Address typo's and refernces to pipeline.

docs/references.md

@@ -16,9 +16,7 @@
   * trimgalore [https://github.com/FelixKrueger/TrimGalore](https://github.com/FelixKrueger/TrimGalore)
 
 6. **hisat2**:
-  * Kim ,D.,Paggi, J.M., Park, C., Bennett, C., Salzberg, S.L. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019 Aug;37(8):907-915. doi: 10.1038/s41587-019-0201-4.
-
-  Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. 2019 Nat Biotechnol. Aug;37(8):907-915. doi:[10.1038/s41587-019-0201-4](https://doi.org/10.1038/s41587-019-0201-4).
+  * Kim ,D.,Paggi, J.M., Park, C., Bennett, C., Salzberg, S.L. 2019 Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. Aug;37(8):907-915. doi:[10.1038/s41587-019-0201-4](https://doi.org/10.1038/s41587-019-0201-4).
 
 7. **samtools**:
   * Li H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin, and 1000 Genome Project Data Processing Subgroup. 2009. The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics 25: 2078-9. doi:[10.1093/bioinformatics/btp352](http://dx.doi.org/10.1093/bioinformatics/btp352)

docs/software_references_mqc.yaml

@@ -4,7 +4,7 @@
         description: 'This section describes references for the tools used.'
         plot_type: 'html'
         data: |
-        
+
                 <h3 id="references">References</h3>
                 <ol style="list-style-type: decimal">
                 <li><strong>python</strong>:</li>
@@ -41,9 +41,8 @@
                 <li><strong>hisat2</strong>:</li>
                 </ol>
                 <ul>
-                <li>Kim ,D.,Paggi, J.M., Park, C., Bennett, C., Salzberg, S.L. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. 2019 Aug;37(8):907-915. doi: 10.1038/s41587-019-0201-4.</li>
+                <li>Kim ,D.,Paggi, J.M., Park, C., Bennett, C., Salzberg, S.L. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. 2019 Nat Biotechnol. 2019 Aug;37(8):907-915. doi:<a href="https://doi.org/10.1038/s41587-019-0201-4">10.1038/s41587-019-0201-4</a></li>
                 </ul>
-                <p>Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. 2019 Nat Biotechnol. Aug;37(8):907-915. doi:<a href="https://doi.org/10.1038/s41587-019-0201-4">10.1038/s41587-019-0201-4</a>.</p>
                 <ol start="7" style="list-style-type: decimal">
                 <li><strong>samtools</strong>:</li>
                 </ol>

docs/software_versions_mqc.yaml

 
         id: 'Software Versions'
         section_name: 'Software Versions'
-        section_href: 'https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/'
+        section_href: 'https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/78-tool_version/docs/RNA-Seq%20Pipeline%20Design%20Process%20Table.pdf'
         plot_type: 'html'
-        description: 'are collected at run time from the software output.'
+        description: 'are collected for pipeline version.'
         data: |
             <dl class="dl-horizontal">
 

workflow/scripts/generate_versions.py

@@ -125,9 +125,9 @@ def main():
         '''
         id: 'Software Versions'
         section_name: 'Software Versions'
-        section_href: 'https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/'
+        section_href: 'https://git.biohpc.swmed.edu/gudmap_rbk/rna-seq/-/blob/78-tool_version/docs/RNA-Seq%20Pipeline%20Design%20Process%20Table.pdf'
         plot_type: 'html'
-        description: 'are collected at run time from the software output.'
+        description: 'are collected for pipeline version.'
         data: |
             <dl class="dl-horizontal">
         '''