change .sif to .img for singularity img

src/singularity_modules/subread/1.6.4/build.sh

 #/bin/sh
-sudo singularity build --force bin/subread:1.6.4.sif docker://quay.io/biocontainers/subread:1.6.4--h84994c4_1 && \
-singularity sign bin/subread:1.6.4.sif
+sudo singularity build --force bin/subread:1.6.4.img docker://quay.io/biocontainers/subread:1.6.4--h84994c4_1 && \
+singularity sign bin/subread:1.6.4.img

src/singularity_modules/tophat/2.1.1/build.sh

 #/bin/sh
-sudo singularity build --force bin/tophat:2.1.1.sif src/singularity_modules/tophat/2.1.1/tophat.def && \
-singularity sign bin/tophat:2.1.1.sif
+sudo singularity build --force bin/tophat:2.1.1.img src/singularity_modules/tophat/2.1.1/tophat.def && \
+singularity sign bin/tophat:2.1.1.img

src/singularity_modules/trimmomatic/0.36/build.sh

 #/bin/sh
-sudo singularity build --force bin/trimmomatic:0.36.sif src/singularity_modules/trimmomatic/0.36/trimmomatic.def && \
-singularity sign bin/trimmomatic:0.36.sif
+sudo singularity build --force bin/trimmomatic:0.36.img src/singularity_modules/trimmomatic/0.36/trimmomatic.def && \
+singularity sign bin/trimmomatic:0.36.img

src/singularity_modules/ucsc/375/build.sh

 #/bin/sh
-sudo singularity build --force bin/ucsc:375.sif src/singularity_modules/ucsc/375/ucsc.def && \
-singularity sign bin/ucsc:375.sif
+sudo singularity build --force bin/ucsc:375.img src/singularity_modules/ucsc/375/ucsc.def && \
+singularity sign bin/ucsc:375.img

src/singularity_modules/umi_tools/1.0.0/build.sh

 #/bin/sh
-sudo singularity build --force bin/umi_tools:1.0.0.sif src/singularity_modules/umi_tools/1.0.0/umi_tools.def && \
-singularity sign bin/umi_tools:1.0.0.sif
+sudo singularity build --force bin/umi_tools:1.0.0.img src/singularity_modules/umi_tools/1.0.0/umi_tools.def && \
+singularity sign bin/umi_tools:1.0.0.img

src/singularity_modules/urqt/d62c1f8/build.sh

 #/bin/sh
-sudo singularity build --force bin/urqt:d62c1f8.sif src/singularity_modules/urqt/d62c1f8/urqt.def && \
-singularity sign bin/urqt:d62c1f8.sif
+sudo singularity build --force bin/urqt:d62c1f8.img src/singularity_modules/urqt/d62c1f8/urqt.def && \
+singularity sign bin/urqt:d62c1f8.img

src/training_dataset.config

@@ -61,55 +61,55 @@ profiles {
     singularity.enabled = true
     process {
       withName: build_synthetic_bed {
-        container = "file://bin/bedtools:2.25.0.sif"
+        container = "file://bin/bedtools:2.25.0.img"
         cpus = 1
       }
       withName: fasta_from_bed {
-        container = "file://bin/bedtools:2.25.0.sif"
+        container = "file://bin/bedtools:2.25.0.img"
         cpus = 1
       }
       withName: index_fasta {
-        container = "file://bin/bowtie2:2.3.4.1.sif"
+        container = "file://bin/bowtie2:2.3.4.1.img"
         cpus = 4
       }
       withName: mapping_fastq_single {
-        container = "file://bin/bowtie2:2.3.4.1.sif"
+        container = "file://bin/bowtie2:2.3.4.1.img"
         cpus = 4
       }
       withName: mapping_fastq_paired {
-        container = "file://bin/bowtie2:2.3.4.1.sif"
+        container = "file://bin/bowtie2:2.3.4.1.img"
         cpus = 4
       }
       withName: bam_2_fastq_paired {
-        container = "file://bin/samtools:1.7.sif"
+        container = "file://bin/samtools:1.7.img"
         cpus = 4
       }
       withName: filter_bam_paired {
-        container = "file://bin/samtools:1.7.sif"
+        container = "file://bin/samtools:1.7.img"
         cpus = 4
       }
       withName: sort_bam_paired {
-        container = "file://bin/samtools:1.7.sif"
+        container = "file://bin/samtools:1.7.img"
         cpus = 4
       }
       withName: index_bam_paired {
-        container = "file://bin/samtools:1.7.sif"
+        container = "file://bin/samtools:1.7.img"
         cpus = 4
       }
       withName: bam_2_fastq_single {
-        container = "file://bin/samtools:1.7.sif"
+        container = "file://bin/samtools:1.7.img"
         cpus = 4
       }
       withName: filter_bam_single {
-        container = "file://bin/samtools:1.7.sif"
+        container = "file://bin/samtools:1.7.img"
         cpus = 4
       }
       withName: sort_bam_single {
-        container = "file://bin/samtools:1.7.sif"
+        container = "file://bin/samtools:1.7.img"
         cpus = 4
       }
       withName: index_bam_single {
-        container = "file://bin/samtools:1.7.sif"
+        container = "file://bin/samtools:1.7.img"
         cpus = 4
       }
     }