From 3a5b57116bc1be78fe8269fc71a9ec90f56e992c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sergio=20Olmos=20Pi=C3=B1ero?= <103578874+OPSergio@users.noreply.github.com> Date: Thu, 19 Sep 2024 16:20:00 +0200 Subject: [PATCH] update sarek version in exomeeb (#341) * update sarek version in exomeeb * Updated sarek version (v3.4.4) in ExomeEB-ExomeTrio-WGSTrio templates * Current version Nextflow --- CHANGELOG.md | 2 +- bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/lablog | 4 ++-- .../templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/lablog | 2 +- bu_isciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/lablog | 4 ++-- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 35bd73635..c899f7d99 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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 diff --git a/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/lablog b/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/lablog index 225026319..edc5cd0eb 100755 --- a/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/lablog +++ b/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/lablog @@ -1,4 +1,4 @@ -# module load Nextflow/22.10.1 singularity +# module load Nextflow singularity ln -s ../00-reads/ . ln -s ../samples_id.txt . @@ -28,7 +28,7 @@ cat < 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 \\ diff --git a/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/lablog b/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/lablog index 179c74934..a7081ffef 100755 --- a/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/lablog +++ b/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/lablog @@ -42,7 +42,7 @@ cat < 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 \\ diff --git a/bu_isciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/lablog b/bu_isciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/lablog index cb6d13302..14528c4fd 100755 --- a/bu_isciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/lablog +++ b/bu_isciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/lablog @@ -1,4 +1,4 @@ -# module load Nextflow/22.10.1 singularity +# module load Nextflow singularity ln -s ../00-reads/ . ln -s ../samples_id.txt . @@ -44,7 +44,7 @@ cat < 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 \\