From 3e2c83f34d2706a2ac1370093075c54d5cc69c6f Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Tue, 23 Oct 2018 16:08:07 +0200
Subject: [PATCH] nf config file update nf syntax for process
---
src/nf_modules/BWA/indexing.config | 4 +-
src/nf_modules/BWA/mapping_paired.config | 4 +-
src/nf_modules/Bowtie/indexing.config | 4 +-
src/nf_modules/Bowtie/mapping_paired.config | 4 +-
src/nf_modules/Bowtie/mapping_single.config | 4 +-
src/nf_modules/Bowtie2/indexing.config | 4 +-
src/nf_modules/Bowtie2/mapping_paired.config | 4 +-
src/nf_modules/Bowtie2/mapping_single.config | 4 +-
src/nf_modules/FastQC/fastqc_paired.config | 4 +-
src/nf_modules/FastQC/fastqc_single.config | 4 +-
src/nf_modules/HTSeq/htseq.config | 8 ++--
.../MUSIC/peak_calling_single.config | 12 ++---
src/nf_modules/MultiQC/multiqc_paired.config | 8 ++--
src/nf_modules/MultiQC/multiqc_single.config | 8 ++--
src/nf_modules/RSEM/indexing.config | 4 +-
.../RSEM/quantification_paired.config | 4 +-
.../RSEM/quantification_single.config | 4 +-
src/nf_modules/SAMtools/filter_bams.config | 4 +-
src/nf_modules/SAMtools/index_bams.config | 4 +-
src/nf_modules/SAMtools/sort_bams.config | 4 +-
src/nf_modules/SAMtools/split_bams.config | 4 +-
src/nf_modules/SRAtoolkit/fastqdump.config | 4 +-
src/nf_modules/UrQt/urqt.config | 4 +-
src/nf_modules/sambamba/index_bams.config | 4 +-
src/nf_modules/sambamba/sort_bams.config | 4 +-
src/nf_modules/sambamba/split_bams.config | 4 +-
src/nf_modules/samblaster/dedup_sams.config | 4 +-
src/training_dataset.config | 44 +++++++++----------
28 files changed, 86 insertions(+), 86 deletions(-)
diff --git a/src/nf_modules/BWA/indexing.config b/src/nf_modules/BWA/indexing.config
index 4f9e6976..66116500 100644
--- a/src/nf_modules/BWA/indexing.config
+++ b/src/nf_modules/BWA/indexing.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $index_fasta {
+ withname: index_fasta {
container = "bwa:0.7.17"
}
}
}
psmn {
process{
- $index_fasta {
+ withname: index_fasta {
beforeScript = "module purge; module load BWA/0.7.17"
executor = "psmn"
cpus = 1
diff --git a/src/nf_modules/BWA/mapping_paired.config b/src/nf_modules/BWA/mapping_paired.config
index d13f1f4e..68df48ed 100644
--- a/src/nf_modules/BWA/mapping_paired.config
+++ b/src/nf_modules/BWA/mapping_paired.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $mapping_fastq {
+ withname: mapping_fastq {
container = "bwa:0.7.17"
}
}
}
psmn {
process{
- $mapping_fastq {
+ withname: mapping_fastq {
beforeScript = "module purge; module load BWA/0.7.17"
executor = "psmn"
cpus = 4
diff --git a/src/nf_modules/Bowtie/indexing.config b/src/nf_modules/Bowtie/indexing.config
index 64df83d8..d97a2ad7 100644
--- a/src/nf_modules/Bowtie/indexing.config
+++ b/src/nf_modules/Bowtie/indexing.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $index_fasta {
+ withname: index_fasta {
container = "bowtie:1.2.2"
}
}
}
psmn {
process{
- $index_fasta {
+ withname: index_fasta {
beforeScript = "module purge; module load Bowtie/1.2.2"
}
}
diff --git a/src/nf_modules/Bowtie/mapping_paired.config b/src/nf_modules/Bowtie/mapping_paired.config
index d2170da7..fbceecea 100644
--- a/src/nf_modules/Bowtie/mapping_paired.config
+++ b/src/nf_modules/Bowtie/mapping_paired.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $mapping_fastq {
+ withname: mapping_fastq {
container = "bowtie:1.2.2"
}
}
}
psmn {
process{
- $mapping_fastq {
+ withname: mapping_fastq {
beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie/1.2.2"
}
}
diff --git a/src/nf_modules/Bowtie/mapping_single.config b/src/nf_modules/Bowtie/mapping_single.config
index d2170da7..fbceecea 100644
--- a/src/nf_modules/Bowtie/mapping_single.config
+++ b/src/nf_modules/Bowtie/mapping_single.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $mapping_fastq {
+ withname: mapping_fastq {
container = "bowtie:1.2.2"
}
}
}
psmn {
process{
- $mapping_fastq {
+ withname: mapping_fastq {
beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie/1.2.2"
}
}
diff --git a/src/nf_modules/Bowtie2/indexing.config b/src/nf_modules/Bowtie2/indexing.config
index 91abd84d..3b87b79e 100644
--- a/src/nf_modules/Bowtie2/indexing.config
+++ b/src/nf_modules/Bowtie2/indexing.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $index_fasta {
+ withname: index_fasta {
container = "bowtie2:2.3.4.1"
}
}
}
psmn {
process{
- $index_fasta {
+ withname: index_fasta {
beforeScript = "module purge; module load Bowtie2/2.3.4.1"
}
}
diff --git a/src/nf_modules/Bowtie2/mapping_paired.config b/src/nf_modules/Bowtie2/mapping_paired.config
index 1f2714a7..840c6d43 100644
--- a/src/nf_modules/Bowtie2/mapping_paired.config
+++ b/src/nf_modules/Bowtie2/mapping_paired.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $mapping_fastq {
+ withname: mapping_fastq {
container = "bowtie2:2.3.4.1"
}
}
}
psmn {
process{
- $mapping_fastq {
+ withname: mapping_fastq {
beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
}
}
diff --git a/src/nf_modules/Bowtie2/mapping_single.config b/src/nf_modules/Bowtie2/mapping_single.config
index 1f2714a7..840c6d43 100644
--- a/src/nf_modules/Bowtie2/mapping_single.config
+++ b/src/nf_modules/Bowtie2/mapping_single.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $mapping_fastq {
+ withname: mapping_fastq {
container = "bowtie2:2.3.4.1"
}
}
}
psmn {
process{
- $mapping_fastq {
+ withname: mapping_fastq {
beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
}
}
diff --git a/src/nf_modules/FastQC/fastqc_paired.config b/src/nf_modules/FastQC/fastqc_paired.config
index 6e869185..875a0fc3 100644
--- a/src/nf_modules/FastQC/fastqc_paired.config
+++ b/src/nf_modules/FastQC/fastqc_paired.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $fastqc_fastq {
+ withname: fastqc_fastq {
container = "fastqc:0.11.5"
}
}
}
psmn {
process{
- $fastqc_fastq {
+ withname: fastqc_fastq {
beforeScript = "module purge; module load FastQC/0.11.5"
executor = "psmn"
cpus = 1
diff --git a/src/nf_modules/FastQC/fastqc_single.config b/src/nf_modules/FastQC/fastqc_single.config
index 6e869185..875a0fc3 100644
--- a/src/nf_modules/FastQC/fastqc_single.config
+++ b/src/nf_modules/FastQC/fastqc_single.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $fastqc_fastq {
+ withname: fastqc_fastq {
container = "fastqc:0.11.5"
}
}
}
psmn {
process{
- $fastqc_fastq {
+ withname: fastqc_fastq {
beforeScript = "module purge; module load FastQC/0.11.5"
executor = "psmn"
cpus = 1
diff --git a/src/nf_modules/HTSeq/htseq.config b/src/nf_modules/HTSeq/htseq.config
index 6dad8c83..42088dd7 100644
--- a/src/nf_modules/HTSeq/htseq.config
+++ b/src/nf_modules/HTSeq/htseq.config
@@ -3,20 +3,20 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $sort_bam {
+ withname: sort_bam {
container = "samtools:1.7"
}
- $counting {
+ withname: counting {
container = "htseq:0.8.0"
}
}
}
psmn {
process{
- $sort_bam {
+ withname: sort_bam {
beforeScript = "module purge; module load SAMtools/1.7"
}
- $trimming {
+ withname: trimming {
beforeScript = "module purge; module load HTSeq/0.8.0"
}
}
diff --git a/src/nf_modules/MUSIC/peak_calling_single.config b/src/nf_modules/MUSIC/peak_calling_single.config
index 70375472..1b53d90d 100644
--- a/src/nf_modules/MUSIC/peak_calling_single.config
+++ b/src/nf_modules/MUSIC/peak_calling_single.config
@@ -3,26 +3,26 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $compute_mappability {
+ withname: compute_mappability {
container = "music:6613c53"
}
- $music_preprocessing {
+ withname: music_preprocessing {
container = "music:6613c53"
}
- $music_computation {
+ withname: music_computation {
container = "music:6613c53"
}
}
}
psmn {
process{
- $compute_mappability {
+ withname: compute_mappability {
beforeScript = "module purge; module load MUSIC/6613c53"
}
- $music_preprocessing {
+ withname: music_preprocessing {
beforeScript = "module purge; module load MUSIC/6613c53"
}
- $music_computation {
+ withname: music_computation {
beforeScript = "module purge; module load MUSIC/6613c53"
}
}
diff --git a/src/nf_modules/MultiQC/multiqc_paired.config b/src/nf_modules/MultiQC/multiqc_paired.config
index a81a361f..d43e99ba 100644
--- a/src/nf_modules/MultiQC/multiqc_paired.config
+++ b/src/nf_modules/MultiQC/multiqc_paired.config
@@ -3,17 +3,17 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $fastqc_fastq {
+ withname: fastqc_fastq {
container = "fastqc:0.11.5"
}
- $multiqc {
+ withname: multiqc {
container = "multiqc:1.0"
}
}
}
psmn {
process{
- $fastqc_fastq {
+ withname: fastqc_fastq {
beforeScript = "module purge; module load FastQC/0.11.5"
executor = "psmn"
cpus = 1
@@ -23,7 +23,7 @@ profiles {
pollInterval = '60sec'
queue = 'monointeldeb128'
}
- $multiqc {
+ withname: multiqc {
beforeScript = "module purge; module load FastQC/1.0"
executor = "psmn"
cpus = 1
diff --git a/src/nf_modules/MultiQC/multiqc_single.config b/src/nf_modules/MultiQC/multiqc_single.config
index a81a361f..d43e99ba 100644
--- a/src/nf_modules/MultiQC/multiqc_single.config
+++ b/src/nf_modules/MultiQC/multiqc_single.config
@@ -3,17 +3,17 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $fastqc_fastq {
+ withname: fastqc_fastq {
container = "fastqc:0.11.5"
}
- $multiqc {
+ withname: multiqc {
container = "multiqc:1.0"
}
}
}
psmn {
process{
- $fastqc_fastq {
+ withname: fastqc_fastq {
beforeScript = "module purge; module load FastQC/0.11.5"
executor = "psmn"
cpus = 1
@@ -23,7 +23,7 @@ profiles {
pollInterval = '60sec'
queue = 'monointeldeb128'
}
- $multiqc {
+ withname: multiqc {
beforeScript = "module purge; module load FastQC/1.0"
executor = "psmn"
cpus = 1
diff --git a/src/nf_modules/RSEM/indexing.config b/src/nf_modules/RSEM/indexing.config
index 52ead0db..4822bb0b 100644
--- a/src/nf_modules/RSEM/indexing.config
+++ b/src/nf_modules/RSEM/indexing.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $index_fasta {
+ withname: index_fasta {
container = "rsem:1.3.0"
}
}
}
psmn {
process{
- $index_fasta {
+ withname: index_fasta {
beforeScript = "module purge; module load RSEM/1.3.0; module load SAMtools/1.7"
}
}
diff --git a/src/nf_modules/RSEM/quantification_paired.config b/src/nf_modules/RSEM/quantification_paired.config
index ad5c0388..5c52dce1 100644
--- a/src/nf_modules/RSEM/quantification_paired.config
+++ b/src/nf_modules/RSEM/quantification_paired.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $mapping_fastq {
+ withname: mapping_fastq {
container = "rsem:1.3.0"
}
}
}
psmn {
process{
- $mapping_fastq {
+ withname: mapping_fastq {
beforeScript = "module purge; module load RSEM/1.3.0; module load SAMtools/1.7"
}
}
diff --git a/src/nf_modules/RSEM/quantification_single.config b/src/nf_modules/RSEM/quantification_single.config
index ad5c0388..5c52dce1 100644
--- a/src/nf_modules/RSEM/quantification_single.config
+++ b/src/nf_modules/RSEM/quantification_single.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $mapping_fastq {
+ withname: mapping_fastq {
container = "rsem:1.3.0"
}
}
}
psmn {
process{
- $mapping_fastq {
+ withname: mapping_fastq {
beforeScript = "module purge; module load RSEM/1.3.0; module load SAMtools/1.7"
}
}
diff --git a/src/nf_modules/SAMtools/filter_bams.config b/src/nf_modules/SAMtools/filter_bams.config
index cee59e8b..15692631 100644
--- a/src/nf_modules/SAMtools/filter_bams.config
+++ b/src/nf_modules/SAMtools/filter_bams.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $filter_bam {
+ withname: filter_bam {
container = "samtools:1.7"
}
}
}
psmn {
process{
- $filter_bam {
+ withname: filter_bam {
beforeScript = "module purge; module load SAMtools/1.7"
}
}
diff --git a/src/nf_modules/SAMtools/index_bams.config b/src/nf_modules/SAMtools/index_bams.config
index 040fee57..277e0a36 100644
--- a/src/nf_modules/SAMtools/index_bams.config
+++ b/src/nf_modules/SAMtools/index_bams.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $index_bam {
+ withname: index_bam {
container = "samtools:1.7"
}
}
}
psmn {
process{
- $index_bam {
+ withname: index_bam {
beforeScript = "module purge; module load SAMtools/1.7"
}
}
diff --git a/src/nf_modules/SAMtools/sort_bams.config b/src/nf_modules/SAMtools/sort_bams.config
index 20dcdccf..d961965c 100644
--- a/src/nf_modules/SAMtools/sort_bams.config
+++ b/src/nf_modules/SAMtools/sort_bams.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $sort_bam {
+ withname: sort_bam {
container = "samtools:1.7"
}
}
}
psmn {
process{
- $sort_bam {
+ withname: sort_bam {
beforeScript = "module purge; module load SAMtools/1.7"
}
}
diff --git a/src/nf_modules/SAMtools/split_bams.config b/src/nf_modules/SAMtools/split_bams.config
index 503d5539..43cba89e 100644
--- a/src/nf_modules/SAMtools/split_bams.config
+++ b/src/nf_modules/SAMtools/split_bams.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $split_bam {
+ withname: split_bam {
container = "samtools:1.7"
}
}
}
psmn {
process{
- $split_bam {
+ withname: split_bam {
beforeScript = "module purge; module load SAMtools/1.7"
}
}
diff --git a/src/nf_modules/SRAtoolkit/fastqdump.config b/src/nf_modules/SRAtoolkit/fastqdump.config
index 1c29984a..9fb28f95 100644
--- a/src/nf_modules/SRAtoolkit/fastqdump.config
+++ b/src/nf_modules/SRAtoolkit/fastqdump.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $fastq_dump {
+ withname: fastq_dump {
container = "sratoolkit:2.8.2"
}
}
}
psmn {
process{
- $fastq_dump {
+ withname: fastq_dump {
beforeScript = "module purge; module load SRAtoolkit/2.8.2"
executor = "psmn"
cpus = 1
diff --git a/src/nf_modules/UrQt/urqt.config b/src/nf_modules/UrQt/urqt.config
index e08a434a..6f2dc8fb 100644
--- a/src/nf_modules/UrQt/urqt.config
+++ b/src/nf_modules/UrQt/urqt.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $trimming {
+ withname: trimming {
container = "urqt:d62c1f8"
}
}
}
psmn {
process{
- $trimming {
+ withname: trimming {
beforeScript = "module purge; module load UrQt/d62c1f8"
executor = "psmn"
cpus = 4
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index cf0c5c7d..2e419215 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $index_bam {
+ withname: index_bam {
container = "sambamba:0.6.7"
}
}
}
psmn {
process{
- $index_bam {
+ withname: index_bam {
beforeScript = "module purge; module load sambamba/0.6.7"
}
}
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index 1303bd68..041a7c7a 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $sort_bam {
+ withname: sort_bam {
container = "sambamba:0.6.7"
}
}
}
psmn {
process{
- $sort_bam {
+ withname: sort_bam {
beforeScript = "module purge; module load sambamba/0.6.7"
}
}
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index c6d211c6..1f10cb45 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $split_bam {
+ withname: split_bam {
container = "sambamba:0.6.7"
}
}
}
psmn {
process{
- $split_bam {
+ withname: split_bam {
beforeScript = "module purge; module load sambamba/0.6.7"
}
}
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index 47ab19e1..646ecb8e 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -3,14 +3,14 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $dedup_sam {
+ withname: dedup_sam {
container = "samblaster:0.1.24"
}
}
}
psmn {
process{
- $dedup_sam {
+ withname: dedup_sam {
beforeScript = "module purge; module load samblaster/0.1.24"
}
}
diff --git a/src/training_dataset.config b/src/training_dataset.config
index 1fb61610..3bddf5fc 100644
--- a/src/training_dataset.config
+++ b/src/training_dataset.config
@@ -3,44 +3,44 @@ profiles {
docker.temp = 'auto'
docker.enabled = true
process {
- $build_synthetic_bed {
+ withname: build_synthetic_bed {
container = "bedtools:2.25.0"
}
- $fasta_from_bed {
+ withname: fasta_from_bed {
container = "bedtools:2.25.0"
}
- $index_fasta {
+ withname: index_fasta {
container = "bowtie2:2.3.4.1"
}
- $mapping_fastq_paired {
+ withname: mapping_fastq_paired {
container = "bowtie2:2.3.4.1"
}
- $bam_2_fastq_paired {
+ withname: bam_2_fastq_paired {
container = "samtools:1.7"
}
- $sort_bam_paired {
+ withname: sort_bam_paired {
container = "samtools:1.7"
}
- $index_bam_paired {
+ withname: index_bam_paired {
container = "samtools:1.7"
}
- $mapping_fastq_single {
+ withname: mapping_fastq_single {
container = "bowtie2:2.3.4.1"
}
- $bam_2_fastq_single {
+ withname: bam_2_fastq_single {
container = "samtools:1.7"
}
- $sort_bam_single {
+ withname: sort_bam_single {
container = "samtools:1.7"
}
- $index_bam_single {
+ withname: index_bam_single {
container = "samtools:1.7"
}
}
}
psmn {
process{
- $build_synthetic_bed {
+ withname: build_synthetic_bed {
beforeScript = "module purge; module load BEDtools/2.25.0"
executor = "psmn"
cpus = 1
@@ -51,7 +51,7 @@ profiles {
queue = 'h6-E5-2667v4deb128'
penv = 'openmp8'
}
- $fasta_from_bed {
+ withname: fasta_from_bed {
beforeScript = "module purge; module load BEDtools/2.25.0"
executor = "psmn"
cpus = 1
@@ -62,31 +62,31 @@ profiles {
queue = 'h6-E5-2667v4deb128'
penv = 'openmp8'
}
- $index_fasta {
+ withname: index_fasta {
beforeScript = "module purge; module load Bowtie2/2.3.4.1"
}
- $mapping_fastq_paired {
+ withname: mapping_fastq_paired {
beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
}
- $bam_2_fastq_paired {
+ withname: bam_2_fastq_paired {
beforeScript = "module purge; module load SAMtools/1.7"
}
- $sort_bam_paired {
+ withname: sort_bam_paired {
beforeScript = "module purge; module load SAMtools/1.7"
}
- $index_bam_paired {
+ withname: index_bam_paired {
beforeScript = "module purge; module load SAMtools/1.7"
}
- $mapping_fastq_single {
+ withname: mapping_fastq_single {
beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
}
- $bam_2_fastq_single {
+ withname: bam_2_fastq_single {
beforeScript = "module purge; module load SAMtools/1.7"
}
- $sort_bam_single {
+ withname: sort_bam_single {
beforeScript = "module purge; module load SAMtools/1.7"
}
- $index_bam_single {
+ withname: index_bam_single {
beforeScript = "module purge; module load SAMtools/1.7"
}
}
--
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