save macs2 fold enrichment signal value in summits

.github/ISSUE_TEMPLATE/bug-report.md → .github/ISSUE_TEMPLATE/bug-error-report---no-usage-questions---feature-requests--use-discussions--.md

@@ -1,13 +1,18 @@
 ---
-name: Bug Report
-about: Create a bug report to help us improve ArchR
+name: Bug/Error Report - NO USAGE QUESTIONS / FEATURE REQUESTS (Use Discussions!)
+about: Create a bug/error report to help us improve ArchR. NOT to be used for usage
+  questions or feature requests!
 title: ''
 labels: bug
 assignees: ''
 
 ---
 
-Before you submit this issue please update ArchR to the latest version and make sure that this issue has not already been fixed in the latest release. ArchR is in *beta* and we will fix problems as they arise. To update ArchR:
+This is an issue template made by the developers of ArchR. You MUST follow these instructions.
+
+Questions related to how to use ArchR or requests for new features should be posted in the Discussions forum (https://github.com/GreenleafLab/ArchR/discussions).
+
+Before you submit this Bug Report please update ArchR to the latest stable version and make sure that this issue has not already been fixed in the latest release. ArchR is still in active development and we will fix problems as they arise. To update ArchR:
 
 devtools::install_github("GreenleafLab/ArchR", ref="master", repos = BiocManager::repositories())
 
@@ -22,13 +27,13 @@ ArchR has a built-in logging functionality for all complex functions. You MUST a
 A clear and concise description of what the bug is.
 
 **To Reproduce**
-To help us optimally address your issue, please try to reproduce this issue using the tutorial hematopoiesis dataset and provide us the command(s) to reproduce your bug.
+To help us optimally address your issue, please try to reproduce this issue using the tutorial hematopoiesis dataset and provide us the command(s) to reproduce your bug. Our first question to you will be "can you reproduce this with the tutorial dataset" so please do this.
 
 **Expected behavior**
 A clear and concise description of what you expected to happen.
 
 **Screenshots**
-If applicable, add screenshots to help explain your problem.
+If applicable, add screenshots to help explain your problem. Do not screenshot code or text but embed this in markdown using triple-backticks.
 
 **Session Info**
 If you do not have a log file because the function that caused the error does not produce one, please paste the output of "sessionInfo()" here.

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1 @@
+blank_issues_enabled: false

.github/workflows/auto-comment.yml

@@ -0,0 +1,25 @@
+name: Auto Comment
+on: [issues]
+jobs:
+  run:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: wow-actions/auto-comment@v1
+        with:
+          GITHUB_TOKEN: ${{ secrets.PERSONAL_ACCESS_TOKEN }}
+          issuesOpened: |
+            Hi @{{ author }}! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the [Discussions](https://github.com/GreenleafLab/ArchR/discussions) section, not in Issues.<br />
+            __Before we help you, you must respond to the following questions__ unless your original post already contained this information:
+            __1.__ If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved?
+            __2.__ Can you recapitulate your error using the tutorial code and dataset? If so, provide a reproducible example.
+            __3.__ Did you post your log file? If not, add it now.
+            __4.__ Remove any screenshots that contain text and instead copy and paste the text using markdown's codeblock syntax (three consecutive backticks). You can do this by editing your original post.
+
+#          issuesOpened: |
+#            Hi @{{ author }}! Thanks for using ArchR! I am currently on paternity leave and will not be responding to any issues or discussion threads. I plan to be back in late January and will do my best to address your issue then.<br />
+#            In the meantime, it is worth noting that there are very few actual bugs in ArchR. If you are getting an error, it is probably something specific to your dataset, usage, or computational environment. Search the previous [Issues](https://github.com/GreenleafLab/ArchR/issues), [Discussions](https://github.com/GreenleafLab/ArchR/discussions), [function definitions](https://www.archrproject.com/reference/index.html), or the [ArchR manual](https://www.archrproject.com/bookdown/index.html) and you will likely find the answers you are looking for.<br />
+#            If you are able to solve your issue, please post the solution and close this issue post. <br />
+#            Otherwise __if you would like my help when I return, you must respond to the following questions__ unless your original post already contained this information:
+#            __1.__ If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved?
+#            __2.__ Can you recapitulate your error using the tutorial code and dataset? If so, provide a reproducible example.
+#            __3.__ Did you post your log file? If not, add it now.

R/ReproduciblePeakSet.R

@@ -788,8 +788,8 @@ addReproduciblePeakSet <- function(
 	run <- system2(pathToMacs2, cmd, wait=TRUE, stdout=NULL, stderr=NULL)
 
 	#Read Summits!
-	out <- data.table::fread(summitsFile, select = c(1,2,3,5))
-	out <- GRanges(out$V1, IRanges(out$V2 + 1, out$V3), score = out$V5)
+	out <- data.table::fread(narrowPeaksFile, select = c(1,2,5,7,10))
+	out <- GRanges(out$V1, IRanges(out$V2 + out$V10 + 1, out$V2 + out$V10 + 1), score = out$V5/10, signalValue = out$V7)
 
 	#Remove Files
 	r2 <- suppressWarnings(file.remove(summitsFile, narrowPeaksFile, xlsFile))