fix internal doc links

Fixing links that were broken from docusaurus update that changes the path construction to internal markdown doc files.

Author: owlang

docusaurus/docs/Tutorials/threebasicplots-exo.md

@@ -159,8 +159,8 @@ Within the [Github repository][github-repo], there is (will be) also an [example
 
 ```
 
-[open-sm]:../static/figs-ex-chipexo/open-sm.png
-[gui-expandbed]:../static/figs-ex-chipexo/gui-expandbed.png
+[open-sm]:/../static/figs-ex-chipexo/open-sm.png
+[gui-expandbed]:/../static/figs-ex-chipexo/gui-expandbed.png
 
 [testdata-reb1-bed]:https://github.com/CEGRcode/2018-Rossi_GenomeResearch/blob/master/Fig1_Reb1/A.Reb1_Rhee_primary_sites_975.bed
 [testdata-reb1-bam]:https://github.com/CEGRcode/2018-Rossi_GenomeResearch/blob/master/Fig1_Reb1/A.Reb1_Rhee_primary_sites_975.bam
@@ -169,10 +169,10 @@ Within the [Github repository][github-repo], there is (will be) also an [example
 [github-repo]:https://www.github.com/CEGRcode/scriptmanager
 [ex-chipexo-bash]:https://www.github.com/CEGRcode/scriptmanager
 
-[bam-indexer]:bam-manipulation/bam-indexer.md
-[expand-bed]:coordinate-manipulation/expand-bed.md
-[tag-pileup]:read-analysis/tag-pileup.md
-[heatmap]:figure-generation/heatmap.md
-[merge-heatmap]:figure-generation/merge-heatmap.md
-[fasta-extract]:sequence-analysis/fasta-extract.md
-[four-color]:figure-generation/four-color.md
+[bam-indexer]:/docs/bam-manipulation/bam-indexer.md
+[expand-bed]:/docs/coordinate-manipulation/expand-bed.md
+[tag-pileup]:/docs/read-analysis/tag-pileup.md
+[heatmap]:/docs/figure-generation/heatmap.md
+[merge-heatmap]:/docs/figure-generation/merge-heatmap.md
+[fasta-extract]:/docs/sequence-analysis/fasta-extract.md
+[four-color]:/docs/figure-generation/four-color.md

docusaurus/docs/coordinate-manipulation/bed-to-gff.md

@@ -1,7 +1,7 @@
 ---
 id: bed-to-gff
 title: Convert BED to GFF
-sidebar_label: bed-to-gff
+sidebar_label: BED to GFF
 ---
 
 Converts [BED file][bed-format]  to [GFF file][gff-format]
@@ -23,5 +23,5 @@ This tool takes a single [BED file][bed-format] for input.
 | -o, --output | specify output directory (default name will be same as original with .gff ext) |
 | -s, --stdout | output gff to STDOUT |
 
-[bed-format]:file-formats.md
-[gff-format]:file-formats.md
+[bed-format]:/docs/file-formats
+[gff-format]:/docs/file-formats

docusaurus/docs/coordinate-manipulation/expand-bed.md

@@ -61,7 +61,7 @@ This tool takes a single [BED file][bed-format] for input.
 
 [bedtools-slop]:https://bedtools.readthedocs.io/en/latest/content/tools/slop.html
 
-[bed-format]:file-formats
-[tag-pileup]:read-analysis/tag-pileup
-[four-color]:sequence-analysis/four-color
-[fasta-extract]:sequence-analysis/fasta-extract
+[bed-format]:/docs/file-formats
+[tag-pileup]:/docs/read-analysis/tag-pileup
+[four-color]:/docs/figure-generation/four-color
+[fasta-extract]:/docs/sequence-analysis/fasta-extract

docusaurus/docs/figure-generation/four-color.md

@@ -38,7 +38,7 @@ Expects a [FASTA][fasta-format] formatted file with many sequences to stack up w
 
 [color-hex-url]:http://www.javascripter.net/faq/rgbtohex.htm
 
-[fasta-extract]:sequence-analysis/fasta-extract.md
+[fasta-extract]:/docs/sequence-analysis/fasta-extract.md
 
-[fasta-format]:file-formats.md
-[png-format]:file-formats.md
+[fasta-format]:/docs/file-formats.md
+[png-format]:/docs/file-formats.md

docusaurus/docs/figure-generation/heatmap-labeler.md

@@ -21,4 +21,4 @@ Clicking "Generate" will execute the script to write `.svg` files, each with one
 
 ## Command Line Interface
 
-[png-format]:file-formats
+[png-format]:/docs/file-formats

docusaurus/docs/figure-generation/heatmap.md

@@ -176,8 +176,8 @@ Expects a [CDT][cdt-format] formatted matrix file of values to generate heatmap
 [color-hex-url]:http://www.javascripter.net/faq/rgbtohex.htm
 [treeview-paper]:https://pubmed.ncbi.nlm.nih.gov/15180930/
 
-[tag-pileup]:read-analysis/tagpileup
-[peak-align-ref]:peak-analysis/peak-align-ref
+[tag-pileup]:/docs/read-analysis/tag-pileup
+[peak-align-ref]:/docs/peak-analysis/peak-align-ref
 
-[cdt-format]:file-formats
-[png-format]:file-formats
+[cdt-format]:/docs/file-formats
+[png-format]:/docs/file-formats

docusaurus/docs/figure-generation/merge-heatmap.md

@@ -98,8 +98,8 @@ Expects two [PNG][png-format] like the output from the [heatmap tool][heatmap].
 
 
 
-[cdt-format]:file-formats
-[png-format]:file-formats
+[cdt-format]:/docs/file-formats
+[png-format]:/docs/file-formats
 
-[heatmap]:figure-generation/heatmap.md
-[chip-exo-tutorial]:threebasicplots-exo.md
+[heatmap]:/docs/figure-generation/heatmap.md
+[chip-exo-tutorial]:/docs/Tutorials/threebasicplots-exo.md