Module	Section	Sample Name	Source
fastp	all_sections	HSC_D12_RU_1uM_1	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/trimming/HSC_D12_RU_1uM_1.fastp.json
fastp	all_sections	HSC_D12_RU_1uM_3	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/trimming/HSC_D12_RU_1uM_3.fastp.json
fastp	all_sections	HSC_D12_RU_1uM_plus_TA_100nM_3	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/trimming/HSC_D12_RU_1uM_plus_TA_100nM_3.fastp.json
fastp	all_sections	HSC_D12_TA_1uM_1	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/trimming/HSC_D12_TA_1uM_1.fastp.json
fastp	all_sections	HSC_D12_RU_1uM_plus_TA_100nM_1	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/trimming/HSC_D12_RU_1uM_plus_TA_100nM_1.fastp.json
fastp	all_sections	HSC_D12_DMSO	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/trimming/HSC_D12_DMSO.fastp.json
fastp	all_sections	HSC_D12_DMSO_2	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/trimming/HSC_D12_DMSO_2.fastp.json
fastp	all_sections	HSC_D12_DMSO_1	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/trimming/HSC_D12_DMSO_1.fastp.json
fastp	all_sections	HSC_D12_TA_100nM_3	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/trimming/HSC_D12_TA_100nM_3.fastp.json
fastp	all_sections	HSC_D12_TA_1uM_3	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/trimming/HSC_D12_TA_1uM_3.fastp.json
fastp	all_sections	HSC_D12_RU_1_uM_plus_TA_1uM_3	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/trimming/HSC_D12_RU_1_uM_plus_TA_1uM_3.fastp.json
fastp	all_sections	HSC_D12_RU_1uM	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/trimming/HSC_D12_RU_1uM.fastp.json
fastp	all_sections	HSC_D12_TA_100nM_2	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/trimming/HSC_D12_TA_100nM_2.fastp.json
fastp	all_sections	HSC_D12_RU_1_uM_plus_TA_1uM_2	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/trimming/HSC_D12_RU_1_uM_plus_TA_1uM_2.fastp.json
fastp	all_sections	HSC_D12_TA_100nM_1	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/trimming/HSC_D12_TA_100nM_1.fastp.json
fastp	all_sections	HSC_D12_TA_100nM	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/trimming/HSC_D12_TA_100nM.fastp.json
fastp	all_sections	HSC_D12_TA_1uM_2	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/trimming/HSC_D12_TA_1uM_2.fastp.json
fastp	all_sections	HSC_D12_TA_1uM	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/trimming/HSC_D12_TA_1uM.fastp.json
fastp	all_sections	HSC_D12_RU_1uM_plus_TA_100nM_2	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/trimming/HSC_D12_RU_1uM_plus_TA_100nM_2.fastp.json
fastp	all_sections	HSC_D12_RU_1uM_2	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/trimming/HSC_D12_RU_1uM_2.fastp.json
fastp	all_sections	HSC_D12_DMSO_3	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/trimming/HSC_D12_DMSO_3.fastp.json
fastp	all_sections	HSC_D12_RU_1_uM_plus_TA_1uM_1	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/trimming/HSC_D12_RU_1_uM_plus_TA_1uM_1.fastp.json
fastp	all_sections	HSC_D12_RU_1uM_plus_TA_100nM	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/trimming/HSC_D12_RU_1uM_plus_TA_100nM.fastp.json
fastp	all_sections	HSC_D12_RU_1_uM_plus_TA_1uM	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/trimming/HSC_D12_RU_1_uM_plus_TA_1uM.fastp.json
Picard	InsertSizeMetrics	HSC_D12_TA_100nM	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/InsertSizeMetrics/GRCh37-HSC_D12_TA_100nM.tsv
Picard	InsertSizeMetrics	HSC_D12_RU_1uM	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/InsertSizeMetrics/GRCh37-HSC_D12_RU_1uM.tsv
Picard	InsertSizeMetrics	HSC_D12_TA_1uM	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/InsertSizeMetrics/GRCh37-HSC_D12_TA_1uM.tsv
Picard	InsertSizeMetrics	HSC_D12_RU_1uM_plus_TA_100nM	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/InsertSizeMetrics/GRCh37-HSC_D12_RU_1uM_plus_TA_100nM.tsv
Picard	InsertSizeMetrics	HSC_D12_RU_1_uM_plus_TA_1uM	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/InsertSizeMetrics/GRCh37-HSC_D12_RU_1_uM_plus_TA_1uM.tsv
Picard	InsertSizeMetrics	HSC_D12_DMSO	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/InsertSizeMetrics/GRCh37-HSC_D12_DMSO.tsv
Picard	DuplicationMetrics	HSC_D12_TA_100nM	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/markdup/GRCh37-HSC_D12_TA_100nM.samtools-coordinate.metrics.txt
Picard	DuplicationMetrics	HSC_D12_RU_1_uM_plus_TA_1uM	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/markdup/GRCh37-HSC_D12_RU_1_uM_plus_TA_1uM.samtools-coordinate.metrics.txt
Picard	DuplicationMetrics	HSC_D12_RU_1uM	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/markdup/GRCh37-HSC_D12_RU_1uM.samtools-coordinate.metrics.txt
Picard	DuplicationMetrics	HSC_D12_RU_1uM_plus_TA_100nM	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/markdup/GRCh37-HSC_D12_RU_1uM_plus_TA_100nM.samtools-coordinate.metrics.txt
Picard	DuplicationMetrics	HSC_D12_TA_1uM	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/markdup/GRCh37-HSC_D12_TA_1uM.samtools-coordinate.metrics.txt
Picard	DuplicationMetrics	HSC_D12_DMSO	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/markdup/GRCh37-HSC_D12_DMSO.samtools-coordinate.metrics.txt
SamTools pre-sieve	stats	HSC_D12_TA_1uM	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/samtools_stats/star/GRCh37-HSC_D12_TA_1uM.samtools-coordinate.samtools_stats.txt
SamTools pre-sieve	stats	HSC_D12_TA_100nM	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/samtools_stats/star/GRCh37-HSC_D12_TA_100nM.samtools-coordinate.samtools_stats.txt
SamTools pre-sieve	stats	HSC_D12_DMSO	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/samtools_stats/star/GRCh37-HSC_D12_DMSO.samtools-coordinate.samtools_stats.txt
SamTools pre-sieve	stats	HSC_D12_RU_1uM	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/samtools_stats/star/GRCh37-HSC_D12_RU_1uM.samtools-coordinate.samtools_stats.txt
SamTools pre-sieve	stats	HSC_D12_RU_1uM_plus_TA_100nM	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/samtools_stats/star/GRCh37-HSC_D12_RU_1uM_plus_TA_100nM.samtools-coordinate.samtools_stats.txt
SamTools pre-sieve	stats	HSC_D12_RU_1_uM_plus_TA_1uM	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/samtools_stats/star/GRCh37-HSC_D12_RU_1_uM_plus_TA_1uM.samtools-coordinate.samtools_stats.txt
SamTools post-sieve	stats	HSC_D12_DMSO	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/samtools_stats/final_bam/GRCh37-HSC_D12_DMSO.samtools-coordinate.samtools_stats.txt
SamTools post-sieve	stats	HSC_D12_RU_1uM_plus_TA_100nM	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/samtools_stats/final_bam/GRCh37-HSC_D12_RU_1uM_plus_TA_100nM.samtools-coordinate.samtools_stats.txt
SamTools post-sieve	stats	HSC_D12_TA_100nM	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/samtools_stats/final_bam/GRCh37-HSC_D12_TA_100nM.samtools-coordinate.samtools_stats.txt
SamTools post-sieve	stats	HSC_D12_RU_1_uM_plus_TA_1uM	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/samtools_stats/final_bam/GRCh37-HSC_D12_RU_1_uM_plus_TA_1uM.samtools-coordinate.samtools_stats.txt
SamTools post-sieve	stats	HSC_D12_TA_1uM	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/samtools_stats/final_bam/GRCh37-HSC_D12_TA_1uM.samtools-coordinate.samtools_stats.txt
SamTools post-sieve	stats	HSC_D12_RU_1uM	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/samtools_stats/final_bam/GRCh37-HSC_D12_RU_1uM.samtools-coordinate.samtools_stats.txt
deepTools	plotPCA	GRCh37	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/plotPCA/GRCh37.tsv
deepTools	plotFingerprint	GRCh37	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/plotFingerprint/GRCh37.tsv
mtnucratio	all_sections	HSC_D12_TA_1uM	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/star/GRCh37-HSC_D12_TA_1uM.samtools-coordinate-unsieved.bam.mtnucratiomtnuc.json
mtnucratio	all_sections	HSC_D12_RU_1uM_plus_TA_100nM	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/star/GRCh37-HSC_D12_RU_1uM_plus_TA_100nM.samtools-coordinate-unsieved.bam.mtnucratiomtnuc.json
mtnucratio	all_sections	HSC_D12_RU_1uM	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/star/GRCh37-HSC_D12_RU_1uM.samtools-coordinate-unsieved.bam.mtnucratiomtnuc.json
mtnucratio	all_sections	HSC_D12_DMSO	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/star/GRCh37-HSC_D12_DMSO.samtools-coordinate-unsieved.bam.mtnucratiomtnuc.json
mtnucratio	all_sections	HSC_D12_RU_1_uM_plus_TA_1uM	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/star/GRCh37-HSC_D12_RU_1_uM_plus_TA_1uM.samtools-coordinate-unsieved.bam.mtnucratiomtnuc.json
mtnucratio	all_sections	HSC_D12_TA_100nM	/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/star/GRCh37-HSC_D12_TA_100nM.samtools-coordinate-unsieved.bam.mtnucratiomtnuc.json