Merge pull request #386 from BU-ISCIII/develop

Develop merge for 2.2.4 release
BU-ISCIII · Dec 27, 2024 · b6916d5 · b6916d5
2 parents 6d9f0a2 + f8774f3
commit b6916d5
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,14 +4,17 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [2.X.Xhot] - 2024-0X-0X : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.X.3
+## [2.2.4] - 2024-12-27 : https://github.com/BU-ISCIII/buisciii-tools/releases/tag/2.2.4
 
 ### Credits
 
-Code contributions to the hotfix:
+- [Victor Lopez](https://github.com/victor5lm)
 
 ### Template fixes and updates
 
+- Replaced /data/bi/ by /data/ucct/bi where necessary [#385](https://github.com/BU-ISCIII/buisciii-tools/pull/385).
+- Removed middle_obx from config files [#385](https://github.com/BU-ISCIII/buisciii-tools/pull/385).
+
 ### Modules
 
 #### Added enhancements

diff --git a/bu_isciii/__main__.py b/bu_isciii/__main__.py
@@ -57,7 +57,7 @@ def run_bu_isciii():
     )
 
     # stderr.print("[green]                                          `._,._,'\n", highlight=False)
-    __version__ = "2.2.3"
+    __version__ = "2.2.4"
     stderr.print(
         "[grey39]    BU-ISCIII-tools version {}".format(__version__), highlight=False
     )

diff --git a/bu_isciii/conf/configuration.json b/bu_isciii/conf/configuration.json
@@ -58,7 +58,7 @@
         ],
         "scratch_path": "/scratch/bi/",
         "srun_settings": {
-            "--partition": "middle_obx,middle_idx",
+            "--partition": "middle_idx",
             "--time": "24:00:00",
             "--chdir": "/scratch/bi/"
         }

diff --git a/bu_isciii/conf/configuration_dev.json b/bu_isciii/conf/configuration_dev.json
@@ -54,7 +54,7 @@
         ],
         "scratch_path": "tests/scratch/bi/",
         "srun_settings": {
-            "--partition": "middle_obx,middle_idx",
+            "--partition": "middle_idx",
             "--time": "24:00:00",
             "--chdir": "tests/scratch/bi/"
         }

diff --git a/bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/01-preproQC/lablog b/bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/01-preproQC/lablog
@@ -2,6 +2,6 @@
 
 mkdir logs
 
-scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
 
 cat ../samples_id.txt | while read in; do echo "mkdir $in; srun --partition short_idx --cpus-per-task 8 --time 01:00:00 --chdir $scratch_dir --output logs/FASTQC.${in}.%j.log singularity exec -B ${scratch_dir}/../../../ -B /srv/fastq_repo/ /data/ucct/bi/pipelines/singularity-images/fastqc:0.11.9--hdfd78af_1 fastqc -o ${scratch_dir}/$in --nogroup -t 8 -k 8 ${scratch_dir}/../00-reads/"$in"_R1.fastq.gz ${scratch_dir}/../00-reads/"$in"_R2.fastq.gz &"; done > _01_rawfastqc.sh
diff --git a/bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/03-procQC/lablog b/bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/03-procQC/lablog
@@ -2,6 +2,6 @@
 
 mkdir logs
 
-scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
 
 cat ../samples_id.txt | while read in; do echo "mkdir $in; srun --partition short_idx --chdir $scratch_dir --output logs/FASTQC.${in}.%j.log singularity exec -B ${scratch_dir}/../../../ /data/ucct/bi/pipelines/singularity-images/fastqc:0.11.9--hdfd78af_1 fastqc -o ${scratch_dir}/$in --nogroup -t 8 -k 8 ${scratch_dir}/../02-preprocessing/${in}/${in}_R1_filtered.fastq.gz ${scratch_dir}/../02-preprocessing/${in}/${in}_R2_filtered.fastq.gz &"; done > _01_rawfastqc.sh
diff --git a/bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/04-irma/lablog b/bu_isciii/templates/IRMA/ANALYSIS/ANALYSIS01_FLU_IRMA/04-irma/lablog
@@ -3,7 +3,7 @@
 
 mkdir logs
 
-scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
 
 cat ../samples_id.txt | while read in; do echo "srun --partition short_idx --cpus-per-task 32 --mem 35000M --chdir $scratch_dir --time 01:00:00 --output logs/IRMA.${in}.%j.log /data/ucct/bi/pipelines/flu-amd/flu-amd-1.1.4/IRMA FLU_AD ../02-preprocessing/${in}/${in}_R1_filtered.fastq.gz ../02-preprocessing/${in}/${in}_R2_filtered.fastq.gz ${in} --external-config ../../../DOC/irma_config.sh &"; done > _01_irma.sh
 

diff --git a/bu_isciii/templates/assembly/ANALYSIS/ANALYSIS01_ASSEMBLY/lablog b/bu_isciii/templates/assembly/ANALYSIS/ANALYSIS01_ASSEMBLY/lablog
@@ -92,7 +92,7 @@ cat samples_id.txt | while read in; do
     fi
 done >> samplesheet.csv
 
-scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
 
 cat <<EOF > assembly.sbatch
 #!/bin/sh

diff --git a/bu_isciii/templates/blast_nt/ANALYSIS/ANALYSIS02_BLAST/lablog b/bu_isciii/templates/blast_nt/ANALYSIS/ANALYSIS02_BLAST/lablog
@@ -1,6 +1,6 @@
 # module load singularity
 
-scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
 mkdir logs
 
 # Location of assemblies to a variable so it only has to be changed here

diff --git a/...sciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/02-ariba/run/lablog b/...sciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/02-ariba/run/lablog
@@ -1,7 +1,7 @@
 # module load singularity
 
 mkdir logs
-scratch_dir=$(echo $PWD | sed 's/\/data\/bi\/scratch_tmp/\/scratch/g')
+scratch_dir=$(echo $PWD | sed 's/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g')
 downloaded_ref=$(find ../../../../REFERENCES/ -type d -name 'ref_db')
 
 # Cartesian product of the two files to avoid double looping

diff --git a/...i/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/02-ariba/summary/lablog b/...i/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/02-ariba/summary/lablog
@@ -1,7 +1,7 @@
 # module load singularity
 
 mkdir -p logs
-scratch_dir=$(echo $PWD | sed 's/\/data\/bi\/scratch_tmp/\/scratch/g')
+scratch_dir=$(echo $PWD | sed 's/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g')
 
 # Ariba summarise data from several runs. View the results in Phandango by dragging and dropping the files out.summary.phandango.tre and out.summary.phandango.csv into the Phandago window.
 # Explanation: 

diff --git a/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/04-emmtyper/lablog b/bu_isciii/templates/characterization/ANALYSIS/ANALYSIS01_CHARACTERIZATION/04-emmtyper/lablog
@@ -12,7 +12,7 @@ ASSEMBLY_LIST=fasta_inputs/assembly_file_list.txt
 # Get the number of files
 num_files=$(wc -l < $ASSEMBLY_LIST)
 
-scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
 
 # STEP 1: Set up jobarray to unzip fasta files
 cat <<EOF > _00_unzip_jobarray.sbatch

diff --git a/bu_isciii/templates/chewbbaca/ANALYSIS/ANALYSIS01_CHEWBBACA/02-chewbbaca/lablog b/bu_isciii/templates/chewbbaca/ANALYSIS/ANALYSIS01_CHEWBBACA/02-chewbbaca/lablog
@@ -1,4 +1,4 @@
-scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
 
 # module load singularity
 

diff --git a/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/02-postprocessing/lablog b/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/02-postprocessing/lablog
@@ -2,7 +2,7 @@
 
 # module load singularity
 
-scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
 
 mkdir -p logs
 

diff --git a/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/03-annotation/lablog b/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/03-annotation/lablog
@@ -1,7 +1,7 @@
 # module load singularity
 # module load Java/17.0.2.lua R/4.2.1
 
-scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
 
 ln -s /data/ucct/bi/references/eukaria/homo_sapiens/cache_vep/custom_databases/dbNSFP/GRCh37/dbNSFP_ENSG_gene_GRCh37.txt .
 mkdir -p vep
@@ -39,9 +39,9 @@ echo "srun --partition short_idx --time 2:00:00 --chdir ${scratch_dir} --output
 echo 'grep -P "(HIGH|MODERATE)" ./variants_annot_all.tab > ./variants_annot_highModerate.tab ' > _05_conseq_filtering.sh
 
 # 9. Running exomiser
-vcf_file=$(realpath ../02-postprocessing/variants_fil.vcf | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+vcf_file=$(realpath ../02-postprocessing/variants_fil.vcf | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
 proband=$(awk 'BEGIN{FS="\t"} $6 == 2 {print $2}' ../../../DOC/family.ped)
-output_folder=$(realpath ./exomiser/exomiser | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+output_folder=$(realpath ./exomiser/exomiser | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
 
 sed -i "s|VCF_FILE|${vcf_file}|g" ./exomiser_configfile.yml
 sed -i "s|PROBAND|${proband}|g" ./exomiser_configfile.yml

diff --git a/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/99-stats/lablog b/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/99-stats/lablog
@@ -1,6 +1,6 @@
 # module load singularity
 
-scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
 mkdir logs
 
 cat ../samples_id.txt | xargs -I @@ echo "srun --partition short_idx --mem 100G --time 2:00:00 --chdir ${scratch_dir} --output logs/PICARDHSMETRICS.@@.%j.log --job-name PICARDHSMETRICS singularity exec -B ${scratch_dir}/../../../ -B /data/ucct/bi/references/eukaria/homo_sapiens/hg19/1000genomes_b37/genome /data/ucct/bi/pipelines/singularity-images/picard:2.25.1--hdfd78af_1 picard CollectHsMetrics -R /data/ucct/bi/references/eukaria/homo_sapiens/hg19/1000genomes_b37/genome/human_g1k_v37_decoy.fasta -BI ${scratch_dir}/../../../REFERENCES/Illumine_Exome_CEX_TargetedRegions_v1.2_modb37.interval_list -TI ${scratch_dir}/../../../REFERENCES/Illumine_Exome_CEX_TargetedRegions_v1.2_modb37.interval_list -I ${scratch_dir}/../01-sarek/preprocessing/recalibrated/@@/@@.recal.cram -O ${scratch_dir}/@@_hsMetrics.out -VALIDATION_STRINGENCY LENIENT &" > _01_picardHsMetrics.sh

diff --git a/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/lablog b/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/lablog
@@ -14,7 +14,7 @@ done < ./samples_id.txt
 
 mkdir -p 02-postprocessing 03-annotation 99-stats
 
-scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
 
 cat <<EOF > sarek.sbatch
 #!/bin/sh

diff --git a/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/02-postprocessing/lablog b/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/02-postprocessing/lablog
@@ -3,7 +3,7 @@
 # Lablog to apply variant filters to combined GVCFs generated by SAREK (HaplotypeCaller)
 
 
-scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
 
 mkdir -p logs
 

diff --git a/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/03-annotation/lablog b/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/03-annotation/lablog
@@ -1,7 +1,7 @@
 # module load singularity
 # module load Java/17.0.2.lua R/4.2.1
 
-scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
 
 ln -s /data/ucct/bi/references/eukaria/homo_sapiens/cache_vep/custom_databases/dbNSFP/GRCh37-4.3/dbNSFP_ENSG_gene_GRCh37.txt
 ln -s /data/ucct/bi/references/eukaria/homo_sapiens/cache_vep/custom_databases/dbNSFP/GRCh37-4.3/dbNSFP_ENSG_plugin_hg19.txt
@@ -58,11 +58,11 @@ echo "rm variants_annot_filterAF.tab" >> aux_03_awk.sh
 #-------------------------------------------------------------------------------------------------------
 
 # 9. Running exomiser
-vcf_file=$(realpath ../02-postprocessing/variants_fil.vcf | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
-ped_file=$(realpath ../../../DOC/family.ped | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+vcf_file=$(realpath ../02-postprocessing/variants_fil.vcf | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
+ped_file=$(realpath ../../../DOC/family.ped | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
 proband=$(awk 'BEGIN{FS="\t"} $6 == 2 {print $2}' ../../../DOC/family.ped)
-bed_file=$(realpath ../../../REFERENCES/Illumine_Exome_CEX_TargetedRegions_v1.2_modb37_mod.bed | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
-output_folder=$(realpath ./exomiser/exomiser | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+bed_file=$(realpath ../../../REFERENCES/Illumine_Exome_CEX_TargetedRegions_v1.2_modb37_mod.bed | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
+output_folder=$(realpath ./exomiser/exomiser | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
 
 sed -i "s|VCF_FILE|${vcf_file}|g" ./exomiser_configfile.yml
 sed -i "s|PED_FILE|${ped_file}|g" ./exomiser_configfile.yml

diff --git a/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/99-stats/lablog b/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/99-stats/lablog
@@ -1,6 +1,6 @@
 # module load singularity
 
-scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
 mkdir logs
 
 cat ../samples_id.txt | xargs -I @@ echo "srun --partition short_idx --mem 100G --time 2:00:00 --chdir ${scratch_dir} --output logs/PICARDHSMETRICS.@@.%j.log --job-name PICARDHSMETRICS singularity exec -B ${scratch_dir}/../../../ -B /data/ucct/bi/references/eukaria/homo_sapiens/hg19/1000genomes_b37/genome/ /data/ucct/bi/pipelines/singularity-images/picard:2.25.1--hdfd78af_1 picard CollectHsMetrics -R /data/ucct/bi/references/eukaria/homo_sapiens/hg19/1000genomes_b37/genome/human_g1k_v37_decoy.fasta -BI ${scratch_dir}/../../../REFERENCES/Illumine_Exome_CEX_TargetedRegions_v1.2_modb37.interval_list -TI ${scratch_dir}/../../../REFERENCES/Illumine_Exome_CEX_TargetedRegions_v1.2_modb37.interval_list -I ${scratch_dir}/../01-sarek/preprocessing/recalibrated/@@/@@.recal.cram -O ${scratch_dir}/@@_hsMetrics.out -VALIDATION_STRINGENCY LENIENT &" > _01_picardHsMetrics.sh

diff --git a/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/lablog b/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/lablog
@@ -28,7 +28,7 @@ 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
 
-scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
 
 cat <<EOF > sarek.sbatch
 #!/bin/sh

diff --git a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/01-preproQC/lablog b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/01-preproQC/lablog
@@ -2,6 +2,6 @@
 
 mkdir logs
 
-scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
 
 cat ../samples_id.txt | while read in; do echo "mkdir $in; srun --partition short_idx --cpus-per-task 8 --time 01:00:00 --chdir $scratch_dir --output logs/FASTQC.${in}.%j.log singularity exec -B ${scratch_dir}/../../../ -B /srv/fastq_repo/ /data/ucct/bi/pipelines/singularity-images/fastqc:0.11.9--hdfd78af_1 fastqc -o ${scratch_dir}/$in --nogroup -t 8 -k 8 ${scratch_dir}/../00-reads/"$in"_R1.fastq.gz ${scratch_dir}/../00-reads/"$in"_R2.fastq.gz &"; done > _01_rawfastqc.sh
diff --git a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/03-procQC/lablog b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/03-procQC/lablog
@@ -2,6 +2,6 @@
 
 mkdir logs
 
-scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
 
 cat ../samples_id.txt | while read in; do echo "mkdir $in; srun --partition short_idx --chdir $scratch_dir --output logs/FASTQC.${in}.%j.log singularity exec -B ${scratch_dir}/../../../ /data/ucct/bi/pipelines/singularity-images/fastqc:0.11.9--hdfd78af_1 fastqc -o ${scratch_dir}/$in --nogroup -t 8 -k 8 ${scratch_dir}/../02-preprocessing/${in}/${in}_R1_filtered.fastq.gz ${scratch_dir}/../02-preprocessing/${in}/${in}_R2_filtered.fastq.gz &"; done > _01_preprofastqc.sh
diff --git a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/04-Alignment/lablog b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/04-Alignment/lablog
@@ -2,7 +2,7 @@
 
 mkdir logs
 
-scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
 
 cat ../samples_id.txt | while read in; do echo "mkdir $in; srun --partition short_idx --chdir $scratch_dir --output logs/BWAMEM.${in}.%j.log --cpus-per-task 20 singularity exec -B ${scratch_dir}/../../../ /data/ucct/bi/pipelines/singularity-images/bwa:0.7.17--he4a0461_11 bwa mem -t 20 REFERENCE_GENOME ${scratch_dir}/../02-preprocessing/${in}/${in}_R1_filtered.fastq.gz ${scratch_dir}/../02-preprocessing/${in}/${in}_R2_filtered.fastq.gz -o ${scratch_dir}/${in}/${in}.sam &"; done >> _01_bwamem.sh
 

diff --git a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/05-mark_dups/lablog b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/05-mark_dups/lablog
@@ -2,7 +2,7 @@
 
 mkdir logs
 
-scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
 
 cat ../samples_id.txt | while read in; do mkdir ${in}; echo "srun --partition short_idx --chdir $scratch_dir --output logs/PICARD_DUPLICATES.${in}.%j.log --mem 251346M --cpus-per-task 20 singularity exec -B ${scratch_dir}/../../../ /data/ucct/bi/pipelines/singularity-images/picard:2.25.1--hdfd78af_1 picard MarkDuplicates ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=false INPUT=${scratch_dir}/../04-Alignment/${in}/${in}_sorted_rg.bam OUTPUT=${scratch_dir}/${in}/${in}_woduplicates.bam METRICS_FILE=${scratch_dir}/${in}/${in}_duplicates.stats TMP_DIR=${scratch_dir}/../../../TMP/${in} &"; done > _01_picard_dups.sh
 

diff --git a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/06-freebayes/lablog b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/06-freebayes/lablog
@@ -2,7 +2,7 @@
 
 mkdir -p logs
 
-scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
 
 cat <<EOF > freebayes.sbatch
 #!/bin/sh

diff --git a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/07-snphylo/lablog b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/07-snphylo/lablog
@@ -1,6 +1,6 @@
 # module load R/4.1.3
 
-scratch_dir=$(echo $PWD | sed 's/\/data\/bi\/scratch_tmp/\/scratch/g')
+scratch_dir=$(echo $PWD | sed 's/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g')
 
 mkdir logs
 

diff --git a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/08-iqtree/lablog b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/08-iqtree/lablog
@@ -1,6 +1,6 @@
 # module load singularity
 
-scratch_dir=$(echo $PWD | sed 's/\/data\/bi\/scratch_tmp/\/scratch/g')
+scratch_dir=$(echo $PWD | sed 's/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g')
 mkdir log
 echo "srun --chdir ${scratch_dir} --output logs/IQTREEMFP.%j.log --job-name IQTREEMFP --cpus-per-task 20 --mem 5G --partition short_idx --time 00:30:00 singularity exec -B ${scratch_dir}/../../../ /data/ucct/bi/pipelines/singularity-images/iqtree:2.1.4_beta--hdcc8f71_0 iqtree -s ${scratch_dir}/../07-snphylo/snphylo.output.fasta -m MFP &" > _00_iqtreemfp.sh
 echo "srun --chdir ${scratch_dir} --output logs/IQTREEFULLALIGN.%j.log --job-name IQTREEFULLALIGN --cpus-per-task 20 --mem 15G --partition short_idx --time 08:00:00 singularity exec -B ${scratch_dir}/../../../ /data/ucct/bi/pipelines/singularity-images/iqtree:2.1.4_beta--hdcc8f71_0 iqtree -s ${scratch_dir}/../07-snphylo/snphylo.output.fasta -m PMB+F+R2 -T 20 -B 1000 -pre phylo.iqtree.bootstrap &" > _01_iqtreeall.sh
diff --git a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/99-stats/lablog b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS01_OUTBREAK/99-stats/lablog
@@ -1,6 +1,6 @@
 # module load singularity
 
-scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
 
 mkdir -p logs
 mkdir samtools_flagstats

diff --git a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS02_MET/99-stats/lablog b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS02_MET/99-stats/lablog
@@ -2,7 +2,7 @@
 
 cat ../../samples_id.txt | while read in; do ln -s ../*_mag/Taxonomy/kraken2/${in}/kraken2_report.txt ./${in}_kraken2_report.txt; done
 
-scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
 
 cat <<EOF > multiqc.sbatch
 #!/bin/sh

diff --git a/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS02_MET/lablog b/bu_isciii/templates/freebayes_outbreak/ANALYSIS/ANALYSIS02_MET/lablog
@@ -3,7 +3,7 @@ ln -s ../samples_id.txt .
 
 #module load Nextflow singularity
 
-scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
 
 cat <<EOF > mag.sbatch
 #!/bin/sh

diff --git a/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/01-fastQC/lablog b/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/01-fastQC/lablog
@@ -1,5 +1,5 @@
 # module load singularity
 
-scratch_dir=$(echo $PWD | sed 's/\/data\/bi\/scratch_tmp/\/scratch/g')
+scratch_dir=$(echo $PWD | sed 's/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g')
 mkdir logs
 cat ../samples_id.txt | xargs -I @@ echo "mkdir @@;srun --chdir ${scratch_dir} --output logs/FASTQC.@@.%j.log --job-name FASTQC --cpus-per-task 8 --mem 8192 --partition short_idx --time 02:00:00 singularity exec -B ${scratch_dir}/../../../ -B /srv/fastq_repo/ /data/ucct/bi/pipelines/singularity-images/fastqc:0.11.9--hdfd78af_1 fastqc -o ${scratch_dir}/@@ --nogroup -t 8 -k 8 ${scratch_dir}/../00-reads/@@_R1.fastq.gz ${scratch_dir}/../00-reads/@@_R2.fastq.gz &" >> _01_fastqc.sh
diff --git a/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/03-preprocQC/lablog b/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/03-preprocQC/lablog
@@ -1,5 +1,5 @@
 # module load singularity
 
-scratch_dir=$(echo $PWD | sed 's/\/data\/bi\/scratch_tmp/\/scratch/g')
+scratch_dir=$(echo $PWD | sed 's/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g')
 mkdir logs
 cat ../samples_id.txt | xargs -I @@ echo "mkdir @@;srun --chdir ${scratch_dir} --output logs/FASTQC.@@.%j.log --job-name FASTQC --cpus-per-task 8 --mem 8192 --partition short_idx --time 02:00:00 singularity exec -B ${scratch_dir}/../../../ /data/ucct/bi/pipelines/singularity-images/fastqc:0.11.9--hdfd78af_1 fastqc -o ${scratch_dir}/@@ --nogroup -t 8 -k 8 ${scratch_dir}/../02-preprocessing/@@/@@_R1_filtered.fastq ${scratch_dir}/../02-preprocessing/@@/@@_R2_filtered.fastq &" >> _01_fastqc.sh
diff --git a/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/04-mapping/lablog b/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/04-mapping/lablog
@@ -2,7 +2,7 @@
 
 mkdir logs
 
-scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
 
 echo "Use bash lablog ../samples_id.txt"
 

diff --git a/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/05-samtools/lablog b/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/05-samtools/lablog
@@ -2,7 +2,7 @@
 
 mkdir logs
 
-scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
 
 echo "Use bash lablog ../samples_id.txt"
 

diff --git a/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/06-VarScan/lablog b/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/06-VarScan/lablog
@@ -2,7 +2,7 @@
 
 mkdir logs
 
-scratch_dir=$(echo $PWD | sed "s/\/data\/bi\/scratch_tmp/\/scratch/g")
+scratch_dir=$(echo $PWD | sed "s/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g")
 
 echo "Use bash lablog ../samples_id.txt"
 

diff --git a/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/07-annotation/lablog b/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/07-annotation/lablog
@@ -1,6 +1,6 @@
 # module load singularity
 
-scratch_dir=$(echo $PWD | sed 's/\/data\/bi\/scratch_tmp/\/scratch/g')
+scratch_dir=$(echo $PWD | sed 's/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g')
 mkdir logs
 
 echo "Use bash lablog ../samples_id.txt"

diff --git a/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/99-stats/lablog b/bu_isciii/templates/lowfreq_panel/ANALYSIS/ANALYSIS01_RBPANEL/99-stats/lablog
@@ -1,6 +1,6 @@
 # module load singularity
 
-scratch_dir=$(echo $PWD | sed 's/\/data\/bi\/scratch_tmp/\/scratch/g')
+scratch_dir=$(echo $PWD | sed 's/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g')
 mkdir logs
 
 cat ../samples_id.txt | xargs -I @@ echo "srun --chdir ${scratch_dir} --output logs/PICARD.@@.%j.log --job-name PICARD --cpus-per-task 1 --mem 8192 --partition short_idx --time 02:00:00 singularity exec -B ${scratch_dir}/../../../ /data/ucct/bi/pipelines/singularity-images/picard:2.25.1--hdfd78af_1 picard CollectHsMetrics -BI ${scratch_dir}/../../../REFERENCES/idt_rb1_panel_20221123.interval_list -TI ${scratch_dir}/../../../REFERENCES/idt_rb1_panel_20221123.interval_list -I ${scratch_dir}/../04-mapping/@@/@@_sorted.bam -O ${scratch_dir}/@@_hsMetrics.out -VALIDATION_STRINGENCY 'LENIENT' &" > _01_picardHsMetrics.sh