docker: change config file to use lbmc/ docker repository

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
       }
     }

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"
       }
     }
   }

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
       }
     }

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
       }
     }

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
       }
     }

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
       }
     }

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
       }
     }

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
       }
     }

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
       }
     }

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
       }
     }

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
       }
     }

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
       }
     }

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
       }
     }

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
       }
     }

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
       }
     }

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
       }
     }

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
       }
     }

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
       }
     }

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
       }
     }

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
       }
     }