From a972f993a389ca6cdc9e5b6d17ac1e0fe4d568fd Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 16 Apr 2019 10:25:45 +0200
Subject: [PATCH] change .sif to .img for singularity img
---
src/nf_modules/bedtools/fasta_from_bed.config | 2 +-
src/nf_modules/bowtie/indexing.config | 2 +-
src/nf_modules/bowtie/mapping_paired.config | 2 +-
src/nf_modules/bowtie/mapping_single.config | 2 +-
src/nf_modules/bowtie2/indexing.config | 2 +-
src/nf_modules/bowtie2/mapping_paired.config | 2 +-
src/nf_modules/bowtie2/mapping_single.config | 2 +-
src/nf_modules/bwa/indexing.config | 2 +-
src/nf_modules/bwa/mapping_paired.config | 2 +-
.../cutadapt/adaptor_removal_paired.config | 2 +-
.../cutadapt/adaptor_removal_single.config | 2 +-
.../cutadapt/trimming_paired.config | 2 +-
.../cutadapt/trimming_single.config | 2 +-
src/nf_modules/deeptools/bam_to_bigwig.config | 4 +--
.../deeptools/compute_matrix.config | 2 +-
src/nf_modules/deeptools/plot_profile.config | 2 +-
src/nf_modules/fastp/fastp_paired.config | 2 +-
src/nf_modules/fastp/fastp_single.config | 2 +-
src/nf_modules/fastqc/fastqc_paired.config | 2 +-
src/nf_modules/fastqc/fastqc_single.config | 2 +-
src/nf_modules/hisat2/indexing.config | 2 +-
src/nf_modules/hisat2/mapping_paired.config | 2 +-
src/nf_modules/hisat2/mapping_single.config | 2 +-
src/nf_modules/htseq/htseq.config | 2 +-
src/nf_modules/kallisto/indexing.config | 2 +-
src/nf_modules/kallisto/mapping_paired.config | 2 +-
src/nf_modules/kallisto/mapping_single.config | 2 +-
src/nf_modules/macs2/peak_calling.config | 2 +-
src/nf_modules/multiqc/multiqc_paired.config | 4 +--
src/nf_modules/multiqc/multiqc_single.config | 4 +--
.../music/peak_calling_single.config | 6 ++---
src/nf_modules/rsem/indexing.config | 2 +-
.../rsem/quantification_paired.config | 2 +-
.../rsem/quantification_single.config | 2 +-
src/nf_modules/sambamba/index_bams.config | 2 +-
src/nf_modules/sambamba/sort_bams.config | 2 +-
src/nf_modules/sambamba/split_bams.config | 2 +-
src/nf_modules/samblaster/dedup_sams.config | 2 +-
src/nf_modules/samtools/filter_bams.config | 2 +-
src/nf_modules/samtools/index_bams.config | 2 +-
src/nf_modules/samtools/sort_bams.config | 2 +-
src/nf_modules/samtools/split_bams.config | 2 +-
src/nf_modules/sratoolkit/fastqdump.config | 2 +-
src/nf_modules/urqt/trimming_paired.config | 2 +-
src/nf_modules/urqt/trimming_single.config | 2 +-
src/singularity_modules/bcftools/1.7/build.sh | 4 +--
.../bedtools/2.25.0/build.sh | 4 +--
src/singularity_modules/bioawk/1.0/build.sh | 4 +--
src/singularity_modules/bowtie/1.2.2/build.sh | 4 +--
.../bowtie2/2.3.4.1/build.sh | 4 +--
src/singularity_modules/bwa/0.7.17/build.sh | 4 +--
src/singularity_modules/canu/1.6/build.sh | 4 +--
.../cutadapt/1.14/build.sh | 4 +--
.../cutadapt/1.15/build.sh | 4 +--
src/singularity_modules/cutadapt/2.1/build.sh | 4 +--
.../deeptools/3.0.2/build.sh | 4 +--
.../deeptools/3.1.1/build.sh | 4 +--
src/singularity_modules/fastp/0.19.7/build.sh | 4 +--
.../fastqc/0.11.5/build.sh | 4 +--
.../file_handle/0.1.1/build.sh | 4 +--
src/singularity_modules/gatk/4.0.8.1/build.sh | 4 +--
src/singularity_modules/hisat2/2.0.0/build.sh | 4 +--
src/singularity_modules/hisat2/2.1.0/build.sh | 4 +--
src/singularity_modules/htseq/0.11.2/build.sh | 4 +--
src/singularity_modules/htseq/0.8.0/build.sh | 4 +--
.../kallisto/0.43.1/build.sh | 4 +--
.../kallisto/0.44.0/build.sh | 4 +--
.../kallisto/0.44.0/kallisto | 2 +-
src/singularity_modules/macs2/2.1.2/build.sh | 4 +--
src/singularity_modules/multiqc/1.0/build.sh | 4 +--
src/singularity_modules/multiqc/1.7/build.sh | 4 +--
.../music/6613c53/build.sh | 4 +--
.../picard/2.18.11/build.sh | 4 +--
src/singularity_modules/pigz/2.4/build.sh | 4 +--
src/singularity_modules/rsem/1.3.0/build.sh | 4 +--
src/singularity_modules/salmon/0.8.2/build.sh | 4 +--
.../sambamba/0.6.7/build.sh | 4 +--
.../samblaster/0.1.24/build.sh | 4 +--
src/singularity_modules/samtools/1.7/build.sh | 4 +--
.../sratoolkit/2.8.2/build.sh | 4 +--
.../subread/1.6.4/build.sh | 4 +--
src/singularity_modules/tophat/2.1.1/build.sh | 4 +--
.../trimmomatic/0.36/build.sh | 4 +--
src/singularity_modules/ucsc/375/build.sh | 4 +--
.../umi_tools/1.0.0/build.sh | 4 +--
src/singularity_modules/urqt/d62c1f8/build.sh | 4 +--
src/training_dataset.config | 26 +++++++++----------
87 files changed, 144 insertions(+), 144 deletions(-)
diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index 1875f439..d0502f57 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/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
}
}
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index 715847fb..c55891bc 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/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"
}
}
}
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index 0936530d..28ce647a 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/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"
}
}
}
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index 0936530d..28ce647a 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/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"
}
}
}
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index 3d0da943..6a9d6071 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/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
}
}
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index 54410c46..63ba18af 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/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
}
}
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index 54410c46..63ba18af 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/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
}
}
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
index f391241a..cae101a5 100644
--- a/src/nf_modules/bwa/indexing.config
+++ b/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
}
}
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
index 700b1983..e3ff6728 100644
--- a/src/nf_modules/bwa/mapping_paired.config
+++ b/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
}
}
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index 46e40043..fefbf0dd 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/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
}
}
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index 46e40043..fefbf0dd 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/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
}
}
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index b3c32aab..cc3e9422 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/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
}
}
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index b3c32aab..cc3e9422 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/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
}
}
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
index 209ae8c9..452ca1c3 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ b/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
}
}
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index 471dde0a..73309d65 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/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
}
}
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index 306f3a90..9f3ce971 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/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
}
}
diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config
index 561a3afa..295d1835 100644
--- a/src/nf_modules/fastp/fastp_paired.config
+++ b/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"
}
}
}
diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config
index 561a3afa..295d1835 100644
--- a/src/nf_modules/fastp/fastp_single.config
+++ b/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"
}
}
}
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
index 9e75046a..08cc9b1b 100644
--- a/src/nf_modules/fastqc/fastqc_paired.config
+++ b/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"
}
}
}
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
index 9e75046a..08cc9b1b 100644
--- a/src/nf_modules/fastqc/fastqc_single.config
+++ b/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"
}
}
}
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
index b259633a..22f41f8d 100644
--- a/src/nf_modules/hisat2/indexing.config
+++ b/src/nf_modules/hisat2/indexing.config
@@ -14,7 +14,7 @@ profiles {
process {
withName: index_fasta {
cpus = 4
- container = "file://bin/hisat2:2.1.0.sif"
+ container = "file://bin/hisat2:2.1.0.img"
}
}
}
diff --git a/src/nf_modules/hisat2/mapping_paired.config b/src/nf_modules/hisat2/mapping_paired.config
index 02c92edf..370f5892 100644
--- a/src/nf_modules/hisat2/mapping_paired.config
+++ b/src/nf_modules/hisat2/mapping_paired.config
@@ -14,7 +14,7 @@ profiles {
process {
withName: mapping_fastq {
cpus = 4
- container = "file://bin/hisat2:2.1.0.sif"
+ container = "file://bin/hisat2:2.1.0.img"
}
}
}
diff --git a/src/nf_modules/hisat2/mapping_single.config b/src/nf_modules/hisat2/mapping_single.config
index 02c92edf..370f5892 100644
--- a/src/nf_modules/hisat2/mapping_single.config
+++ b/src/nf_modules/hisat2/mapping_single.config
@@ -14,7 +14,7 @@ profiles {
process {
withName: mapping_fastq {
cpus = 4
- container = "file://bin/hisat2:2.1.0.sif"
+ container = "file://bin/hisat2:2.1.0.img"
}
}
}
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index 30646614..bd55d6a6 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/src/nf_modules/htseq/htseq.config
@@ -17,7 +17,7 @@ profiles {
singularity.enabled = true
process {
withName: sort_bam {
- container = "file://bin/htseq:0.11.2.sif"
+ container = "file://bin/htseq:0.11.2.img"
cpus = 1
}
}
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index 35dffe67..403d9426 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
process {
withName: index_fasta {
- container = "file://bin/kallisto:0.44.0.sif"
+ container = "file://bin/kallisto:0.44.0.img"
cpus = 4
}
}
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index ef499149..a8c439b9 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
process {
withName: mapping_fastq {
- container = "file://bin/kallisto:0.44.0.sif"
+ container = "file://bin/kallisto:0.44.0.img"
cpus = 4
}
}
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index ef499149..a8c439b9 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
process {
withName: mapping_fastq {
- container = "file://bin/kallisto:0.44.0.sif"
+ container = "file://bin/kallisto:0.44.0.img"
cpus = 4
}
}
diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config
index 8462ab86..fe712a6a 100644
--- a/src/nf_modules/macs2/peak_calling.config
+++ b/src/nf_modules/macs2/peak_calling.config
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
process {
withName: peak_calling {
- container = "file://bin/macs2:2.1.2.sif"
+ container = "file://bin/macs2:2.1.2.img"
cpus = 4
}
}
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index aaa32da1..c6af2012 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -18,11 +18,11 @@ profiles {
singularity.enabled = true
process {
withName: fastqc_fastq {
- container = "file://bin/fastqc:0.11.5.sif"
+ container = "file://bin/fastqc:0.11.5.img"
cpus = 1
}
withName: multiqc {
- container = "file://bin/multiqc:1.7.sif"
+ container = "file://bin/multiqc:1.7.img"
cpus = 1
}
}
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index bdf60504..42d1406c 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -17,11 +17,11 @@ profiles {
singularity.enabled = true
process {
withName: fastqc_fastq {
- container = "file://bin/fastqc:0.11.5.sif"
+ container = "file://bin/fastqc:0.11.5.img"
cpus = 1
}
withName: multiqc {
- container = "file://bin/multiqc:1.7.sif"
+ container = "file://bin/multiqc:1.7.img"
cpus = 1
}
}
diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config
index d21fe81d..cf15eab2 100644
--- a/src/nf_modules/music/peak_calling_single.config
+++ b/src/nf_modules/music/peak_calling_single.config
@@ -21,15 +21,15 @@ profiles {
singularity.enabled = true
process {
withName: compute_mappability {
- container = "file://bin/music:6613c53.sif"
+ container = "file://bin/music:6613c53.img"
cpus = 1
}
withName: music_preprocessing {
- container = "file://bin/music:6613c53.sif"
+ container = "file://bin/music:6613c53.img"
cpus = 1
}
withName: music_computation {
- container = "file://bin/music:6613c53.sif"
+ container = "file://bin/music:6613c53.img"
cpus = 1
}
}
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
index aeea35fe..d0aea317 100644
--- a/src/nf_modules/rsem/indexing.config
+++ b/src/nf_modules/rsem/indexing.config
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
process {
withName: index_fasta {
- container = "file://bin/rsem:1.3.0.sif"
+ container = "file://bin/rsem:1.3.0.img"
cpus = 4
}
}
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
index 812167ed..035db80f 100644
--- a/src/nf_modules/rsem/quantification_paired.config
+++ b/src/nf_modules/rsem/quantification_paired.config
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
process {
withName: mapping_fastq {
- container = "file://bin/rsem:1.3.0.sif"
+ container = "file://bin/rsem:1.3.0.img"
cpus = 4
}
}
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
index 812167ed..035db80f 100644
--- a/src/nf_modules/rsem/quantification_single.config
+++ b/src/nf_modules/rsem/quantification_single.config
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
process {
withName: mapping_fastq {
- container = "file://bin/rsem:1.3.0.sif"
+ container = "file://bin/rsem:1.3.0.img"
cpus = 4
}
}
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index 8cbbd24b..06c3fcc5 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -13,7 +13,7 @@ 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
}
}
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index 11811d97..73f2bcd1 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
process {
withName: sort_bam {
- container = "file://bin/sambamba:0.6.7.sif"
+ container = "file://bin/sambamba:0.6.7.img"
cpus = 4
}
}
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index 6df50fc7..95173ec2 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
process {
withName: split_bam {
- container = "file://bin/sambamba:0.6.7.sif"
+ container = "file://bin/sambamba:0.6.7.img"
cpus = 4
}
}
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index 75efda22..c7e1525c 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
process {
withName: split_bam {
- container = "file://bin/sambamba:0.6.7.sif"
+ container = "file://bin/sambamba:0.6.7.img"
cpus = 4
}
}
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
index 87d99007..2b3a814a 100644
--- a/src/nf_modules/samtools/filter_bams.config
+++ b/src/nf_modules/samtools/filter_bams.config
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
process {
withName: filter_bam {
- container = "file://bin/samtools:1.7.sif"
+ container = "file://bin/samtools:1.7.img"
cpus = 4
}
}
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
index 762773b4..5cec951b 100644
--- a/src/nf_modules/samtools/index_bams.config
+++ b/src/nf_modules/samtools/index_bams.config
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
process {
withName: index_bam {
- container = "file://bin/samtools:1.7.sif"
+ container = "file://bin/samtools:1.7.img"
cpus = 1
}
}
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
index 63c23123..9f420077 100644
--- a/src/nf_modules/samtools/sort_bams.config
+++ b/src/nf_modules/samtools/sort_bams.config
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
process {
withName: sort_bam {
- container = "file://bin/samtools:1.7.sif"
+ container = "file://bin/samtools:1.7.img"
cpus = 4
}
}
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
index de924648..91b2f1ac 100644
--- a/src/nf_modules/samtools/split_bams.config
+++ b/src/nf_modules/samtools/split_bams.config
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
process {
withName: split_bam {
- container = "file://bin/samtools:1.7.sif"
+ container = "file://bin/samtools:1.7.img"
cpus = 2
}
}
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
index 2fc5039f..043a3784 100644
--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ b/src/nf_modules/sratoolkit/fastqdump.config
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
process {
withName: split_bam {
- container = "file://bin/sambamba:0.6.7.sif"
+ container = "file://bin/sambamba:0.6.7.img"
cpus = 1
}
}
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index f0b084b8..cd6a5151 100644
--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -14,7 +14,7 @@ profiles {
process {
withName: trimming {
cpus = 4
- container = "file://bin/urqt:d62c1f8.sif"
+ container = "file://bin/urqt:d62c1f8.img"
}
}
}
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index 02788fcb..237737cf 100644
--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -13,7 +13,7 @@ profiles {
singularity.enabled = true
process {
withName: trimming {
- container = "file://bin/urqt:d62c1f8.sif"
+ container = "file://bin/urqt:d62c1f8.img"
cpus = 4
}
}
diff --git a/src/singularity_modules/bcftools/1.7/build.sh b/src/singularity_modules/bcftools/1.7/build.sh
index bee821bd..96ecae55 100755
--- a/src/singularity_modules/bcftools/1.7/build.sh
+++ b/src/singularity_modules/bcftools/1.7/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/bcftools:1.7.sif src/singularity_modules/bcftools/1.7/bcftools.def && \
-singularity sign bin/bcftools:1.7.sif
+sudo singularity build --force bin/bcftools:1.7.img src/singularity_modules/bcftools/1.7/bcftools.def && \
+singularity sign bin/bcftools:1.7.img
diff --git a/src/singularity_modules/bedtools/2.25.0/build.sh b/src/singularity_modules/bedtools/2.25.0/build.sh
index 60644b46..936a71be 100755
--- a/src/singularity_modules/bedtools/2.25.0/build.sh
+++ b/src/singularity_modules/bedtools/2.25.0/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/bedtools:2.25.0.sif src/singularity_modules/bedtools/2.25.0/bedtools.def && \
-singularity sign bin/bedtools:2.25.0.sif
+sudo singularity build --force bin/bedtools:2.25.0.img src/singularity_modules/bedtools/2.25.0/bedtools.def && \
+singularity sign bin/bedtools:2.25.0.img
diff --git a/src/singularity_modules/bioawk/1.0/build.sh b/src/singularity_modules/bioawk/1.0/build.sh
index 3f8adc04..be5a5098 100755
--- a/src/singularity_modules/bioawk/1.0/build.sh
+++ b/src/singularity_modules/bioawk/1.0/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/bioawk:1.0.sif src/singularity_modules/bioawk/1.0/bioawk.def && \
-singularity sign bin/bioawk:1.0.sif
+sudo singularity build --force bin/bioawk:1.0.img src/singularity_modules/bioawk/1.0/bioawk.def && \
+singularity sign bin/bioawk:1.0.img
diff --git a/src/singularity_modules/bowtie/1.2.2/build.sh b/src/singularity_modules/bowtie/1.2.2/build.sh
index 3470fca0..a5a5c54d 100755
--- a/src/singularity_modules/bowtie/1.2.2/build.sh
+++ b/src/singularity_modules/bowtie/1.2.2/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/bowtie:1.2.2.sif src/singularity_modules/bowtie/1.2.2/bowtie.def && \
-singularity sign bin/bowtie:1.2.2.sif
+sudo singularity build --force bin/bowtie:1.2.2.img src/singularity_modules/bowtie/1.2.2/bowtie.def && \
+singularity sign bin/bowtie:1.2.2.img
diff --git a/src/singularity_modules/bowtie2/2.3.4.1/build.sh b/src/singularity_modules/bowtie2/2.3.4.1/build.sh
index f9f58ae6..c01beabb 100755
--- a/src/singularity_modules/bowtie2/2.3.4.1/build.sh
+++ b/src/singularity_modules/bowtie2/2.3.4.1/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/bowtie2:2.3.4.1.sif src/singularity_modules/bowtie2/2.3.4.1/bowtie2.def && \
-singularity sign bin/bowtie2:2.3.4.1.sif
+sudo singularity build --force bin/bowtie2:2.3.4.1.img src/singularity_modules/bowtie2/2.3.4.1/bowtie2.def && \
+singularity sign bin/bowtie2:2.3.4.1.img
diff --git a/src/singularity_modules/bwa/0.7.17/build.sh b/src/singularity_modules/bwa/0.7.17/build.sh
index a340c5f8..0392a0c1 100755
--- a/src/singularity_modules/bwa/0.7.17/build.sh
+++ b/src/singularity_modules/bwa/0.7.17/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/bwa:0.7.17.sif src/singularity_modules/bwa/0.7.17/bwa.def && \
-singularity sign bin/bwa:0.7.17.sif
+sudo singularity build --force bin/bwa:0.7.17.img src/singularity_modules/bwa/0.7.17/bwa.def && \
+singularity sign bin/bwa:0.7.17.img
diff --git a/src/singularity_modules/canu/1.6/build.sh b/src/singularity_modules/canu/1.6/build.sh
index 591cb660..78805dac 100755
--- a/src/singularity_modules/canu/1.6/build.sh
+++ b/src/singularity_modules/canu/1.6/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/canu:1.6.sif src/singularity_modules/canu/1.6/canu.def && \
-singularity sign bin/canu:1.6.sif
+sudo singularity build --force bin/canu:1.6.img src/singularity_modules/canu/1.6/canu.def && \
+singularity sign bin/canu:1.6.img
diff --git a/src/singularity_modules/cutadapt/1.14/build.sh b/src/singularity_modules/cutadapt/1.14/build.sh
index 5327f7c4..0369e0df 100755
--- a/src/singularity_modules/cutadapt/1.14/build.sh
+++ b/src/singularity_modules/cutadapt/1.14/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/cutadapt:1.14.sif src/singularity_modules/cutadapt/1.14/cutadapt.def && \
-singularity sign bin/cutadapt:1.14.sif
+sudo singularity build --force bin/cutadapt:1.14.img src/singularity_modules/cutadapt/1.14/cutadapt.def && \
+singularity sign bin/cutadapt:1.14.img
diff --git a/src/singularity_modules/cutadapt/1.15/build.sh b/src/singularity_modules/cutadapt/1.15/build.sh
index c002354b..95883b04 100755
--- a/src/singularity_modules/cutadapt/1.15/build.sh
+++ b/src/singularity_modules/cutadapt/1.15/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/cutadapt:1.15.sif src/singularity_modules/cutadapt/1.15/cutadapt.def && \
-singularity sign bin/cutadapt:1.15.sif
+sudo singularity build --force bin/cutadapt:1.15.img src/singularity_modules/cutadapt/1.15/cutadapt.def && \
+singularity sign bin/cutadapt:1.15.img
diff --git a/src/singularity_modules/cutadapt/2.1/build.sh b/src/singularity_modules/cutadapt/2.1/build.sh
index fdb8c4d0..5a7070ec 100755
--- a/src/singularity_modules/cutadapt/2.1/build.sh
+++ b/src/singularity_modules/cutadapt/2.1/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/cutadapt:2.1.sif src/singularity_modules/cutadapt/2.1/cutadapt.def && \
-singularity sign bin/cutadapt:2.1.sif
+sudo singularity build --force bin/cutadapt:2.1.img src/singularity_modules/cutadapt/2.1/cutadapt.def && \
+singularity sign bin/cutadapt:2.1.img
diff --git a/src/singularity_modules/deeptools/3.0.2/build.sh b/src/singularity_modules/deeptools/3.0.2/build.sh
index 9e59a81d..2ffc9937 100755
--- a/src/singularity_modules/deeptools/3.0.2/build.sh
+++ b/src/singularity_modules/deeptools/3.0.2/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/deeptools:3.0.2.sif src/singularity_modules/deeptools/3.0.2/deeptools.def && \
-singularity sign bin/deeptools:3.0.2.sif
+sudo singularity build --force bin/deeptools:3.0.2.img src/singularity_modules/deeptools/3.0.2/deeptools.def && \
+singularity sign bin/deeptools:3.0.2.img
diff --git a/src/singularity_modules/deeptools/3.1.1/build.sh b/src/singularity_modules/deeptools/3.1.1/build.sh
index b9210571..78304343 100755
--- a/src/singularity_modules/deeptools/3.1.1/build.sh
+++ b/src/singularity_modules/deeptools/3.1.1/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/deeptools:3.1.1.sif src/singularity_modules/deeptools/3.1.1/deeptools.def && \
-singularity sign bin/deeptools:3.1.1.sif
+sudo singularity build --force bin/deeptools:3.1.1.img src/singularity_modules/deeptools/3.1.1/deeptools.def && \
+singularity sign bin/deeptools:3.1.1.img
diff --git a/src/singularity_modules/fastp/0.19.7/build.sh b/src/singularity_modules/fastp/0.19.7/build.sh
index 01a0d812..58127ff0 100755
--- a/src/singularity_modules/fastp/0.19.7/build.sh
+++ b/src/singularity_modules/fastp/0.19.7/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/fastp:0.19.7.sif docker://quay.io/biocontainers/fastp:0.19.7--hdbcaa40_0 && \
-singularity sign bin/fastp:0.19.7.sif
+sudo singularity build --force bin/fastp:0.19.7.img docker://quay.io/biocontainers/fastp:0.19.7--hdbcaa40_0 && \
+singularity sign bin/fastp:0.19.7.img
diff --git a/src/singularity_modules/fastqc/0.11.5/build.sh b/src/singularity_modules/fastqc/0.11.5/build.sh
index b3983367..ef313d4e 100755
--- a/src/singularity_modules/fastqc/0.11.5/build.sh
+++ b/src/singularity_modules/fastqc/0.11.5/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/fastqc:0.11.5.sif src/singularity_modules/fastqc/0.11.5/fastqc.def && \
-singularity sign bin/fastqc:0.11.5.sif
+sudo singularity build --force bin/fastqc:0.11.5.img src/singularity_modules/fastqc/0.11.5/fastqc.def && \
+singularity sign bin/fastqc:0.11.5.img
diff --git a/src/singularity_modules/file_handle/0.1.1/build.sh b/src/singularity_modules/file_handle/0.1.1/build.sh
index 17122f24..b48ae449 100755
--- a/src/singularity_modules/file_handle/0.1.1/build.sh
+++ b/src/singularity_modules/file_handle/0.1.1/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/file_handle:0.1.1.sif src/singularity_modules/file_handle/0.1.1/file_handle.def && \
-singularity sign bin/file_handle:0.1.1.sif
+sudo singularity build --force bin/file_handle:0.1.1.img src/singularity_modules/file_handle/0.1.1/file_handle.def && \
+singularity sign bin/file_handle:0.1.1.img
diff --git a/src/singularity_modules/gatk/4.0.8.1/build.sh b/src/singularity_modules/gatk/4.0.8.1/build.sh
index 5158959f..87e095b7 100755
--- a/src/singularity_modules/gatk/4.0.8.1/build.sh
+++ b/src/singularity_modules/gatk/4.0.8.1/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/gatk:4.0.8.1.sif src/singularity_modules/gatk/4.0.8.1/gatk.def && \
-singularity sign bin/gatk:4.0.8.1.sif
+sudo singularity build --force bin/gatk:4.0.8.1.img src/singularity_modules/gatk/4.0.8.1/gatk.def && \
+singularity sign bin/gatk:4.0.8.1.img
diff --git a/src/singularity_modules/hisat2/2.0.0/build.sh b/src/singularity_modules/hisat2/2.0.0/build.sh
index e2b18756..4ba74ed4 100755
--- a/src/singularity_modules/hisat2/2.0.0/build.sh
+++ b/src/singularity_modules/hisat2/2.0.0/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/hisat2:2.0.0.sif src/singularity_modules/hisat2/2.0.0/hisat2.def && \
-singularity sign bin/hisat2:2.0.0.sif
+sudo singularity build --force bin/hisat2:2.0.0.img src/singularity_modules/hisat2/2.0.0/hisat2.def && \
+singularity sign bin/hisat2:2.0.0.img
diff --git a/src/singularity_modules/hisat2/2.1.0/build.sh b/src/singularity_modules/hisat2/2.1.0/build.sh
index 074f4ce6..5a23a144 100755
--- a/src/singularity_modules/hisat2/2.1.0/build.sh
+++ b/src/singularity_modules/hisat2/2.1.0/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/hisat2:2.1.0.sif src/singularity_modules/hisat2/2.1.0/hisat2.def && \
-singularity sign bin/hisat2:2.1.0.sif
+sudo singularity build --force bin/hisat2:2.1.0.img src/singularity_modules/hisat2/2.1.0/hisat2.def && \
+singularity sign bin/hisat2:2.1.0.img
diff --git a/src/singularity_modules/htseq/0.11.2/build.sh b/src/singularity_modules/htseq/0.11.2/build.sh
index 1c3c8170..116d41a8 100755
--- a/src/singularity_modules/htseq/0.11.2/build.sh
+++ b/src/singularity_modules/htseq/0.11.2/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/htseq:0.11.2.sif src/singularity_modules/htseq/0.11.2/htseq.def && \
-singularity sign bin/htseq:0.11.2.sif
+sudo singularity build --force bin/htseq:0.11.2.img src/singularity_modules/htseq/0.11.2/htseq.def && \
+singularity sign bin/htseq:0.11.2.img
diff --git a/src/singularity_modules/htseq/0.8.0/build.sh b/src/singularity_modules/htseq/0.8.0/build.sh
index 73b14c96..19aed8a6 100755
--- a/src/singularity_modules/htseq/0.8.0/build.sh
+++ b/src/singularity_modules/htseq/0.8.0/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/htseq:0.8.0.sif src/singularity_modules/htseq/0.8.0/htseq.def && \
-singularity sign bin/htseq:0.8.0.sif
+sudo singularity build --force bin/htseq:0.8.0.img src/singularity_modules/htseq/0.8.0/htseq.def && \
+singularity sign bin/htseq:0.8.0.img
diff --git a/src/singularity_modules/kallisto/0.43.1/build.sh b/src/singularity_modules/kallisto/0.43.1/build.sh
index 8ecfe6e4..1a83c7c6 100755
--- a/src/singularity_modules/kallisto/0.43.1/build.sh
+++ b/src/singularity_modules/kallisto/0.43.1/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/kallisto:0.43.1.sif src/singularity_modules/kallisto/0.43.1/kallisto.def && \
-singularity sign bin/kallisto:0.43.1.sif
+sudo singularity build --force bin/kallisto:0.43.1.img src/singularity_modules/kallisto/0.43.1/kallisto.def && \
+singularity sign bin/kallisto:0.43.1.img
diff --git a/src/singularity_modules/kallisto/0.44.0/build.sh b/src/singularity_modules/kallisto/0.44.0/build.sh
index 10a6cc08..bf884fb9 100755
--- a/src/singularity_modules/kallisto/0.44.0/build.sh
+++ b/src/singularity_modules/kallisto/0.44.0/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/kallisto:0.44.0.sif src/singularity_modules/kallisto/0.44.0/kallisto.def && \
-singularity sign bin/kallisto:0.44.0.sif
+sudo singularity build --force bin/kallisto:0.44.0.img src/singularity_modules/kallisto/0.44.0/kallisto.def && \
+singularity sign bin/kallisto:0.44.0.img
diff --git a/src/singularity_modules/kallisto/0.44.0/kallisto b/src/singularity_modules/kallisto/0.44.0/kallisto
index b5083b6e..c5d5177f 100755
--- a/src/singularity_modules/kallisto/0.44.0/kallisto
+++ b/src/singularity_modules/kallisto/0.44.0/kallisto
@@ -1,2 +1,2 @@
#/bin/bash
-singularity exec /sps/lbmc/common/singularity/kallisto:0.44.0.sif kallisto $@
+singularity exec /sps/lbmc/common/singularity/kallisto:0.44.0.img kallisto $@
diff --git a/src/singularity_modules/macs2/2.1.2/build.sh b/src/singularity_modules/macs2/2.1.2/build.sh
index 1ca31100..260c2fef 100755
--- a/src/singularity_modules/macs2/2.1.2/build.sh
+++ b/src/singularity_modules/macs2/2.1.2/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/macs2:2.1.2.sif docker://quay.io/biocontainers/macs2:2.1.2--py27r351h14c3975_1 && \
-singularity sign bin/macs2:2.1.2.sif
+sudo singularity build --force bin/macs2:2.1.2.img docker://quay.io/biocontainers/macs2:2.1.2--py27r351h14c3975_1 && \
+singularity sign bin/macs2:2.1.2.img
diff --git a/src/singularity_modules/multiqc/1.0/build.sh b/src/singularity_modules/multiqc/1.0/build.sh
index 36f62981..4622469f 100755
--- a/src/singularity_modules/multiqc/1.0/build.sh
+++ b/src/singularity_modules/multiqc/1.0/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/multiqc:1.0.sif src/singularity_modules/multiqc/1.0/multiqc.def && \
-singularity sign bin/multiqc:1.0.sif
+sudo singularity build --force bin/multiqc:1.0.img src/singularity_modules/multiqc/1.0/multiqc.def && \
+singularity sign bin/multiqc:1.0.img
diff --git a/src/singularity_modules/multiqc/1.7/build.sh b/src/singularity_modules/multiqc/1.7/build.sh
index 7c2ae670..89176b32 100755
--- a/src/singularity_modules/multiqc/1.7/build.sh
+++ b/src/singularity_modules/multiqc/1.7/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/multiqc:1.7.sif src/singularity_modules/multiqc/1.7/multiqc.def && \
-singularity sign bin/multiqc:1.7.sif
+sudo singularity build --force bin/multiqc:1.7.img src/singularity_modules/multiqc/1.7/multiqc.def && \
+singularity sign bin/multiqc:1.7.img
diff --git a/src/singularity_modules/music/6613c53/build.sh b/src/singularity_modules/music/6613c53/build.sh
index 94b5e31a..49d7d42e 100755
--- a/src/singularity_modules/music/6613c53/build.sh
+++ b/src/singularity_modules/music/6613c53/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/music:6613c53.sif src/singularity_modules/music/6613c53/music.def && \
-singularity sign bin/music:6613c53.sif
+sudo singularity build --force bin/music:6613c53.img src/singularity_modules/music/6613c53/music.def && \
+singularity sign bin/music:6613c53.img
diff --git a/src/singularity_modules/picard/2.18.11/build.sh b/src/singularity_modules/picard/2.18.11/build.sh
index 2c985f4e..e6752395 100755
--- a/src/singularity_modules/picard/2.18.11/build.sh
+++ b/src/singularity_modules/picard/2.18.11/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/picard:2.18.11.sif src/singularity_modules/picard/2.18.11/picard.def && \
-singularity sign bin/picard:2.18.11.sif
+sudo singularity build --force bin/picard:2.18.11.img src/singularity_modules/picard/2.18.11/picard.def && \
+singularity sign bin/picard:2.18.11.img
diff --git a/src/singularity_modules/pigz/2.4/build.sh b/src/singularity_modules/pigz/2.4/build.sh
index 9c1bfee0..d5cb798f 100755
--- a/src/singularity_modules/pigz/2.4/build.sh
+++ b/src/singularity_modules/pigz/2.4/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/pigz:2.4.sif src/singularity_modules/pigz/2.4/pigz.def && \
-singularity sign bin/pigz:2.4.sif
+sudo singularity build --force bin/pigz:2.4.img src/singularity_modules/pigz/2.4/pigz.def && \
+singularity sign bin/pigz:2.4.img
diff --git a/src/singularity_modules/rsem/1.3.0/build.sh b/src/singularity_modules/rsem/1.3.0/build.sh
index de64794a..841decce 100755
--- a/src/singularity_modules/rsem/1.3.0/build.sh
+++ b/src/singularity_modules/rsem/1.3.0/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/rsem:1.3.0.sif src/singularity_modules/rsem/1.3.0/rsem.def && \
-singularity sign bin/rsem:1.3.0.sif
+sudo singularity build --force bin/rsem:1.3.0.img src/singularity_modules/rsem/1.3.0/rsem.def && \
+singularity sign bin/rsem:1.3.0.img
diff --git a/src/singularity_modules/salmon/0.8.2/build.sh b/src/singularity_modules/salmon/0.8.2/build.sh
index 42464c1c..a87d021a 100755
--- a/src/singularity_modules/salmon/0.8.2/build.sh
+++ b/src/singularity_modules/salmon/0.8.2/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/salmon:0.8.2.sif src/singularity_modules/salmon/0.8.2/salmon.def && \
-singularity sign bin/salmon:0.8.2.sif
+sudo singularity build --force bin/salmon:0.8.2.img src/singularity_modules/salmon/0.8.2/salmon.def && \
+singularity sign bin/salmon:0.8.2.img
diff --git a/src/singularity_modules/sambamba/0.6.7/build.sh b/src/singularity_modules/sambamba/0.6.7/build.sh
index fad93ead..d70f385c 100755
--- a/src/singularity_modules/sambamba/0.6.7/build.sh
+++ b/src/singularity_modules/sambamba/0.6.7/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/sambamba:0.6.7.sif src/singularity_modules/sambamba/0.6.7/sambamba.def && \
-singularity sign bin/sambamba:0.6.7.sif
+sudo singularity build --force bin/sambamba:0.6.7.img src/singularity_modules/sambamba/0.6.7/sambamba.def && \
+singularity sign bin/sambamba:0.6.7.img
diff --git a/src/singularity_modules/samblaster/0.1.24/build.sh b/src/singularity_modules/samblaster/0.1.24/build.sh
index 9a5b9fec..6761f501 100755
--- a/src/singularity_modules/samblaster/0.1.24/build.sh
+++ b/src/singularity_modules/samblaster/0.1.24/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/samblaster:0.1.24.sif src/singularity_modules/samblaster/0.1.24/samblaster.def && \
-singularity sign bin/samblaster:0.1.24.sif
+sudo singularity build --force bin/samblaster:0.1.24.img src/singularity_modules/samblaster/0.1.24/samblaster.def && \
+singularity sign bin/samblaster:0.1.24.img
diff --git a/src/singularity_modules/samtools/1.7/build.sh b/src/singularity_modules/samtools/1.7/build.sh
index 5e720251..7121a402 100755
--- a/src/singularity_modules/samtools/1.7/build.sh
+++ b/src/singularity_modules/samtools/1.7/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/samtools:1.7.sif src/singularity_modules/samtools/1.7/samtools.def && \
-singularity sign bin/samtools:1.7.sif
+sudo singularity build --force bin/samtools:1.7.img src/singularity_modules/samtools/1.7/samtools.def && \
+singularity sign bin/samtools:1.7.img
diff --git a/src/singularity_modules/sratoolkit/2.8.2/build.sh b/src/singularity_modules/sratoolkit/2.8.2/build.sh
index fd8586e3..c71c8a5f 100755
--- a/src/singularity_modules/sratoolkit/2.8.2/build.sh
+++ b/src/singularity_modules/sratoolkit/2.8.2/build.sh
@@ -1,3 +1,3 @@
#/bin/sh
-sudo singularity build --force bin/sratoolkit:2.8.2.sif src/singularity_modules/sratoolkit/2.8.2/sratoolkit.def && \
-singularity sign bin/sratoolkit:2.8.2.sif
+sudo singularity build --force bin/sratoolkit:2.8.2.img src/singularity_modules/sratoolkit/2.8.2/sratoolkit.def && \
+singularity sign bin/sratoolkit:2.8.2.img
diff --git a/src/singularity_modules/subread/1.6.4/build.sh b/src/singularity_modules/subread/1.6.4/build.sh
index 029a7d84..455172af 100755
--- a/src/singularity_modules/subread/1.6.4/build.sh
+++ b/src/singularity_modules/subread/1.6.4/build.sh
@@ -1,3 +1,3 @@
#/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
diff --git a/src/singularity_modules/tophat/2.1.1/build.sh b/src/singularity_modules/tophat/2.1.1/build.sh
index d0e21445..002911a7 100755
--- a/src/singularity_modules/tophat/2.1.1/build.sh
+++ b/src/singularity_modules/tophat/2.1.1/build.sh
@@ -1,3 +1,3 @@
#/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
diff --git a/src/singularity_modules/trimmomatic/0.36/build.sh b/src/singularity_modules/trimmomatic/0.36/build.sh
index 3b3d8728..e911a1c2 100755
--- a/src/singularity_modules/trimmomatic/0.36/build.sh
+++ b/src/singularity_modules/trimmomatic/0.36/build.sh
@@ -1,3 +1,3 @@
#/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
diff --git a/src/singularity_modules/ucsc/375/build.sh b/src/singularity_modules/ucsc/375/build.sh
index ab60035f..9546fa68 100755
--- a/src/singularity_modules/ucsc/375/build.sh
+++ b/src/singularity_modules/ucsc/375/build.sh
@@ -1,3 +1,3 @@
#/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
diff --git a/src/singularity_modules/umi_tools/1.0.0/build.sh b/src/singularity_modules/umi_tools/1.0.0/build.sh
index b9781cb9..011337df 100755
--- a/src/singularity_modules/umi_tools/1.0.0/build.sh
+++ b/src/singularity_modules/umi_tools/1.0.0/build.sh
@@ -1,3 +1,3 @@
#/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
diff --git a/src/singularity_modules/urqt/d62c1f8/build.sh b/src/singularity_modules/urqt/d62c1f8/build.sh
index 7ad1eb6c..7d8d0a1c 100755
--- a/src/singularity_modules/urqt/d62c1f8/build.sh
+++ b/src/singularity_modules/urqt/d62c1f8/build.sh
@@ -1,3 +1,3 @@
#/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
diff --git a/src/training_dataset.config b/src/training_dataset.config
index baebb4cf..98f32abe 100644
--- a/src/training_dataset.config
+++ b/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
}
}
--
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