Merge pull request #70 from UMCUGenetics/release/v0.7.0

v0.7.0

Author: melferink

Mosdepth/0.3.3/Mosdepth.nf

@@ -0,0 +1,19 @@
+process Mosdepth {
+    tag {"Mosdepth ${sample_id}"}
+    label 'Mosdepth_0_3_3'
+    container = 'quay.io/biocontainers/mosdepth:0.3.3--h37c5b7d_2'
+    shell = ['/bin/bash', '-euo', 'pipefail']
+
+    input:
+        tuple(val(sample_id), path(bam_file), path(bai_file))
+
+    output:
+        tuple(val(sample_id), path("${sample_id}.mosdepth.summary.txt"), emit: summary_file)
+        tuple(val(sample_id), path("${sample_id}.mosdepth.*.txt"), emit: txt_files)
+        tuple(val(sample_id), path("${sample_id}*bed*"), emit: bed_files, optional: true)
+
+    script:
+        """
+        mosdepth -t ${task.cpus} ${params.optional} ${sample_id} ${bam_file}
+        """
+}

Sambamba/0.7.0/ViewSubsample.nf

@@ -0,0 +1,18 @@
+process Subsample {
+    tag {"Sambamba Subsample ${sample_id}"}
+    label 'Sambamba_0_7_0'
+    label 'Sambamba_0_7_0_ViewSubsample'
+    container = 'quay.io/biocontainers/sambamba:0.7.0--h89e63da_1'
+    shell = ['/bin/bash', '-euo', 'pipefail']
+
+    input:
+        tuple(sample_id, val(fraction), path(bam_file), path(bai_file))
+
+    output:
+        tuple(sample_id, path("${bam_file.baseName}.subsample.bam"), path("${bam_file.baseName}.subsample.bam.bai"), emit: bam_file)
+
+    script:
+        """
+        sambamba view -t ${task.cpus} -f bam -s ${fraction} ${params.optional} ${bam_file} -o ${bam_file.baseName}.subsample.bam
+        """
+}