diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index 220cdce3419562f18858cc73be58157e901dac8d..41c1dac9c0b9d177d14fb72448668a007935751d 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -52,8 +52,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: fasta_from_bed {
+ container = "/sps/lbmc/common/singularity/bedtools:2.25.0.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index e1b0262d050bbf2799ffda390eacb44a1ad7386a..73217f9acad643d3e4f6ddec51ae86ab0af77f21 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/src/nf_modules/bowtie/indexing.config
@@ -54,7 +54,7 @@ profiles {
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ container = "/sps/lbmc/common/singularity/bowtie:1.2.2.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index d24ba5d8a6cdee52b50027ea59b5c639480aab63..44ab8bcbae3895d5671ecff3d641f3b6a405fb85 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/src/nf_modules/bowtie/mapping_paired.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: mapping_fastq {
+ container = "/sps/lbmc/common/singularity/bowtie:1.2.2.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index d24ba5d8a6cdee52b50027ea59b5c639480aab63..44ab8bcbae3895d5671ecff3d641f3b6a405fb85 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/src/nf_modules/bowtie/mapping_single.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: mapping_fastq {
+ container = "/sps/lbmc/common/singularity/bowtie:1.2.2.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index 98b7cdac14765aea04a052599b22c9e238e9802b..20487563f1931d316ddd4ea266f33ef21a7fae51 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/src/nf_modules/bowtie2/indexing.config
@@ -54,7 +54,7 @@ profiles {
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ container = "/sps/lbmc/common/singularity/bowtie2:2.3.4.1.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index 7d8e543f0abf1b898484739b99cd26d90166481d..7874ae45bd8965e6d763a48d79eb1424b11b3bb6 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/src/nf_modules/bowtie2/mapping_paired.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: mapping_fastq {
+ container = "/sps/lbmc/common/singularity/bowtie2:2.3.4.1.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index 7d8e543f0abf1b898484739b99cd26d90166481d..7874ae45bd8965e6d763a48d79eb1424b11b3bb6 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/src/nf_modules/bowtie2/mapping_single.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: mapping_fastq {
+ container = "/sps/lbmc/common/singularity/bowtie2:2.3.4.1.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
index 89574aa8bd1bb0c3fd658a2e73103a239544048a..72274ad40def0a40ced26cbe604a8890051c604f 100644
--- a/src/nf_modules/bwa/indexing.config
+++ b/src/nf_modules/bwa/indexing.config
@@ -54,7 +54,7 @@ profiles {
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ container = "/sps/lbmc/common/singularity//bwa:0.7.17.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
index 4f013608bd6530836ea03c9db9b5c756c78ae385..a3e5c6282833019f29879ac01d3b450e819633e2 100644
--- a/src/nf_modules/bwa/mapping_paired.config
+++ b/src/nf_modules/bwa/mapping_paired.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: mapping_fastq {
+ container = "/sps/lbmc/common/singularity/bwa:0.7.17.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index 7317fb7b29a512c9c95c51b7a5792bd1e8aab5e5..e58c385a19462b9ffe19816ee1e3e68599c5f47e 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -52,8 +52,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: adaptor_removal {
+ container = "/sps/lbmc/common/singularity/cutadapt:2.1.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index 7317fb7b29a512c9c95c51b7a5792bd1e8aab5e5..e58c385a19462b9ffe19816ee1e3e68599c5f47e 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -52,8 +52,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: adaptor_removal {
+ container = "/sps/lbmc/common/singularity/cutadapt:2.1.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index f201a5719c6e2d08f17dc3dedc958d5d3a3a441d..9b49fcee87d3de5d362d861671de26f326d711ed 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -52,8 +52,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: trimming {
+ container = "/sps/lbmc/common/singularity/cutadapt:2.1.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index f201a5719c6e2d08f17dc3dedc958d5d3a3a441d..9b49fcee87d3de5d362d861671de26f326d711ed 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -52,8 +52,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: trimming {
+ container = "/sps/lbmc/common/singularity/cutadapt:2.1.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index 66be28dd24c4092466f55eb15b392b709ab9d2bc..fb1cd0483b4d9a7a9192e11696c1a93149c5af45 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/src/nf_modules/deeptools/compute_matrix.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: compute_matrix {
+ container = "/sps/lbmc/common/singularity/deeptools:3.0.2.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index bb1feb2e709b48911185b75bcfb0e6f6cc23e926..08d20977b90e7395f3e4691aa420d1ef96fd23a5 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/src/nf_modules/deeptools/plot_profile.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: plot_profile {
+ container = "/sps/lbmc/common/singularity/deeptools:3.0.2.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config
index 67af9be59231f40d553a13f0eb4c24f87006bf12..7d9c83e45cf27d1819728e34818179a281756d1e 100644
--- a/src/nf_modules/fastp/fastp_paired.config
+++ b/src/nf_modules/fastp/fastp_paired.config
@@ -52,8 +52,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: fastp_fastq {
+ container = "/sps/lbmc/common/singularity/fastp:0.19.7.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config
index 67af9be59231f40d553a13f0eb4c24f87006bf12..7d9c83e45cf27d1819728e34818179a281756d1e 100644
--- a/src/nf_modules/fastp/fastp_single.config
+++ b/src/nf_modules/fastp/fastp_single.config
@@ -52,8 +52,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: fastp_fastq {
+ container = "/sps/lbmc/common/singularity/fastp:0.19.7.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
index 70c9b99628065576415c11f11031fae165185355..6e9dcaf7a72af01b35500485568cf0b15886b0aa 100644
--- a/src/nf_modules/fastqc/fastqc_paired.config
+++ b/src/nf_modules/fastqc/fastqc_paired.config
@@ -52,8 +52,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: fastqc_fastq {
+ container = "/sps/lbmc/common/singularity/fastqc:0.11.5.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
index 70c9b99628065576415c11f11031fae165185355..6e9dcaf7a72af01b35500485568cf0b15886b0aa 100644
--- a/src/nf_modules/fastqc/fastqc_single.config
+++ b/src/nf_modules/fastqc/fastqc_single.config
@@ -52,8 +52,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: fastqc_fastq {
+ container = "/sps/lbmc/common/singularity/fastqc:0.11.5.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
index c3784d3132cde31b73bb0d57a3f38f619a4ff0c6..6d39e60ac10ae949693ac487b996e731cb7acf74 100644
--- a/src/nf_modules/hisat2/indexing.config
+++ b/src/nf_modules/hisat2/indexing.config
@@ -54,7 +54,7 @@ profiles {
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ container = "/sps/lbmc/common/singularity/hisat2:2.1.0.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/hisat2/mapping_paired.config b/src/nf_modules/hisat2/mapping_paired.config
index 993ef10b16b725e0e8b00b4abdc7b4c40da6f17b..97b4807dc83054b2bd17a31205887e7ebe408141 100644
--- a/src/nf_modules/hisat2/mapping_paired.config
+++ b/src/nf_modules/hisat2/mapping_paired.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: mapping_fastq {
+ container = "/sps/lbmc/common/singularity/hisat2:2.1.0.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/hisat2/mapping_single.config b/src/nf_modules/hisat2/mapping_single.config
index 993ef10b16b725e0e8b00b4abdc7b4c40da6f17b..97b4807dc83054b2bd17a31205887e7ebe408141 100644
--- a/src/nf_modules/hisat2/mapping_single.config
+++ b/src/nf_modules/hisat2/mapping_single.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: mapping_fastq {
+ container = "/sps/lbmc/common/singularity/hisat2:2.1.0.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index 7349c5f04d0fc638ae053a8739251120e85ef720..09b368ae47a9f29ad42cc7ae6a0f2dae548034e6 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/src/nf_modules/htseq/htseq.config
@@ -78,8 +78,19 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: sort_bam {
+ container = "/sps/lbmc/common/singularity/samtools:1.7.img"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
+ cpus = 1
+ queue = 'huge'
+ }
+ withName: counting {
+ container = "/sps/lbmc/common/singularity/htseq:0.11.2.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index 2599af596033ba29a0df72ba7b6783f1cd107450..801dfdc17bcba182fc6894b07ce55c1eeb03dc03 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -53,7 +53,7 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
+ withName: mapping_fastq {
container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index 2599af596033ba29a0df72ba7b6783f1cd107450..801dfdc17bcba182fc6894b07ce55c1eeb03dc03 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -53,7 +53,7 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
+ withName: mapping_fastq {
container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config
index d5223cd11c15e691b1eb82fb9d51af7b682a65d2..93697c70ce2f6179f5ec8ac4f39ce6ca6b3acf6a 100644
--- a/src/nf_modules/macs2/peak_calling.config
+++ b/src/nf_modules/macs2/peak_calling.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: peak_calling {
+ container = "/sps/lbmc/common/singularity/macs2:2.1.2.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index 813b55e29eee267f31fc605ae06f2588ce5207dc..86ead2c4f4a1a29e1164b7ea5ab870cead90f496 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -87,8 +87,19 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: fastq_fastqc {
+ container = "/sps/lbmc/common/singularity/fastqc:0.11.5.img"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
+ cpus = 1
+ queue = 'huge'
+ }
+ withName: multiqc {
+ container = "/sps/lbmc/common/singularity/multiqc:1.7.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index 304ea3e08b400045c9b108a0aa4fb9c7dce0f298..e296853fb7d7addfbfc1e22a6c483a85b9ac8427 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -86,8 +86,19 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: fastq_fastqc {
+ container = "/sps/lbmc/common/singularity/fastqc:0.11.5.img"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
+ cpus = 1
+ queue = 'huge'
+ }
+ withName: multiqc {
+ container = "/sps/lbmc/common/singularity/multiqc:1.7.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config
index 64a55bd0b53a335a17a989983501a9417f355852..972de3d7961ba73e4a38521e940a3a9891e1525a 100644
--- a/src/nf_modules/music/peak_calling_single.config
+++ b/src/nf_modules/music/peak_calling_single.config
@@ -112,8 +112,30 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: compute_mappability {
+ container = "/sps/lbmc/common/singularity/music:6613c53.img"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
+ cpus = 1
+ queue = 'huge'
+ }
+ withName: music_preprocessing {
+ container = "/sps/lbmc/common/singularity/music:6613c53.img"
+ scratch = true
+ stageInMode = "copy"
+ stageOutMode = "rsync"
+ executor = "sge"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
+ cpus = 1
+ queue = 'huge'
+ }
+ withName: music_computation {
+ container = "/sps/lbmc/common/singularity/music:6613c53.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
index 1149d299a8d52923da7dc6e7aa7369cfc7a92dbb..b9de25369f632eaf3607339be219a9d0667feb3e 100644
--- a/src/nf_modules/rsem/indexing.config
+++ b/src/nf_modules/rsem/indexing.config
@@ -54,7 +54,7 @@ profiles {
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ container = "/sps/lbmc/common/singularity/rsem:1.3.0.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
index 3519333078b1d0713ddcd42214173fba6eec9718..03152ccaf28ebc6aa76e6f4f2dd582913ce169f7 100644
--- a/src/nf_modules/rsem/quantification_paired.config
+++ b/src/nf_modules/rsem/quantification_paired.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: mapping_fastq {
+ container = "/sps/lbmc/common/singularity/rsem:1.3.0.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
index 3519333078b1d0713ddcd42214173fba6eec9718..03152ccaf28ebc6aa76e6f4f2dd582913ce169f7 100644
--- a/src/nf_modules/rsem/quantification_single.config
+++ b/src/nf_modules/rsem/quantification_single.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: mapping_fastq {
+ container = "/sps/lbmc/common/singularity/rsem:1.3.0.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index 7055c98c5be5516493b5ea8d52ac7c7038936e6d..cb3d4308e153f4bdea2d63bc41b359e679e8a6f6 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: index_bam {
+ container = "/sps/lbmc/common/singularity/sambamba:0.6.9.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index 2ccdc387a36f77ae271f39be463023183360170a..de2eb6e80e9ed05d755792b76af0c07d5cbc328e 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: sort_bam {
+ container = "/sps/lbmc/common/singularity/sambamba:0.6.9.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
@@ -64,6 +64,7 @@ profiles {
cpus = 1
queue = 'huge'
}
+
}
}
}
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index 57346f105efafc03785ebf517fbd7800bc5a91ed..74dd96d055ea9b6a61a8e0851b85e824c71cca57 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: split_bam {
+ container = "/sps/lbmc/common/singularity/sambamba:0.6.9.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index 6911ff9301e3cf4b1a8a422cf6fdf8d1b2b93378..a47c35ac6a744507e7ea68e577e1b45484b0163a 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: dedup_sam {
+ container = "/sps/lbmc/common/singularity/sambamba:0.6.7.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
index 0116e7c66ec2a1faf2dd2a6a96acbe5637bacefa..dfc5d68f5b6202ec40f72e7b1ce1da51be617bc4 100644
--- a/src/nf_modules/samtools/filter_bams.config
+++ b/src/nf_modules/samtools/filter_bams.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: filter_bam {
+ container = "/sps/lbmc/common/singularity/samtools:1.7.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
index dfab8d3d1f95a504ebae7a848219e6168a27a29c..3c0e876cfb9a4636221c5eb9fe21873ecec393cd 100644
--- a/src/nf_modules/samtools/index_bams.config
+++ b/src/nf_modules/samtools/index_bams.config
@@ -52,8 +52,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: index_bam {
+ container = "/sps/lbmc/common/singularity/samtools:1.7.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
index 45c69f8ae7b8a381bbe2139dea8cf7525702ec92..690dc9038c4c13cd9d71bc3f835bb844ab391396 100644
--- a/src/nf_modules/samtools/sort_bams.config
+++ b/src/nf_modules/samtools/sort_bams.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: sort_bam {
+ container = "/sps/lbmc/common/singularity/samtools:1.7.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
index f03bc1a85d2b1e74d0088cade99222d5d6146eaf..6afd888004da99b66fd6125e38d6b10b4fa59eb5 100644
--- a/src/nf_modules/samtools/split_bams.config
+++ b/src/nf_modules/samtools/split_bams.config
@@ -52,8 +52,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: split_bam {
+ container = "/sps/lbmc/common/singularity/samtools:1.7.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
index 1538b1a06a35020a5d3ac8cef1824b99555f276d..6abc3955f8ee8a8ed1c603978b916ca4c142afad 100644
--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ b/src/nf_modules/sratoolkit/fastqdump.config
@@ -52,8 +52,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: fastq_dump {
+ container = "/sps/lbmc/common/singularity/sambamba:0.6.7.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index 2073efc271fba3d71b02dc52aadfbbadf7534125..976921f2975f502092589e07156b1c5080c14030 100644
--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: trimming {
+ container = "/sps/lbmc/common/singularity/urqt:d62c1f8.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index e82bd35f96edf31a78c2cd7b62892ec6bb1b367a..99fb7d9465afa3ca4245ba002062d08ae90af0e8 100644
--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -53,8 +53,8 @@ profiles {
singularity.enabled = true
singularity.runOptions = "--bind /pbs,/sps,/scratch"
process{
- withName: index_fasta {
- container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
+ withName: trimming {
+ container = "/sps/lbmc/common/singularity/urqt:d62c1f8.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"