fix loss if last chr in make ref and some other bugs

cellgeni · Dec 10, 2024 · 6579a2d · 6579a2d
1 parent a8a44ba
commit 6579a2d
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Showing 2 changed files with 5 additions and 1 deletion.
diff --git a/bin/sajr.ss.jar b/bin/sajr.ss.jar
diff --git a/main.nf b/main.nf
@@ -53,6 +53,8 @@ process get_data {
 
 
 process run_sajr {
+  publishDir "${params.outdir}/sajr/", mode: 'copy', pattern: "${id}"
+
   input:
   tuple val(id), path(bam_path), path(bam_path_id), val(strand), path(ref)
 
@@ -70,6 +72,8 @@ process run_sajr {
     -ann_in=!{ref}/segments.sajr \
     -stranded=!{strand} \
     -count_only_border_reads=true
+  
+  gzip !{id}/*
   '''
 }
 
@@ -181,4 +185,4 @@ workflow repseudobulk {
 
 workflow reference {
   make_ref(params.gtf)
-}
+}