Merge pull request #39 from CCBR/dev

Dev
CCBR · Feb 10, 2023 · b018de9 · b018de9
2 parents e0d7769 + 208afae
commit b018de9
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diff --git a/docs/user-guide/output.md b/docs/user-guide/output.md
@@ -1,9 +1,10 @@
 # 4. Expected Outputs
 The following directories are created under the WORKDIR/results directory:
 
+- annotation: this directory will include annotations from HOMER and ROSE. It contains a sub-directory that relates to the quality threshold used.
 - alignment_stats: this directory include information on the alignment of each sample
 - bigwig: this directory includes the bigwig files for each sample 
-- peaks:
+- peaks: It contains a sub-directory that relates to the quality threshold used.
     - contrasts: this includes the contrasts for each line listed in the contrast manifest
     - seacr: this includes all peak calls from SEACR for each sample
     - macs2: this includes all peak calls from MACS2 for each sample

diff --git a/workflow/scripts/_diff_markdown.Rmd b/workflow/scripts/_diff_markdown.Rmd
@@ -381,9 +381,11 @@ deg %>% rownames_to_column(var="Annotation") -> deg
 pander(deg)
 
 # add catch for hs1 which names SYMBOLS col as geneId
-lookup <- c(SYMBOL = "geneId")
-results_df=results_df %>%
-   dplyr::rename(any_of(lookup))
+if(params$species == "hs1"){
+  lookup <- c(SYMBOL = "geneId")
+  results_df=results_df %>%
+     dplyr::rename(any_of(lookup))
+}
 ```
 
 ### DESeq Volcano