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fmortreu
nextflow
Commits
30b52060
Unverified
Commit
30b52060
authored
Nov 28, 2019
by
Laurent Modolo
Browse files
*.config: fix singularity cacheDir path for in2p3
parent
75b8a82d
Changes
49
Hide whitespace changes
Inline
Side-by-side
src/nf_modules/bedtools/fasta_from_bed.config
View file @
30b52060
...
...
@@ -35,7 +35,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"$baseDir/.
src/
singularity_in2p3/"
singularity
.
cacheDir
=
"$baseDir/.singularity_in2p3/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
fasta_from_bed
{
...
...
src/nf_modules/bowtie/indexing.config
View file @
30b52060
...
...
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"$baseDir/.
src/
singularity_in2p3/"
singularity
.
cacheDir
=
"$baseDir/.singularity_in2p3/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
index_fasta
{
...
...
src/nf_modules/bowtie/mapping_paired.config
View file @
30b52060
...
...
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"$baseDir/.
src/
singularity_in2p3/"
singularity
.
cacheDir
=
"$baseDir/.singularity_in2p3/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
mapping_fastq
{
...
...
src/nf_modules/bowtie/mapping_single.config
View file @
30b52060
...
...
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"$baseDir/.
src/
singularity_in2p3/"
singularity
.
cacheDir
=
"$baseDir/.singularity_in2p3/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
mapping_fastq
{
...
...
src/nf_modules/bowtie2/indexing.config
View file @
30b52060
...
...
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"$baseDir/.
src/
singularity_in2p3/"
singularity
.
cacheDir
=
"$baseDir/.singularity_in2p3/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
index_fasta
{
...
...
src/nf_modules/bowtie2/mapping_paired.config
View file @
30b52060
...
...
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"$baseDir/.
src/
singularity_in2p3/"
singularity
.
cacheDir
=
"$baseDir/.singularity_in2p3/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
mapping_fastq
{
...
...
src/nf_modules/bowtie2/mapping_single.config
View file @
30b52060
...
...
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"$baseDir/.
src/
singularity_in2p3/"
singularity
.
cacheDir
=
"$baseDir/.singularity_in2p3/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
mapping_fastq
{
...
...
src/nf_modules/bwa/indexing.config
View file @
30b52060
...
...
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"$baseDir/.
src/
singularity_in2p3/"
singularity
.
cacheDir
=
"$baseDir/.singularity_in2p3/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
index_fasta
{
...
...
src/nf_modules/bwa/mapping_paired.config
View file @
30b52060
...
...
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"$baseDir/.
src/
singularity_in2p3/"
singularity
.
cacheDir
=
"$baseDir/.singularity_in2p3/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
mapping_fastq
{
...
...
src/nf_modules/cutadapt/adaptor_removal_paired.config
View file @
30b52060
...
...
@@ -35,7 +35,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"$baseDir/.
src/
singularity_in2p3/"
singularity
.
cacheDir
=
"$baseDir/.singularity_in2p3/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
adaptor_removal
{
...
...
src/nf_modules/cutadapt/adaptor_removal_single.config
View file @
30b52060
...
...
@@ -35,7 +35,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"$baseDir/.
src/
singularity_in2p3/"
singularity
.
cacheDir
=
"$baseDir/.singularity_in2p3/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
adaptor_removal
{
...
...
src/nf_modules/cutadapt/trimming_paired.config
View file @
30b52060
...
...
@@ -35,7 +35,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"$baseDir/.
src/
singularity_in2p3/"
singularity
.
cacheDir
=
"$baseDir/.singularity_in2p3/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
trimming
{
...
...
src/nf_modules/cutadapt/trimming_single.config
View file @
30b52060
...
...
@@ -35,7 +35,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"$baseDir/.
src/
singularity_in2p3/"
singularity
.
cacheDir
=
"$baseDir/.singularity_in2p3/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
trimming
{
...
...
src/nf_modules/deeptools/bam_to_bigwig.config
View file @
30b52060
...
...
@@ -55,7 +55,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"$baseDir/.
src/
singularity_in2p3/"
singularity
.
cacheDir
=
"$baseDir/.singularity_in2p3/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
index_bam
{
...
...
src/nf_modules/deeptools/compute_matrix.config
View file @
30b52060
...
...
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"$baseDir/.
src/
singularity_in2p3/"
singularity
.
cacheDir
=
"$baseDir/.singularity_in2p3/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
compute_matrix
{
...
...
src/nf_modules/deeptools/plot_profile.config
View file @
30b52060
...
...
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"$baseDir/.
src/
singularity_in2p3/"
singularity
.
cacheDir
=
"$baseDir/.singularity_in2p3/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
plot_profile
{
...
...
src/nf_modules/fastp/fastp_paired.config
View file @
30b52060
...
...
@@ -35,7 +35,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"$baseDir/.
src/
singularity_in2p3/"
singularity
.
cacheDir
=
"$baseDir/.singularity_in2p3/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
fastp_fastq
{
...
...
src/nf_modules/fastp/fastp_single.config
View file @
30b52060
...
...
@@ -35,7 +35,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"$baseDir/.
src/
singularity_in2p3/"
singularity
.
cacheDir
=
"$baseDir/.singularity_in2p3/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
fastp_fastq
{
...
...
src/nf_modules/fastqc/fastqc_paired.config
View file @
30b52060
...
...
@@ -35,7 +35,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"$baseDir/.
src/
singularity_in2p3/"
singularity
.
cacheDir
=
"$baseDir/.singularity_in2p3/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
fastqc_fastq
{
...
...
src/nf_modules/fastqc/fastqc_single.config
View file @
30b52060
...
...
@@ -35,7 +35,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"$baseDir/.
src/
singularity_in2p3/"
singularity
.
cacheDir
=
"$baseDir/.singularity_in2p3/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
fastqc_fastq
{
...
...
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