ucsc: add bedgraph_to_wig.pl script

src/.docker_modules/ucsc/407/Dockerfile

@@ -25,3 +25,6 @@ cd .. &&\
 mv userApps/bin/* /usr/bin/ &&\
 rm -R userApps.v${UCSC_VERSION}.src.tgz &&\
 rm -R userApps
+
+COPY bedgraph_to_wig.pl /usr/bin/
+RUN chmod +x /usr/bin/bedgraph_to_wig.pl
\ No newline at end of file

src/nf_modules/ucsc/main.nf

@@ -30,3 +30,52 @@ sort -T ./ -k1,1 -k2,2n ${bg} > \
     ${bg.simpleName}_norm.bw
 """
 }
+
+
+params.bigwig_to_wig = ""
+params.bigwig_to_wig_out = ""
+process bigwig_to_wig {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "${file_id}"
+  if (params.bigwig_to_wig_out != "") {
+    publishDir "results/${params.bigwig_to_wig_out}", mode: 'copy'
+  }
+
+  input:
+  tuple val(file_id) path(bw)
+
+  output:
+  tuple val(file_id), path("*.wig"), emit: wig
+
+  script:
+"""
+bigWigToBedGraph ${bw} ${bw.simpleName}.bg
+bedgraph_to_wig.pl --bedgraph ${bw.simpleName}.bg --wig ${bw.simpleName}.wig --step 1
+"""
+}
+
+params.bigwig2_to_wig2 = ""
+params.bigwig2_to_wig2_out = ""
+process bigwig2_to_wig2 {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+  tag "${file_id}"
+  if (params.bigwig_to_wig_out != "") {
+    publishDir "results/${params.bigwig_to_wig_out}", mode: 'copy'
+  }
+
+  input:
+  tuple val(file_id), path(bw_a), path(bw_b)
+
+  output:
+  tuple val(file_id), path("${bw_a.simpleName}.wig"), path("${bw_b.simpleName}.wig"), emit: wig
+
+  script:
+"""
+bigWigToBedGraph ${bw_a} ${bw_a.simpleName}.bg
+bedgraph_to_wig.pl --bedgraph ${bw_a.simpleName}.bg --wig ${bw_a.simpleName}.wig --step 1
+bigWigToBedGraph ${bw_b} ${bw_b.simpleName}.bg
+bedgraph_to_wig.pl --bedgraph ${bw_b.simpleName}.bg --wig ${bw_b.simpleName}.wig --step 1
+"""
+}
\ No newline at end of file