deeptools: add singularity to files

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'

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:

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'

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:

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'

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:

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