diff --git a/src/.update_config.sh b/src/.update_config.sh
index e8f4fc9b5b655e95aed72d42cce2c4d203be4c57..0beb2b1bc658a13270be203f5673aefcf9ac2475 100644
--- a/src/.update_config.sh
+++ b/src/.update_config.sh
@@ -28,3 +28,5 @@ fd ".*config" src/ -x perl -0777pe "s|'|\"|mg" -i {}
# we update the psmn config to singularity
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 {}
+
diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index a59f2573d12f69acbf78b016d14a7b1febad05b4..6b642d67e2c87d0addcfa92e94424a3125ec5ab2 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: fasta_from_bed {
container = "lbmc/bedtools:2.25.0"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index 10e15a389eb6a662ccaa926aa780bc948668283c..56d24810c481425592e98cdaba43fbaa2de2ee0e 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/src/nf_modules/bowtie/indexing.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: index_fasta {
container = "lbmc/bowtie:1.2.2"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index 591528f9a6dd6b51eb658bf75534a25767327548..7f564233df64a881adf281bc1cef31ebc6a175b6 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/src/nf_modules/bowtie/mapping_paired.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/bowtie:1.2.2"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index 591528f9a6dd6b51eb658bf75534a25767327548..7f564233df64a881adf281bc1cef31ebc6a175b6 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/src/nf_modules/bowtie/mapping_single.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/bowtie:1.2.2"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index 9c3fc8ec670b3fbcda54b8fe683bacb6aed5116c..5248f81c6c99813484260920facf194254e3fab3 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/src/nf_modules/bowtie2/indexing.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: index_fasta {
container = "lbmc/bowtie2:2.3.4.1"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index 140f6740b7e048b6592869eeb5d71334f6d83487..e3d7b7c6e85a223aa4e1af2dce945aa20148378b 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/src/nf_modules/bowtie2/mapping_paired.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/bowtie2:2.3.4.1"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index 140f6740b7e048b6592869eeb5d71334f6d83487..e3d7b7c6e85a223aa4e1af2dce945aa20148378b 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/src/nf_modules/bowtie2/mapping_single.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/bowtie2:2.3.4.1"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
index 03b85b1c7bb8851d2c71548bc4429981c22fba32..ba8af39e6a148c5ef64769cc1e6019c962d5e310 100644
--- a/src/nf_modules/bwa/indexing.config
+++ b/src/nf_modules/bwa/indexing.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: index_fasta {
container = "lbmc/bwa:0.7.17"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
index 73da47575b537890a00ade13d7be3ecf708a4f46..94f3904d31033af65be1fa92ef5dee2a507cfbb1 100644
--- a/src/nf_modules/bwa/mapping_paired.config
+++ b/src/nf_modules/bwa/mapping_paired.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/bwa:0.7.17"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index 6def97522a81b797e9246c32a266643865abb58d..8eb321088b58f58c6af22a901632e250e6dbb143 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: adaptor_removal {
container = "lbmc/cutadapt:2.4"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index 6def97522a81b797e9246c32a266643865abb58d..8eb321088b58f58c6af22a901632e250e6dbb143 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: adaptor_removal {
container = "lbmc/cutadapt:2.4"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index f813ab4f588f1c298ff7aa1dbf0af7e809f92c0d..0d27d53f88a3483c67ee94bec24814f0506c82fb 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: trimming {
container = "lbmc/cutadapt:2.4"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index f813ab4f588f1c298ff7aa1dbf0af7e809f92c0d..0d27d53f88a3483c67ee94bec24814f0506c82fb 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: trimming {
container = "lbmc/cutadapt:2.4"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
index 81fac55dda2a64f18e86223d322a5483888f4d92..99461159da4e4d899c651ee138e8952432729b55 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ b/src/nf_modules/deeptools/bam_to_bigwig.config
@@ -34,7 +34,6 @@ profiles {
process{
withName: index_bam {
container = "lbmc/deeptools:3.0.2"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index d020de9af4d9d095a15b095f00512578b819c483..36279710aaca525f1b0ceac02120110cf0db16ca 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/src/nf_modules/deeptools/compute_matrix.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: compute_matrix {
container = "lbmc/deeptools:3.0.2"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index 5dec8218244e4daf68c81902c317f95dfbf39f05..627384e03eb23f3003fbcb7639b1ae798ea4b9d5 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/src/nf_modules/deeptools/plot_profile.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: plot_profile {
container = "lbmc/deeptools:3.0.2"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config
index 68f316c51add2572a966c7333d45a151c0ab473e..4545a98852c99f41295458c015fb91da88e8cf8e 100644
--- a/src/nf_modules/fastp/fastp_paired.config
+++ b/src/nf_modules/fastp/fastp_paired.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: fastp_fastq {
container = "lbmc/fastp:0.19.7"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config
index 68f316c51add2572a966c7333d45a151c0ab473e..4545a98852c99f41295458c015fb91da88e8cf8e 100644
--- a/src/nf_modules/fastp/fastp_single.config
+++ b/src/nf_modules/fastp/fastp_single.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: fastp_fastq {
container = "lbmc/fastp:0.19.7"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
index 98e4c1dfdf962c31d9481eebe772ff5dc7379d3f..fb8c8b2e00dfc0b8a5568603e33427668f1d00d7 100644
--- a/src/nf_modules/fastqc/fastqc_paired.config
+++ b/src/nf_modules/fastqc/fastqc_paired.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: fastqc_fastq {
container = "lbmc/fastqc:0.11.5"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
index 98e4c1dfdf962c31d9481eebe772ff5dc7379d3f..fb8c8b2e00dfc0b8a5568603e33427668f1d00d7 100644
--- a/src/nf_modules/fastqc/fastqc_single.config
+++ b/src/nf_modules/fastqc/fastqc_single.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: fastqc_fastq {
container = "lbmc/fastqc:0.11.5"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
index ba2915cbb61ebfb758b14b400dda2e520d0c823e..074e5311bb965d282c28a0d4e54d6ec38a1e422a 100644
--- a/src/nf_modules/hisat2/indexing.config
+++ b/src/nf_modules/hisat2/indexing.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: index_fasta {
container = "lbmc/hisat2:2.1.0"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index 72d14beca17c1ec2bf1a28659df650036fc5b091..354c26072b79904a2ad420c418c4209680013efb 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/src/nf_modules/htseq/htseq.config
@@ -34,7 +34,6 @@ profiles {
process{
withName: sort_bam {
container = "lbmc/htseq:0.11.2"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index ef535de88ce92d3df027b3af4fab52b01d610ee8..3b60bf84a9875c36ce466f7aa50f62bd16c475e6 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: index_fasta {
container = "lbmc/kallisto:0.44.0"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index d4bc1680edf121079a49c5dfc3d84360a20bcde2..a74e8ea3e13b26e0844be1bfde30729c5ad1bd64 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/kallisto:0.44.0"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index d4bc1680edf121079a49c5dfc3d84360a20bcde2..a74e8ea3e13b26e0844be1bfde30729c5ad1bd64 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/kallisto:0.44.0"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config
index 2d250ef0ac44216f3cc5f08f582be0479b8b88c1..e272f0382ae45ee9e36ae40180c3e31e1d58d4d6 100644
--- a/src/nf_modules/macs2/peak_calling.config
+++ b/src/nf_modules/macs2/peak_calling.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: peak_calling {
container = "lbmc/macs2:2.1.2"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index 68d4b992dd00286589269435dab2e787802a9b21..370a3e0677063cf77b4aeb862b3d2b96c007c4db 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -35,7 +35,6 @@ profiles {
process{
withName: fastqc_fastq {
container = "lbmc/multiqc:1.7"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index 7dbea6c6dd043e8d71a7634100474ae869d9de42..6926341dc0f978b7a319350b16dff934b7be111a 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -34,7 +34,6 @@ profiles {
process{
withName: fastqc_fastq {
container = "lbmc/multiqc:1.7"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config
index 19d8002b07f8e744bd8b972a2b0051d94cd14b7e..16df88bce60ee9a6da8280a67d47de93e7006826 100644
--- a/src/nf_modules/music/peak_calling_single.config
+++ b/src/nf_modules/music/peak_calling_single.config
@@ -42,7 +42,6 @@ profiles {
process{
withName: compute_mappability {
container = "lbmc/music:6613c53"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
index 9a3d570c4f4f3f37215996f301b3711f30772231..004755f57c6703f308c274a39bd76971790b8f53 100644
--- a/src/nf_modules/rsem/indexing.config
+++ b/src/nf_modules/rsem/indexing.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: index_fasta {
container = "lbmc/rsem:1.3.0"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
index 5371df44c9ed0fc22abf8cbec1eeab0bdb063304..3570af32b00200be2ae2a1f96cbc2adc16bd2021 100644
--- a/src/nf_modules/rsem/quantification_paired.config
+++ b/src/nf_modules/rsem/quantification_paired.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/rsem:1.3.0"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
index 5371df44c9ed0fc22abf8cbec1eeab0bdb063304..3570af32b00200be2ae2a1f96cbc2adc16bd2021 100644
--- a/src/nf_modules/rsem/quantification_single.config
+++ b/src/nf_modules/rsem/quantification_single.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/rsem:1.3.0"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index 5e710fca6cbaf83456bfc4249b20e6b76663f67b..baa6c562b4727e4fe18546336d2c485b8f614f25 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: index_bam {
container = "lbmc/sambamba:0.6.9"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index 4a55199346834c01820437a125932a534b3a77a2..17ed79c462b4483e23e8d7c82bdcf05938bea93b 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: sort_bam {
container = "lbmc/sambamba:0.6.9"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index 86934b58e59f153d6c67ee9efb64f530a7fc8357..3394ef09b95337fb96cb7db7f7e877ad9e98c14e 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: split_bam {
container = "lbmc/sambamba:0.6.9"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index c7f2dc36b1ff8e1a3090e0b7ceef930710938adb..bb2612c63e60e0116f5f3c5bc2f282ca940eeb4d 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: dedup_sam {
container = "lbmc/sambamba:0.6.7"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
index 17e7fefdebe0c426592a096fb44938924b63bbc3..a5cce9ded4494e47144006bece659504dc97131d 100644
--- a/src/nf_modules/samtools/filter_bams.config
+++ b/src/nf_modules/samtools/filter_bams.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: filter_bam {
container = "lbmc/samtools:1.7"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
index 234119a0147b7783a1976a5d84e7b81f1abff83a..fb3624808f2e38b4e7e3cd95cfac49831e476332 100644
--- a/src/nf_modules/samtools/index_bams.config
+++ b/src/nf_modules/samtools/index_bams.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: index_bam {
container = "lbmc/samtools:1.7"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
index dd020ab0b6b3b39d142e2ae567bd40e9f41411ef..c1ee3f37987c70f9a314306feeb4fb75143fe110 100644
--- a/src/nf_modules/samtools/sort_bams.config
+++ b/src/nf_modules/samtools/sort_bams.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: sort_bam {
container = "lbmc/samtools:1.7"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
index cd34b08512b08ae59572df25732fb07afdb32b84..6507405f272951de58bccc085db2ce19f1f93c32 100644
--- a/src/nf_modules/samtools/split_bams.config
+++ b/src/nf_modules/samtools/split_bams.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: split_bam {
container = "lbmc/samtools:1.7"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
index cc260862131e5002f7dea3c17eb50b6e23981a4c..e0708d7a368ee7c447967cf97e30acf3f9416e7d 100644
--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ b/src/nf_modules/sratoolkit/fastqdump.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: fastq_dump {
container = "lbmc/sratoolkit:2.8.2"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/star/indexing.config b/src/nf_modules/star/indexing.config
index 490aea021cd9318742f826c022db2fe3fdb47768..d3d5edae2dd80ee7eca854f113b5606b31426e41 100644
--- a/src/nf_modules/star/indexing.config
+++ b/src/nf_modules/star/indexing.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: index_fasta {
container = "lbmc/star:2.7.3a"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/star/mapping_paired.config b/src/nf_modules/star/mapping_paired.config
index e737ad12fffc9f55f92b918a819d97a3f243b9ed..2787b425f9b85ef514377d3ecd6483db31f2c7e7 100644
--- a/src/nf_modules/star/mapping_paired.config
+++ b/src/nf_modules/star/mapping_paired.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/star:2.7.3a"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/star/mapping_single.config b/src/nf_modules/star/mapping_single.config
index e737ad12fffc9f55f92b918a819d97a3f243b9ed..2787b425f9b85ef514377d3ecd6483db31f2c7e7 100644
--- a/src/nf_modules/star/mapping_single.config
+++ b/src/nf_modules/star/mapping_single.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: mapping_fastq {
container = "lbmc/star:2.7.3a"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/subread/subread.config b/src/nf_modules/subread/subread.config
index 9ddbadb0d9fc6586d2e621bb9c26d40400a2c028..715e6136bc2e5d68b2575e82e877764b5ac99f31 100644
--- a/src/nf_modules/subread/subread.config
+++ b/src/nf_modules/subread/subread.config
@@ -34,7 +34,6 @@ profiles {
process{
withName: sort_bam {
container = "lbmc/subread:1.6.4"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index a7dd1111faf84eb9c12b1722ca39dfe57768af54..e740020e1b6ac34b054fcb3ce87b47b9b027745e 100644
--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: trimming {
container = "lbmc/urqt:d62c1f8"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index a2719bd38cf9969a7aa46b15da7678889ec54969..8df07c4ec085da916e5154aac13b3ce906413fdb 100644
--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -26,7 +26,6 @@ profiles {
process{
withName: trimming {
container = "lbmc/urqt:d62c1f8"
- scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"