diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index 1a2252127e23a53e0511cc743b1233ec5d558b33..7230e0a448f5e71bee117993ec421d8701118918 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: fasta_from_bed {
- container = "bedtools:2.25.0"
+ container = "lbmc/bedtools:2.25.0"
cpus = 1
}
}
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index 06b57209094a1f13ef56cec8174cc5249430014d..aca112597cee0d5b3b5147096c3420e2df1ea174 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/src/nf_modules/bowtie/indexing.config
@@ -5,7 +5,7 @@ profiles {
process {
withName: index_fasta {
cpus = 4
- container = "bowtie:1.2.2"
+ container = "lbmc/bowtie:1.2.2"
}
}
}
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index 61f40f9e4b7bdacd779a26ee496001d84bf5e18e..b3c8e31c77d95a11932c0635b36fa84fbe61a240 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/src/nf_modules/bowtie/mapping_paired.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: mapping_fastq {
- container = "bowtie:1.2.2"
+ container = "lbmc/bowtie:1.2.2"
cpus = 4
}
}
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index 61f40f9e4b7bdacd779a26ee496001d84bf5e18e..b3c8e31c77d95a11932c0635b36fa84fbe61a240 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/src/nf_modules/bowtie/mapping_single.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: mapping_fastq {
- container = "bowtie:1.2.2"
+ container = "lbmc/bowtie:1.2.2"
cpus = 4
}
}
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index 2d52dc48f5523e18a7b803374d0d28be55f99b55..597f971cd9164c188b6107e1b9c82e5ebc32e729 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/src/nf_modules/bowtie2/indexing.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: index_fasta {
- container = "bowtie2:2.3.4.1"
+ container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
}
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index 85655e48219db38ca8e2e21c7851ada62ebe9f20..10dcb684cbb6d61d6131c2d0594424c5d8444d43 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/src/nf_modules/bowtie2/mapping_paired.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: mapping_fastq {
- container = "bowtie2:2.3.4.1"
+ container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
}
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index 85655e48219db38ca8e2e21c7851ada62ebe9f20..10dcb684cbb6d61d6131c2d0594424c5d8444d43 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/src/nf_modules/bowtie2/mapping_single.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: mapping_fastq {
- container = "bowtie2:2.3.4.1"
+ container = "lbmc/bowtie2:2.3.4.1"
cpus = 4
}
}
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
index c970b5bbc084e90662d9af3766db67d40a6dcc8c..6f01a5001535d8ccf9b70d6e365ddc0f164d23e8 100644
--- a/src/nf_modules/bwa/indexing.config
+++ b/src/nf_modules/bwa/indexing.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: index_fasta {
- container = "bwa:0.7.17"
+ container = "lbmc/bwa:0.7.17"
cpus = 4
}
}
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
index af4f9683709cbe62745472fbc14d49451e1cfb09..d475bf7a76d69c96fb4a17e3e6c5c20f69c1b34f 100644
--- a/src/nf_modules/bwa/mapping_paired.config
+++ b/src/nf_modules/bwa/mapping_paired.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: mapping_fastq {
- container = "bwa:0.7.17"
+ container = "lbmc/bwa:0.7.17"
cpus = 4
}
}
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index 8add46ca97a05ec35723d7a481bd4ed4b0870a19..852779a8ca7cca7c07d90d52e761dc7c7b5df20e 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: adaptor_removal {
- container = "cutadapt:2.1"
+ container = "lbmc/cutadapt:2.1"
cpus = 1
}
}
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index 8add46ca97a05ec35723d7a481bd4ed4b0870a19..852779a8ca7cca7c07d90d52e761dc7c7b5df20e 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: adaptor_removal {
- container = "cutadapt:2.1"
+ container = "lbmc/cutadapt:2.1"
cpus = 1
}
}
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index 721d88051a7106d01eb57308460d0c27a8df40a2..3dfeb1835646c7e8067fd02277b5ef7b91fd32e3 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: trimming {
- container = "cutadapt:2.1"
+ container = "lbmc/cutadapt:2.1"
cpus = 1
}
}
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index 721d88051a7106d01eb57308460d0c27a8df40a2..3dfeb1835646c7e8067fd02277b5ef7b91fd32e3 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: trimming {
- container = "cutadapt:2.1"
+ container = "lbmc/cutadapt:2.1"
cpus = 1
}
}
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
index 5be6a4cbeff21f70c6ccb314b7ded8e03af73b9d..b5276da8d418c7ad2404803a7275075e188e2bac 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ b/src/nf_modules/deeptools/bam_to_bigwig.config
@@ -4,11 +4,11 @@ profiles {
docker.enabled = true
process {
withName: index_bam {
- container = "sambamba:0.6.7"
+ container = "lbmc/sambamba:0.6.7"
cpus = 4
}
withName: bam_to_bigwig {
- container = "deeptools:3.0.2"
+ container = "lbmc/deeptools:3.0.2"
cpus = 4
}
}
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index b09867699daf264e2b5c33d103243cf7f4d30e82..55c03e3f12166d0c7fe3a4b93e90e075454a83f9 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/src/nf_modules/deeptools/compute_matrix.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: compute_matrix {
- container = "deeptools:3.0.2"
+ container = "lbmc/deeptools:3.0.2"
cpus = 4
}
}
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index e9fe1504b5f9dc17d337ea04a5c16240820653d9..2dd2466506b53f3f7d420f3fabd0222b899b36ad 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/src/nf_modules/deeptools/plot_profile.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: plot_profile {
- container = "deeptools:3.0.2"
+ container = "lbmc/deeptools:3.0.2"
cpus = 4
}
}
diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config
index df041cb9df4262756b3701b9b291419abd88a643..c8a289fad4885c1987a8637c441a532ab71b1f39 100644
--- a/src/nf_modules/fastp/fastp_paired.config
+++ b/src/nf_modules/fastp/fastp_paired.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: fastp_fastq {
- container = "fastp:0.19.7"
+ container = "lbmc/fastp:0.19.7"
cpus = 1
}
}
diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config
index df041cb9df4262756b3701b9b291419abd88a643..c8a289fad4885c1987a8637c441a532ab71b1f39 100644
--- a/src/nf_modules/fastp/fastp_single.config
+++ b/src/nf_modules/fastp/fastp_single.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: fastp_fastq {
- container = "fastp:0.19.7"
+ container = "lbmc/fastp:0.19.7"
cpus = 1
}
}
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
index 2ed15c542eef76cc7c0ed7fdcaa9ce9bc6dc4613..1c02c54830961ec16aec0f0e37c0127e31df1ed6 100644
--- a/src/nf_modules/fastqc/fastqc_paired.config
+++ b/src/nf_modules/fastqc/fastqc_paired.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: fastqc_fastq {
- container = "fastqc:0.11.5"
+ container = "lbmc/fastqc:0.11.5"
cpus = 1
}
}
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
index 2ed15c542eef76cc7c0ed7fdcaa9ce9bc6dc4613..1c02c54830961ec16aec0f0e37c0127e31df1ed6 100644
--- a/src/nf_modules/fastqc/fastqc_single.config
+++ b/src/nf_modules/fastqc/fastqc_single.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: fastqc_fastq {
- container = "fastqc:0.11.5"
+ container = "lbmc/fastqc:0.11.5"
cpus = 1
}
}
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
index d97e7c7490044ab754a995d30fd949d40306e827..db0217aa45eb268ef4516a9c7853a311dcdaa96c 100644
--- a/src/nf_modules/hisat2/indexing.config
+++ b/src/nf_modules/hisat2/indexing.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: index_fasta {
- container = "hisat2:2.1.0"
+ container = "lbmc/hisat2:2.1.0"
cpus = 4
}
}
diff --git a/src/nf_modules/hisat2/mapping_paired.config b/src/nf_modules/hisat2/mapping_paired.config
index c0b9c8085f558a6733b001b339565dbc40a57ac3..d496d8608fa3c7791eaf6171a78e9e80cf07201f 100644
--- a/src/nf_modules/hisat2/mapping_paired.config
+++ b/src/nf_modules/hisat2/mapping_paired.config
@@ -5,7 +5,7 @@ profiles {
process {
withName: mapping_fastq {
cpus = 4
- container = "hisat2:2.1.0"
+ container = "lbmc/hisat2:2.1.0"
}
}
}
diff --git a/src/nf_modules/hisat2/mapping_single.config b/src/nf_modules/hisat2/mapping_single.config
index c0b9c8085f558a6733b001b339565dbc40a57ac3..d496d8608fa3c7791eaf6171a78e9e80cf07201f 100644
--- a/src/nf_modules/hisat2/mapping_single.config
+++ b/src/nf_modules/hisat2/mapping_single.config
@@ -5,7 +5,7 @@ profiles {
process {
withName: mapping_fastq {
cpus = 4
- container = "hisat2:2.1.0"
+ container = "lbmc/hisat2:2.1.0"
}
}
}
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index a04f0851f357f7f3cf7f71acab1602f973d6d7a4..d20648c740c0ea0538ff20ec70b13bc02b1e9a12 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/src/nf_modules/htseq/htseq.config
@@ -4,11 +4,11 @@ profiles {
docker.enabled = true
process {
withName: sort_bam {
- container = "samtools:1.7"
+ container = "lbmc/samtools:1.7"
cpus = 1
}
withName: counting {
- container = "htseq:0.11.2"
+ container = "lbmc/htseq:0.11.2"
cpus = 1
}
}
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index b677b616e70579432463360369e9f7bfd45ee305..5b126bbe50713c058be01968e1cebe144e492443 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withNamek index_fasta {
- container = "kallisto:0.44.0"
+ container = "lbmc/kallisto:0.44.0"
cpus = 4
}
}
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index 620e506d463f56e03aa9baaa566037dda1a047f6..7680223470d6fad16917d6786252264dc32d0844 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: mapping_fastq {
- container = "kallisto:0.44.0"
+ container = "lbmc/kallisto:0.44.0"
cpus = 4
}
}
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index 620e506d463f56e03aa9baaa566037dda1a047f6..7680223470d6fad16917d6786252264dc32d0844 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: mapping_fastq {
- container = "kallisto:0.44.0"
+ container = "lbmc/kallisto:0.44.0"
cpus = 4
}
}
diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config
index 8e3965f8666807fe531eb0ad2d005aa4000e5442..18b639e7d5c14fd07a75c54a97186823eb772a97 100644
--- a/src/nf_modules/macs2/peak_calling.config
+++ b/src/nf_modules/macs2/peak_calling.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: peak_calling {
- container = "macs2:2.1.2"
+ container = "lbmc/macs2:2.1.2"
cpus = 4
}
}
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index 1825a1355594ec0cc3aadbd8007f4cf271a3ba67..53442413b98e69e316ada977f08cc04a64efed05 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -5,11 +5,11 @@ profiles {
docker.enabled = true
process {
withName: fastqc_fastq {
- container = "fastqc:0.11.5"
+ container = "lbmc/fastqc:0.11.5"
cpus = 1
}
withName: multiqc {
- container = "multiqc:1.7"
+ container = "lbmc/multiqc:1.7"
cpus = 1
}
}
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index 6a2edfb6a7f3b2349ac4042ca94b0bdd44aa8a33..a52a9a4174753ee34628779fbd3abfacbde4f4c8 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -4,11 +4,11 @@ profiles {
docker.enabled = true
process {
withName: fastqc_fastq {
- container = "fastqc:0.11.5"
+ container = "lbmc/fastqc:0.11.5"
cpus = 1
}
withName: multiqc {
- container = "multiqc:1.7"
+ container = "lbmc/multiqc:1.7"
cpus = 1
}
}
diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config
index dc46d8c8281d8ce74a2ff2733df4864ec33e1529..613fdc4d6cdfe3e0778b538ceea46373ecb15501 100644
--- a/src/nf_modules/music/peak_calling_single.config
+++ b/src/nf_modules/music/peak_calling_single.config
@@ -4,15 +4,15 @@ profiles {
docker.enabled = true
process {
withName: compute_mappability {
- container = "music:6613c53"
+ container = "lbmc/music:6613c53"
cpus = 1
}
withName: music_preprocessing {
- container = "music:6613c53"
+ container = "lbmc/music:6613c53"
cpus = 1
}
withName: music_computation{
- container = "music:6613c53"
+ container = "lbmc/music:6613c53"
cpus = 1
}
}
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
index d58a310d88e5d160f597f15afc884b4dcc10fcec..602f8319a647711507b5f11be59353d8f8355ac5 100644
--- a/src/nf_modules/rsem/indexing.config
+++ b/src/nf_modules/rsem/indexing.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: index_fasta {
- container = "rsem:1.3.0"
+ container = "lbmc/rsem:1.3.0"
cpus = 4
}
}
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
index 75aae6edaa335d8a0cc1f6405b0c35d4be1800d8..9a2f21015b3bbb4959f3b7fa673f2ecd9fea981d 100644
--- a/src/nf_modules/rsem/quantification_paired.config
+++ b/src/nf_modules/rsem/quantification_paired.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: mapping_fastq {
- container = "rsem:1.3.0"
+ container = "lbmc/rsem:1.3.0"
cpus = 4
}
}
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
index 75aae6edaa335d8a0cc1f6405b0c35d4be1800d8..9a2f21015b3bbb4959f3b7fa673f2ecd9fea981d 100644
--- a/src/nf_modules/rsem/quantification_single.config
+++ b/src/nf_modules/rsem/quantification_single.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: mapping_fastq {
- container = "rsem:1.3.0"
+ container = "lbmc/rsem:1.3.0"
cpus = 4
}
}
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index 9199b7a4d958830dddd269764ceebc0d0993def3..6de14fb09a50c5668b72afeaa82b202ee931d1e6 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: index_bam {
- container = "sambamba:0.6.9"
+ container = "lbmc/sambamba:0.6.9"
cpus = 4
}
}
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index 0a71fc389f479c3597b7cf53751348aab7e70448..ed485d3ea604f3bfc5b7f447da6c6ed2d54eb319 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: sort_bam {
- container = "sambamba:0.6.9"
+ container = "lbmc/sambamba:0.6.9"
cpus = 4
}
}
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index 8a3e4ab57c962728c577778a1f155e69ce8e60c3..78752eddd679dbb81bd23e3ad748c7f0280b2666 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: split_bam {
- container = "sambamba:0.6.9"
+ container = "lbmc/sambamba:0.6.9"
cpus = 4
}
}
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index 7fd05167e1565fdd54716481d08e970172dc1a72..e850a3fff71c0b9a30f6a52c10fc73aa1121001e 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: dedup_sam {
- container = "samblaster:0.1.24"
+ container = "lbmc/samblaster:0.1.24"
cpus = 4
}
}
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
index fc7a216c9a8bb175a4a427ead760d1e32e30bf56..53b8e45f1b2671c386632a59c8e6a1067d422f40 100644
--- a/src/nf_modules/samtools/filter_bams.config
+++ b/src/nf_modules/samtools/filter_bams.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: filter_bam {
- container = "samtools:1.7"
+ container = "lbmc/samtools:1.7"
cpus = 4
}
}
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
index 8b910b604136284756c752065f49a8c1705ddaa7..692cd174369a32c3229f8becb680a9da1efb43f3 100644
--- a/src/nf_modules/samtools/index_bams.config
+++ b/src/nf_modules/samtools/index_bams.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: index_bam {
- container = "samtools:1.7"
+ container = "lbmc/samtools:1.7"
cpus = 1
}
}
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
index d5e06e31e6ee28efd21c698133604e0cb5188b1f..9955a3532c199e719d0c3939cc6824006f8205a8 100644
--- a/src/nf_modules/samtools/sort_bams.config
+++ b/src/nf_modules/samtools/sort_bams.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: sort_bam {
- container = "samtools:1.7"
+ container = "lbmc/samtools:1.7"
cpus = 4
}
}
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
index c145bf33c4441a84c413eeba43dcce45ea2a5c1e..fcb6c20c1e9c317090c919d0ff7489d1c313e8ad 100644
--- a/src/nf_modules/samtools/split_bams.config
+++ b/src/nf_modules/samtools/split_bams.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: split_bam {
- container = "samtools:1.7"
+ container = "lbmc/samtools:1.7"
cpus = 2
}
}
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
index ee6ed1fa378034ef2bccb1e643cab9cfb7e3ea5d..d6c5b48a3b0cd3f69ebb48a0fc5556afd3a6dbf7 100644
--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ b/src/nf_modules/sratoolkit/fastqdump.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: fastq_dump {
- container = "sratoolkit:2.8.2"
+ container = "lbmc/sratoolkit:2.8.2"
cpus = 1
}
}
diff --git a/src/nf_modules/subread/subread.config b/src/nf_modules/subread/subread.config
index 19f20463dd9f908edd35771ad578e2dc7be0e6d0..e9debde156a26b92faa0f6aa2b8e1b376abfc45c 100644
--- a/src/nf_modules/subread/subread.config
+++ b/src/nf_modules/subread/subread.config
@@ -4,11 +4,11 @@ profiles {
docker.enabled = true
process {
withName: sort_bam {
- container = "samtools:1.7"
+ container = "lbmc/samtools:1.7"
cpus = 1
}
withName: counting {
- container = "subread:1.6.4"
+ container = "lbmc/subread:1.6.4"
cpus = 1
}
}
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index dbe4e11ccc1d77caf8fa3f346c344eeca27ae4f7..3e9227c8c2792acdcb369c353cdcf25a28d72b3d 100644
--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -5,7 +5,7 @@ profiles {
process {
withName: trimming {
cpus = 4
- container = "urqt:d62c1f8"
+ container = "lbmc/urqt:d62c1f8"
}
}
}
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index 016d65033739a5b850f368ef00a98c94a513f449..34bf633bbc7a1e1db4f41bb10542826eb7a8b3e5 100644
--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -4,7 +4,7 @@ profiles {
docker.enabled = true
process {
withName: trimming {
- container = "urqt:d62c1f8"
+ container = "lbmc/urqt:d62c1f8"
cpus = 4
}
}