change .sif to .img for singularity img

src/nf_modules/bedtools/fasta_from_bed.config

@@ -13,7 +13,7 @@ profiles {
     singularity.enabled = true
     process {
       withName: fasta_from_bed {
-        container = "file://bin/bedtools:2.25.0.sif"
+        container = "file://bin/bedtools:2.25.0.img"
         cpus = 1
       }
     }

src/nf_modules/bowtie/indexing.config

@@ -14,7 +14,7 @@ profiles {
     process {
       withName: index_fasta {
         cpus = 4
-        container = "file://bin/bowtie:1.2.2.sif"
+        container = "file://bin/bowtie:1.2.2.img"
       }
     }
   }

src/nf_modules/bowtie/mapping_paired.config

@@ -14,7 +14,7 @@ profiles {
     process {
       withName: mapping_fastq {
         cpus = 4
-        container = "file://bin/bowtie:1.2.2.sif"
+        container = "file://bin/bowtie:1.2.2.img"
       }
     }
   }

src/nf_modules/bowtie/mapping_single.config

@@ -14,7 +14,7 @@ profiles {
     process {
       withName: mapping_fastq {
         cpus = 4
-        container = "file://bin/bowtie:1.2.2.sif"
+        container = "file://bin/bowtie:1.2.2.img"
       }
     }
   }

src/nf_modules/bowtie2/indexing.config

@@ -13,7 +13,7 @@ profiles {
     singularity.enabled = true
     process {
       withName: index_fasta {
-        container = "file://bin/bowtie2:2.3.4.1.sif"
+        container = "file://bin/bowtie2:2.3.4.1.img"
         cpus = 4
       }
     }

src/nf_modules/bowtie2/mapping_paired.config

@@ -13,7 +13,7 @@ profiles {
     singularity.enabled = true
     process {
       withName: mapping_fastq {
-        container = "file://bin/bowtie2:2.3.4.1.sif"
+        container = "file://bin/bowtie2:2.3.4.1.img"
         cpus = 4
       }
     }

src/nf_modules/bowtie2/mapping_single.config

@@ -13,7 +13,7 @@ profiles {
     singularity.enabled = true
     process {
       withName: mapping_fastq {
-        container = "file://bin/bowtie2:2.3.4.1.sif"
+        container = "file://bin/bowtie2:2.3.4.1.img"
         cpus = 4
       }
     }

src/nf_modules/bwa/indexing.config

@@ -13,7 +13,7 @@ profiles {
     singularity.enabled = true
     process {
       withName: index_fasta {
-        container = "file://bin/bwa:0.7.17.sif"
+        container = "file://bin/bwa:0.7.17.img"
         cpus = 4
       }
     }

src/nf_modules/bwa/mapping_paired.config

@@ -13,7 +13,7 @@ profiles {
     singularity.enabled = true
     process {
       withName: mapping_fastq {
-        container = "file://bin/bwa:0.7.17.sif"
+        container = "file://bin/bwa:0.7.17.img"
         cpus = 4
       }
     }

src/nf_modules/cutadapt/adaptor_removal_paired.config

@@ -13,7 +13,7 @@ profiles {
     singularity.enabled = true
     process {
       withName: adaptor_removal {
-        container = "file://bin/cutadapt:2.1.sif"
+        container = "file://bin/cutadapt:2.1.img"
         cpus = 1
       }
     }

src/nf_modules/cutadapt/adaptor_removal_single.config

@@ -13,7 +13,7 @@ profiles {
     singularity.enabled = true
     process {
       withName: adaptor_removal {
-        container = "file://bin/cutadapt:2.1.sif"
+        container = "file://bin/cutadapt:2.1.img"
         cpus = 1
       }
     }

src/nf_modules/cutadapt/trimming_paired.config

@@ -13,7 +13,7 @@ profiles {
     singularity.enabled = true
     process {
       withName: trimming {
-        container = "file://bin/cutadapt:2.1.sif"
+        container = "file://bin/cutadapt:2.1.img"
         cpus = 1
       }
     }

src/nf_modules/cutadapt/trimming_single.config

@@ -13,7 +13,7 @@ profiles {
     singularity.enabled = true
     process {
       withName: trimming {
-        container = "file://bin/cutadapt:2.1.sif"
+        container = "file://bin/cutadapt:2.1.img"
         cpus = 1
       }
     }

src/nf_modules/deeptools/bam_to_bigwig.config

@@ -17,11 +17,11 @@ profiles {
     singularity.enabled = true
     process {
       withName: index_bam {
-        container = "file://bin/sambamba:0.6.7.sif"
+        container = "file://bin/sambamba:0.6.7.img"
         cpus = 4
       }
       withName: bam_to_bigwig {
-        container = "file://bin/deeptools:3.0.2.sif"
+        container = "file://bin/deeptools:3.0.2.img"
         cpus = 4
       }
     }

src/nf_modules/deeptools/compute_matrix.config

@@ -13,7 +13,7 @@ profiles {
     singularity.enabled = true
     process {
       withName: compute_matrix {
-        container = "file://bin/deeptools:3.0.2.sif"
+        container = "file://bin/deeptools:3.0.2.img"
         cpus = 4
       }
     }

src/nf_modules/deeptools/plot_profile.config

@@ -13,7 +13,7 @@ profiles {
     singularity.enabled = true
     process {
       withName: compute_matrix {
-        container = "file://bin/deeptools:3.0.2.sif"
+        container = "file://bin/deeptools:3.0.2.img"
         cpus = 4
       }
     }

src/nf_modules/fastp/fastp_paired.config

@@ -14,7 +14,7 @@ profiles {
     process {
       withName: fastp_fastq {
         cpus = 1
-        container = "file://bin/fastp:0.19.7.sif"
+        container = "file://bin/fastp:0.19.7.img"
       }
     }
   }

src/nf_modules/fastp/fastp_single.config

@@ -14,7 +14,7 @@ profiles {
     process {
       withName: fastp_fastq {
         cpus = 1
-        container = "file://bin/fastp:0.19.7.sif"
+        container = "file://bin/fastp:0.19.7.img"
       }
     }
   }

src/nf_modules/fastqc/fastqc_paired.config

@@ -14,7 +14,7 @@ profiles {
     process {
       withName: fastqc_fastq {
         cpus = 1
-        container = "file://bin/fastqc:0.11.5.sif"
+        container = "file://bin/fastqc:0.11.5.img"
       }
     }
   }

src/nf_modules/fastqc/fastqc_single.config

@@ -14,7 +14,7 @@ profiles {
     process {
       withName: fastqc_fastq {
         cpus = 1
-        container = "file://bin/fastqc:0.11.5.sif"
+        container = "file://bin/fastqc:0.11.5.img"
       }
     }
   }