Module	Section	Sample Name	Source
FastQC (pre-Trimming)	all_sections	L2_4_CD2_S74_R2_001	/work/project/crucial/Sarah/7-EAGER/NC_009263.1_RESULTS/work/ea/80b47d09899ebc219f554c909b97c1/fastqc_raw/L2_4_CD2_S74_R2_001_raw_fastqc.zip
FastQC (pre-Trimming)	all_sections	L2_4_CD2_S74_R1_001	/work/project/crucial/Sarah/7-EAGER/NC_009263.1_RESULTS/work/ea/80b47d09899ebc219f554c909b97c1/fastqc_raw/L2_4_CD2_S74_R1_001_raw_fastqc.zip
Adapter Removal	all_sections	L2_4_CD2_S74_R1_001	/work/project/crucial/Sarah/7-EAGER/NC_009263.1_RESULTS/work/ea/80b47d09899ebc219f554c909b97c1/adapter_removal/L2_4_CD2_S74_R1_001.fastq_L0.pe.settings
FastQC (post-Trimming)	all_sections	L2_4_CD2_S74_R1_001	/work/project/crucial/Sarah/7-EAGER/NC_009263.1_RESULTS/work/ea/80b47d09899ebc219f554c909b97c1/fastqc/L2_4_CD2_S74_R1_001.fastq_L0.pe.combined_fastqc.zip
Samtools Flagstat (pre-samtools filter)	flagstat	L2_4_CD2_S74	/work/project/crucial/Sarah/7-EAGER/NC_009263.1_RESULTS/work/ea/80b47d09899ebc219f554c909b97c1/flagstat/L2_4_CD2_S74_flagstat.stats
Samtools Flagstat (post-samtools filter)	flagstat	L2_4_CD2_S74	/work/project/crucial/Sarah/7-EAGER/NC_009263.1_RESULTS/work/ea/80b47d09899ebc219f554c909b97c1/flagstat_filtered/L2_4_CD2_S74_postfilterflagstat.stats
Picard	DuplicationMetrics	L2_4_CD2_S74	/work/project/crucial/Sarah/7-EAGER/NC_009263.1_RESULTS/work/ea/80b47d09899ebc219f554c909b97c1/markdup/L2_4_CD2_S74_rmdup.metrics
Preseq	all_sections	L2_4_CD2_S74	/work/project/crucial/Sarah/7-EAGER/NC_009263.1_RESULTS/work/ea/80b47d09899ebc219f554c909b97c1/preseq/L2_4_CD2_S74.filtered.preseq
DamageProfiler	all_sections	L2_4_CD2_S74	/work/project/crucial/Sarah/7-EAGER/NC_009263.1_RESULTS/work/ea/80b47d09899ebc219f554c909b97c1/damageprofiler/dmgprof8/dmgprof.json
mtnucratio	all_sections	L2_4_CD2_S74	/work/project/crucial/Sarah/7-EAGER/NC_009263.1_RESULTS/work/ea/80b47d09899ebc219f554c909b97c1/mutnucratio/L2_4_CD2_S74_rmdup.bam.mtnucratiomtnuc.json
QualiMap	genome_results	L2_4_CD2_S74	/work/project/crucial/Sarah/7-EAGER/NC_009263.1_RESULTS/work/ea/80b47d09899ebc219f554c909b97c1/qualimap/qualimap8/L2_4_CD2_S74_rmdup_stats/genome_results.txt
QualiMap	coverage_histogram	L2_4_CD2_S74	/work/project/crucial/Sarah/7-EAGER/NC_009263.1_RESULTS/work/ea/80b47d09899ebc219f554c909b97c1/qualimap/qualimap8/L2_4_CD2_S74_rmdup_stats/raw_data_qualimapReport/coverage_histogram.txt
QualiMap	mapped_gc_distribution	L2_4_CD2_S74	/work/project/crucial/Sarah/7-EAGER/NC_009263.1_RESULTS/work/ea/80b47d09899ebc219f554c909b97c1/qualimap/qualimap8/L2_4_CD2_S74_rmdup_stats/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt
Bcftools	stats	L2_4_CD2_S74	/work/project/crucial/Sarah/7-EAGER/NC_009263.1_RESULTS/work/ea/80b47d09899ebc219f554c909b97c1/bcftools_stats8