diff --git a/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/lablog b/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/lablog index 7ec5fae9..acca0e08 100644 --- a/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/lablog +++ b/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/lablog @@ -1,3 +1,5 @@ +# module load Nextflow/22.10.1 singularity + ln -s ../00-reads/ . ln -s ../samples_id.txt . @@ -6,8 +8,6 @@ cat samples_id.txt | xargs -I % echo -e "%,XY,0,%,1,00-reads/%_R1.fastq.gz,00-re mkdir -p 02-postprocessing 03-annotation 99-stats -#module load Nextflow singularity - scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") cat < sarek.sbatch diff --git a/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/lablog b/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/lablog index 9c249408..18a30679 100644 --- a/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/lablog +++ b/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/lablog @@ -1,3 +1,5 @@ +# module load Nextflow/22.10.1 singularity + ln -s ../00-reads/ . ln -s ../samples_id.txt . @@ -22,13 +24,10 @@ do done < ./samples_id.txt - echo -e "patient,sex,status,sample,lane,fastq_1,fastq_2" > samplesheet.csv cat samples_id.txt | xargs -I % echo -e "%,XY,0,%,1,00-reads/%_R1.fastq.gz,00-reads/%_R2.fastq.gz" >> samplesheet.csv mkdir -p 02-postprocessing 03-annotation 99-stats -#module load Nextflow singularity - scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g") cat < sarek.sbatch diff --git a/bu_isciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/lablog b/bu_isciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/lablog index 372a1b25..f85f3675 100644 --- a/bu_isciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/lablog +++ b/bu_isciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/lablog @@ -1,3 +1,4 @@ +# module load Nextflow/22.10.1 singularity ln -s ../00-reads/ . ln -s ../samples_id.txt . @@ -28,7 +29,6 @@ echo -e "patient,sex,status,sample,lane,fastq_1,fastq_2" > samplesheet.csv cat samples_id.txt | xargs -I % echo -e "%,XY,0,%,1,00-reads/%_R1.fastq.gz,00-reads/%_R2.fastq.gz" >> samplesheet.csv mkdir -p 02-postprocessing 03-annotation 99-stats -#module load Nextflow singularity scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")