Sample	command
D10_supernatant_DMSO_1	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D10_supernatant_DMSO_1_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D10_supernatant_DMSO_1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D10_supernatant_DMSO_1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D10_supernatant_DMSO_1.fastp.json 
D10_supernatant_DMSO_2	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D10_supernatant_DMSO_2_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D10_supernatant_DMSO_2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D10_supernatant_DMSO_2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D10_supernatant_DMSO_2.fastp.json 
D10_supernatant_DMSO_3	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D10_supernatant_DMSO_3_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D10_supernatant_DMSO_3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D10_supernatant_DMSO_3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D10_supernatant_DMSO_3.fastp.json 
D10_supernatant_TA_1	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D10_supernatant_TA_1_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D10_supernatant_TA_1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D10_supernatant_TA_1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D10_supernatant_TA_1.fastp.json 
D10_supernatant_TA_2	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D10_supernatant_TA_2_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D10_supernatant_TA_2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D10_supernatant_TA_2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D10_supernatant_TA_2.fastp.json 
D10_supernatant_TA_3	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D10_supernatant_TA_3_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D10_supernatant_TA_3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D10_supernatant_TA_3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D10_supernatant_TA_3.fastp.json 
D12_adherent_DMSO_1	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_adherent_DMSO_1_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_adherent_DMSO_1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_adherent_DMSO_1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_adherent_DMSO_1.fastp.json 
D12_adherent_DMSO_2	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_adherent_DMSO_2_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_adherent_DMSO_2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_adherent_DMSO_2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_adherent_DMSO_2.fastp.json 
D12_adherent_DMSO_3	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_adherent_DMSO_3_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_adherent_DMSO_3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_adherent_DMSO_3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_adherent_DMSO_3.fastp.json 
D12_adherent_TA_1	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_adherent_TA_1_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_adherent_TA_1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_adherent_TA_1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_adherent_TA_1.fastp.json 
D12_adherent_TA_2	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_adherent_TA_2_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_adherent_TA_2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_adherent_TA_2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_adherent_TA_2.fastp.json 
D12_adherent_TA_3	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_adherent_TA_3_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_adherent_TA_3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_adherent_TA_3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_adherent_TA_3.fastp.json 
D12_supernatant_DMSO_1	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_DMSO_1_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_DMSO_1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_DMSO_1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_DMSO_1.fastp.json 
D12_supernatant_DMSO_2	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_DMSO_2_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_DMSO_2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_DMSO_2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_DMSO_2.fastp.json 
D12_supernatant_DMSO_3	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_DMSO_3_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_DMSO_3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_DMSO_3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_DMSO_3.fastp.json 
D12_supernatant_RU1uMTA100nM_1	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_RU1uMTA100nM_1_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_RU1uMTA100nM_1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_RU1uMTA100nM_1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_RU1uMTA100nM_1.fastp.json 
D12_supernatant_RU1uMTA100nM_2	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_RU1uMTA100nM_2_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_RU1uMTA100nM_2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_RU1uMTA100nM_2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_RU1uMTA100nM_2.fastp.json 
D12_supernatant_RU1uMTA100nM_3	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_RU1uMTA100nM_3_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_RU1uMTA100nM_3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_RU1uMTA100nM_3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_RU1uMTA100nM_3.fastp.json 
D12_supernatant_RU1uMTA1uM_1	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_RU1uMTA1uM_1_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_RU1uMTA1uM_1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_RU1uMTA1uM_1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_RU1uMTA1uM_1.fastp.json 
D12_supernatant_RU1uMTA1uM_2	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_RU1uMTA1uM_2_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_RU1uMTA1uM_2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_RU1uMTA1uM_2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_RU1uMTA1uM_2.fastp.json 
D12_supernatant_RU1uMTA1uM_3	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_RU1uMTA1uM_3_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_RU1uMTA1uM_3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_RU1uMTA1uM_3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_RU1uMTA1uM_3.fastp.json 
D12_supernatant_RU1uM_1	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_RU1uM_1_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_RU1uM_1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_RU1uM_1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_RU1uM_1.fastp.json 
D12_supernatant_RU1uM_2	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_RU1uM_2_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_RU1uM_2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_RU1uM_2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_RU1uM_2.fastp.json 
D12_supernatant_RU1uM_3	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_RU1uM_3_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_RU1uM_3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_RU1uM_3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_RU1uM_3.fastp.json 
D12_supernatant_TA100nM_1	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_TA100nM_1_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_TA100nM_1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_TA100nM_1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_TA100nM_1.fastp.json 
D12_supernatant_TA100nM_2	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_TA100nM_2_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_TA100nM_2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_TA100nM_2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_TA100nM_2.fastp.json 
D12_supernatant_TA100nM_3	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_TA100nM_3_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_TA100nM_3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_TA100nM_3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_TA100nM_3.fastp.json 
D12_supernatant_TA1uM_1	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_TA1uM_1_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_TA1uM_1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_TA1uM_1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_TA1uM_1.fastp.json 
D12_supernatant_TA1uM_2	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_TA1uM_2_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_TA1uM_2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_TA1uM_2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_TA1uM_2.fastp.json 
D12_supernatant_TA1uM_3	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_TA1uM_3_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_TA1uM_3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_TA1uM_3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_TA1uM_3.fastp.json 
D12_supernatant_TA_1	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_TA_1_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_TA_1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_TA_1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_TA_1.fastp.json 
D12_supernatant_TA_2	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_TA_2_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_TA_2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_TA_2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_TA_2.fastp.json 
D12_supernatant_TA_3	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_TA_3_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D12_supernatant_TA_3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_TA_3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D12_supernatant_TA_3.fastp.json 
D18_adherent_DMSO_2	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D18_adherent_DMSO_2_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D18_adherent_DMSO_2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D18_adherent_DMSO_2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D18_adherent_DMSO_2.fastp.json 
D18_adherent_DMSO_3	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D18_adherent_DMSO_3_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D18_adherent_DMSO_3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D18_adherent_DMSO_3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D18_adherent_DMSO_3.fastp.json 
D18_adherent_TA_2	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D18_adherent_TA_2_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D18_adherent_TA_2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D18_adherent_TA_2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D18_adherent_TA_2.fastp.json 
D18_adherent_TA_3	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D18_adherent_TA_3_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D18_adherent_TA_3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D18_adherent_TA_3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D18_adherent_TA_3.fastp.json 
D18_supernatant_DMSO_2	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D18_supernatant_DMSO_2_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D18_supernatant_DMSO_2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D18_supernatant_DMSO_2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D18_supernatant_DMSO_2.fastp.json 
D18_supernatant_DMSO_3	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D18_supernatant_DMSO_3_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D18_supernatant_DMSO_3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D18_supernatant_DMSO_3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D18_supernatant_DMSO_3.fastp.json 
D18_supernatant_TA_2	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D18_supernatant_TA_2_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D18_supernatant_TA_2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D18_supernatant_TA_2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D18_supernatant_TA_2.fastp.json 
D18_supernatant_TA_3	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D18_supernatant_TA_3_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D18_supernatant_TA_3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D18_supernatant_TA_3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D18_supernatant_TA_3.fastp.json 
D19_adherent_DMSO_1	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D19_adherent_DMSO_1_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D19_adherent_DMSO_1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D19_adherent_DMSO_1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D19_adherent_DMSO_1.fastp.json 
D19_adherent_TA_1	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D19_adherent_TA_1_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D19_adherent_TA_1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D19_adherent_TA_1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D19_adherent_TA_1.fastp.json 
D19_supernatant_DMSO_1	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D19_supernatant_DMSO_1_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D19_supernatant_DMSO_1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D19_supernatant_DMSO_1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D19_supernatant_DMSO_1.fastp.json 
D19_supernatant_TA_1	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D19_supernatant_TA_1_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D19_supernatant_TA_1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D19_supernatant_TA_1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D19_supernatant_TA_1.fastp.json 
D1_adherent_TA_1	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D1_adherent_TA_1_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D1_adherent_TA_1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D1_adherent_TA_1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D1_adherent_TA_1.fastp.json 
D1_adherent_TA_2	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D1_adherent_TA_2_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D1_adherent_TA_2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D1_adherent_TA_2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D1_adherent_TA_2.fastp.json 
D1_adherent_TA_3	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D1_adherent_TA_3_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D1_adherent_TA_3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D1_adherent_TA_3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D1_adherent_TA_3.fastp.json 
D1_adherent_TA_DMSO_1	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D1_adherent_TA_DMSO_1_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D1_adherent_TA_DMSO_1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D1_adherent_TA_DMSO_1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D1_adherent_TA_DMSO_1.fastp.json 
D1_adherent_TA_DMSO_2	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D1_adherent_TA_DMSO_2_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D1_adherent_TA_DMSO_2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D1_adherent_TA_DMSO_2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D1_adherent_TA_DMSO_2.fastp.json 
D1_adherent_TA_DMSO_3	fastp -w 1 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D1_adherent_TA_DMSO_3_R1_trimmed.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/D1_adherent_TA_DMSO_3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D1_adherent_TA_DMSO_3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/D1_adherent_TA_DMSO_3.fastp.json 
HSCD12_DMSO_1bio	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/HSCD12_DMSO_1bio_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/HSCD12_DMSO_1bio_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_DMSO_1bio_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_DMSO_1bio_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_DMSO_1bio.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_DMSO_1bio.fastp.json 
HSCD12_DMSO_2bio	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/HSCD12_DMSO_2bio_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/HSCD12_DMSO_2bio_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_DMSO_2bio_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_DMSO_2bio_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_DMSO_2bio.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_DMSO_2bio.fastp.json 
HSCD12_DMSO_3bio	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/HSCD12_DMSO_3bio_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/HSCD12_DMSO_3bio_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_DMSO_3bio_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_DMSO_3bio_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_DMSO_3bio.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_DMSO_3bio.fastp.json 
HSCD12_RU1uMTA100nM_1bio	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/HSCD12_RU1uMTA100nM_1bio_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/HSCD12_RU1uMTA100nM_1bio_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_RU1uMTA100nM_1bio_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_RU1uMTA100nM_1bio_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_RU1uMTA100nM_1bio.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_RU1uMTA100nM_1bio.fastp.json 
HSCD12_RU1uMTA100nM_2bio	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/HSCD12_RU1uMTA100nM_2bio_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/HSCD12_RU1uMTA100nM_2bio_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_RU1uMTA100nM_2bio_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_RU1uMTA100nM_2bio_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_RU1uMTA100nM_2bio.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_RU1uMTA100nM_2bio.fastp.json 
HSCD12_RU1uMTA100nM_3bio	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/HSCD12_RU1uMTA100nM_3bio_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/HSCD12_RU1uMTA100nM_3bio_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_RU1uMTA100nM_3bio_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_RU1uMTA100nM_3bio_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_RU1uMTA100nM_3bio.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_RU1uMTA100nM_3bio.fastp.json 
HSCD12_RU1uMTA1uM_1bio	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/HSCD12_RU1uMTA1uM_1bio_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/HSCD12_RU1uMTA1uM_1bio_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_RU1uMTA1uM_1bio_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_RU1uMTA1uM_1bio_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_RU1uMTA1uM_1bio.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_RU1uMTA1uM_1bio.fastp.json 
HSCD12_RU1uMTA1uM_2bio	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/HSCD12_RU1uMTA1uM_2bio_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/HSCD12_RU1uMTA1uM_2bio_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_RU1uMTA1uM_2bio_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_RU1uMTA1uM_2bio_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_RU1uMTA1uM_2bio.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_RU1uMTA1uM_2bio.fastp.json 
HSCD12_RU1uMTA1uM_3bio	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/HSCD12_RU1uMTA1uM_3bio_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/HSCD12_RU1uMTA1uM_3bio_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_RU1uMTA1uM_3bio_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_RU1uMTA1uM_3bio_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_RU1uMTA1uM_3bio.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_RU1uMTA1uM_3bio.fastp.json 
HSCD12_RU1uM_1bio	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/HSCD12_RU1uM_1bio_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/HSCD12_RU1uM_1bio_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_RU1uM_1bio_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_RU1uM_1bio_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_RU1uM_1bio.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_RU1uM_1bio.fastp.json 
HSCD12_RU1uM_2bio	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/HSCD12_RU1uM_2bio_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/HSCD12_RU1uM_2bio_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_RU1uM_2bio_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_RU1uM_2bio_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_RU1uM_2bio.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_RU1uM_2bio.fastp.json 
HSCD12_RU1uM_3bio	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/HSCD12_RU1uM_3bio_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/HSCD12_RU1uM_3bio_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_RU1uM_3bio_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_RU1uM_3bio_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_RU1uM_3bio.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_RU1uM_3bio.fastp.json 
HSCD12_TA100nM_1bio	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/HSCD12_TA100nM_1bio_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/HSCD12_TA100nM_1bio_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_TA100nM_1bio_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_TA100nM_1bio_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_TA100nM_1bio.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_TA100nM_1bio.fastp.json 
HSCD12_TA100nM_2bio	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/HSCD12_TA100nM_2bio_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/HSCD12_TA100nM_2bio_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_TA100nM_2bio_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_TA100nM_2bio_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_TA100nM_2bio.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_TA100nM_2bio.fastp.json 
HSCD12_TA100nM_3bio	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/HSCD12_TA100nM_3bio_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/HSCD12_TA100nM_3bio_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_TA100nM_3bio_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_TA100nM_3bio_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_TA100nM_3bio.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_TA100nM_3bio.fastp.json 
HSCD12_TA1uM_1bio	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/HSCD12_TA1uM_1bio_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/HSCD12_TA1uM_1bio_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_TA1uM_1bio_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_TA1uM_1bio_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_TA1uM_1bio.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_TA1uM_1bio.fastp.json 
HSCD12_TA1uM_2bio	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/HSCD12_TA1uM_2bio_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/HSCD12_TA1uM_2bio_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_TA1uM_2bio_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_TA1uM_2bio_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_TA1uM_2bio.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_TA1uM_2bio.fastp.json 
HSCD12_TA1uM_3bio	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/HSCD12_TA1uM_3bio_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/HSCD12_TA1uM_3bio_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_TA1uM_3bio_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/HSCD12_TA1uM_3bio_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_TA1uM_3bio.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/HSCD12_TA1uM_3bio.fastp.json 
NP_Day10_supernatant_DMSO_1	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day10_supernatant_DMSO_1_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day10_supernatant_DMSO_1_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day10_supernatant_DMSO_1_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day10_supernatant_DMSO_1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day10_supernatant_DMSO_1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day10_supernatant_DMSO_1.fastp.json 
NP_Day10_supernatant_DMSO_2	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day10_supernatant_DMSO_2_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day10_supernatant_DMSO_2_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day10_supernatant_DMSO_2_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day10_supernatant_DMSO_2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day10_supernatant_DMSO_2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day10_supernatant_DMSO_2.fastp.json 
NP_Day10_supernatant_DMSO_3	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day10_supernatant_DMSO_3_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day10_supernatant_DMSO_3_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day10_supernatant_DMSO_3_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day10_supernatant_DMSO_3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day10_supernatant_DMSO_3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day10_supernatant_DMSO_3.fastp.json 
NP_Day10_supernatant_TA_1	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day10_supernatant_TA_1_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day10_supernatant_TA_1_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day10_supernatant_TA_1_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day10_supernatant_TA_1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day10_supernatant_TA_1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day10_supernatant_TA_1.fastp.json 
NP_Day10_supernatant_TA_2	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day10_supernatant_TA_2_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day10_supernatant_TA_2_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day10_supernatant_TA_2_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day10_supernatant_TA_2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day10_supernatant_TA_2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day10_supernatant_TA_2.fastp.json 
NP_Day10_supernatant_TA_3	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day10_supernatant_TA_3_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day10_supernatant_TA_3_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day10_supernatant_TA_3_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day10_supernatant_TA_3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day10_supernatant_TA_3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day10_supernatant_TA_3.fastp.json 
NP_Day12_adherent_DMSO_1	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day12_adherent_DMSO_1_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day12_adherent_DMSO_1_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day12_adherent_DMSO_1_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day12_adherent_DMSO_1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day12_adherent_DMSO_1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day12_adherent_DMSO_1.fastp.json 
NP_Day12_adherent_DMSO_2	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day12_adherent_DMSO_2_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day12_adherent_DMSO_2_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day12_adherent_DMSO_2_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day12_adherent_DMSO_2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day12_adherent_DMSO_2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day12_adherent_DMSO_2.fastp.json 
NP_Day12_adherent_DMSO_3	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day12_adherent_DMSO_3_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day12_adherent_DMSO_3_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day12_adherent_DMSO_3_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day12_adherent_DMSO_3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day12_adherent_DMSO_3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day12_adherent_DMSO_3.fastp.json 
NP_Day12_adherent_TA_1	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day12_adherent_TA_1_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day12_adherent_TA_1_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day12_adherent_TA_1_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day12_adherent_TA_1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day12_adherent_TA_1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day12_adherent_TA_1.fastp.json 
NP_Day12_adherent_TA_2	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day12_adherent_TA_2_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day12_adherent_TA_2_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day12_adherent_TA_2_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day12_adherent_TA_2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day12_adherent_TA_2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day12_adherent_TA_2.fastp.json 
NP_Day12_adherent_TA_3	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day12_adherent_TA_3_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day12_adherent_TA_3_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day12_adherent_TA_3_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day12_adherent_TA_3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day12_adherent_TA_3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day12_adherent_TA_3.fastp.json 
NP_Day12_supernatant_DMSO_1	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day12_supernatant_DMSO_1_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day12_supernatant_DMSO_1_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day12_supernatant_DMSO_1_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day12_supernatant_DMSO_1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day12_supernatant_DMSO_1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day12_supernatant_DMSO_1.fastp.json 
NP_Day12_supernatant_DMSO_2	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day12_supernatant_DMSO_2_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day12_supernatant_DMSO_2_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day12_supernatant_DMSO_2_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day12_supernatant_DMSO_2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day12_supernatant_DMSO_2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day12_supernatant_DMSO_2.fastp.json 
NP_Day12_supernatant_DMSO_3	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day12_supernatant_DMSO_3_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day12_supernatant_DMSO_3_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day12_supernatant_DMSO_3_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day12_supernatant_DMSO_3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day12_supernatant_DMSO_3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day12_supernatant_DMSO_3.fastp.json 
NP_Day12_supernatant_TA_1	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day12_supernatant_TA_1_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day12_supernatant_TA_1_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day12_supernatant_TA_1_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day12_supernatant_TA_1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day12_supernatant_TA_1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day12_supernatant_TA_1.fastp.json 
NP_Day12_supernatant_TA_2	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day12_supernatant_TA_2_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day12_supernatant_TA_2_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day12_supernatant_TA_2_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day12_supernatant_TA_2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day12_supernatant_TA_2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day12_supernatant_TA_2.fastp.json 
NP_Day12_supernatant_TA_3	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day12_supernatant_TA_3_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day12_supernatant_TA_3_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day12_supernatant_TA_3_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day12_supernatant_TA_3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day12_supernatant_TA_3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day12_supernatant_TA_3.fastp.json 
NP_Day18_adherent_DMSO_2	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day18_adherent_DMSO_2_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day18_adherent_DMSO_2_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day18_adherent_DMSO_2_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day18_adherent_DMSO_2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day18_adherent_DMSO_2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day18_adherent_DMSO_2.fastp.json 
NP_Day18_adherent_DMSO_3	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day18_adherent_DMSO_3_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day18_adherent_DMSO_3_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day18_adherent_DMSO_3_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day18_adherent_DMSO_3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day18_adherent_DMSO_3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day18_adherent_DMSO_3.fastp.json 
NP_Day18_adherent_TA_2	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day18_adherent_TA_2_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day18_adherent_TA_2_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day18_adherent_TA_2_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day18_adherent_TA_2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day18_adherent_TA_2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day18_adherent_TA_2.fastp.json 
NP_Day18_adherent_TA_3	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day18_adherent_TA_3_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day18_adherent_TA_3_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day18_adherent_TA_3_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day18_adherent_TA_3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day18_adherent_TA_3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day18_adherent_TA_3.fastp.json 
NP_Day18_supernatant_DMSO_2	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day18_supernatant_DMSO_2_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day18_supernatant_DMSO_2_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day18_supernatant_DMSO_2_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day18_supernatant_DMSO_2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day18_supernatant_DMSO_2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day18_supernatant_DMSO_2.fastp.json 
NP_Day18_supernatant_DMSO_3	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day18_supernatant_DMSO_3_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day18_supernatant_DMSO_3_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day18_supernatant_DMSO_3_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day18_supernatant_DMSO_3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day18_supernatant_DMSO_3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day18_supernatant_DMSO_3.fastp.json 
NP_Day18_supernatant_TA_2	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day18_supernatant_TA_2_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day18_supernatant_TA_2_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day18_supernatant_TA_2_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day18_supernatant_TA_2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day18_supernatant_TA_2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day18_supernatant_TA_2.fastp.json 
NP_Day18_supernatant_TA_3	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day18_supernatant_TA_3_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day18_supernatant_TA_3_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day18_supernatant_TA_3_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day18_supernatant_TA_3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day18_supernatant_TA_3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day18_supernatant_TA_3.fastp.json 
NP_Day19_adherent_DMSO_1	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day19_adherent_DMSO_1_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day19_adherent_DMSO_1_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day19_adherent_DMSO_1_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day19_adherent_DMSO_1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day19_adherent_DMSO_1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day19_adherent_DMSO_1.fastp.json 
NP_Day19_adherent_TA_1	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day19_adherent_TA_1_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day19_adherent_TA_1_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day19_adherent_TA_1_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day19_adherent_TA_1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day19_adherent_TA_1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day19_adherent_TA_1.fastp.json 
NP_Day19_supernatant_DMSO_1	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day19_supernatant_DMSO_1_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day19_supernatant_DMSO_1_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day19_supernatant_DMSO_1_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day19_supernatant_DMSO_1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day19_supernatant_DMSO_1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day19_supernatant_DMSO_1.fastp.json 
NP_Day19_supernatant_TA_1	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day19_supernatant_TA_1_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day19_supernatant_TA_1_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day19_supernatant_TA_1_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day19_supernatant_TA_1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day19_supernatant_TA_1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day19_supernatant_TA_1.fastp.json 
NP_Day1_adherentcells_DMSO_1	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day1_adherentcells_DMSO_1_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day1_adherentcells_DMSO_1_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day1_adherentcells_DMSO_1_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day1_adherentcells_DMSO_1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day1_adherentcells_DMSO_1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day1_adherentcells_DMSO_1.fastp.json 
NP_Day1_adherentcells_DMSO_2	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day1_adherentcells_DMSO_2_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day1_adherentcells_DMSO_2_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day1_adherentcells_DMSO_2_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day1_adherentcells_DMSO_2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day1_adherentcells_DMSO_2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day1_adherentcells_DMSO_2.fastp.json 
NP_Day1_adherentcells_DMSO_3	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day1_adherentcells_DMSO_3_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day1_adherentcells_DMSO_3_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day1_adherentcells_DMSO_3_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day1_adherentcells_DMSO_3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day1_adherentcells_DMSO_3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day1_adherentcells_DMSO_3.fastp.json 
NP_Day1_adherentcells_TA_1	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day1_adherentcells_TA_1_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day1_adherentcells_TA_1_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day1_adherentcells_TA_1_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day1_adherentcells_TA_1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day1_adherentcells_TA_1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day1_adherentcells_TA_1.fastp.json 
NP_Day1_adherentcells_TA_2	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day1_adherentcells_TA_2_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day1_adherentcells_TA_2_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day1_adherentcells_TA_2_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day1_adherentcells_TA_2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day1_adherentcells_TA_2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day1_adherentcells_TA_2.fastp.json 
NP_Day1_adherentcells_TA_3	fastp -w 2 --in1 /home/slrinzema/ceph/ghe/samples/NP_Day1_adherentcells_TA_3_R1.fastq.gz --in2 /home/slrinzema/ceph/ghe/samples/NP_Day1_adherentcells_TA_3_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day1_adherentcells_TA_3_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/fastq_trimmed/NP_Day1_adherentcells_TA_3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day1_adherentcells_TA_3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/trimming/NP_Day1_adherentcells_TA_3.fastp.json