Module	Section	Sample Name	Source
FastQC (pre-Trimming)	all_sections	L0_5_EG10_S85_R2_001	/work/project/crucial/Sarah/7-EAGER/NC_020762.1_RESULTS/work/73/d6611528884a41b464d71ba41337d5/fastqc_raw/L0_5_EG10_S85_R2_001_raw_fastqc.zip
FastQC (pre-Trimming)	all_sections	L7_14_22d_S48_R2_001	/work/project/crucial/Sarah/7-EAGER/NC_020762.1_RESULTS/work/73/d6611528884a41b464d71ba41337d5/fastqc_raw/L7_14_22d_S48_R2_001_raw_fastqc.zip
FastQC (pre-Trimming)	all_sections	L0_5_EG10_S85_R1_001	/work/project/crucial/Sarah/7-EAGER/NC_020762.1_RESULTS/work/73/d6611528884a41b464d71ba41337d5/fastqc_raw/L0_5_EG10_S85_R1_001_raw_fastqc.zip
FastQC (pre-Trimming)	all_sections	L7_14_22d_S48_R1_001	/work/project/crucial/Sarah/7-EAGER/NC_020762.1_RESULTS/work/73/d6611528884a41b464d71ba41337d5/fastqc_raw/L7_14_22d_S48_R1_001_raw_fastqc.zip
Adapter Removal	all_sections	L7_14_22d_S48_R1_001	/work/project/crucial/Sarah/7-EAGER/NC_020762.1_RESULTS/work/73/d6611528884a41b464d71ba41337d5/adapter_removal/L7_14_22d_S48_R1_001.fastq_L0.pe.settings
Adapter Removal	all_sections	L0_5_EG10_S85_R1_001	/work/project/crucial/Sarah/7-EAGER/NC_020762.1_RESULTS/work/73/d6611528884a41b464d71ba41337d5/adapter_removal/L0_5_EG10_S85_R1_001.fastq_L0.pe.settings
FastQC (post-Trimming)	all_sections	L7_14_22d_S48_R1_001	/work/project/crucial/Sarah/7-EAGER/NC_020762.1_RESULTS/work/73/d6611528884a41b464d71ba41337d5/fastqc/L7_14_22d_S48_R1_001.fastq_L0.pe.combined_fastqc.zip
FastQC (post-Trimming)	all_sections	L0_5_EG10_S85_R1_001	/work/project/crucial/Sarah/7-EAGER/NC_020762.1_RESULTS/work/73/d6611528884a41b464d71ba41337d5/fastqc/L0_5_EG10_S85_R1_001.fastq_L0.pe.combined_fastqc.zip
Samtools Flagstat (pre-samtools filter)	flagstat	L0_5_EG10_S85	/work/project/crucial/Sarah/7-EAGER/NC_020762.1_RESULTS/work/73/d6611528884a41b464d71ba41337d5/flagstat/L0_5_EG10_S85_flagstat.stats
Samtools Flagstat (pre-samtools filter)	flagstat	L7_14_22d_S48	/work/project/crucial/Sarah/7-EAGER/NC_020762.1_RESULTS/work/73/d6611528884a41b464d71ba41337d5/flagstat/L7_14_22d_S48_flagstat.stats
Samtools Flagstat (post-samtools filter)	flagstat	L0_5_EG10_S85	/work/project/crucial/Sarah/7-EAGER/NC_020762.1_RESULTS/work/73/d6611528884a41b464d71ba41337d5/flagstat_filtered/L0_5_EG10_S85_postfilterflagstat.stats
Samtools Flagstat (post-samtools filter)	flagstat	L7_14_22d_S48	/work/project/crucial/Sarah/7-EAGER/NC_020762.1_RESULTS/work/73/d6611528884a41b464d71ba41337d5/flagstat_filtered/L7_14_22d_S48_postfilterflagstat.stats
Picard	DuplicationMetrics	L0_5_EG10_S85	/work/project/crucial/Sarah/7-EAGER/NC_020762.1_RESULTS/work/73/d6611528884a41b464d71ba41337d5/markdup/L0_5_EG10_S85_rmdup.metrics
Picard	DuplicationMetrics	L7_14_22d_S48	/work/project/crucial/Sarah/7-EAGER/NC_020762.1_RESULTS/work/73/d6611528884a41b464d71ba41337d5/markdup/L7_14_22d_S48_rmdup.metrics
Preseq	all_sections	L7_14_22d_S48	/work/project/crucial/Sarah/7-EAGER/NC_020762.1_RESULTS/work/73/d6611528884a41b464d71ba41337d5/preseq/L7_14_22d_S48.filtered.preseq
Preseq	all_sections	L0_5_EG10_S85	/work/project/crucial/Sarah/7-EAGER/NC_020762.1_RESULTS/work/73/d6611528884a41b464d71ba41337d5/preseq/L0_5_EG10_S85.filtered.preseq
DamageProfiler	all_sections	L0_5_EG10_S85	/work/project/crucial/Sarah/7-EAGER/NC_020762.1_RESULTS/work/73/d6611528884a41b464d71ba41337d5/damageprofiler/dmgprof8/dmgprof.json
DamageProfiler	all_sections	L7_14_22d_S48	/work/project/crucial/Sarah/7-EAGER/NC_020762.1_RESULTS/work/73/d6611528884a41b464d71ba41337d5/damageprofiler/dmgprof16/dmgprof.json
mtnucratio	all_sections	L0_5_EG10_S85	/work/project/crucial/Sarah/7-EAGER/NC_020762.1_RESULTS/work/73/d6611528884a41b464d71ba41337d5/mutnucratio/L0_5_EG10_S85_rmdup.bam.mtnucratiomtnuc.json
mtnucratio	all_sections	L7_14_22d_S48	/work/project/crucial/Sarah/7-EAGER/NC_020762.1_RESULTS/work/73/d6611528884a41b464d71ba41337d5/mutnucratio/L7_14_22d_S48_rmdup.bam.mtnucratiomtnuc.json
QualiMap	genome_results	L7_14_22d_S48	/work/project/crucial/Sarah/7-EAGER/NC_020762.1_RESULTS/work/73/d6611528884a41b464d71ba41337d5/qualimap/qualimap16/L7_14_22d_S48_rmdup_stats/genome_results.txt
QualiMap	genome_results	L0_5_EG10_S85	/work/project/crucial/Sarah/7-EAGER/NC_020762.1_RESULTS/work/73/d6611528884a41b464d71ba41337d5/qualimap/qualimap8/L0_5_EG10_S85_rmdup_stats/genome_results.txt
QualiMap	coverage_histogram	L7_14_22d_S48	/work/project/crucial/Sarah/7-EAGER/NC_020762.1_RESULTS/work/73/d6611528884a41b464d71ba41337d5/qualimap/qualimap16/L7_14_22d_S48_rmdup_stats/raw_data_qualimapReport/coverage_histogram.txt
QualiMap	coverage_histogram	L0_5_EG10_S85	/work/project/crucial/Sarah/7-EAGER/NC_020762.1_RESULTS/work/73/d6611528884a41b464d71ba41337d5/qualimap/qualimap8/L0_5_EG10_S85_rmdup_stats/raw_data_qualimapReport/coverage_histogram.txt
QualiMap	mapped_gc_distribution	L7_14_22d_S48	/work/project/crucial/Sarah/7-EAGER/NC_020762.1_RESULTS/work/73/d6611528884a41b464d71ba41337d5/qualimap/qualimap16/L7_14_22d_S48_rmdup_stats/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt
QualiMap	mapped_gc_distribution	L0_5_EG10_S85	/work/project/crucial/Sarah/7-EAGER/NC_020762.1_RESULTS/work/73/d6611528884a41b464d71ba41337d5/qualimap/qualimap8/L0_5_EG10_S85_rmdup_stats/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt
Bcftools	stats	L0_5_EG10_S85	/work/project/crucial/Sarah/7-EAGER/NC_020762.1_RESULTS/work/73/d6611528884a41b464d71ba41337d5/bcftools_stats16
Bcftools	stats	L7_14_22d_S48	/work/project/crucial/Sarah/7-EAGER/NC_020762.1_RESULTS/work/73/d6611528884a41b464d71ba41337d5/bcftools_stats8