Module	Section	Sample Name	Source
FastQC (pre-Trimming)	all_sections	L11_7_SCO_1354_S70_R1_001	/work/project/crucial/Sarah/7-EAGER/NC_006531.1_RESULTS/work/21/7fd9d6b15ddd5772a87d1f73c919ae/fastqc_raw/L11_7_SCO_1354_S70_R1_001_raw_fastqc.zip
FastQC (pre-Trimming)	all_sections	L11_7_SCO_1354_S70_R2_001	/work/project/crucial/Sarah/7-EAGER/NC_006531.1_RESULTS/work/21/7fd9d6b15ddd5772a87d1f73c919ae/fastqc_raw/L11_7_SCO_1354_S70_R2_001_raw_fastqc.zip
Adapter Removal	all_sections	L11_7_SCO_1354_S70_R1_001	/work/project/crucial/Sarah/7-EAGER/NC_006531.1_RESULTS/work/21/7fd9d6b15ddd5772a87d1f73c919ae/adapter_removal/L11_7_SCO_1354_S70_R1_001.fastq_L0.pe.settings
FastQC (post-Trimming)	all_sections	L11_7_SCO_1354_S70_R1_001	/work/project/crucial/Sarah/7-EAGER/NC_006531.1_RESULTS/work/21/7fd9d6b15ddd5772a87d1f73c919ae/fastqc/L11_7_SCO_1354_S70_R1_001.fastq_L0.pe.combined_fastqc.zip
Samtools Flagstat (pre-samtools filter)	flagstat	L11_7_SCO_1354_S70	/work/project/crucial/Sarah/7-EAGER/NC_006531.1_RESULTS/work/21/7fd9d6b15ddd5772a87d1f73c919ae/flagstat/L11_7_SCO_1354_S70_flagstat.stats
Samtools Flagstat (post-samtools filter)	flagstat	L11_7_SCO_1354_S70	/work/project/crucial/Sarah/7-EAGER/NC_006531.1_RESULTS/work/21/7fd9d6b15ddd5772a87d1f73c919ae/flagstat_filtered/L11_7_SCO_1354_S70_postfilterflagstat.stats
Picard	DuplicationMetrics	L11_7_SCO_1354_S70	/work/project/crucial/Sarah/7-EAGER/NC_006531.1_RESULTS/work/21/7fd9d6b15ddd5772a87d1f73c919ae/markdup/L11_7_SCO_1354_S70_rmdup.metrics
Preseq	all_sections	L11_7_SCO_1354_S70	/work/project/crucial/Sarah/7-EAGER/NC_006531.1_RESULTS/work/21/7fd9d6b15ddd5772a87d1f73c919ae/preseq/L11_7_SCO_1354_S70.filtered.preseq
DamageProfiler	all_sections	L11_7_SCO_1354_S70	/work/project/crucial/Sarah/7-EAGER/NC_006531.1_RESULTS/work/21/7fd9d6b15ddd5772a87d1f73c919ae/damageprofiler/dmgprof8/dmgprof.json
mtnucratio	all_sections	L11_7_SCO_1354_S70	/work/project/crucial/Sarah/7-EAGER/NC_006531.1_RESULTS/work/21/7fd9d6b15ddd5772a87d1f73c919ae/mutnucratio/L11_7_SCO_1354_S70_rmdup.bam.mtnucratiomtnuc.json
QualiMap	genome_results	L11_7_SCO_1354_S70	/work/project/crucial/Sarah/7-EAGER/NC_006531.1_RESULTS/work/21/7fd9d6b15ddd5772a87d1f73c919ae/qualimap/qualimap8/L11_7_SCO_1354_S70_rmdup_stats/genome_results.txt
QualiMap	coverage_histogram	L11_7_SCO_1354_S70	/work/project/crucial/Sarah/7-EAGER/NC_006531.1_RESULTS/work/21/7fd9d6b15ddd5772a87d1f73c919ae/qualimap/qualimap8/L11_7_SCO_1354_S70_rmdup_stats/raw_data_qualimapReport/coverage_histogram.txt
QualiMap	mapped_gc_distribution	L11_7_SCO_1354_S70	/work/project/crucial/Sarah/7-EAGER/NC_006531.1_RESULTS/work/21/7fd9d6b15ddd5772a87d1f73c919ae/qualimap/qualimap8/L11_7_SCO_1354_S70_rmdup_stats/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt
Bcftools	stats	L11_7_SCO_1354_S70	/work/project/crucial/Sarah/7-EAGER/NC_006531.1_RESULTS/work/21/7fd9d6b15ddd5772a87d1f73c919ae/bcftools_stats8