Merge branch 'Alia' into 'master'

Ajout de la fonction sort_index_bam

See merge request testoni-lab/bolero!1

src/nf_modules/samtools/main.nf

@@ -14,7 +14,7 @@ process sort_bam {
     path(bam)
 
   output:
-    path("*sorted.bam*"), emit: sorted_bam
+    path("*sorted.bam"), emit: sorted_bam
 
   script:
 """
@@ -29,7 +29,7 @@ process start_position_counts {
     publishDir "results/${params.start_position_counts_out}", mode: 'copy'
 
     input:
-        path(bam)
+        tuple path(bam), path(index)
 
     output:
         path "*", emit: count
@@ -61,4 +61,26 @@ process index_bam {
 """
 samtools index -@ ${task.cpus} ${bam}
 """
+}
+
+params.indexed_bam_out =""
+process sort_index_bam {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "sorting"
+  if (params.indexed_bam_out != "") {
+    publishDir "results/${params.indexed_bam_out}", mode: 'copy'
+  }
+
+  input:
+    path(bam)
+
+  output:
+    tuple path("*sorted.bam"), path("*.bai"), emit: indexed_bam
+
+  script:
+"""
+samtools sort -@ ${task.cpus} ${bam} -o ${bam.simpleName}_sorted.bam
+samtools index -@ ${task.cpus} ${bam.simpleName}_sorted.bam
+"""
 }
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