diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
index ab28edcb57900abc1f77900e2e76a7a1fad19dd0..c3edbc6fcb96f0edad85ce57786cf3d3072b45c7 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ b/src/nf_modules/deeptools/bam_to_bigwig.config
@@ -5,9 +5,24 @@ profiles {
     process {
       withName: index_bam {
         container = "sambamba:0.6.7"
+        cpus = 4
       }
       withName: bam_to_bigwig {
         container = "deeptools:3.0.2"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: index_bam {
+        container = "file://bin/sambamba:0.6.7.sif"
+        cpus = 4
+      }
+      withName: bam_to_bigwig {
+        container = "file://bin/deeptools:3.0.2.sif"
+        cpus = 4
       }
     }
   }
@@ -18,6 +33,7 @@ profiles {
         module = "sambamba/0.6.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
+        cpus = 16
         memory = "30GB"
         time = "24h"
         queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
@@ -28,6 +44,7 @@ profiles {
         module = "deeptools/3.0.2"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
+        cpus = 16
         memory = "30GB"
         time = "24h"
         queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.nf b/src/nf_modules/deeptools/bam_to_bigwig.nf
index 85fa78705f7b2bea012948f6eb8b23627c03bb62..4c30ee0eed193fba70ea3b236a8bfde800993697 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.nf
+++ b/src/nf_modules/deeptools/bam_to_bigwig.nf
@@ -15,7 +15,6 @@ bam_files.into{
 
 process index_bam {
   tag "$file_id"
-  cpus 4
 
   input:
     set file_id, file(bam) from bam_files_index
@@ -33,7 +32,7 @@ bam_files_indexed = bam_files_bigwig.join(indexed_bam_file, by: 0)
 
 process bam_to_bigwig {
   tag "$file_id"
-  cpus 4
+
   publishDir "results/mapping/bigwig/", mode: 'copy'
 
   input:
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index 7159cbc7bff8bec00caee83ec53e415ecb51a5b1..c2c64bf432870a7b514dcc02d50ef420d1668c61 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/src/nf_modules/deeptools/compute_matrix.config
@@ -5,6 +5,16 @@ profiles {
     process {
       withName: compute_matrix {
         container = "deeptools:3.0.2"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: compute_matrix {
+        container = "file://bin/deeptools:3.0.2.sif"
+        cpus = 4
       }
     }
   }
@@ -15,6 +25,7 @@ profiles {
         module = "deeptools/3.0.2"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
+        cpus = 16
         memory = "30GB"
         time = "24h"
         queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
diff --git a/src/nf_modules/deeptools/compute_matrix.nf b/src/nf_modules/deeptools/compute_matrix.nf
index d1d0ae07def09062c93f57dfac54b75734cfdb55..2b6e0e915b00fd1f475818352e11e4ce97225ee0 100644
--- a/src/nf_modules/deeptools/compute_matrix.nf
+++ b/src/nf_modules/deeptools/compute_matrix.nf
@@ -17,7 +17,6 @@ Channel
 
 process compute_matrix {
   tag "$bed_file_id"
-  cpus 4
   publishDir "results/mapping/region_matrix/", mode: 'copy'
 
   input:
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index 984575cc24a3b7a001a91d5c7fe096c7b17fd284..11626d8b52e05342fc6b239589e2b01ef1c4e229 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/src/nf_modules/deeptools/plot_profile.config
@@ -5,6 +5,16 @@ profiles {
     process {
       withName: plot_profile {
         container = "deeptools:3.0.2"
+        cpus = 4
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: compute_matrix {
+        container = "file://bin/deeptools:3.0.2.sif"
+        cpus = 4
       }
     }
   }
@@ -15,6 +25,7 @@ profiles {
         module = "deeptools/3.0.2"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
+        cpus = 16
         memory = "30GB"
         time = "24h"
         queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
diff --git a/src/nf_modules/deeptools/plot_profile.nf b/src/nf_modules/deeptools/plot_profile.nf
index eb089714827a8163185fea8fa64cd892e03b6b7d..dfce4e5504bdd4cede56fa156ffa4fa268a7fede 100644
--- a/src/nf_modules/deeptools/plot_profile.nf
+++ b/src/nf_modules/deeptools/plot_profile.nf
@@ -12,7 +12,6 @@ Channel
 
 process plot_profile {
   tag "$file_id"
-  cpus 4
   publishDir "results/mapping/region_matrix/", mode: 'copy'
 
   input:
diff --git a/src/nf_modules/deeptools/tests.sh b/src/nf_modules/deeptools/tests.sh
index 8c95d4057cafe10a040e9320065d2e490e8ab318..4253689a7c94a62feec6be1536f11d394fec909b 100755
--- a/src/nf_modules/deeptools/tests.sh
+++ b/src/nf_modules/deeptools/tests.sh
@@ -22,3 +22,25 @@ cp data/tiny_dataset/map/tiny_v2.sort.bam \
   --matrix "results/mapping/region_matrix/*.mat.gz" \
   --title "plot title" \
   -resume
+
+if [ -x "$(command -v singularity)" ]; then
+./nextflow src/nf_modules/deeptools/bam_to_bigwig.nf \
+  -c src/nf_modules/deeptools/bam_to_bigwig.config \
+  -profile docker \
+  --bam "data/tiny_dataset/map/tiny_v2*.sort.bam" \
+  -resume
+
+./nextflow src/nf_modules/deeptools/compute_matrix.nf \
+  -c src/nf_modules/deeptools/compute_matrix.config \
+  -profile docker \
+  --bw "results/mapping/bigwig/*.bw" \
+  --bed "data/tiny_dataset/annot/tiny.bed" \
+  -resume
+
+./nextflow src/nf_modules/deeptools/plot_profile.nf \
+  -c src/nf_modules/deeptools/plot_profile.config \
+  -profile docker \
+  --matrix "results/mapping/region_matrix/*.mat.gz" \
+  --title "plot title" \
+  -resume
+fi