Sample	command
BoneMarrow	fastp -w 1 --in1 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/BoneMarrow_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2022/metta/qc/trimming/BoneMarrow.fastp.html -j /scratch/slrinzema/ghe_2022/metta/qc/trimming/BoneMarrow.fastp.json 
CRISPR	fastp -w 1 --in1 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/CRISPR_R1_trimmed.fastq.gz --in2 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/CRISPR_R2_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2022/metta/qc/trimming/CRISPR.fastp.html -j /scratch/slrinzema/ghe_2022/metta/qc/trimming/CRISPR.fastp.json 
CordBlood	fastp -w 1 --in1 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/CordBlood_R1_trimmed.fastq.gz --in2 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/CordBlood_R2_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2022/metta/qc/trimming/CordBlood.fastp.html -j /scratch/slrinzema/ghe_2022/metta/qc/trimming/CordBlood.fastp.json 
DMSO_1	fastp -w 1 --in1 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/DMSO_1_R1_trimmed.fastq.gz --in2 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/DMSO_1_R2_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2022/metta/qc/trimming/DMSO_1.fastp.html -j /scratch/slrinzema/ghe_2022/metta/qc/trimming/DMSO_1.fastp.json 
DMSO_2	fastp -w 1 --in1 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/DMSO_2_R1_trimmed.fastq.gz --in2 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/DMSO_2_R2_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2022/metta/qc/trimming/DMSO_2.fastp.html -j /scratch/slrinzema/ghe_2022/metta/qc/trimming/DMSO_2.fastp.json 
DMSO_3	fastp -w 1 --in1 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/DMSO_3_R1_trimmed.fastq.gz --in2 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/DMSO_3_R2_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2022/metta/qc/trimming/DMSO_3.fastp.html -j /scratch/slrinzema/ghe_2022/metta/qc/trimming/DMSO_3.fastp.json 
GSM5034742	fastp -w 2 --in1 /scratch/slrinzema/ghe_2022/fastqs_all/GSM5034742_R1.fastq.gz --in2 /scratch/slrinzema/ghe_2022/fastqs_all/GSM5034742_R2.fastq.gz --out1 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/GSM5034742_R1_trimmed.fastq.gz --out2 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/GSM5034742_R2_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM5034742.fastp.html -j /scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM5034742.fastp.json 
GSM5034743	fastp -w 2 --in1 /scratch/slrinzema/ghe_2022/fastqs_all/GSM5034743_R1.fastq.gz --in2 /scratch/slrinzema/ghe_2022/fastqs_all/GSM5034743_R2.fastq.gz --out1 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/GSM5034743_R1_trimmed.fastq.gz --out2 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/GSM5034743_R2_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM5034743.fastp.html -j /scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM5034743.fastp.json 
GSM5739833	fastp -w 2 --in1 /scratch/slrinzema/ghe_2022/fastqs_all/GSM5739833_R1.fastq.gz --in2 /scratch/slrinzema/ghe_2022/fastqs_all/GSM5739833_R2.fastq.gz --out1 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/GSM5739833_R1_trimmed.fastq.gz --out2 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/GSM5739833_R2_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM5739833.fastp.html -j /scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM5739833.fastp.json 
GSM5739838	fastp -w 2 --in1 /scratch/slrinzema/ghe_2022/fastqs_all/GSM5739838_R1.fastq.gz --in2 /scratch/slrinzema/ghe_2022/fastqs_all/GSM5739838_R2.fastq.gz --out1 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/GSM5739838_R1_trimmed.fastq.gz --out2 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/GSM5739838_R2_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM5739838.fastp.html -j /scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM5739838.fastp.json 
GSM5739842	fastp -w 2 --in1 /scratch/slrinzema/ghe_2022/fastqs_all/GSM5739842_R1.fastq.gz --in2 /scratch/slrinzema/ghe_2022/fastqs_all/GSM5739842_R2.fastq.gz --out1 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/GSM5739842_R1_trimmed.fastq.gz --out2 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/GSM5739842_R2_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM5739842.fastp.html -j /scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM5739842.fastp.json 
GSM5772725	fastp -w 2 --in1 /scratch/slrinzema/ghe_2022/fastqs_all/GSM5772725.fastq.gz --out1 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/GSM5772725_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM5772725.fastp.html -j /scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM5772725.fastp.json 
GSM5772761	fastp -w 2 --in1 /scratch/slrinzema/ghe_2022/fastqs_all/GSM5772761.fastq.gz --out1 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/GSM5772761_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM5772761.fastp.html -j /scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM5772761.fastp.json 
GSM5772762	fastp -w 2 --in1 /scratch/slrinzema/ghe_2022/fastqs_all/GSM5772762.fastq.gz --out1 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/GSM5772762_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM5772762.fastp.html -j /scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM5772762.fastp.json 
GSM5772763	fastp -w 2 --in1 /scratch/slrinzema/ghe_2022/fastqs_all/GSM5772763.fastq.gz --out1 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/GSM5772763_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM5772763.fastp.html -j /scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM5772763.fastp.json 
GSM5772764	fastp -w 2 --in1 /scratch/slrinzema/ghe_2022/fastqs_all/GSM5772764.fastq.gz --out1 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/GSM5772764_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM5772764.fastp.html -j /scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM5772764.fastp.json 
GSM6133152	fastp -w 2 --in1 /scratch/slrinzema/ghe_2022/fastqs_all/GSM6133152.fastq.gz --out1 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/GSM6133152_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM6133152.fastp.html -j /scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM6133152.fastp.json 
GSM6133153	fastp -w 2 --in1 /scratch/slrinzema/ghe_2022/fastqs_all/GSM6133153.fastq.gz --out1 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/GSM6133153_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM6133153.fastp.html -j /scratch/slrinzema/ghe_2022/metta/qc/trimming/GSM6133153.fastp.json 
HSCD12_DMSO_1tec	fastp -w 2 --in1 /scratch/slrinzema/ghe_2022/fastqs_all/HSCD12_DMSO_1tec_R1.fastq.gz --in2 /scratch/slrinzema/ghe_2022/fastqs_all/HSCD12_DMSO_1tec_R2.fastq.gz --out1 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/HSCD12_DMSO_1tec_R1_trimmed.fastq.gz --out2 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/HSCD12_DMSO_1tec_R2_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2022/metta/qc/trimming/HSCD12_DMSO_1tec.fastp.html -j /scratch/slrinzema/ghe_2022/metta/qc/trimming/HSCD12_DMSO_1tec.fastp.json 
HSCD12_DMSO_2tec	fastp -w 2 --in1 /scratch/slrinzema/ghe_2022/fastqs_all/HSCD12_DMSO_2tec_R1.fastq.gz --in2 /scratch/slrinzema/ghe_2022/fastqs_all/HSCD12_DMSO_2tec_R2.fastq.gz --out1 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/HSCD12_DMSO_2tec_R1_trimmed.fastq.gz --out2 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/HSCD12_DMSO_2tec_R2_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2022/metta/qc/trimming/HSCD12_DMSO_2tec.fastp.html -j /scratch/slrinzema/ghe_2022/metta/qc/trimming/HSCD12_DMSO_2tec.fastp.json 
HSCD12_DMSO_3tec	fastp -w 2 --in1 /scratch/slrinzema/ghe_2022/fastqs_all/HSCD12_DMSO_3tec_R1.fastq.gz --in2 /scratch/slrinzema/ghe_2022/fastqs_all/HSCD12_DMSO_3tec_R2.fastq.gz --out1 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/HSCD12_DMSO_3tec_R1_trimmed.fastq.gz --out2 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/HSCD12_DMSO_3tec_R2_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2022/metta/qc/trimming/HSCD12_DMSO_3tec.fastp.html -j /scratch/slrinzema/ghe_2022/metta/qc/trimming/HSCD12_DMSO_3tec.fastp.json 
Neutrophil	fastp -w 1 --in1 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/Neutrophil_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2022/metta/qc/trimming/Neutrophil.fastp.html -j /scratch/slrinzema/ghe_2022/metta/qc/trimming/Neutrophil.fastp.json 
Skin	fastp -w 1 --in1 /scratch/slrinzema/ghe_2022/metta/fastq_trimmed/Skin_trimmed.fastq.gz -h /scratch/slrinzema/ghe_2022/metta/qc/trimming/Skin.fastp.html -j /scratch/slrinzema/ghe_2022/metta/qc/trimming/Skin.fastp.json