence_length_distribution_plot_1.pdf → ...c_sequence_length_distribution_plot_1.pdf b/...c_sequence_length_distribution_plot_1.pdf → ...c_sequence_length_distribution_plot_1.pdf
diff --git a/...png/mqc_fastqc_adapter_content_plot_1.png → ...png/mqc_fastqc_adapter_content_plot_1.png b/...png/mqc_fastqc_adapter_content_plot_1.png → ...png/mqc_fastqc_adapter_content_plot_1.png
diff --git a/.../mqc_fastqc_per_base_n_content_plot_1.png → .../mqc_fastqc_per_base_n_content_plot_1.png b/.../mqc_fastqc_per_base_n_content_plot_1.png → .../mqc_fastqc_per_base_n_content_plot_1.png
diff --git a/...stqc_per_base_sequence_quality_plot_1.png → ...stqc_per_base_sequence_quality_plot_1.png b/...stqc_per_base_sequence_quality_plot_1.png → ...stqc_per_base_sequence_quality_plot_1.png
diff --git a/...c_per_sequence_gc_content_plot_Counts.png → ...c_per_sequence_gc_content_plot_Counts.png b/...c_per_sequence_gc_content_plot_Counts.png → ...c_per_sequence_gc_content_plot_Counts.png
diff --git a/..._sequence_gc_content_plot_Percentages.png → ..._sequence_gc_content_plot_Percentages.png b/..._sequence_gc_content_plot_Percentages.png → ..._sequence_gc_content_plot_Percentages.png
diff --git a/...qc_per_sequence_quality_scores_plot_1.png → ...qc_per_sequence_quality_scores_plot_1.png b/...qc_per_sequence_quality_scores_plot_1.png → ...qc_per_sequence_quality_scores_plot_1.png
diff --git a/...png/mqc_fastqc_sequence_counts_plot_1.png → ...png/mqc_fastqc_sequence_counts_plot_1.png b/...png/mqc_fastqc_sequence_counts_plot_1.png → ...png/mqc_fastqc_sequence_counts_plot_1.png
diff --git a/.../mqc_fastqc_sequence_counts_plot_1_pc.png → .../mqc_fastqc_sequence_counts_plot_1_pc.png b/.../mqc_fastqc_sequence_counts_plot_1_pc.png → .../mqc_fastqc_sequence_counts_plot_1_pc.png
diff --git a/...qc_sequence_duplication_levels_plot_1.png → ...qc_sequence_duplication_levels_plot_1.png b/...qc_sequence_duplication_levels_plot_1.png → ...qc_sequence_duplication_levels_plot_1.png
diff --git a/...c_sequence_length_distribution_plot_1.png → ...c_sequence_length_distribution_plot_1.png b/...c_sequence_length_distribution_plot_1.png → ...c_sequence_length_distribution_plot_1.png
diff --git a/...svg/mqc_fastqc_adapter_content_plot_1.svg → ...svg/mqc_fastqc_adapter_content_plot_1.svg b/...svg/mqc_fastqc_adapter_content_plot_1.svg → ...svg/mqc_fastqc_adapter_content_plot_1.svg
diff --git a/.../mqc_fastqc_per_base_n_content_plot_1.svg → .../mqc_fastqc_per_base_n_content_plot_1.svg b/.../mqc_fastqc_per_base_n_content_plot_1.svg → .../mqc_fastqc_per_base_n_content_plot_1.svg
diff --git a/...stqc_per_base_sequence_quality_plot_1.svg → ...stqc_per_base_sequence_quality_plot_1.svg b/...stqc_per_base_sequence_quality_plot_1.svg → ...stqc_per_base_sequence_quality_plot_1.svg
diff --git a/...c_per_sequence_gc_content_plot_Counts.svg → ...c_per_sequence_gc_content_plot_Counts.svg b/...c_per_sequence_gc_content_plot_Counts.svg → ...c_per_sequence_gc_content_plot_Counts.svg
diff --git a/..._sequence_gc_content_plot_Percentages.svg → ..._sequence_gc_content_plot_Percentages.svg b/..._sequence_gc_content_plot_Percentages.svg → ..._sequence_gc_content_plot_Percentages.svg
diff --git a/...qc_per_sequence_quality_scores_plot_1.svg → ...qc_per_sequence_quality_scores_plot_1.svg b/...qc_per_sequence_quality_scores_plot_1.svg → ...qc_per_sequence_quality_scores_plot_1.svg
diff --git a/...svg/mqc_fastqc_sequence_counts_plot_1.svg → ...svg/mqc_fastqc_sequence_counts_plot_1.svg b/...svg/mqc_fastqc_sequence_counts_plot_1.svg → ...svg/mqc_fastqc_sequence_counts_plot_1.svg
diff --git a/.../mqc_fastqc_sequence_counts_plot_1_pc.svg → .../mqc_fastqc_sequence_counts_plot_1_pc.svg b/.../mqc_fastqc_sequence_counts_plot_1_pc.svg → .../mqc_fastqc_sequence_counts_plot_1_pc.svg
diff --git a/...qc_sequence_duplication_levels_plot_1.svg → ...qc_sequence_duplication_levels_plot_1.svg b/...qc_sequence_duplication_levels_plot_1.svg → ...qc_sequence_duplication_levels_plot_1.svg
diff --git a/...c_sequence_length_distribution_plot_1.svg → ...c_sequence_length_distribution_plot_1.svg b/...c_sequence_length_distribution_plot_1.svg → ...c_sequence_length_distribution_plot_1.svg
diff --git a/...2_331_assembly/aligned_stats/NAx_plot.pdf → ...2_331_assembly/aligned_stats/NAx_plot.pdf b/...2_331_assembly/aligned_stats/NAx_plot.pdf → ...2_331_assembly/aligned_stats/NAx_plot.pdf
diff --git a/..._331_assembly/aligned_stats/NGAx_plot.pdf → ..._331_assembly/aligned_stats/NGAx_plot.pdf b/..._331_assembly/aligned_stats/NGAx_plot.pdf → ..._331_assembly/aligned_stats/NGAx_plot.pdf
diff --git a/...ssembly/aligned_stats/cumulative_plot.pdf → ...ssembly/aligned_stats/cumulative_plot.pdf b/...ssembly/aligned_stats/cumulative_plot.pdf → ...ssembly/aligned_stats/cumulative_plot.pdf
diff --git a/...stats/22-299_filtered_GC_content_plot.pdf → ...stats/22-299_filtered_GC_content_plot.pdf b/...stats/22-299_filtered_GC_content_plot.pdf → ...stats/22-299_filtered_GC_content_plot.pdf
diff --git a/...ts/22-299_filtered_coverage_histogram.pdf → ...ts/22-299_filtered_coverage_histogram.pdf b/...ts/22-299_filtered_coverage_histogram.pdf → ...ts/22-299_filtered_coverage_histogram.pdf
diff --git a/...stats/22-300_filtered_GC_content_plot.pdf → ...stats/22-300_filtered_GC_content_plot.pdf b/...stats/22-300_filtered_GC_content_plot.pdf → ...stats/22-300_filtered_GC_content_plot.pdf
diff --git a/...ts/22-300_filtered_coverage_histogram.pdf → ...ts/22-300_filtered_coverage_histogram.pdf b/...ts/22-300_filtered_coverage_histogram.pdf → ...ts/22-300_filtered_coverage_histogram.pdf
diff --git a/...stats/22-301_filtered_GC_content_plot.pdf → ...stats/22-301_filtered_GC_content_plot.pdf b/...stats/22-301_filtered_GC_content_plot.pdf → ...stats/22-301_filtered_GC_content_plot.pdf
diff --git a/...ts/22-301_filtered_coverage_histogram.pdf → ...ts/22-301_filtered_coverage_histogram.pdf b/...ts/22-301_filtered_coverage_histogram.pdf → ...ts/22-301_filtered_coverage_histogram.pdf
diff --git a/...stats/22-324_filtered_GC_content_plot.pdf → ...stats/22-324_filtered_GC_content_plot.pdf b/...stats/22-324_filtered_GC_content_plot.pdf → ...stats/22-324_filtered_GC_content_plot.pdf
diff --git a/...ts/22-324_filtered_coverage_histogram.pdf → ...ts/22-324_filtered_coverage_histogram.pdf b/...ts/22-324_filtered_coverage_histogram.pdf → ...ts/22-324_filtered_coverage_histogram.pdf
diff --git a/...tats/22-329A_filtered_GC_content_plot.pdf → ...tats/22-329A_filtered_GC_content_plot.pdf b/...tats/22-329A_filtered_GC_content_plot.pdf → ...tats/22-329A_filtered_GC_content_plot.pdf
diff --git a/...s/22-329A_filtered_coverage_histogram.pdf → ...s/22-329A_filtered_coverage_histogram.pdf b/...s/22-329A_filtered_coverage_histogram.pdf → ...s/22-329A_filtered_coverage_histogram.pdf
diff --git a/...tats/22-329B_filtered_GC_content_plot.pdf → ...tats/22-329B_filtered_GC_content_plot.pdf b/...tats/22-329B_filtered_GC_content_plot.pdf → ...tats/22-329B_filtered_GC_content_plot.pdf
diff --git a/...s/22-329B_filtered_coverage_histogram.pdf → ...s/22-329B_filtered_coverage_histogram.pdf b/...s/22-329B_filtered_coverage_histogram.pdf → ...s/22-329B_filtered_coverage_histogram.pdf
diff --git a/...stats/22-330_filtered_GC_content_plot.pdf → ...stats/22-330_filtered_GC_content_plot.pdf b/...stats/22-330_filtered_GC_content_plot.pdf → ...stats/22-330_filtered_GC_content_plot.pdf
diff --git a/...ts/22-330_filtered_coverage_histogram.pdf → ...ts/22-330_filtered_coverage_histogram.pdf b/...ts/22-330_filtered_coverage_histogram.pdf → ...ts/22-330_filtered_coverage_histogram.pdf
diff --git a/..._assembly/basic_stats/GC_content_plot.pdf → ..._assembly/basic_stats/GC_content_plot.pdf b/..._assembly/basic_stats/GC_content_plot.pdf → ..._assembly/basic_stats/GC_content_plot.pdf
diff --git a/.../22_331_assembly/basic_stats/NGx_plot.pdf → .../22_331_assembly/basic_stats/NGx_plot.pdf b/.../22_331_assembly/basic_stats/NGx_plot.pdf → .../22_331_assembly/basic_stats/NGx_plot.pdf
diff --git a/...t/22_331_assembly/basic_stats/Nx_plot.pdf → ...t/22_331_assembly/basic_stats/Nx_plot.pdf b/...t/22_331_assembly/basic_stats/Nx_plot.pdf → ...t/22_331_assembly/basic_stats/Nx_plot.pdf
diff --git a/.../SRR17286018_filtered_GC_content_plot.pdf → .../SRR17286018_filtered_GC_content_plot.pdf b/.../SRR17286018_filtered_GC_content_plot.pdf → .../SRR17286018_filtered_GC_content_plot.pdf
diff --git a/...R17286018_filtered_coverage_histogram.pdf → ...R17286018_filtered_coverage_histogram.pdf b/...R17286018_filtered_coverage_histogram.pdf → ...R17286018_filtered_coverage_histogram.pdf
diff --git a/...sembly/basic_stats/coverage_histogram.pdf → ...sembly/basic_stats/coverage_histogram.pdf b/...sembly/basic_stats/coverage_histogram.pdf → ...sembly/basic_stats/coverage_histogram.pdf
diff --git a/..._assembly/basic_stats/cumulative_plot.pdf → ..._assembly/basic_stats/cumulative_plot.pdf b/..._assembly/basic_stats/cumulative_plot.pdf → ..._assembly/basic_stats/cumulative_plot.pdf
diff --git a/...22_331_assembly/basic_stats/gc.icarus.txt → ...22_331_assembly/basic_stats/gc.icarus.txt b/...22_331_assembly/basic_stats/gc.icarus.txt → ...22_331_assembly/basic_stats/gc.icarus.txt
diff --git a/...gs_reports/22-299_filtered.mis_contigs.fa → ...gs_reports/22-299_filtered.mis_contigs.fa b/...gs_reports/22-299_filtered.mis_contigs.fa → ...gs_reports/22-299_filtered.mis_contigs.fa
diff --git a/...gs_reports/22-300_filtered.mis_contigs.fa → ...gs_reports/22-300_filtered.mis_contigs.fa b/...gs_reports/22-300_filtered.mis_contigs.fa → ...gs_reports/22-300_filtered.mis_contigs.fa
diff --git a/...gs_reports/22-301_filtered.mis_contigs.fa → ...gs_reports/22-301_filtered.mis_contigs.fa b/...gs_reports/22-301_filtered.mis_contigs.fa → ...gs_reports/22-301_filtered.mis_contigs.fa
diff --git a/...gs_reports/22-324_filtered.mis_contigs.fa → ...gs_reports/22-324_filtered.mis_contigs.fa b/...gs_reports/22-324_filtered.mis_contigs.fa → ...gs_reports/22-324_filtered.mis_contigs.fa
diff --git a/...s_reports/22-329A_filtered.mis_contigs.fa → ...s_reports/22-329A_filtered.mis_contigs.fa b/...s_reports/22-329A_filtered.mis_contigs.fa → ...s_reports/22-329A_filtered.mis_contigs.fa
diff --git a/...s_reports/22-329B_filtered.mis_contigs.fa → ...s_reports/22-329B_filtered.mis_contigs.fa b/...s_reports/22-329B_filtered.mis_contigs.fa → ...s_reports/22-329B_filtered.mis_contigs.fa
diff --git a/...gs_reports/22-330_filtered.mis_contigs.fa → ...gs_reports/22-330_filtered.mis_contigs.fa b/...gs_reports/22-330_filtered.mis_contigs.fa → ...gs_reports/22-330_filtered.mis_contigs.fa
diff --git a/...ports/SRR17286018_filtered.mis_contigs.fa → ...ports/SRR17286018_filtered.mis_contigs.fa b/...ports/SRR17286018_filtered.mis_contigs.fa → ...ports/SRR17286018_filtered.mis_contigs.fa
diff --git a/...eports/all_alignments_22-299_filtered.tsv → ...eports/all_alignments_22-299_filtered.tsv b/...eports/all_alignments_22-299_filtered.tsv → ...eports/all_alignments_22-299_filtered.tsv
diff --git a/...eports/all_alignments_22-300_filtered.tsv → ...eports/all_alignments_22-300_filtered.tsv b/...eports/all_alignments_22-300_filtered.tsv → ...eports/all_alignments_22-300_filtered.tsv
diff --git a/...eports/all_alignments_22-301_filtered.tsv → ...eports/all_alignments_22-301_filtered.tsv b/...eports/all_alignments_22-301_filtered.tsv → ...eports/all_alignments_22-301_filtered.tsv
diff --git a/...eports/all_alignments_22-324_filtered.tsv → ...eports/all_alignments_22-324_filtered.tsv b/...eports/all_alignments_22-324_filtered.tsv → ...eports/all_alignments_22-324_filtered.tsv
diff --git a/...ports/all_alignments_22-329A_filtered.tsv → ...ports/all_alignments_22-329A_filtered.tsv b/...ports/all_alignments_22-329A_filtered.tsv → ...ports/all_alignments_22-329A_filtered.tsv
diff --git a/...ports/all_alignments_22-329B_filtered.tsv → ...ports/all_alignments_22-329B_filtered.tsv b/...ports/all_alignments_22-329B_filtered.tsv → ...ports/all_alignments_22-329B_filtered.tsv
diff --git a/...eports/all_alignments_22-330_filtered.tsv → ...eports/all_alignments_22-330_filtered.tsv b/...eports/all_alignments_22-330_filtered.tsv → ...eports/all_alignments_22-330_filtered.tsv
diff --git a/...s/all_alignments_SRR17286018_filtered.tsv → ...s/all_alignments_SRR17286018_filtered.tsv b/...s/all_alignments_SRR17286018_filtered.tsv → ...s/all_alignments_SRR17286018_filtered.tsv
diff --git a/...s_report_22-299_filtered.mis_contigs.info → ...s_report_22-299_filtered.mis_contigs.info b/...s_report_22-299_filtered.mis_contigs.info → ...s_report_22-299_filtered.mis_contigs.info
diff --git a/...rts/contigs_report_22-299_filtered.stderr → ...rts/contigs_report_22-299_filtered.stderr b/...rts/contigs_report_22-299_filtered.stderr → ...rts/contigs_report_22-299_filtered.stderr
diff --git a/...rts/contigs_report_22-299_filtered.stdout → ...rts/contigs_report_22-299_filtered.stdout b/...rts/contigs_report_22-299_filtered.stdout → ...rts/contigs_report_22-299_filtered.stdout
diff --git a/...igs_report_22-299_filtered.unaligned.info → ...igs_report_22-299_filtered.unaligned.info b/...igs_report_22-299_filtered.unaligned.info → ...igs_report_22-299_filtered.unaligned.info
diff --git a/...s_report_22-300_filtered.mis_contigs.info → ...s_report_22-300_filtered.mis_contigs.info b/...s_report_22-300_filtered.mis_contigs.info → ...s_report_22-300_filtered.mis_contigs.info
diff --git a/...rts/contigs_report_22-300_filtered.stderr → ...rts/contigs_report_22-300_filtered.stderr b/...rts/contigs_report_22-300_filtered.stderr → ...rts/contigs_report_22-300_filtered.stderr
diff --git a/...rts/contigs_report_22-300_filtered.stdout → ...rts/contigs_report_22-300_filtered.stdout b/...rts/contigs_report_22-300_filtered.stdout → ...rts/contigs_report_22-300_filtered.stdout
diff --git a/...igs_report_22-300_filtered.unaligned.info → ...igs_report_22-300_filtered.unaligned.info b/...igs_report_22-300_filtered.unaligned.info → ...igs_report_22-300_filtered.unaligned.info
diff --git a/...s_report_22-301_filtered.mis_contigs.info → ...s_report_22-301_filtered.mis_contigs.info b/...s_report_22-301_filtered.mis_contigs.info → ...s_report_22-301_filtered.mis_contigs.info
diff --git a/...rts/contigs_report_22-301_filtered.stderr → ...rts/contigs_report_22-301_filtered.stderr b/...rts/contigs_report_22-301_filtered.stderr → ...rts/contigs_report_22-301_filtered.stderr
diff --git a/...rts/contigs_report_22-301_filtered.stdout → ...rts/contigs_report_22-301_filtered.stdout b/...rts/contigs_report_22-301_filtered.stdout → ...rts/contigs_report_22-301_filtered.stdout
diff --git a/...igs_report_22-301_filtered.unaligned.info → ...igs_report_22-301_filtered.unaligned.info b/...igs_report_22-301_filtered.unaligned.info → ...igs_report_22-301_filtered.unaligned.info
diff --git a/...s_report_22-324_filtered.mis_contigs.info → ...s_report_22-324_filtered.mis_contigs.info b/...s_report_22-324_filtered.mis_contigs.info → ...s_report_22-324_filtered.mis_contigs.info
diff --git a/...rts/contigs_report_22-324_filtered.stderr → ...rts/contigs_report_22-324_filtered.stderr b/...rts/contigs_report_22-324_filtered.stderr → ...rts/contigs_report_22-324_filtered.stderr
diff --git a/...rts/contigs_report_22-324_filtered.stdout → ...rts/contigs_report_22-324_filtered.stdout b/...rts/contigs_report_22-324_filtered.stdout → ...rts/contigs_report_22-324_filtered.stdout
diff --git a/...igs_report_22-324_filtered.unaligned.info → ...igs_report_22-324_filtered.unaligned.info b/...igs_report_22-324_filtered.unaligned.info → ...igs_report_22-324_filtered.unaligned.info
diff --git a/..._report_22-329A_filtered.mis_contigs.info → ..._report_22-329A_filtered.mis_contigs.info b/..._report_22-329A_filtered.mis_contigs.info → ..._report_22-329A_filtered.mis_contigs.info
diff --git a/...ts/contigs_report_22-329A_filtered.stderr → ...ts/contigs_report_22-329A_filtered.stderr b/...ts/contigs_report_22-329A_filtered.stderr → ...ts/contigs_report_22-329A_filtered.stderr
diff --git a/...ts/contigs_report_22-329A_filtered.stdout → ...ts/contigs_report_22-329A_filtered.stdout b/...ts/contigs_report_22-329A_filtered.stdout → ...ts/contigs_report_22-329A_filtered.stdout
diff --git a/...gs_report_22-329A_filtered.unaligned.info → ...gs_report_22-329A_filtered.unaligned.info b/...gs_report_22-329A_filtered.unaligned.info → ...gs_report_22-329A_filtered.unaligned.info
diff --git a/..._report_22-329B_filtered.mis_contigs.info → ..._report_22-329B_filtered.mis_contigs.info b/..._report_22-329B_filtered.mis_contigs.info → ..._report_22-329B_filtered.mis_contigs.info
diff --git a/...ts/contigs_report_22-329B_filtered.stderr → ...ts/contigs_report_22-329B_filtered.stderr b/...ts/contigs_report_22-329B_filtered.stderr → ...ts/contigs_report_22-329B_filtered.stderr
diff --git a/...ts/contigs_report_22-329B_filtered.stdout → ...ts/contigs_report_22-329B_filtered.stdout b/...ts/contigs_report_22-329B_filtered.stdout → ...ts/contigs_report_22-329B_filtered.stdout
diff --git a/...gs_report_22-329B_filtered.unaligned.info → ...gs_report_22-329B_filtered.unaligned.info b/...gs_report_22-329B_filtered.unaligned.info → ...gs_report_22-329B_filtered.unaligned.info
diff --git a/...s_report_22-330_filtered.mis_contigs.info → ...s_report_22-330_filtered.mis_contigs.info b/...s_report_22-330_filtered.mis_contigs.info → ...s_report_22-330_filtered.mis_contigs.info
diff --git a/...rts/contigs_report_22-330_filtered.stderr → ...rts/contigs_report_22-330_filtered.stderr b/...rts/contigs_report_22-330_filtered.stderr → ...rts/contigs_report_22-330_filtered.stderr
diff --git a/...rts/contigs_report_22-330_filtered.stdout → ...rts/contigs_report_22-330_filtered.stdout b/...rts/contigs_report_22-330_filtered.stdout → ...rts/contigs_report_22-330_filtered.stdout
diff --git a/...igs_report_22-330_filtered.unaligned.info → ...igs_report_22-330_filtered.unaligned.info b/...igs_report_22-330_filtered.unaligned.info → ...igs_report_22-330_filtered.unaligned.info
diff --git a/...ort_SRR17286018_filtered.mis_contigs.info → ...ort_SRR17286018_filtered.mis_contigs.info b/...ort_SRR17286018_filtered.mis_contigs.info → ...ort_SRR17286018_filtered.mis_contigs.info
diff --git a/...ontigs_report_SRR17286018_filtered.stderr → ...ontigs_report_SRR17286018_filtered.stderr b/...ontigs_report_SRR17286018_filtered.stderr → ...ontigs_report_SRR17286018_filtered.stderr
diff --git a/...ontigs_report_SRR17286018_filtered.stdout → ...ontigs_report_SRR17286018_filtered.stdout b/...ontigs_report_SRR17286018_filtered.stdout → ...ontigs_report_SRR17286018_filtered.stdout
diff --git a/...eport_SRR17286018_filtered.unaligned.info → ...eport_SRR17286018_filtered.unaligned.info b/...eport_SRR17286018_filtered.unaligned.info → ...eport_SRR17286018_filtered.unaligned.info
diff --git a/...rts/minimap_output/22-299_filtered.coords → ...rts/minimap_output/22-299_filtered.coords b/...rts/minimap_output/22-299_filtered.coords → ...rts/minimap_output/22-299_filtered.coords
diff --git a/...ap_output/22-299_filtered.coords.filtered → ...ap_output/22-299_filtered.coords.filtered b/...ap_output/22-299_filtered.coords.filtered → ...ap_output/22-299_filtered.coords.filtered
diff --git a/...minimap_output/22-299_filtered.coords_tmp → ...minimap_output/22-299_filtered.coords_tmp b/...minimap_output/22-299_filtered.coords_tmp → ...minimap_output/22-299_filtered.coords_tmp
diff --git a/...reports/minimap_output/22-299_filtered.sf → ...reports/minimap_output/22-299_filtered.sf b/...reports/minimap_output/22-299_filtered.sf → ...reports/minimap_output/22-299_filtered.sf
diff --git a/.../minimap_output/22-299_filtered.unaligned → .../minimap_output/22-299_filtered.unaligned b/.../minimap_output/22-299_filtered.unaligned → .../minimap_output/22-299_filtered.unaligned
diff --git a/.../minimap_output/22-299_filtered.used_snps → .../minimap_output/22-299_filtered.used_snps b/.../minimap_output/22-299_filtered.used_snps → .../minimap_output/22-299_filtered.used_snps
diff --git a/...rts/minimap_output/22-300_filtered.coords → ...rts/minimap_output/22-300_filtered.coords b/...rts/minimap_output/22-300_filtered.coords → ...rts/minimap_output/22-300_filtered.coords
diff --git a/...ap_output/22-300_filtered.coords.filtered → ...ap_output/22-300_filtered.coords.filtered b/...ap_output/22-300_filtered.coords.filtered → ...ap_output/22-300_filtered.coords.filtered
diff --git a/...minimap_output/22-300_filtered.coords_tmp → ...minimap_output/22-300_filtered.coords_tmp b/...minimap_output/22-300_filtered.coords_tmp → ...minimap_output/22-300_filtered.coords_tmp
diff --git a/...reports/minimap_output/22-300_filtered.sf → ...reports/minimap_output/22-300_filtered.sf b/...reports/minimap_output/22-300_filtered.sf → ...reports/minimap_output/22-300_filtered.sf
diff --git a/.../minimap_output/22-300_filtered.unaligned → .../minimap_output/22-300_filtered.unaligned b/.../minimap_output/22-300_filtered.unaligned → .../minimap_output/22-300_filtered.unaligned
diff --git a/.../minimap_output/22-300_filtered.used_snps → .../minimap_output/22-300_filtered.used_snps b/.../minimap_output/22-300_filtered.used_snps → .../minimap_output/22-300_filtered.used_snps
diff --git a/...rts/minimap_output/22-301_filtered.coords → ...rts/minimap_output/22-301_filtered.coords b/...rts/minimap_output/22-301_filtered.coords → ...rts/minimap_output/22-301_filtered.coords
diff --git a/...ap_output/22-301_filtered.coords.filtered → ...ap_output/22-301_filtered.coords.filtered b/...ap_output/22-301_filtered.coords.filtered → ...ap_output/22-301_filtered.coords.filtered
diff --git a/...minimap_output/22-301_filtered.coords_tmp → ...minimap_output/22-301_filtered.coords_tmp b/...minimap_output/22-301_filtered.coords_tmp → ...minimap_output/22-301_filtered.coords_tmp
diff --git a/...reports/minimap_output/22-301_filtered.sf → ...reports/minimap_output/22-301_filtered.sf b/...reports/minimap_output/22-301_filtered.sf → ...reports/minimap_output/22-301_filtered.sf
diff --git a/.../minimap_output/22-301_filtered.unaligned → .../minimap_output/22-301_filtered.unaligned b/.../minimap_output/22-301_filtered.unaligned → .../minimap_output/22-301_filtered.unaligned
diff --git a/.../minimap_output/22-301_filtered.used_snps → .../minimap_output/22-301_filtered.used_snps b/.../minimap_output/22-301_filtered.used_snps → .../minimap_output/22-301_filtered.used_snps
diff --git a/...rts/minimap_output/22-324_filtered.coords → ...rts/minimap_output/22-324_filtered.coords b/...rts/minimap_output/22-324_filtered.coords → ...rts/minimap_output/22-324_filtered.coords
diff --git a/...ap_output/22-324_filtered.coords.filtered → ...ap_output/22-324_filtered.coords.filtered b/...ap_output/22-324_filtered.coords.filtered → ...ap_output/22-324_filtered.coords.filtered
diff --git a/...minimap_output/22-324_filtered.coords_tmp → ...minimap_output/22-324_filtered.coords_tmp b/...minimap_output/22-324_filtered.coords_tmp → ...minimap_output/22-324_filtered.coords_tmp
diff --git a/...reports/minimap_output/22-324_filtered.sf → ...reports/minimap_output/22-324_filtered.sf b/...reports/minimap_output/22-324_filtered.sf → ...reports/minimap_output/22-324_filtered.sf
diff --git a/.../minimap_output/22-324_filtered.unaligned → .../minimap_output/22-324_filtered.unaligned b/.../minimap_output/22-324_filtered.unaligned → .../minimap_output/22-324_filtered.unaligned
diff --git a/.../minimap_output/22-324_filtered.used_snps → .../minimap_output/22-324_filtered.used_snps b/.../minimap_output/22-324_filtered.used_snps → .../minimap_output/22-324_filtered.used_snps
diff --git a/...ts/minimap_output/22-329A_filtered.coords → ...ts/minimap_output/22-329A_filtered.coords b/...ts/minimap_output/22-329A_filtered.coords → ...ts/minimap_output/22-329A_filtered.coords
diff --git a/...p_output/22-329A_filtered.coords.filtered → ...p_output/22-329A_filtered.coords.filtered b/...p_output/22-329A_filtered.coords.filtered → ...p_output/22-329A_filtered.coords.filtered
diff --git a/...inimap_output/22-329A_filtered.coords_tmp → ...inimap_output/22-329A_filtered.coords_tmp b/...inimap_output/22-329A_filtered.coords_tmp → ...inimap_output/22-329A_filtered.coords_tmp
diff --git a/...eports/minimap_output/22-329A_filtered.sf → ...eports/minimap_output/22-329A_filtered.sf b/...eports/minimap_output/22-329A_filtered.sf → ...eports/minimap_output/22-329A_filtered.sf
diff --git a/...minimap_output/22-329A_filtered.unaligned → ...minimap_output/22-329A_filtered.unaligned b/...minimap_output/22-329A_filtered.unaligned → ...minimap_output/22-329A_filtered.unaligned
diff --git a/...minimap_output/22-329A_filtered.used_snps → ...minimap_output/22-329A_filtered.used_snps b/...minimap_output/22-329A_filtered.used_snps → ...minimap_output/22-329A_filtered.used_snps
diff --git a/...ts/minimap_output/22-329B_filtered.coords → ...ts/minimap_output/22-329B_filtered.coords b/...ts/minimap_output/22-329B_filtered.coords → ...ts/minimap_output/22-329B_filtered.coords
diff --git a/...p_output/22-329B_filtered.coords.filtered → ...p_output/22-329B_filtered.coords.filtered b/...p_output/22-329B_filtered.coords.filtered → ...p_output/22-329B_filtered.coords.filtered
diff --git a/...inimap_output/22-329B_filtered.coords_tmp → ...inimap_output/22-329B_filtered.coords_tmp b/...inimap_output/22-329B_filtered.coords_tmp → ...inimap_output/22-329B_filtered.coords_tmp
diff --git a/...eports/minimap_output/22-329B_filtered.sf → ...eports/minimap_output/22-329B_filtered.sf b/...eports/minimap_output/22-329B_filtered.sf → ...eports/minimap_output/22-329B_filtered.sf
diff --git a/...minimap_output/22-329B_filtered.unaligned → ...minimap_output/22-329B_filtered.unaligned b/...minimap_output/22-329B_filtered.unaligned → ...minimap_output/22-329B_filtered.unaligned
diff --git a/...minimap_output/22-329B_filtered.used_snps → ...minimap_output/22-329B_filtered.used_snps b/...minimap_output/22-329B_filtered.used_snps → ...minimap_output/22-329B_filtered.used_snps
diff --git a/...rts/minimap_output/22-330_filtered.coords → ...rts/minimap_output/22-330_filtered.coords b/...rts/minimap_output/22-330_filtered.coords → ...rts/minimap_output/22-330_filtered.coords
diff --git a/...ap_output/22-330_filtered.coords.filtered → ...ap_output/22-330_filtered.coords.filtered b/...ap_output/22-330_filtered.coords.filtered → ...ap_output/22-330_filtered.coords.filtered
diff --git a/...minimap_output/22-330_filtered.coords_tmp → ...minimap_output/22-330_filtered.coords_tmp b/...minimap_output/22-330_filtered.coords_tmp → ...minimap_output/22-330_filtered.coords_tmp
diff --git a/...reports/minimap_output/22-330_filtered.sf → ...reports/minimap_output/22-330_filtered.sf b/...reports/minimap_output/22-330_filtered.sf → ...reports/minimap_output/22-330_filtered.sf
diff --git a/.../minimap_output/22-330_filtered.unaligned → .../minimap_output/22-330_filtered.unaligned b/.../minimap_output/22-330_filtered.unaligned → .../minimap_output/22-330_filtered.unaligned
diff --git a/.../minimap_output/22-330_filtered.used_snps → .../minimap_output/22-330_filtered.used_snps b/.../minimap_output/22-330_filtered.used_snps → .../minimap_output/22-330_filtered.used_snps
diff --git a/...inimap_output/SRR17286018_filtered.coords → ...inimap_output/SRR17286018_filtered.coords b/...inimap_output/SRR17286018_filtered.coords → ...inimap_output/SRR17286018_filtered.coords
diff --git a/...tput/SRR17286018_filtered.coords.filtered → ...tput/SRR17286018_filtered.coords.filtered b/...tput/SRR17286018_filtered.coords.filtered → ...tput/SRR17286018_filtered.coords.filtered
diff --git a/...ap_output/SRR17286018_filtered.coords_tmp → ...ap_output/SRR17286018_filtered.coords_tmp b/...ap_output/SRR17286018_filtered.coords_tmp → ...ap_output/SRR17286018_filtered.coords_tmp
diff --git a/...ts/minimap_output/SRR17286018_filtered.sf → ...ts/minimap_output/SRR17286018_filtered.sf b/...ts/minimap_output/SRR17286018_filtered.sf → ...ts/minimap_output/SRR17286018_filtered.sf
diff --git a/...map_output/SRR17286018_filtered.unaligned → ...map_output/SRR17286018_filtered.unaligned b/...map_output/SRR17286018_filtered.unaligned → ...map_output/SRR17286018_filtered.unaligned
diff --git a/...map_output/SRR17286018_filtered.used_snps → ...map_output/SRR17286018_filtered.used_snps b/...map_output/SRR17286018_filtered.used_snps → ...map_output/SRR17286018_filtered.used_snps
diff --git a/...gs_reports/misassemblies_frcurve_plot.pdf → ...gs_reports/misassemblies_frcurve_plot.pdf b/...gs_reports/misassemblies_frcurve_plot.pdf → ...gs_reports/misassemblies_frcurve_plot.pdf
diff --git a/...ly/contigs_reports/misassemblies_plot.pdf → ...ly/contigs_reports/misassemblies_plot.pdf b/...ly/contigs_reports/misassemblies_plot.pdf → ...ly/contigs_reports/misassemblies_plot.pdf
diff --git a/.../contigs_reports/misassemblies_report.tex → .../contigs_reports/misassemblies_report.tex b/.../contigs_reports/misassemblies_report.tex → .../contigs_reports/misassemblies_report.tex
diff --git a/.../contigs_reports/misassemblies_report.tsv → .../contigs_reports/misassemblies_report.tsv b/.../contigs_reports/misassemblies_report.tsv → .../contigs_reports/misassemblies_report.tsv
diff --git a/.../contigs_reports/misassemblies_report.txt → .../contigs_reports/misassemblies_report.txt b/.../contigs_reports/misassemblies_report.txt → .../contigs_reports/misassemblies_report.txt
diff --git a/...ports/transposed_report_misassemblies.tex → ...ports/transposed_report_misassemblies.tex b/...ports/transposed_report_misassemblies.tex → ...ports/transposed_report_misassemblies.tex
diff --git a/...ports/transposed_report_misassemblies.tsv → ...ports/transposed_report_misassemblies.tsv b/...ports/transposed_report_misassemblies.tsv → ...ports/transposed_report_misassemblies.tsv
diff --git a/...ports/transposed_report_misassemblies.txt → ...ports/transposed_report_misassemblies.txt b/...ports/transposed_report_misassemblies.txt → ...ports/transposed_report_misassemblies.txt
diff --git a/...mbly/contigs_reports/unaligned_report.tex → ...mbly/contigs_reports/unaligned_report.tex b/...mbly/contigs_reports/unaligned_report.tex → ...mbly/contigs_reports/unaligned_report.tex
diff --git a/...mbly/contigs_reports/unaligned_report.tsv → ...mbly/contigs_reports/unaligned_report.tsv b/...mbly/contigs_reports/unaligned_report.tsv → ...mbly/contigs_reports/unaligned_report.tsv
diff --git a/...mbly/contigs_reports/unaligned_report.txt → ...mbly/contigs_reports/unaligned_report.txt b/...mbly/contigs_reports/unaligned_report.txt → ...mbly/contigs_reports/unaligned_report.txt
diff --git a/...bly/genome_stats/22-299_filtered_gaps.txt → ...bly/genome_stats/22-299_filtered_gaps.txt b/...bly/genome_stats/22-299_filtered_gaps.txt → ...bly/genome_stats/22-299_filtered_gaps.txt
diff --git a/...bly/genome_stats/22-300_filtered_gaps.txt → ...bly/genome_stats/22-300_filtered_gaps.txt b/...bly/genome_stats/22-300_filtered_gaps.txt → ...bly/genome_stats/22-300_filtered_gaps.txt
diff --git a/...bly/genome_stats/22-301_filtered_gaps.txt → ...bly/genome_stats/22-301_filtered_gaps.txt b/...bly/genome_stats/22-301_filtered_gaps.txt → ...bly/genome_stats/22-301_filtered_gaps.txt
diff --git a/...bly/genome_stats/22-324_filtered_gaps.txt → ...bly/genome_stats/22-324_filtered_gaps.txt b/...bly/genome_stats/22-324_filtered_gaps.txt → ...bly/genome_stats/22-324_filtered_gaps.txt
diff --git a/...ly/genome_stats/22-329A_filtered_gaps.txt → ...ly/genome_stats/22-329A_filtered_gaps.txt b/...ly/genome_stats/22-329A_filtered_gaps.txt → ...ly/genome_stats/22-329A_filtered_gaps.txt
diff --git a/...ly/genome_stats/22-329B_filtered_gaps.txt → ...ly/genome_stats/22-329B_filtered_gaps.txt b/...ly/genome_stats/22-329B_filtered_gaps.txt → ...ly/genome_stats/22-329B_filtered_gaps.txt
diff --git a/...bly/genome_stats/22-330_filtered_gaps.txt → ...bly/genome_stats/22-330_filtered_gaps.txt b/...bly/genome_stats/22-330_filtered_gaps.txt → ...bly/genome_stats/22-330_filtered_gaps.txt
diff --git a/...enome_stats/SRR17286018_filtered_gaps.txt → ...enome_stats/SRR17286018_filtered_gaps.txt b/...enome_stats/SRR17286018_filtered_gaps.txt → ...enome_stats/SRR17286018_filtered_gaps.txt
diff --git a/...enome_stats/genome_fraction_histogram.pdf → ...enome_stats/genome_fraction_histogram.pdf b/...enome_stats/genome_fraction_histogram.pdf → ...enome_stats/genome_fraction_histogram.pdf
diff --git a/...331_assembly/genome_stats/genome_info.txt → ...331_assembly/genome_stats/genome_info.txt b/...331_assembly/genome_stats/genome_info.txt → ...331_assembly/genome_stats/genome_info.txt
diff --git a/.../1/inputs/quast/22_331_assembly/quast.log → .../1/inputs/quast/22_331_assembly/quast.log b/.../1/inputs/quast/22_331_assembly/quast.log → .../1/inputs/quast/22_331_assembly/quast.log
diff --git a/...1/inputs/quast/22_331_assembly/report.pdf → ...1/inputs/quast/22_331_assembly/report.pdf b/...1/inputs/quast/22_331_assembly/report.pdf → ...1/inputs/quast/22_331_assembly/report.pdf
diff --git a/...1/inputs/quast/22_331_assembly/report.tex → ...1/inputs/quast/22_331_assembly/report.tex b/...1/inputs/quast/22_331_assembly/report.tex → ...1/inputs/quast/22_331_assembly/report.tex
diff --git a/...1/inputs/quast/22_331_assembly/report.tsv → ...1/inputs/quast/22_331_assembly/report.tsv b/...1/inputs/quast/22_331_assembly/report.tsv → ...1/inputs/quast/22_331_assembly/report.tsv
diff --git a/...1/inputs/quast/22_331_assembly/report.txt → ...1/inputs/quast/22_331_assembly/report.txt b/...1/inputs/quast/22_331_assembly/report.txt → ...1/inputs/quast/22_331_assembly/report.txt
diff --git a/...ast/22_331_assembly/transposed_report.tex → ...ast/22_331_assembly/transposed_report.tex b/...ast/22_331_assembly/transposed_report.tex → ...ast/22_331_assembly/transposed_report.tex
diff --git a/...ast/22_331_assembly/transposed_report.tsv → ...ast/22_331_assembly/transposed_report.tsv b/...ast/22_331_assembly/transposed_report.tsv → ...ast/22_331_assembly/transposed_report.tsv
diff --git a/...ast/22_331_assembly/transposed_report.txt → ...ast/22_331_assembly/transposed_report.txt b/...ast/22_331_assembly/transposed_report.txt → ...ast/22_331_assembly/transposed_report.txt
diff --git a/...port_old/_test_data/1/inputs/ref_data.tsv → ...port_new/_test_data/1/inputs/ref_data.tsv b/...port_old/_test_data/1/inputs/ref_data.tsv → ...port_new/_test_data/1/inputs/ref_data.tsv
diff --git a/...eport_old/_test_data/1/inputs/ref_ids.txt → ...eport_new/_test_data/1/inputs/ref_ids.txt b/...eport_old/_test_data/1/inputs/ref_ids.txt → ...eport_new/_test_data/1/inputs/ref_ids.txt
diff --git a/...ort_old/_test_data/1/inputs/samp_data.csv → ...ort_new/_test_data/1/inputs/samp_data.csv b/...ort_old/_test_data/1/inputs/samp_data.csv → ...ort_new/_test_data/1/inputs/samp_data.csv
diff --git a/..._test_data/1/inputs/sendsketch/22-299.txt → ..._test_data/1/inputs/sendsketch/22-299.txt b/..._test_data/1/inputs/sendsketch/22-299.txt → ..._test_data/1/inputs/sendsketch/22-299.txt
diff --git a/..._test_data/1/inputs/sendsketch/22-300.txt → ..._test_data/1/inputs/sendsketch/22-300.txt b/..._test_data/1/inputs/sendsketch/22-300.txt → ..._test_data/1/inputs/sendsketch/22-300.txt
diff --git a/..._test_data/1/inputs/sendsketch/22-301.txt → ..._test_data/1/inputs/sendsketch/22-301.txt b/..._test_data/1/inputs/sendsketch/22-301.txt → ..._test_data/1/inputs/sendsketch/22-301.txt
diff --git a/..._test_data/1/inputs/sendsketch/22-324.txt → ..._test_data/1/inputs/sendsketch/22-324.txt b/..._test_data/1/inputs/sendsketch/22-324.txt → ..._test_data/1/inputs/sendsketch/22-324.txt
diff --git a/...test_data/1/inputs/sendsketch/22-329A.txt → ...test_data/1/inputs/sendsketch/22-329A.txt b/...test_data/1/inputs/sendsketch/22-329A.txt → ...test_data/1/inputs/sendsketch/22-329A.txt
diff --git a/...test_data/1/inputs/sendsketch/22-329B.txt → ...test_data/1/inputs/sendsketch/22-329B.txt b/...test_data/1/inputs/sendsketch/22-329B.txt → ...test_data/1/inputs/sendsketch/22-329B.txt
diff --git a/..._test_data/1/inputs/sendsketch/22-330.txt → ..._test_data/1/inputs/sendsketch/22-330.txt b/..._test_data/1/inputs/sendsketch/22-330.txt → ..._test_data/1/inputs/sendsketch/22-330.txt
diff --git a/..._data/1/inputs/sendsketch/SRR17286018.txt → ..._data/1/inputs/sendsketch/SRR17286018.txt b/..._data/1/inputs/sendsketch/SRR17286018.txt → ..._data/1/inputs/sendsketch/SRR17286018.txt
diff --git a/...riant_data/xan_test_22_331_assembly.fasta → ...riant_data/xan_test_22_331_assembly.fasta b/...riant_data/xan_test_22_331_assembly.fasta → ...riant_data/xan_test_22_331_assembly.fasta
diff --git a/...nt_data/xan_test_22_331_assembly.treefile → ...nt_data/xan_test_22_331_assembly.treefile b/...nt_data/xan_test_22_331_assembly.treefile → ...nt_data/xan_test_22_331_assembly.treefile
diff --git a/...22_331_assembly.vcffilter.filtered.vcf.gz → ...22_331_assembly.vcffilter.filtered.vcf.gz b/...22_331_assembly.vcffilter.filtered.vcf.gz → ...22_331_assembly.vcffilter.filtered.vcf.gz
diff --git a/...port_old/_test_data/1/inputs/versions.yml → ...port_new/_test_data/1/inputs/versions.yml b/...port_old/_test_data/1/inputs/versions.yml → ...port_new/_test_data/1/inputs/versions.yml
diff --git a/...rt_old/_test_data/2/inputs/ani_matrix.csv → ...rt_new/_test_data/2/inputs/ani_matrix.csv b/...rt_old/_test_data/2/inputs/ani_matrix.csv → ...rt_new/_test_data/2/inputs/ani_matrix.csv
diff --git a/...d/_test_data/2/inputs/core_phylo.treefile → ...w/_test_data/2/inputs/core_phylo.treefile b/...d/_test_data/2/inputs/core_phylo.treefile → ...w/_test_data/2/inputs/core_phylo.treefile
diff --git a/...port_old/_test_data/2/inputs/group_id.txt → ...port_new/_test_data/2/inputs/group_id.txt b/...port_old/_test_data/2/inputs/group_id.txt → ...port_new/_test_data/2/inputs/group_id.txt
diff --git a/...ata/mqc_fastqc_adapter_content_plot_1.txt → ...ata/mqc_fastqc_adapter_content_plot_1.txt b/...ata/mqc_fastqc_adapter_content_plot_1.txt → ...ata/mqc_fastqc_adapter_content_plot_1.txt
diff --git a/.../mqc_fastqc_per_base_n_content_plot_1.txt → .../mqc_fastqc_per_base_n_content_plot_1.txt b/.../mqc_fastqc_per_base_n_content_plot_1.txt → .../mqc_fastqc_per_base_n_content_plot_1.txt
diff --git a/...stqc_per_base_sequence_quality_plot_1.txt → ...stqc_per_base_sequence_quality_plot_1.txt b/...stqc_per_base_sequence_quality_plot_1.txt → ...stqc_per_base_sequence_quality_plot_1.txt
diff --git a/...c_per_sequence_gc_content_plot_Counts.txt → ...c_per_sequence_gc_content_plot_Counts.txt b/...c_per_sequence_gc_content_plot_Counts.txt → ...c_per_sequence_gc_content_plot_Counts.txt
diff --git a/..._sequence_gc_content_plot_Percentages.txt → ..._sequence_gc_content_plot_Percentages.txt b/..._sequence_gc_content_plot_Percentages.txt → ..._sequence_gc_content_plot_Percentages.txt
diff --git a/...qc_per_sequence_quality_scores_plot_1.txt → ...qc_per_sequence_quality_scores_plot_1.txt b/...qc_per_sequence_quality_scores_plot_1.txt → ...qc_per_sequence_quality_scores_plot_1.txt
diff --git a/...ata/mqc_fastqc_sequence_counts_plot_1.txt → ...ata/mqc_fastqc_sequence_counts_plot_1.txt b/...ata/mqc_fastqc_sequence_counts_plot_1.txt → ...ata/mqc_fastqc_sequence_counts_plot_1.txt
diff --git a/...qc_sequence_duplication_levels_plot_1.txt → ...qc_sequence_duplication_levels_plot_1.txt b/...qc_sequence_duplication_levels_plot_1.txt → ...qc_sequence_duplication_levels_plot_1.txt
diff --git a/...c_sequence_length_distribution_plot_1.txt → ...c_sequence_length_distribution_plot_1.txt b/...c_sequence_length_distribution_plot_1.txt → ...c_sequence_length_distribution_plot_1.txt
diff --git a/...2/inputs/multiqc/multiqc_data/multiqc.log → ...2/inputs/multiqc/multiqc_data/multiqc.log b/...2/inputs/multiqc/multiqc_data/multiqc.log → ...2/inputs/multiqc/multiqc_data/multiqc.log
diff --git a/...ultiqc/multiqc_data/multiqc_citations.txt → ...ultiqc/multiqc_data/multiqc_citations.txt b/...ultiqc/multiqc_data/multiqc_citations.txt → ...ultiqc/multiqc_data/multiqc_citations.txt
diff --git a/...ts/multiqc/multiqc_data/multiqc_data.json → ...ts/multiqc/multiqc_data/multiqc_data.json b/...ts/multiqc/multiqc_data/multiqc_data.json → ...ts/multiqc/multiqc_data/multiqc_data.json
diff --git a/...s/multiqc/multiqc_data/multiqc_fastqc.txt → ...s/multiqc/multiqc_data/multiqc_fastqc.txt b/...s/multiqc/multiqc_data/multiqc_fastqc.txt → ...s/multiqc/multiqc_data/multiqc_fastqc.txt
diff --git a/...qc/multiqc_data/multiqc_general_stats.txt → ...qc/multiqc_data/multiqc_general_stats.txt b/...qc/multiqc_data/multiqc_general_stats.txt → ...qc/multiqc_data/multiqc_general_stats.txt
diff --git a/.../multiqc/multiqc_data/multiqc_sources.txt → .../multiqc/multiqc_data/multiqc_sources.txt b/.../multiqc/multiqc_data/multiqc_sources.txt → .../multiqc/multiqc_data/multiqc_sources.txt
diff --git a/...pdf/mqc_fastqc_adapter_content_plot_1.pdf → ...pdf/mqc_fastqc_adapter_content_plot_1.pdf b/...pdf/mqc_fastqc_adapter_content_plot_1.pdf → ...pdf/mqc_fastqc_adapter_content_plot_1.pdf
diff --git a/.../mqc_fastqc_per_base_n_content_plot_1.pdf → .../mqc_fastqc_per_base_n_content_plot_1.pdf b/.../mqc_fastqc_per_base_n_content_plot_1.pdf → .../mqc_fastqc_per_base_n_content_plot_1.pdf
diff --git a/...stqc_per_base_sequence_quality_plot_1.pdf → ...stqc_per_base_sequence_quality_plot_1.pdf b/...stqc_per_base_sequence_quality_plot_1.pdf → ...stqc_per_base_sequence_quality_plot_1.pdf
diff --git a/...c_per_sequence_gc_content_plot_Counts.pdf → ...c_per_sequence_gc_content_plot_Counts.pdf b/...c_per_sequence_gc_content_plot_Counts.pdf → ...c_per_sequence_gc_content_plot_Counts.pdf
diff --git a/..._sequence_gc_content_plot_Percentages.pdf → ..._sequence_gc_content_plot_Percentages.pdf b/..._sequence_gc_content_plot_Percentages.pdf → ..._sequence_gc_content_plot_Percentages.pdf
diff --git a/...qc_per_sequence_quality_scores_plot_1.pdf → ...qc_per_sequence_quality_scores_plot_1.pdf b/...qc_per_sequence_quality_scores_plot_1.pdf → ...qc_per_sequence_quality_scores_plot_1.pdf
diff --git a/...pdf/mqc_fastqc_sequence_counts_plot_1.pdf → ...pdf/mqc_fastqc_sequence_counts_plot_1.pdf b/...pdf/mqc_fastqc_sequence_counts_plot_1.pdf → ...pdf/mqc_fastqc_sequence_counts_plot_1.pdf
diff --git a/.../mqc_fastqc_sequence_counts_plot_1_pc.pdf → .../mqc_fastqc_sequence_counts_plot_1_pc.pdf b/.../mqc_fastqc_sequence_counts_plot_1_pc.pdf → .../mqc_fastqc_sequence_counts_plot_1_pc.pdf
diff --git a/...qc_sequence_duplication_levels_plot_1.pdf → ...qc_sequence_duplication_levels_plot_1.pdf b/...qc_sequence_duplication_levels_plot_1.pdf → ...qc_sequence_duplication_levels_plot_1.pdf
diff --git a/...c_sequence_length_distribution_plot_1.pdf → ...c_sequence_length_distribution_plot_1.pdf b/...c_sequence_length_distribution_plot_1.pdf → ...c_sequence_length_distribution_plot_1.pdf
diff --git a/...png/mqc_fastqc_adapter_content_plot_1.png → ...png/mqc_fastqc_adapter_content_plot_1.png b/...png/mqc_fastqc_adapter_content_plot_1.png → ...png/mqc_fastqc_adapter_content_plot_1.png
diff --git a/.../mqc_fastqc_per_base_n_content_plot_1.png → .../mqc_fastqc_per_base_n_content_plot_1.png b/.../mqc_fastqc_per_base_n_content_plot_1.png → .../mqc_fastqc_per_base_n_content_plot_1.png
diff --git a/...stqc_per_base_sequence_quality_plot_1.png → ...stqc_per_base_sequence_quality_plot_1.png b/...stqc_per_base_sequence_quality_plot_1.png → ...stqc_per_base_sequence_quality_plot_1.png
diff --git a/...c_per_sequence_gc_content_plot_Counts.png → ...c_per_sequence_gc_content_plot_Counts.png b/...c_per_sequence_gc_content_plot_Counts.png → ...c_per_sequence_gc_content_plot_Counts.png
diff --git a/..._sequence_gc_content_plot_Percentages.png → ..._sequence_gc_content_plot_Percentages.png b/..._sequence_gc_content_plot_Percentages.png → ..._sequence_gc_content_plot_Percentages.png
diff --git a/...qc_per_sequence_quality_scores_plot_1.png → ...qc_per_sequence_quality_scores_plot_1.png b/...qc_per_sequence_quality_scores_plot_1.png → ...qc_per_sequence_quality_scores_plot_1.png
diff --git a/...png/mqc_fastqc_sequence_counts_plot_1.png → ...png/mqc_fastqc_sequence_counts_plot_1.png b/...png/mqc_fastqc_sequence_counts_plot_1.png → ...png/mqc_fastqc_sequence_counts_plot_1.png
diff --git a/.../mqc_fastqc_sequence_counts_plot_1_pc.png → .../mqc_fastqc_sequence_counts_plot_1_pc.png b/.../mqc_fastqc_sequence_counts_plot_1_pc.png → .../mqc_fastqc_sequence_counts_plot_1_pc.png
diff --git a/...qc_sequence_duplication_levels_plot_1.png → ...qc_sequence_duplication_levels_plot_1.png b/...qc_sequence_duplication_levels_plot_1.png → ...qc_sequence_duplication_levels_plot_1.png
diff --git a/...c_sequence_length_distribution_plot_1.png → ...c_sequence_length_distribution_plot_1.png b/...c_sequence_length_distribution_plot_1.png → ...c_sequence_length_distribution_plot_1.png
diff --git a/...svg/mqc_fastqc_adapter_content_plot_1.svg → ...svg/mqc_fastqc_adapter_content_plot_1.svg b/...svg/mqc_fastqc_adapter_content_plot_1.svg → ...svg/mqc_fastqc_adapter_content_plot_1.svg
diff --git a/.../mqc_fastqc_per_base_n_content_plot_1.svg → .../mqc_fastqc_per_base_n_content_plot_1.svg b/.../mqc_fastqc_per_base_n_content_plot_1.svg → .../mqc_fastqc_per_base_n_content_plot_1.svg
diff --git a/...stqc_per_base_sequence_quality_plot_1.svg → ...stqc_per_base_sequence_quality_plot_1.svg b/...stqc_per_base_sequence_quality_plot_1.svg → ...stqc_per_base_sequence_quality_plot_1.svg
diff --git a/...c_per_sequence_gc_content_plot_Counts.svg → ...c_per_sequence_gc_content_plot_Counts.svg b/...c_per_sequence_gc_content_plot_Counts.svg → ...c_per_sequence_gc_content_plot_Counts.svg
diff --git a/..._sequence_gc_content_plot_Percentages.svg → ..._sequence_gc_content_plot_Percentages.svg b/..._sequence_gc_content_plot_Percentages.svg → ..._sequence_gc_content_plot_Percentages.svg
diff --git a/...qc_per_sequence_quality_scores_plot_1.svg → ...qc_per_sequence_quality_scores_plot_1.svg b/...qc_per_sequence_quality_scores_plot_1.svg → ...qc_per_sequence_quality_scores_plot_1.svg
diff --git a/...svg/mqc_fastqc_sequence_counts_plot_1.svg → ...svg/mqc_fastqc_sequence_counts_plot_1.svg b/...svg/mqc_fastqc_sequence_counts_plot_1.svg → ...svg/mqc_fastqc_sequence_counts_plot_1.svg
diff --git a/.../mqc_fastqc_sequence_counts_plot_1_pc.svg → .../mqc_fastqc_sequence_counts_plot_1_pc.svg b/.../mqc_fastqc_sequence_counts_plot_1_pc.svg → .../mqc_fastqc_sequence_counts_plot_1_pc.svg
diff --git a/...qc_sequence_duplication_levels_plot_1.svg → ...qc_sequence_duplication_levels_plot_1.svg b/...qc_sequence_duplication_levels_plot_1.svg → ...qc_sequence_duplication_levels_plot_1.svg
diff --git a/...c_sequence_length_distribution_plot_1.svg → ...c_sequence_length_distribution_plot_1.svg b/...c_sequence_length_distribution_plot_1.svg → ...c_sequence_length_distribution_plot_1.svg
diff --git a/...CF_001908775.1/aligned_stats/NAx_plot.pdf → ...CF_001908775.1/aligned_stats/NAx_plot.pdf b/...CF_001908775.1/aligned_stats/NAx_plot.pdf → ...CF_001908775.1/aligned_stats/NAx_plot.pdf
diff --git a/...F_001908775.1/aligned_stats/NGAx_plot.pdf → ...F_001908775.1/aligned_stats/NGAx_plot.pdf b/...F_001908775.1/aligned_stats/NGAx_plot.pdf → ...F_001908775.1/aligned_stats/NGAx_plot.pdf
diff --git a/...08775.1/aligned_stats/cumulative_plot.pdf → ...08775.1/aligned_stats/cumulative_plot.pdf b/...08775.1/aligned_stats/cumulative_plot.pdf → ...08775.1/aligned_stats/cumulative_plot.pdf
diff --git a/...stats/22-299_filtered_GC_content_plot.pdf → ...stats/22-299_filtered_GC_content_plot.pdf b/...stats/22-299_filtered_GC_content_plot.pdf → ...stats/22-299_filtered_GC_content_plot.pdf