# echo processing raw reads with fastp
# pancancer_singlesample boold
fastp \
-i /dataseq/T7/result/OutputFq/upload/E150013722/L01/*_JM-181200004530_*1.fq.gz \
-o /home/jm001/project/pancancer_singlesample/160/Blood/JM-181200004530/qc/JM-181200004530_clean_R1.fq.gz \
-I /dataseq/T7/result/OutputFq/upload/E150013722/L01/*_JM-181200004530_*2.fq.gz \
-O /home/jm001/project/pancancer_singlesample/160/Blood/JM-181200004530/qc/JM-181200004530_clean_R2.fq.gz \
-j /home/jm001/project/pancancer_singlesample/160/Blood/JM-181200004530/qc/JM-181200004530.json \
-h /home/jm001/project/pancancer_singlesample/160/Blood/JM-181200004530/qc/JM-181200004530.html \
--disable_trim_poly_g \
--disable_quality_filtering \
-w 10 \
--adapter_sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCA \
--adapter_sequence_r2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT \
--report_title JM-181200004530

# singlecancer_singlesample_umi boold
fastp \
-i ${inputDir}/*_${tumor}_*1.fq.gz \
-o ${outputDir}/qc/${tumor}_clean_R1.fq.gz \
-I ${inputDir}/*_${tumor}_*2.fq.gz \
-O ${outputDir}/qc/${tumor}_clean_R2.fq.gz \
-j ${outputDir}/qc/${tumor}.json \
-h ${outputDir}/qc/${tumor}.html --report_title ${tumor}\
-w 10 \
--disable_trim_poly_g \
--disable_quality_filtering \
--adapter_sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCA \
--adapter_sequence_r2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT \

# comcancer_singelsample_cfDNA

# 替换头部
sekit ...
fastp -i ${outputDir}/qc/${tumor}_changehead_R1.fq \
-o ${outputDir}/qc/${tumor}_clean_R1.fq.gz \
-I ${outputDir}/qc/${tumor}_changehead_R2.fq \
-O ${outputDir}/qc/${tumor}_clean_R2.fq.gz \
-w 10 \
-U --umi_loc=per_read \
--umi_len=4 \
--umi_prefix=UMI \
--umi_skip=3 \
--disable_trim_poly_g \
--correction \
--overlap_len_require 10 \
-j ${outputDir}/qc/${tumor}.json \
-h ${outputDir}/qc/${tumor}.html \
--report_title ${tumor} -e 20

# UMI
python3 ${codes_dir}/UMI_Project.py -i ${inputDir} -o ${outputDir} -t ${tumor}
rm ${outputDir}/qc/${tumor}_changehead_R1.fq ${outputDir}/qc/${tumor}_changehead_R2.fq


# 624
fastp -i ${outputDir}/qc/${tumor}_changehead_R1.fq \
-o ${outputDir}/qc/${tumor}_clean_R1.fq.gz \
-I ${outputDir}/qc/${tumor}_changehead_R2.fq \
-O ${outputDir}/qc/${tumor}_clean_R2.fq.gz \
-w 10 \
-U \
--umi_loc=per_read \
--umi_len=4\
--umi_prefix=UMI\
--umi_skip=3 \
--disable_trim_poly_g \
--disable_quality_filtering \
--adapter_sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCA \
--adapter_sequence_r2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT \
--correction \
--overlap_len_require 10 \
-j ${outputDir}/qc/${tumor}.json \
-h ${outputDir}/qc/${tumor}.html --report_title ${tumor}
# UMI
python3 ${codes_dir}/UMI_Project.py -i ${inputDir} -o ${outputDir} -t ${tumor}
rm ${outputDir}/qc/${tumor}_changehead_R1.fq ${outputDir}/qc/${tumor}_changehead_R2.fq

# 682
fastp \
-i ${inputDir}/*_${name}_*1.fq.gz \
-o ${outputDir}/qc/${name}_clean_R1.fq.gz \
-I ${inputDir}/*_${name}_*2.fq.gz -O ${outputDir}/qc/${name}_clean_R2.fq.gz \
-w 10 \
--correction \
--overlap_len_require 10 \
-j ${outputDir}/qc/${name}.json \
-h ${outputDir}/qc/${name}.html \
--report_title ${name} \
-e 20