Module	Section	Sample Name	Source
FastQC (pre-Trimming)	all_sections	L0_4_EG9_S84_R2_001	/work/project/crucial/Sarah/7-EAGER/NC_012928.1_RESULTS/work/6a/13056e089d598d4084c76d2632ccad/fastqc_raw/L0_4_EG9_S84_R2_001_raw_fastqc.zip
FastQC (pre-Trimming)	all_sections	L0_4_EG9_S84_R1_001	/work/project/crucial/Sarah/7-EAGER/NC_012928.1_RESULTS/work/6a/13056e089d598d4084c76d2632ccad/fastqc_raw/L0_4_EG9_S84_R1_001_raw_fastqc.zip
Adapter Removal	all_sections	L0_4_EG9_S84_R1_001	/work/project/crucial/Sarah/7-EAGER/NC_012928.1_RESULTS/work/6a/13056e089d598d4084c76d2632ccad/adapter_removal/L0_4_EG9_S84_R1_001.fastq_L0.pe.settings
FastQC (post-Trimming)	all_sections	L0_4_EG9_S84_R1_001	/work/project/crucial/Sarah/7-EAGER/NC_012928.1_RESULTS/work/6a/13056e089d598d4084c76d2632ccad/fastqc/L0_4_EG9_S84_R1_001.fastq_L0.pe.combined_fastqc.zip
Samtools Flagstat (pre-samtools filter)	flagstat	L0_4_EG9_S84	/work/project/crucial/Sarah/7-EAGER/NC_012928.1_RESULTS/work/6a/13056e089d598d4084c76d2632ccad/flagstat/L0_4_EG9_S84_flagstat.stats
Samtools Flagstat (post-samtools filter)	flagstat	L0_4_EG9_S84	/work/project/crucial/Sarah/7-EAGER/NC_012928.1_RESULTS/work/6a/13056e089d598d4084c76d2632ccad/flagstat_filtered/L0_4_EG9_S84_postfilterflagstat.stats
Picard	DuplicationMetrics	L0_4_EG9_S84	/work/project/crucial/Sarah/7-EAGER/NC_012928.1_RESULTS/work/6a/13056e089d598d4084c76d2632ccad/markdup/L0_4_EG9_S84_rmdup.metrics
Preseq	all_sections	L0_4_EG9_S84	/work/project/crucial/Sarah/7-EAGER/NC_012928.1_RESULTS/work/6a/13056e089d598d4084c76d2632ccad/preseq/L0_4_EG9_S84.filtered.preseq
DamageProfiler	all_sections	L0_4_EG9_S84	/work/project/crucial/Sarah/7-EAGER/NC_012928.1_RESULTS/work/6a/13056e089d598d4084c76d2632ccad/damageprofiler/dmgprof8/dmgprof.json
mtnucratio	all_sections	L0_4_EG9_S84	/work/project/crucial/Sarah/7-EAGER/NC_012928.1_RESULTS/work/6a/13056e089d598d4084c76d2632ccad/mutnucratio/L0_4_EG9_S84_rmdup.bam.mtnucratiomtnuc.json
QualiMap	genome_results	L0_4_EG9_S84	/work/project/crucial/Sarah/7-EAGER/NC_012928.1_RESULTS/work/6a/13056e089d598d4084c76d2632ccad/qualimap/qualimap8/L0_4_EG9_S84_rmdup_stats/genome_results.txt
QualiMap	coverage_histogram	L0_4_EG9_S84	/work/project/crucial/Sarah/7-EAGER/NC_012928.1_RESULTS/work/6a/13056e089d598d4084c76d2632ccad/qualimap/qualimap8/L0_4_EG9_S84_rmdup_stats/raw_data_qualimapReport/coverage_histogram.txt
QualiMap	mapped_gc_distribution	L0_4_EG9_S84	/work/project/crucial/Sarah/7-EAGER/NC_012928.1_RESULTS/work/6a/13056e089d598d4084c76d2632ccad/qualimap/qualimap8/L0_4_EG9_S84_rmdup_stats/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt
Bcftools	stats	L0_4_EG9_S84	/work/project/crucial/Sarah/7-EAGER/NC_012928.1_RESULTS/work/6a/13056e089d598d4084c76d2632ccad/bcftools_stats8