mkdir logs and idx instead of obx

bu_isciii/templates/mtbseq/ANALYSIS/ANALYSIS01_MTBSEQ/03-MTBSeq/lablog

@@ -3,11 +3,12 @@
 # srun parameters
 scratch_dir=$(echo $(pwd) | sed "s@/data/bi/scratch_tmp/@/scratch/@g" )
 
+mkdir logs
 cat ../samples_id.txt | xargs -I % echo "mkdir %; ln -s ../../01-preprocessing/%/%_R1_filtered.fastq.gz %/%_lib1_R1.fastq.gz" > _00_prepareRaw.sh
 cat ../samples_id.txt | xargs -I % echo "ln -s ../../01-preprocessing/%/%_R2_filtered.fastq.gz %/%_lib1_R2.fastq.gz" >> _00_prepareRaw.sh
 cat ../samples_id.txt | xargs -I % echo "cd %;ls *.fastq.gz | tr '_' '\t' | cut -f 1,2 | sort -u > samples.txt;cd -" > _01_preparesamples.sh
 
-cat ../samples_id.txt | xargs -I @@ echo -e "srun --job-name MTBSEQ.@@  --output logs/MTBSEQ.@@.%j.log --partition middle_obx --mem 48G --chdir ${scratch_dir}/@@ --cpus-per-task 10 MTBseq --step TBfull --threads 10 --samples samples.txt &" > _02_mtbseq.sh
+cat ../samples_id.txt | xargs -I @@ echo -e "srun --job-name MTBSEQ.@@  --output logs/MTBSEQ.@@.%j.log --partition middle_idx --mem 48G --chdir ${scratch_dir}/@@ --cpus-per-task 10 MTBseq --step TBfull --threads 10 --samples samples.txt &" > _02_mtbseq.sh
 
 # classification
 echo "mkdir classification_all" > _03_gather_results.sh