Update lablog_viralrecon with QC scripts

BU-ISCIII · Jan 28, 2025 · b32dac5 · b32dac5
1 parent 47bcd87
commit b32dac5
Showing 1 changed file with 6 additions and 0 deletions.
diff --git a/buisciii/templates/viralrecon/ANALYSIS/lablog_viralrecon b/buisciii/templates/viralrecon/ANALYSIS/lablog_viralrecon
@@ -602,6 +602,8 @@ do
     cp deduplicate_long_table.sh ${FOLDER_NAME}/
     cp percentajeNs.py ${FOLDER_NAME}/
     cp remove_columns_mapping_table.sh ${FOLDER_NAME}/
+    cp get_percentage_LDM.py ${FOLDER_NAME}/
+    cp Sgene_metrics.sh ${FOLDER_NAME}/
     grep -i ${in} samples_ref.txt | cut -f1,2 > ${FOLDER_NAME}/samples_ref.txt
     echo "ln -s ../00-reads ." > ${FOLDER_NAME}/lablog
     printf "ln -s ../samples_id.txt .\n\n" >> ${FOLDER_NAME}/lablog
@@ -660,13 +662,17 @@ do
     echo "#module load R/4.2.1" >> ${FOLDER_NAME}/lablog
     printf 'echo "Rscript create_assembly_stats.R" > _05_create_stats_assembly.sh\n\n' >> ${FOLDER_NAME}/lablog
     printf 'echo "bash deduplicate_long_table.sh" > _06_deduplicate_long_table.sh\n\n' >> ${FOLDER_NAME}/lablog
+    printf 'echo "bash Sgene_metrics.sh" > _07_create_Sgene_metrics.sh\n\n' >> ${FOLDER_NAME}/lablog
+    printf 'echo "srun --partition short_idx --chdir ${scratch_dir} --output logs/LDM.log --job-name LDM python3 ${scratch_dir}/get_percentage_LDM.py" > _08_create_quality_control_summary.sh\n\n' >> ${FOLDER_NAME}/lablog
 
     i=$((i+1))
 done
 rm host_list.tmp
 rm create_summary_report.sh
 rm deduplicate_long_table.sh
 rm percentajeNs.py
+rm get_percentage_LDM.py
+rm Sgene_metrics.sh
 rm _02_create_run_percentage_Ns.sh
 cd 00-reads; cat ../samples_id.txt | xargs -I % echo "ln -s ../../RAW/%_*R1*.fastq.gz %_R1.fastq.gz" | bash; cat ../samples_id.txt | xargs -I % echo "ln -s ../../RAW/%_*R2*.fastq.gz %_R2.fastq.gz" | bash; cd ..