BU-ISCIII · GuilleGorines · Sep 19, 2023 · Sep 7, 2023 · Sep 12, 2023 · Sep 12, 2023
diff --git a/bu_isciii/drylab_api.py b/bu_isciii/drylab_api.py
@@ -38,7 +38,7 @@ def get_request(
             if req.status_code > 201:
                 if safe:
                     log.info(
-                        "Resolution id does not exist. Status code: " + req.status_code
+                        f"Resolution id does not exist. Status code: {req.status_code}"
                     )
                     sys.exit()
                 else:

diff --git a/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/03-annotation/lablog b/bu_isciii/templates/exomeeb/ANALYSIS/ANALYSIS01_EXOME/03-annotation/lablog
@@ -48,7 +48,7 @@ sed -i "s|OUTPUT_FOLDER|${output_folder}|g" ./exomiser_configfile.yml
 
 # THE FILE "spring.log" MUST BE DELETED IN THE CORRESPONDING NODE
 echo "java -Xms2g -Xmx4g -jar exomiser-cli-13.0.0.jar --analysis ${scratch_dir}/exomiser_configfile.yml; rm /tmp/spring.log" > aux_06_exomiser_exome.sh
-echo "srun --partition short_idx --mem 100G --time 2:00:00 --chdir /data/bi/pipelines/exomiser/exomiser-cli-13.0.0 --output logs/EXOMISER.log --job-name EXOMISER bash aux_06_exomiser_exome.sh" > _06_exomiser_exome.sh
+echo "srun --partition short_idx --mem 100G --time 2:00:00 --chdir /data/bi/pipelines/exomiser/exomiser-cli-13.0.0 --output logs/EXOMISER.log --job-name EXOMISER bash ${scratch_dir}/aux_06_exomiser_exome.sh" > _06_exomiser_exome.sh
 
 # annot_all table is huge, lets shrink it a little bit
 echo "srun --partition short_idx --chdir ${scratch_dir} --output logs/COMPRESS_ALL.log --job-name COMPRESS_ANNOT_ALL gzip variants_annot_all.tab &" >> _07_gzip_table.sh
diff --git 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 <<EOF > sarek.sbatch

diff --git a/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/03-annotation/lablog b/bu_isciii/templates/exometrio/ANALYSIS/ANALYSIS01_EXOME/03-annotation/lablog
@@ -71,7 +71,7 @@ sed -i "s|OUTPUT_FOLDER|${output_folder}|g" ./exomiser_configfile.yml
 
 # THE FILE "spring.log" MUST BE DELETED IN THE CORRESPONDING NODE
 echo "java -Xms2g -Xmx4g -jar exomiser-cli-13.0.0.jar --analysis ${scratch_dir}/exomiser_configfile.yml; rm /tmp/spring.log" > aux_04_exomiser_exome.sh
-echo "srun --partition short_idx --mem 100G --time 2:00:00 --chdir /data/bi/pipelines/exomiser/exomiser-cli-13.0.0 --output logs/EXOMISER.log --job-name EXOMISER bash aux_04_exomiser_exome.sh" > _04_exomiser_exome.sh
+echo "srun --partition short_idx --mem 100G --time 2:00:00 --chdir /data/bi/pipelines/exomiser/exomiser-cli-13.0.0 --output logs/EXOMISER.log --job-name EXOMISER bash ${scratch_dir}/aux_04_exomiser_exome.sh &" > _04_exomiser_exome.sh
 
 #---------------------------------------------------------------------------------------------------------
 

diff --git 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 <<EOF > sarek.sbatch

diff --git a/bu_isciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/03-annotation/lablog b/bu_isciii/templates/wgstrio/ANALYSIS/ANALYSIS01_GENOME/03-annotation/lablog
@@ -60,12 +60,9 @@ echo "rm variants_annot_filterAF.tab" >> aux_03_awk.sh
 #---------------------------------------------------------------------------------------------------------------------------------
 
 ## 7. Running exomiser
-## NOTE: CHANGE HERE THE NODES
-EXOMISER_FULL_NODE="ideafix04"
 EXOMISER_EXOME_NODE="ideafix06"
 EXOMISER_GENES_NODE="ideafix10"
 
-
 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")
 proband=$(awk 'BEGIN{FS="\t"} $6 == 2 {print $2}' ../../../DOC/family.ped)
@@ -77,7 +74,8 @@ sed -i "s|PROBAND|${proband}|g" ./exomiser_configfile.yml
 #sed -i "s|BED_FILE|${bed_file}|g" ./exomiser_configfile.yml
 sed -i "s|OUTPUT_FOLDER|${output_folder}|g" ./exomiser_configfile.yml
 
-echo "srun --partition short_idx --nodelist ${EXOMISER_FULL_NODE} --mem 350G --time 12:00:00 --chdir /data/bi/pipelines/exomiser/exomiser-cli-13.0.0 --output logs/EXOMISER.log --job-name EXOMISER java -Xms300g -Xmx300g -jar exomiser-cli-13.0.0.jar --analysis ${scratch_dir}/exomiser_configfile.yml &" > _04_exomiser_ALL.sh
+echo "java -Xms300g -Xmx300g -jar exomiser-cli-13.0.0.jar --analysis ${scratch_dir}/exomiser_configfile.yml; rm /tmp/spring.log" > aux1_04_exomiser_ALL.sh
+echo "srun --partition short_idx --mem 350G --time 12:00:00 --chdir /data/bi/pipelines/exomiser/exomiser-cli-13.0.0 --output logs/EXOMISER.log --job-name EXOMISER bash ${scratch_dir}/aux1_04_exomiser_ALL.sh &" > _04_exomiser_ALL.sh
 
 ## 8. Running exomiser_exome
 
@@ -93,7 +91,8 @@ sed -i "s|PROBAND|${proband}|g" ./exomiser_configfile_exome.yml
 sed -i "s|BED_FILE|${bed_file}|g" ./exomiser_configfile_exome.yml
 sed -i "s|OUTPUT_FOLDER|${output_folder}|g" ./exomiser_configfile_exome.yml
 
-echo "srun --partition short_idx --nodelist ${EXOMISER_EXOME_NODE} --mem 350G --time 12:00:00 --chdir /data/bi/pipelines/exomiser/exomiser-cli-13.0.0 --output logs/EXOMISER_exome.log --job-name EXOMISER java -Xms300g -Xmx300g -jar exomiser-cli-13.0.0.jar --analysis ${scratch_dir}/exomiser_configfile_exome.yml &" >> _04_exomiser_ALL.sh
+echo "java -Xms300g -Xmx300g -jar exomiser-cli-13.0.0.jar --analysis ${scratch_dir}/exomiser_configfile_exome.yml; rm /tmp/spring.log" > aux2_04_exomiser_exome.sh
+echo "srun --partition short_idx --mem 350G --time 12:00:00 --chdir /data/bi/pipelines/exomiser/exomiser-cli-13.0.0 --output logs/EXOMISER_exome.log --job-name EXOMISER bash ${scratch_dir}/aux2_04_exomiser_exome.sh &" >> _04_exomiser_ALL.sh
 
 ## 9. Running exomiser_genes
 
@@ -109,23 +108,16 @@ sed -i "s|PROBAND|${proband}|g" ./exomiser_configfile_genes.yml
 sed -i "s|BED_FILE|${bed_file}|g" ./exomiser_configfile_genes.yml
 sed -i "s|OUTPUT_FOLDER|${output_folder}|g" ./exomiser_configfile_genes.yml
 
-echo "srun --partition short_idx --nodelist ${EXOMISER_GENES_NODE} --mem 350G --time 12:00:00 --chdir /data/bi/pipelines/exomiser/exomiser-cli-13.0.0 --output logs/EXOMISER_genes.log --job-name EXOMISER java -Xms300g -Xmx300g -jar exomiser-cli-13.0.0.jar --analysis ${scratch_dir}/exomiser_configfile_genes.yml &" >> _04_exomiser_ALL.sh
+echo "java -Xms300g -Xmx300g -jar exomiser-cli-13.0.0.jar --analysis ${scratch_dir}/exomiser_configfile_genes.yml; rm /tmp/spring.log" > aux3_04_exomiser_genes.sh
+echo "srun --partition short_idx --mem 350G --time 12:00:00 --chdir /data/bi/pipelines/exomiser/exomiser-cli-13.0.0 --output logs/EXOMISER_genes.log --job-name EXOMISER bash ${scratch_dir}/aux3_04_exomiser_genes.sh &" >> _04_exomiser_ALL.sh
 
 #--------------------------------------------------------------------------------------------------------
 
-## 9.1 Exomiser leaves some ugly spring.log that must be deleted for other users to run exomizer
-## so we do that here
-
-echo "srun --chdir /tmp --partition short_idx --nodelist ${EXOMISER_FULL_NODE} rm spring.log &" > _05_filter_heritance_ALL.sh
-echo "srun --chdir /tmp --partition short_idx --nodelist ${EXOMISER_EXOME_NODE} rm spring.log &" >> _05_filter_heritance_ALL.sh
-echo "srun --chdir /tmp --partition short_idx --nodelist ${EXOMISER_GENES_NODE} rm spring.log &" >> _05_filter_heritance_ALL.sh
-
-
 #10. Lablog to modify the output reported by exomiser and create a final file with a personalized format. For each exomiser analysis (whole genome, exome, genes)
 
 # Grep variant id for each inheritance model
 
-cat inheritance_types.txt | xargs -I % echo "grep 'PASS' ./exomiser/exomiser/exomiser_%.variants.tsv | awk '{print \$1\"_\"\$2\"_\"\$3\"_\"\$4}' > ./filter_heritance/filter_heritance/id_%.txt " >> _05_filter_heritance_ALL.sh
+cat inheritance_types.txt | xargs -I % echo "grep 'PASS' ./exomiser/exomiser/exomiser_%.variants.tsv | awk '{print \$1\"_\"\$2\"_\"\$3\"_\"\$4}' > ./filter_heritance/filter_heritance/id_%.txt " > _05_filter_heritance_ALL.sh
 cat inheritance_types.txt | xargs -I % echo "grep 'PASS' ./exomiser/exomiser_genes/exomiser_genes_%.variants.tsv | awk '{print \$1\"_\"\$2\"_\"\$3\"_\"\$4}' > ./filter_heritance/filter_heritance_genes/id_%_genes.txt " >> _05_filter_heritance_ALL.sh
 cat inheritance_types.txt | xargs -I % echo "grep 'PASS' ./exomiser/exomiser_exome/exomiser_exome_%.variants.tsv | awk '{print \$1\"_\"\$2\"_\"\$3\"_\"\$4}' > ./filter_heritance/filter_heritance_exome/id_%_exome.txt " >> _05_filter_heritance_ALL.sh
 

diff --git 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")
 

diff --git a/bu_isciii/templates/wgstrio/ANALYSIS/lablog → ...iii/templates/wgstrio/ANALYSIS/lablog_wgs b/bu_isciii/templates/wgstrio/ANALYSIS/lablog → ...iii/templates/wgstrio/ANALYSIS/lablog_wgs
@@ -1,6 +1,5 @@
 mkdir 00-reads
 ls ../RAW/*.gz | cut -d "/" -f3 | cut -d "_" -f 1 | sort -u | grep -v "md5" > samples_id.txt
-mkdir -p 00-reads
-mkdir -p $(date '+%Y%m%d')_ANALYSIS01_GENOME
+mv ANALYSIS01_GENOME $(date '+%Y%m%d')_ANALYSIS01_GENOME
 cd 00-reads; cat ../samples_id.txt | xargs -I % echo "ln -s ../../RAW/%_*R1*.fastq.gz %_R1.fastq.gz" | bash; cd -
 cd 00-reads; cat ../samples_id.txt | xargs -I % echo "ln -s ../../RAW/%_*R2*.fastq.gz %_R2.fastq.gz" | bash; cd -