Sample	command
NP_Day10_supernatant_DMSO_A72_S3	fastp -w 2 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/fastq/NP_Day10_supernatant_DMSO_A72_S3_R1.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/fastq/NP_Day10_supernatant_DMSO_A72_S3_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/fastq_trimmed/NP_Day10_supernatant_DMSO_A72_S3_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/fastq_trimmed/NP_Day10_supernatant_DMSO_A72_S3_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/trimming/NP_Day10_supernatant_DMSO_A72_S3.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/trimming/NP_Day10_supernatant_DMSO_A72_S3.fastp.json 
NP_Day10_supernatant_TA_A71_S7	fastp -w 2 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/fastq/NP_Day10_supernatant_TA_A71_S7_R1.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/fastq/NP_Day10_supernatant_TA_A71_S7_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/fastq_trimmed/NP_Day10_supernatant_TA_A71_S7_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/fastq_trimmed/NP_Day10_supernatant_TA_A71_S7_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/trimming/NP_Day10_supernatant_TA_A71_S7.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/trimming/NP_Day10_supernatant_TA_A71_S7.fastp.json 
NP_Day12_adherent_DMSO_A61_S9	fastp -w 2 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/fastq/NP_Day12_adherent_DMSO_A61_S9_R1.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/fastq/NP_Day12_adherent_DMSO_A61_S9_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/fastq_trimmed/NP_Day12_adherent_DMSO_A61_S9_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/fastq_trimmed/NP_Day12_adherent_DMSO_A61_S9_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/trimming/NP_Day12_adherent_DMSO_A61_S9.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/trimming/NP_Day12_adherent_DMSO_A61_S9.fastp.json 
NP_Day12_adherent_TA_A60_S4	fastp -w 2 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/fastq/NP_Day12_adherent_TA_A60_S4_R1.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/fastq/NP_Day12_adherent_TA_A60_S4_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/fastq_trimmed/NP_Day12_adherent_TA_A60_S4_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/fastq_trimmed/NP_Day12_adherent_TA_A60_S4_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/trimming/NP_Day12_adherent_TA_A60_S4.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/trimming/NP_Day12_adherent_TA_A60_S4.fastp.json 
NP_Day12_supernatant_DMSO_A74_S8	fastp -w 2 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/fastq/NP_Day12_supernatant_DMSO_A74_S8_R1.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/fastq/NP_Day12_supernatant_DMSO_A74_S8_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/fastq_trimmed/NP_Day12_supernatant_DMSO_A74_S8_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/fastq_trimmed/NP_Day12_supernatant_DMSO_A74_S8_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/trimming/NP_Day12_supernatant_DMSO_A74_S8.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/trimming/NP_Day12_supernatant_DMSO_A74_S8.fastp.json 
NP_Day12_supernatant_TA_A73_S10	fastp -w 2 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/fastq/NP_Day12_supernatant_TA_A73_S10_R1.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/fastq/NP_Day12_supernatant_TA_A73_S10_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/fastq_trimmed/NP_Day12_supernatant_TA_A73_S10_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/fastq_trimmed/NP_Day12_supernatant_TA_A73_S10_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/trimming/NP_Day12_supernatant_TA_A73_S10.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/trimming/NP_Day12_supernatant_TA_A73_S10.fastp.json 
NP_Day19_adherent_DMSO_A65_S2	fastp -w 2 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/fastq/NP_Day19_adherent_DMSO_A65_S2_R1.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/fastq/NP_Day19_adherent_DMSO_A65_S2_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/fastq_trimmed/NP_Day19_adherent_DMSO_A65_S2_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/fastq_trimmed/NP_Day19_adherent_DMSO_A65_S2_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/trimming/NP_Day19_adherent_DMSO_A65_S2.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/trimming/NP_Day19_adherent_DMSO_A65_S2.fastp.json 
NP_Day19_adherent_TA_A64_S1	fastp -w 2 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/fastq/NP_Day19_adherent_TA_A64_S1_R1.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/fastq/NP_Day19_adherent_TA_A64_S1_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/fastq_trimmed/NP_Day19_adherent_TA_A64_S1_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/fastq_trimmed/NP_Day19_adherent_TA_A64_S1_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/trimming/NP_Day19_adherent_TA_A64_S1.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/trimming/NP_Day19_adherent_TA_A64_S1.fastp.json 
NP_Day19_supernatant_DMSO_A63_S6	fastp -w 2 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/fastq/NP_Day19_supernatant_DMSO_A63_S6_R1.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/fastq/NP_Day19_supernatant_DMSO_A63_S6_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/fastq_trimmed/NP_Day19_supernatant_DMSO_A63_S6_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/fastq_trimmed/NP_Day19_supernatant_DMSO_A63_S6_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/trimming/NP_Day19_supernatant_DMSO_A63_S6.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/trimming/NP_Day19_supernatant_DMSO_A63_S6.fastp.json 
NP_Day19_supernatant_TA_A62_S5	fastp -w 2 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/fastq/NP_Day19_supernatant_TA_A62_S5_R1.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/fastq/NP_Day19_supernatant_TA_A62_S5_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/fastq_trimmed/NP_Day19_supernatant_TA_A62_S5_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/fastq_trimmed/NP_Day19_supernatant_TA_A62_S5_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/trimming/NP_Day19_supernatant_TA_A62_S5.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/trimming/NP_Day19_supernatant_TA_A62_S5.fastp.json 
NP_Day1_adherentcells_DMSO_A70_S14	fastp -w 2 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/fastq/NP_Day1_adherentcells_DMSO_A70_S14_R1.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/fastq/NP_Day1_adherentcells_DMSO_A70_S14_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/fastq_trimmed/NP_Day1_adherentcells_DMSO_A70_S14_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/fastq_trimmed/NP_Day1_adherentcells_DMSO_A70_S14_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/trimming/NP_Day1_adherentcells_DMSO_A70_S14.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/trimming/NP_Day1_adherentcells_DMSO_A70_S14.fastp.json 
NP_Day1_adherentcells_TA_A66_S11	fastp -w 2 --in1 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/fastq/NP_Day1_adherentcells_TA_A66_S11_R1.fastq.gz --in2 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/fastq/NP_Day1_adherentcells_TA_A66_S11_R2.fastq.gz --out1 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/fastq_trimmed/NP_Day1_adherentcells_TA_A66_S11_R1_trimmed.fastq.gz --out2 /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/fastq_trimmed/NP_Day1_adherentcells_TA_A66_S11_R2_trimmed.fastq.gz -h /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/trimming/NP_Day1_adherentcells_TA_A66_S11.fastp.html -j /ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/trimming/NP_Day1_adherentcells_TA_A66_S11.fastp.json