diff --git a/src/.update_config.sh b/src/.update_config.sh
index 0beb2b1bc658a13270be203f5673aefcf9ac2475..2ea29fcf25727fdddaa062fbc7c047f89f9e4af5 100644
--- a/src/.update_config.sh
+++ b/src/.update_config.sh
@@ -29,4 +29,4 @@ fd ".*config" src/ -x perl -0777pe "s|'|\"|mg" -i {}
fd ".*config" src/ -x perl -0777pe 's|psmn{|psmn{\n singularity.enabled = true\n singularity.cacheDir = "$baseDir/.singularity_psmn/"\n singularity.runOptions = "--bind /Xnfs,/scratch"|mg' -i {}
fd ".*config" src/ -x perl -0777pe 's|beforeScript.*conda.*(\n\s*clusterOptions = "-cwd -V".*)(container .*executor = "sge")|\2\1\2|gs' -i {}
fd ".*config" src/nf_modules/ -x perl -0777pe 's|\s*scratch = true(\n.*clusterOptions = "-cwd -V")|\1|gs' -i {}
-
+fd ".*config" src/nf_modules/ -x perl -0777pe 's|\s*stageInMode = "copy"\n\s*stageOutMode = "rsync"(\n.*clusterOptions = "-cwd -V")|\1|gs' -i {}
diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index 6b642d67e2c87d0addcfa92e94424a3125ec5ab2..a04494e663516f7643d786da08e7e6229a5b4f37 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: fasta_from_bed {
container = "lbmc/bedtools:2.25.0"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index 56d24810c481425592e98cdaba43fbaa2de2ee0e..ccf47042bc019c4d8a601543ec7bc7213cbb738c 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/src/nf_modules/bowtie/indexing.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: index_fasta {
container = "lbmc/bowtie:1.2.2"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
memory = "20GB"
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index 7f564233df64a881adf281bc1cef31ebc6a175b6..e6c7c6dadd4625a6affeabcfc68e50aa30f8f227 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/src/nf_modules/bowtie/mapping_paired.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/bowtie:1.2.2"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index 7f564233df64a881adf281bc1cef31ebc6a175b6..e6c7c6dadd4625a6affeabcfc68e50aa30f8f227 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/src/nf_modules/bowtie/mapping_single.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/bowtie:1.2.2"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index 5248f81c6c99813484260920facf194254e3fab3..773c5eae572785d6a7fea6ed1e3ccb9b8d14e00d 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/src/nf_modules/bowtie2/indexing.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: index_fasta {
container = "lbmc/bowtie2:2.3.4.1"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index e3d7b7c6e85a223aa4e1af2dce945aa20148378b..b9f515f11cbc300b8208d7033a90f40bb75ef774 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/src/nf_modules/bowtie2/mapping_paired.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/bowtie2:2.3.4.1"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index e3d7b7c6e85a223aa4e1af2dce945aa20148378b..b9f515f11cbc300b8208d7033a90f40bb75ef774 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/src/nf_modules/bowtie2/mapping_single.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/bowtie2:2.3.4.1"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
index ba8af39e6a148c5ef64769cc1e6019c962d5e310..b3b90059b1cb324f5b792f811079002aabd8acd2 100644
--- a/src/nf_modules/bwa/indexing.config
+++ b/src/nf_modules/bwa/indexing.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: index_fasta {
container = "lbmc/bwa:0.7.17"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
index 94f3904d31033af65be1fa92ef5dee2a507cfbb1..b28e5b9cf21573fc04a6fcf103fff13fee1b8ffa 100644
--- a/src/nf_modules/bwa/mapping_paired.config
+++ b/src/nf_modules/bwa/mapping_paired.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/bwa:0.7.17"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index 8eb321088b58f58c6af22a901632e250e6dbb143..02b23b5526e1e42e9e44c6171075f7519fd4f0cf 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: adaptor_removal {
container = "lbmc/cutadapt:2.4"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index 8eb321088b58f58c6af22a901632e250e6dbb143..02b23b5526e1e42e9e44c6171075f7519fd4f0cf 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: adaptor_removal {
container = "lbmc/cutadapt:2.4"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index 0d27d53f88a3483c67ee94bec24814f0506c82fb..839bce094e92762fe98094881310b319bc445c8e 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: trimming {
container = "lbmc/cutadapt:2.4"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index 0d27d53f88a3483c67ee94bec24814f0506c82fb..839bce094e92762fe98094881310b319bc445c8e 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: trimming {
container = "lbmc/cutadapt:2.4"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
index 99461159da4e4d899c651ee138e8952432729b55..9dd57e691ea71e368e4835e5b37d6a8c8c04a175 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ b/src/nf_modules/deeptools/bam_to_bigwig.config
@@ -34,8 +34,6 @@ profiles {
process{
withName: index_bam {
container = "lbmc/deeptools:3.0.2"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index 36279710aaca525f1b0ceac02120110cf0db16ca..8c9c1b7a6cf50cb012569ffabc605d666af11fac 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/src/nf_modules/deeptools/compute_matrix.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: compute_matrix {
container = "lbmc/deeptools:3.0.2"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index 627384e03eb23f3003fbcb7639b1ae798ea4b9d5..9320784680c101ee6bf0b8fa77aff11afcd0f2a4 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/src/nf_modules/deeptools/plot_profile.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: plot_profile {
container = "lbmc/deeptools:3.0.2"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config
index 4545a98852c99f41295458c015fb91da88e8cf8e..dc9bf8cde93bdc0e51dc318d2e4d9f9fb321ae82 100644
--- a/src/nf_modules/fastp/fastp_paired.config
+++ b/src/nf_modules/fastp/fastp_paired.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: fastp_fastq {
container = "lbmc/fastp:0.19.7"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config
index 4545a98852c99f41295458c015fb91da88e8cf8e..dc9bf8cde93bdc0e51dc318d2e4d9f9fb321ae82 100644
--- a/src/nf_modules/fastp/fastp_single.config
+++ b/src/nf_modules/fastp/fastp_single.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: fastp_fastq {
container = "lbmc/fastp:0.19.7"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
index fb8c8b2e00dfc0b8a5568603e33427668f1d00d7..5f12694b8f34eea4b873cd8ddc4cccdc680002a9 100644
--- a/src/nf_modules/fastqc/fastqc_paired.config
+++ b/src/nf_modules/fastqc/fastqc_paired.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: fastqc_fastq {
container = "lbmc/fastqc:0.11.5"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
index fb8c8b2e00dfc0b8a5568603e33427668f1d00d7..5f12694b8f34eea4b873cd8ddc4cccdc680002a9 100644
--- a/src/nf_modules/fastqc/fastqc_single.config
+++ b/src/nf_modules/fastqc/fastqc_single.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: fastqc_fastq {
container = "lbmc/fastqc:0.11.5"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
index 074e5311bb965d282c28a0d4e54d6ec38a1e422a..5d154dd49c0a40d51046a5134e71621a0f6db6f6 100644
--- a/src/nf_modules/hisat2/indexing.config
+++ b/src/nf_modules/hisat2/indexing.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: index_fasta {
container = "lbmc/hisat2:2.1.0"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
memory = "20GB"
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index 354c26072b79904a2ad420c418c4209680013efb..931ca7848e8c382befe60caf281b46dd723d6f19 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/src/nf_modules/htseq/htseq.config
@@ -34,8 +34,6 @@ profiles {
process{
withName: sort_bam {
container = "lbmc/htseq:0.11.2"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index 3b60bf84a9875c36ce466f7aa50f62bd16c475e6..52d83cf298c9daee3d767a8b93ba6be28076d3e2 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: index_fasta {
container = "lbmc/kallisto:0.44.0"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index a74e8ea3e13b26e0844be1bfde30729c5ad1bd64..839ae33192e5c9ca4c72ff83f64e89abed05d5ac 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/kallisto:0.44.0"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index a74e8ea3e13b26e0844be1bfde30729c5ad1bd64..839ae33192e5c9ca4c72ff83f64e89abed05d5ac 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/kallisto:0.44.0"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config
index e272f0382ae45ee9e36ae40180c3e31e1d58d4d6..d3cbbdb98ced18dd2756bc4f96b18f0e6d28647a 100644
--- a/src/nf_modules/macs2/peak_calling.config
+++ b/src/nf_modules/macs2/peak_calling.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: peak_calling {
container = "lbmc/macs2:2.1.2"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index 370a3e0677063cf77b4aeb862b3d2b96c007c4db..c8fe4a1d9c3cc85287d80a6e578b780178ac6dd6 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -35,8 +35,6 @@ profiles {
process{
withName: fastqc_fastq {
container = "lbmc/multiqc:1.7"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index 6926341dc0f978b7a319350b16dff934b7be111a..641a65e3d359b581b9860b548fe71bfa55a6a0e7 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -34,8 +34,6 @@ profiles {
process{
withName: fastqc_fastq {
container = "lbmc/multiqc:1.7"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config
index 16df88bce60ee9a6da8280a67d47de93e7006826..dea6fa7b77851ace3272ac460a9db888acb2bb31 100644
--- a/src/nf_modules/music/peak_calling_single.config
+++ b/src/nf_modules/music/peak_calling_single.config
@@ -42,8 +42,6 @@ profiles {
process{
withName: compute_mappability {
container = "lbmc/music:6613c53"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
index 004755f57c6703f308c274a39bd76971790b8f53..86f57dde734750c4e55857b645cd60f231dd72ed 100644
--- a/src/nf_modules/rsem/indexing.config
+++ b/src/nf_modules/rsem/indexing.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: index_fasta {
container = "lbmc/rsem:1.3.0"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
index 3570af32b00200be2ae2a1f96cbc2adc16bd2021..a959b00faf62fd63965be66d1efbab61c70b1772 100644
--- a/src/nf_modules/rsem/quantification_paired.config
+++ b/src/nf_modules/rsem/quantification_paired.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/rsem:1.3.0"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
index 3570af32b00200be2ae2a1f96cbc2adc16bd2021..a959b00faf62fd63965be66d1efbab61c70b1772 100644
--- a/src/nf_modules/rsem/quantification_single.config
+++ b/src/nf_modules/rsem/quantification_single.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/rsem:1.3.0"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index baa6c562b4727e4fe18546336d2c485b8f614f25..da8f84fc81c1eb17176d16fd04af21c886661477 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: index_bam {
container = "lbmc/sambamba:0.6.9"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index 17ed79c462b4483e23e8d7c82bdcf05938bea93b..610573272475384df4ad0d0ee46f7dd053f1aa3c 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: sort_bam {
container = "lbmc/sambamba:0.6.9"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 4
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index 3394ef09b95337fb96cb7db7f7e877ad9e98c14e..e9df7d6965eb7a88c9f8d196888c05a8ec6d8c03 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: split_bam {
container = "lbmc/sambamba:0.6.9"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index bb2612c63e60e0116f5f3c5bc2f282ca940eeb4d..e35185c15749ec3a4c91d4497e29391cb6180018 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: dedup_sam {
container = "lbmc/sambamba:0.6.7"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
index a5cce9ded4494e47144006bece659504dc97131d..dfd7f8bf183336f1168e3c93e755f153ca2f410d 100644
--- a/src/nf_modules/samtools/filter_bams.config
+++ b/src/nf_modules/samtools/filter_bams.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: filter_bam {
container = "lbmc/samtools:1.7"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
index fb3624808f2e38b4e7e3cd95cfac49831e476332..173af8fe0940a96d9fe03c0179eb62aaca76dace 100644
--- a/src/nf_modules/samtools/index_bams.config
+++ b/src/nf_modules/samtools/index_bams.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: index_bam {
container = "lbmc/samtools:1.7"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
index c1ee3f37987c70f9a314306feeb4fb75143fe110..48f18580754cd776a7c409206963dbd5a55a50f8 100644
--- a/src/nf_modules/samtools/sort_bams.config
+++ b/src/nf_modules/samtools/sort_bams.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: sort_bam {
container = "lbmc/samtools:1.7"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
index 6507405f272951de58bccc085db2ce19f1f93c32..757a946a3888bc801aeef5a68eb90c3695197192 100644
--- a/src/nf_modules/samtools/split_bams.config
+++ b/src/nf_modules/samtools/split_bams.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: split_bam {
container = "lbmc/samtools:1.7"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
index e0708d7a368ee7c447967cf97e30acf3f9416e7d..4287e92f36e6b2774f39ce3d38191c76881f312f 100644
--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ b/src/nf_modules/sratoolkit/fastqdump.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: fastq_dump {
container = "lbmc/sratoolkit:2.8.2"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/star/indexing.config b/src/nf_modules/star/indexing.config
index d3d5edae2dd80ee7eca854f113b5606b31426e41..503c1b8c9fa6c21261530c8d3f9c78a5a30c207e 100644
--- a/src/nf_modules/star/indexing.config
+++ b/src/nf_modules/star/indexing.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: index_fasta {
container = "lbmc/star:2.7.3a"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/star/mapping_paired.config b/src/nf_modules/star/mapping_paired.config
index 2787b425f9b85ef514377d3ecd6483db31f2c7e7..d9d43b943740d4f714e05075827b843a606e02e3 100644
--- a/src/nf_modules/star/mapping_paired.config
+++ b/src/nf_modules/star/mapping_paired.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/star:2.7.3a"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/star/mapping_single.config b/src/nf_modules/star/mapping_single.config
index 2787b425f9b85ef514377d3ecd6483db31f2c7e7..d9d43b943740d4f714e05075827b843a606e02e3 100644
--- a/src/nf_modules/star/mapping_single.config
+++ b/src/nf_modules/star/mapping_single.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/star:2.7.3a"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/nf_modules/subread/subread.config b/src/nf_modules/subread/subread.config
index 715e6136bc2e5d68b2575e82e877764b5ac99f31..2d09601a5bc48e9ff0f65edde7fb56d978ffd90b 100644
--- a/src/nf_modules/subread/subread.config
+++ b/src/nf_modules/subread/subread.config
@@ -34,8 +34,6 @@ profiles {
process{
withName: sort_bam {
container = "lbmc/subread:1.6.4"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index e740020e1b6ac34b054fcb3ce87b47b9b027745e..f5ca80843af2ead8ca438a839765a77497e7a337 100644
--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: trimming {
container = "lbmc/urqt:d62c1f8"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
memory = "5GB"
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index 8df07c4ec085da916e5154aac13b3ce906413fdb..374112e5218fa5916800f3c92bd6f989d59a9aa2 100644
--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -26,8 +26,6 @@ profiles {
process{
withName: trimming {
container = "lbmc/urqt:d62c1f8"
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
diff --git a/src/solution_RNASeq.config b/src/solution_RNASeq.config
index 77142cab816aacd6efe5dfebd1237f424df9c4a7..fadfceb4bef905feafb1df7fbf1f2d3101ebb822 100644
--- a/src/solution_RNASeq.config
+++ b/src/solution_RNASeq.config
@@ -58,9 +58,6 @@ profiles {
process{
withName: adaptor_removal {
container = "lbmc/cutadapt:2.1"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
@@ -71,8 +68,6 @@ profiles {
withName: trimming {
container = "lbmc/urqt:d62c1f8"
scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
@@ -84,9 +79,6 @@ profiles {
}
withName: fasta_from_bed {
container = "lbmc/bedtools:2.25.0"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
@@ -96,9 +88,6 @@ profiles {
}
withName: index_fasta {
container = "lbmc/kallisto:0.44.0"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32
@@ -109,9 +98,6 @@ profiles {
}
withName: mapping_fastq {
container = "lbmc/kallisto:0.44.0"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 32