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fduveau
nextflow
Commits
32312418
Unverified
Commit
32312418
authored
Nov 27, 2019
by
Laurent Modolo
Browse files
add .signularity_in2p3 folder to fix lock problem in nf
parent
3192a86d
Changes
50
Hide whitespace changes
Inline
Side-by-side
src/.update_config.sh
View file @
32312418
...
...
@@ -5,11 +5,12 @@ fd ".*config" -E "nf_modules" src/ -x perl -0777pe 's|container = "|container =
fd
".*config"
-E
"nf_modules"
src/
-x
perl
-pe
's|container = "lbmc/file://bin/(.*).img"|container = "lbmc/\1"|g'
-i
{}
# update singularity config
fd
".*config"
-E
"nf_modules"
src/
-x
perl
-077
6
pe
's|\n\s*singularity {\n\s*singularity.enabled = true|\n singularity {\n singularity.enabled = true\n singularity.cacheDir = "./bin/"|mg'
-i
{}
fd
".*config"
-E
"nf_modules"
src/
-x
perl
-077
7
pe
's|\n\s*singularity {\n\s*singularity.enabled = true|\n singularity {\n singularity.enabled = true\n singularity.cacheDir = "./bin/"|mg'
-i
{}
# update in2p3 config
fd
".*config"
-E
"nf_modules"
src/
-x
perl
-0777pe
's|\n\s*ccin2p3 {\n\s*singularity.enabled = true|\n ccin2p3 {\n singularity.enabled = true\n singularity.cacheDir = "/sps/lbmc/common/singularity/"|mg'
-i
{}
fd
".*config"
src/
-x
perl
-pe
's|container = "lbmc//sps/lbmc/common/singularity/(.*).img"|container = "lbmc/\1"|g'
-i
{}
fd
".*config"
src/
-x
perl
-0777pe
's|singularity.cacheDir = "/sps/lbmc/common/singularity/"|singularity.cacheDir = "\$baseDir/.src/singularity_in2p3/"|mg'
-i
{}
# we remove the ccin2p3_conda section
fd
".*config"
-E
"nf_modules"
src/
-x
perl
-0777pe
"s|
\s
*ccin2p3_conda {.*ccin2p3 {
\n
|
\n
ccin2p3 {
\n
|msg"
-i
{}
...
...
src/nf_modules/bedtools/fasta_from_bed.config
View file @
32312418
...
...
@@ -35,7 +35,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"
/sps/lbmc/common
/singularity/"
singularity
.
cacheDir
=
"
$baseDir/.src
/singularity
_in2p3
/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
fasta_from_bed
{
...
...
src/nf_modules/bowtie/indexing.config
View file @
32312418
...
...
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"
/sps/lbmc/common
/singularity/"
singularity
.
cacheDir
=
"
$baseDir/.src
/singularity
_in2p3
/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
index_fasta
{
...
...
src/nf_modules/bowtie/mapping_paired.config
View file @
32312418
...
...
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"
/sps/lbmc/common
/singularity/"
singularity
.
cacheDir
=
"
$baseDir/.src
/singularity
_in2p3
/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
mapping_fastq
{
...
...
src/nf_modules/bowtie/mapping_single.config
View file @
32312418
...
...
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"
/sps/lbmc/common
/singularity/"
singularity
.
cacheDir
=
"
$baseDir/.src
/singularity
_in2p3
/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
mapping_fastq
{
...
...
src/nf_modules/bowtie2/indexing.config
View file @
32312418
...
...
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"
/sps/lbmc/common
/singularity/"
singularity
.
cacheDir
=
"
$baseDir/.src
/singularity
_in2p3
/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
index_fasta
{
...
...
src/nf_modules/bowtie2/mapping_paired.config
View file @
32312418
...
...
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"
/sps/lbmc/common
/singularity/"
singularity
.
cacheDir
=
"
$baseDir/.src
/singularity
_in2p3
/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
mapping_fastq
{
...
...
src/nf_modules/bowtie2/mapping_single.config
View file @
32312418
...
...
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"
/sps/lbmc/common
/singularity/"
singularity
.
cacheDir
=
"
$baseDir/.src
/singularity
_in2p3
/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
mapping_fastq
{
...
...
src/nf_modules/bwa/indexing.config
View file @
32312418
...
...
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"
/sps/lbmc/common
/singularity/"
singularity
.
cacheDir
=
"
$baseDir/.src
/singularity
_in2p3
/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
index_fasta
{
...
...
src/nf_modules/bwa/mapping_paired.config
View file @
32312418
...
...
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"
/sps/lbmc/common
/singularity/"
singularity
.
cacheDir
=
"
$baseDir/.src
/singularity
_in2p3
/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
mapping_fastq
{
...
...
src/nf_modules/cutadapt/adaptor_removal_paired.config
View file @
32312418
...
...
@@ -35,7 +35,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"
/sps/lbmc/common
/singularity/"
singularity
.
cacheDir
=
"
$baseDir/.src
/singularity
_in2p3
/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
adaptor_removal
{
...
...
src/nf_modules/cutadapt/adaptor_removal_single.config
View file @
32312418
...
...
@@ -35,7 +35,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"
/sps/lbmc/common
/singularity/"
singularity
.
cacheDir
=
"
$baseDir/.src
/singularity
_in2p3
/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
adaptor_removal
{
...
...
src/nf_modules/cutadapt/trimming_paired.config
View file @
32312418
...
...
@@ -35,7 +35,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"
/sps/lbmc/common
/singularity/"
singularity
.
cacheDir
=
"
$baseDir/.src
/singularity
_in2p3
/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
trimming
{
...
...
src/nf_modules/cutadapt/trimming_single.config
View file @
32312418
...
...
@@ -35,7 +35,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"
/sps/lbmc/common
/singularity/"
singularity
.
cacheDir
=
"
$baseDir/.src
/singularity
_in2p3
/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
trimming
{
...
...
src/nf_modules/deeptools/bam_to_bigwig.config
View file @
32312418
...
...
@@ -55,7 +55,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"
/sps/lbmc/common
/singularity/"
singularity
.
cacheDir
=
"
$baseDir/.src
/singularity
_in2p3
/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
index_bam
{
...
...
src/nf_modules/deeptools/compute_matrix.config
View file @
32312418
...
...
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"
/sps/lbmc/common
/singularity/"
singularity
.
cacheDir
=
"
$baseDir/.src
/singularity
_in2p3
/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
compute_matrix
{
...
...
src/nf_modules/deeptools/plot_profile.config
View file @
32312418
...
...
@@ -36,7 +36,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"
/sps/lbmc/common
/singularity/"
singularity
.
cacheDir
=
"
$baseDir/.src
/singularity
_in2p3
/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
plot_profile
{
...
...
src/nf_modules/fastp/fastp_paired.config
View file @
32312418
...
...
@@ -35,7 +35,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"
/sps/lbmc/common
/singularity/"
singularity
.
cacheDir
=
"
$baseDir/.src
/singularity
_in2p3
/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
fastp_fastq
{
...
...
src/nf_modules/fastp/fastp_single.config
View file @
32312418
...
...
@@ -35,7 +35,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"
/sps/lbmc/common
/singularity/"
singularity
.
cacheDir
=
"
$baseDir/.src
/singularity
_in2p3
/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
fastp_fastq
{
...
...
src/nf_modules/fastqc/fastqc_paired.config
View file @
32312418
...
...
@@ -35,7 +35,7 @@ profiles {
}
ccin2p3
{
singularity
.
enabled
=
true
singularity
.
cacheDir
=
"
/sps/lbmc/common
/singularity/"
singularity
.
cacheDir
=
"
$baseDir/.src
/singularity
_in2p3
/"
singularity
.
runOptions
=
"--bind /pbs,/sps,/scratch"
process
{
withName
:
fastqc_fastq
{
...
...
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