diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index 1875f439afb83ec770c22556d488024135cfda53..d0502f572f9af375dbb0de6c146b68a69d14aee0 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 715847fb1031980d9bb7a4ef6ebd14a366cce717..c55891bc0258987c293bad3255620b994ce12644 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 0936530df60624419e4682d686d10ea873f44a32..28ce647adc1887832efb0035b9c59adce4bb8307 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 0936530df60624419e4682d686d10ea873f44a32..28ce647adc1887832efb0035b9c59adce4bb8307 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 3d0da943a3a54a33c845e8ef042d7c95946cf69f..6a9d607102705bf3fd72b8ec55d70a62779ce762 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 54410c46293bde9d1ac2a1e75366de06abd317f9..63ba18af26d8973f09f63693e3a3eb16691eac0e 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 54410c46293bde9d1ac2a1e75366de06abd317f9..63ba18af26d8973f09f63693e3a3eb16691eac0e 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 f391241a8848c8d91e1b4ce0e4089d27196cc05e..cae101a51a4adc1f118d7321aa92db9d1630156a 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 700b1983129258bd2419287862acce50a8bdf0c4..e3ff6728be10872184b86554afdaf563891b41df 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 46e4004354b8f4b988c19ffcd077f8d8b3884c04..fefbf0dd262dfc968f9c52a60d96644e9bd07b00 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 46e4004354b8f4b988c19ffcd077f8d8b3884c04..fefbf0dd262dfc968f9c52a60d96644e9bd07b00 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 b3c32aab3df3e41bc4775c9f84662bfa301436da..cc3e9422fa8e05d9a2c67821d0dff51489a7f5f8 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 b3c32aab3df3e41bc4775c9f84662bfa301436da..cc3e9422fa8e05d9a2c67821d0dff51489a7f5f8 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 209ae8c924bf15bd24b010b0b8a3eec393da72e0..452ca1c338ae072a84f6f5863bc49fc45e38dabf 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 471dde0a4ba33b022b46bd6ee4c3bf246bc0a40d..73309d65df3121c016a40fd5a9f14f181bb8aad5 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 306f3a90156b367c72301e0f2973fe8538d80e7d..9f3ce971b921757a5a9abdff1753b1a6e0800602 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 561a3afa0d4aea85daaf76ea2d2bf0f488cce718..295d1835c536ed458e0b0921e1bbf9a55420b18e 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 561a3afa0d4aea85daaf76ea2d2bf0f488cce718..295d1835c536ed458e0b0921e1bbf9a55420b18e 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 9e75046a9c9a7f0d1e9e6f62d266a3c857ba67c3..08cc9b1b79204a178d9a1bb7880b1eddb7e66935 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 9e75046a9c9a7f0d1e9e6f62d266a3c857ba67c3..08cc9b1b79204a178d9a1bb7880b1eddb7e66935 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 b259633a356075cabc4a621d7b13b1a683cc4db7..22f41f8d0e42a89b7967d414ad616e5982df2526 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 02c92edfdf20563dc0114608af27072c0c68c023..370f5892c4b01e600cc403abf95fa2ef07811d79 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 02c92edfdf20563dc0114608af27072c0c68c023..370f5892c4b01e600cc403abf95fa2ef07811d79 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 30646614ba5baef156f337ca61b4061cc4031b49..bd55d6a6ab5a546f68ce748ab20ff9795c9c5037 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 35dffe6716c12fb95f2ed7a9350b36a21b98509b..403d94263b80aecdf743250d93d0bc68f63554da 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 ef4991498ca24bbb1d8ff14b28c93b2efbaa0bf4..a8c439b950c294cc3ebad6ed0855e5dfd697f1d6 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 ef4991498ca24bbb1d8ff14b28c93b2efbaa0bf4..a8c439b950c294cc3ebad6ed0855e5dfd697f1d6 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 8462ab8651cbbeb0b23d3cc213d6f9142be5e5c0..fe712a6a5fc2036cfd236266228a542d41bcfa9d 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 aaa32da19c1ef5b6b3a0108cf97a54e7ac191e71..c6af20124ed843db63b2c9a36f63f37fc174c38a 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 bdf605046e60e22feb08e8a332a69c5834332570..42d1406c8223b98d22e9fa87b4585578662ffb5e 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 d21fe81da5cee0f002abba1993293c789cc50f86..cf15eab2fdf2632257ce95124490ae7db7637bcf 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 aeea35fe8614f890077faaba3fb65bef3cc216bb..d0aea31710b4a652c8bb673969395a4f49ccb29c 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 812167ed15e95cea57dbc0e7d4540df942bcc733..035db80fa396f1c07cef03e2b142ed0e5902bc12 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 812167ed15e95cea57dbc0e7d4540df942bcc733..035db80fa396f1c07cef03e2b142ed0e5902bc12 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 8cbbd24b2129f2ec3a52acaedba253f17f34160c..06c3fcc5ea2074ee69b44ccf96167581b7afec2f 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 11811d97cfa36527c48414459c4be7d3cdf20d82..73f2bcd16faf8a52847acb3061dbfcc96f45c029 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 6df50fc7397bf2e76ef75531f77c361b98435dc9..95173ec226c71587b30f62a015fbf45bc0d34279 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 75efda223362e7f0d6594bc4e3c339f2b3c9857f..c7e1525c483efdccf1ecd9cea73f055159f69845 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 87d99007b08d77f57d5edf576ff288da1f78ec99..2b3a814aeeb8a98e79c4018876ecb5cf6d123ab7 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 762773b473e61d7d863c344dad284b38c50f1f31..5cec951ba634f96dbca2aa121497b2df57a11cfb 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 63c23123cb2798e306d1163bd3999c0922726f04..9f420077d2877a8d4f89873d835ebe0e703b640d 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 de924648525a4b23e4717102f8c566338d895a25..91b2f1ac1c69bc9ec8788f0db291a16cbfb96e73 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 2fc5039ff3fae99cbbc5bf5af69456834188d4b1..043a378494ccebf2351db163a87cc69ee632844a 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 f0b084b8e3048736787d405678edf1e7db7a2577..cd6a51517d4326eaf640e414013ad608010c0d7e 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 02788fcb559b010c2856920828b0f651de215d11..237737cfda805d4a970d553a794c3dd1a8e3a593 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 bee821bdc4f9791ea199ffe11a72643f745ce26d..96ecae5578d87feea685b260167cfeb1056989e4 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 60644b467833cde7327376293de5700d95358081..936a71be2f68a8f06061216dad3f2448f38f596e 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 3f8adc0419f1556b31a349761e8b6bd995181ea4..be5a5098f61c617db40b2e9f5bacb7299a9fafcd 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 3470fca0a1764c0fb4eda3f57097328563c05dc4..a5a5c54de96ed09e45b17b33ee218a906483b192 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 f9f58ae6044cf3241d16974e06a19678ccaad710..c01beabb54124f4b9f5d79a8410330e8206e56b5 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 a340c5f8698caf67031934f912fad2cb45d22578..0392a0c13c69399a0c95f8e838dc2114113a27f7 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 591cb660b7b84e69eb4ec1acbc3ba04de0d2baf4..78805dac402711a96131cffef808fb01d3e63b70 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 5327f7c468b5e3a800f42d46e89ae6f1bcafa2c4..0369e0dfd33740fd7c6ad99eda36ac3bb9f5ec16 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 c002354b7e4c92bf9a03e7fafe89214f74a98012..95883b041fe741e6482d3dbaec4078b7b453046c 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 fdb8c4d03a336ce6bcc1856d4cade58c2284ecd8..5a7070ec2e72a3cae9276d8a208dcba1dcd7a0eb 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 9e59a81d43cae27b5278dc5cc18a39016ab8c8e1..2ffc99376f780286b44fc2ad5015cb7da14dc5ad 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 b9210571f8a0e2e0bdbb4fd837db41261ed4984e..78304343c115bb7eaa3773e1ee16eea3de700bf0 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 01a0d8121ac842dc84113b94aa6a6f7c1ca4c043..58127ff089d25f62c22269a935e630749efc3356 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 b3983367f70e5b7aa19b699d81dd0198b2b9c4da..ef313d4e3bd1a19519227c5677c8bfa7ca4bf927 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 17122f2430e98679a97d1eaadfdacbc0a980a346..b48ae449778ba2afe084269b3eb50e645f5067f2 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 5158959fe830919751ce2906eddea4c29e99444e..87e095b7ad5eba073b4b5d92ad50f865889a7df8 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 e2b18756a8540739fa815f1ff3e3b4960b3e803b..4ba74ed48f773c6cd96c580e5d0031e6f33af320 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 074f4ce61f6e8e6f98d7c496d9c42b5b72ac5311..5a23a14463d2463fc2f8bd6a52330468daecfa55 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 1c3c8170a944815df67c3157123737e7839cc10a..116d41a811b1dfc384b65e146c50ec91f0a2eae5 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 73b14c96de04064668445e3c309eddd4df269d67..19aed8a6cbf1be1e9534ca2344a9462e012f87fe 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 8ecfe6e4b7121c57a6c03d72f149a6eca29c7f37..1a83c7c621874535db355448941b98710cad8d97 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 10a6cc0815f13d40ecb5a7f7919df27ffabc7fb3..bf884fb987b05902e653cde3a4e119c3d5f1d0a0 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 b5083b6e74a2284856e719ce129ca71f3500095a..c5d5177fad1a9ad70886eb849c1cf57f71f7bbd2 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 1ca311007fed8ba5497328078d7891b69efc5277..260c2fef9d41210d65221c8eaf6931aed1e04569 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 36f629810e3a7af6b5fae1904fa9f2f15a8b8e19..4622469f01cc28bbf86a3003d9035c71e407b71f 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 7c2ae6706849dff18a1fc20648d1146dbae74270..89176b32c0ceb1dd974c5445d3988bfadecf4ff0 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 94b5e31a1735262c32af79c281ddcccfb25702fb..49d7d42e6eb9491f31be809f6cf1db63454efda1 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 2c985f4e7ba9e7c1d74eef126c5597edde831235..e6752395713ba40fbefc0b54b7fed9e78512a7b9 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 9c1bfee094062d8c9b1d40965d7a6ac5924958c1..d5cb798fc49422c3d53b8609131884c7eabf3eb7 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 de64794a33d098c07e4f959679af258e48eb462d..841decceb4c7e47c070373d5d878b264a0d3a751 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 42464c1c83e52c9260679edeef33ccc9faab07c8..a87d021ad9a5a2d29ec522aef105b907f7243b7e 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 fad93ead5827ff2fe6aadd0504a43d11ede728e6..d70f385c79942e53bf9bee5ca40bac87469b994c 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 9a5b9fecc61d3a78de5a0d18a4b73baa7c2004a1..6761f50108b43bace04b6d1a11a0b8cb74ef6e70 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 5e720251c9994a202703928605b323f19d51387c..7121a402411b0375e2f0074bb61e07ddc45bae8e 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 fd8586e38a57fbb56262a081215ce95070c555e1..c71c8a5f7da1f911f602d849b4f9cdd112c00421 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 029a7d84e5bd22e314eb2fa7d912b2771af66ac8..455172afb856a4044319267226fbe90e2e707dd9 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 d0e2144537fd3f9a09180a92f6a2b74961e4f85b..002911a76f89fc08aed5d83f6f62d3eb0b95f5ad 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 3b3d8728817016dd928bca2a10c8b45743ad7d70..e911a1c2d30b59da8274ef0fd7217c709864880a 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 ab60035f4e9f3bfa9b33a221c348c4b7de02538b..9546fa685da95b8d6fe7090cedb2173fdb9669dd 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 b9781cb9d59992321bcb07fe82329e99674f9e08..011337df0d6dd979474c65a8aab271e1dda8dc64 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 7ad1eb6c41f15b94e7fb8294e34984a53d6f9c19..7d8d0a1c2e292a545166c04207d4b59c3669861d 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 baebb4cf2fcebc4001c04c5f53842a3b74ebbf27..98f32abedf02fa385b0b8bf8bc2223e7a8e3bad3 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
}
}