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update sarek version in exomeeb #341

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Sep 19, 2024
Merged

update sarek version in exomeeb #341

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b6560c8
update sarek version in exomeeb
OPSergio Sep 12, 2024
02d8917
Updated sarek version (v3.4.4) in ExomeEB-ExomeTrio-WGSTrio templates
OPSergio Sep 12, 2024
1cfd838
Current version Nextflow
OPSergio Sep 12, 2024
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2 changes: 1 addition & 1 deletion CHANGELOG.md
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Expand Up @@ -14,7 +14,7 @@ Code contributions to the new version:

### Template fixes and updates
- Fixed path to blast database and update Emmtyper params [#339](https://github.com/BU-ISCIII/buisciii-tools/pull/339)

- Updated sarek version (v3.4.4) in ExomeEB-ExomeTrio-WGSTrio templates [#341] (https://github.com/BU-ISCIII/buisciii-tools/pull/341)
### Modules

#### Added enhancements
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4 changes: 2 additions & 2 deletions bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/lablog
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@@ -1,4 +1,4 @@
# module load Nextflow/22.10.1 singularity
# module load Nextflow singularity

ln -s ../00-reads/ .
ln -s ../samples_id.txt .
Expand Down Expand Up @@ -28,7 +28,7 @@ cat <<EOF > sarek.sbatch

export NXF_OPTS="-Xms500M -Xmx4G"

nextflow run /data/bi/pipelines/nf-core-sarek/nf-core-sarek-3.4.2/workflow/main.nf \\
nextflow run /data/bi/pipelines/nf-core-sarek/nf-core-sarek_3.4.4/3_4_4/main.nf \\
-c ../../DOC/hpc_slurm_sarek.config \\
--input 'samplesheet.csv' \\
--outdir 01-sarek \\
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2 changes: 1 addition & 1 deletion bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/lablog
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Expand Up @@ -42,7 +42,7 @@ cat <<EOF > sarek.sbatch

export NXF_OPTS="-Xms500M -Xmx4G"

nextflow run /data/bi/pipelines/nf-core-sarek/nf-core-sarek-3.4.2/workflow/main.nf \\
nextflow run /data/bi/pipelines/nf-core-sarek/nf-core-sarek_3.4.4/3_4_4/main.nf \\
-c ../../DOC/hpc_slurm_sarek.config \\
--input 'samplesheet.csv' \\
--outdir 01-sarek \\
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4 changes: 2 additions & 2 deletions bu_isciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/lablog
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# module load Nextflow/22.10.1 singularity
# module load Nextflow singularity

ln -s ../00-reads/ .
ln -s ../samples_id.txt .
Expand Down Expand Up @@ -44,7 +44,7 @@ cat <<EOF > sarek.sbatch

export NXF_OPTS="-Xms500M -Xmx4G"

nextflow run /data/bi/pipelines/nf-core-sarek/nf-core-sarek-3.4.2/workflow/main.nf \\
nextflow run /data/bi/pipelines/nf-core-sarek/nf-core-sarek_3.4.4/3_4_4/main.nf \\
-c ../../DOC/hpc_slurm_sarek.config \\
--input 'samplesheet.csv' \\
--outdir 01-sarek \\
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