bump to v0.2.3

angelovangel · Jan 9, 2025 · 444c6e8 · 444c6e8
1 parent 42c7cbf
commit 444c6e8
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Showing 3 changed files with 16 additions and 16 deletions.
diff --git a/bin/coverage_summary.R b/bin/coverage_summary.R
@@ -55,9 +55,9 @@ finaltable <-
     caption = htmltools::tags$caption(
       style = 'caption-side: bottom; text-align: left; color: grey;',
       htmltools::HTML(
-        "Ref size: <b>", refsize, 
-        "bp </b><br/>Run id:&nbsp&nbsp <b>", arg[2],
-        "</b><br/>Date:&nbsp&nbsp&nbsp&nbsp&nbsp <b>", format.POSIXct(Sys.time(), format = "%Y-%m-%d")
+        "Ref size: <i>", refsize, 
+        "bp </i><br/>Run id:&nbsp&nbsp <i>", arg[2],
+        "</i><br/>Date:&nbsp&nbsp&nbsp&nbsp&nbsp <i>", format.POSIXct(Sys.time(), format = "%Y-%m-%d")
         )
     ),
     # style = 'bootstrap',
@@ -80,4 +80,4 @@ finaltable <-
   spk_add_deps()
 
 #write.csv(df, file = '00-alignment-summary.tsv', sep = '\t', row.names = F, col.names = T)
-DT::saveWidget(finaltable, '00-alignment-summary.html')
+DT::saveWidget(finaltable, file = '00-alignment-summary.html', title = "minimapper-summary")
diff --git a/main.nf b/main.nf
@@ -182,6 +182,17 @@ workflow {
     .combine(reads_ch) \
     | (MINIMAP & MEDAKA_VARIANT) 
 
+    MINIMAP.out.bam_ch
+    .flatten()
+    .filter( ~/.*bam$/ )
+    //.view()
+    | COVERAGE_STATS
+
+    COVERAGE_STATS.out.coverage_ch
+    .collect()
+    //.view()
+    | COVERAGE_SUMMARY
+
     MINIMAP.out.bam_ch \
     .map{ [ it.toString().split("/").last().split("\\.")[0], it ] } //make keys for join
     .set { minimap_ch }
@@ -196,15 +207,4 @@ workflow {
     //.view()
     | IGV
 
-    MINIMAP.out.bam_ch
-    .flatten()
-    .filter( ~/.*bam$/ )
-    //.view()
-    | COVERAGE_STATS
-
-    COVERAGE_STATS.out.coverage_ch
-    .collect()
-    //.view()
-    | COVERAGE_SUMMARY
-
 }
diff --git a/nextflow.config b/nextflow.config
@@ -6,7 +6,7 @@ manifest {
     description     = "Map long reads to reference"
     mainScript      = "main.nf"
     nextflowVersion = ">=23.04.2"
-    version         = "v0.2.2"
+    version         = "v0.2.3"
 }