Module	Section	Sample Name	Source
QualiMap	mapped_gc_distribution	ea1 | map | 1EA_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-smds_stats | raw_data_qualimapReport | asm_pair-smds_stats	/data/m/ea1/map/1EA_L7_R1_001_dedup.fastq.gz/bowtie2/asm_pair-smds_stats/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt
QualiMap	mapped_gc_distribution	ea1 | map | 3EA_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-smds_stats | raw_data_qualimapReport | asm_pair-smds_stats	/data/m/ea1/map/3EA_L7_R1_001_dedup.fastq.gz/bowtie2/asm_pair-smds_stats/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt
QualiMap	mapped_gc_distribution	ea1 | map | 2EA_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-smds_stats | raw_data_qualimapReport | asm_pair-smds_stats	/data/m/ea1/map/2EA_L7_R1_001_dedup.fastq.gz/bowtie2/asm_pair-smds_stats/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt
QualiMap	coverage_histogram	ea1 | map | 1EA_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-smds_stats | raw_data_qualimapReport | asm_pair-smds_stats	/data/m/ea1/map/1EA_L7_R1_001_dedup.fastq.gz/bowtie2/asm_pair-smds_stats/raw_data_qualimapReport/coverage_histogram.txt
QualiMap	coverage_histogram	ea1 | map | 3EA_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-smds_stats | raw_data_qualimapReport | asm_pair-smds_stats	/data/m/ea1/map/3EA_L7_R1_001_dedup.fastq.gz/bowtie2/asm_pair-smds_stats/raw_data_qualimapReport/coverage_histogram.txt
QualiMap	coverage_histogram	ea1 | map | 2EA_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-smds_stats | raw_data_qualimapReport | asm_pair-smds_stats	/data/m/ea1/map/2EA_L7_R1_001_dedup.fastq.gz/bowtie2/asm_pair-smds_stats/raw_data_qualimapReport/coverage_histogram.txt
QualiMap	insert_size_histogram	ea1 | map | 1EA_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-smds_stats | raw_data_qualimapReport | asm_pair-smds_stats	/data/m/ea1/map/1EA_L7_R1_001_dedup.fastq.gz/bowtie2/asm_pair-smds_stats/raw_data_qualimapReport/insert_size_histogram.txt
QualiMap	insert_size_histogram	ea1 | map | 3EA_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-smds_stats | raw_data_qualimapReport | asm_pair-smds_stats	/data/m/ea1/map/3EA_L7_R1_001_dedup.fastq.gz/bowtie2/asm_pair-smds_stats/raw_data_qualimapReport/insert_size_histogram.txt
QualiMap	insert_size_histogram	ea1 | map | 2EA_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-smds_stats | raw_data_qualimapReport | asm_pair-smds_stats	/data/m/ea1/map/2EA_L7_R1_001_dedup.fastq.gz/bowtie2/asm_pair-smds_stats/raw_data_qualimapReport/insert_size_histogram.txt
QualiMap	genome_results	ea1 | map | 2EA_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-smds_stats | asm_pair-smds.bam	/data/m/ea1/map/2EA_L7_R1_001_dedup.fastq.gz/bowtie2/asm_pair-smds_stats/genome_results.txt
QualiMap	genome_results	ea1 | map | 1EA_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-smds_stats | asm_pair-smds.bam	/data/m/ea1/map/1EA_L7_R1_001_dedup.fastq.gz/bowtie2/asm_pair-smds_stats/genome_results.txt
QualiMap	genome_results	ea1 | map | 3EA_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-smds_stats | asm_pair-smds.bam	/data/m/ea1/map/3EA_L7_R1_001_dedup.fastq.gz/bowtie2/asm_pair-smds_stats/genome_results.txt
Picard	DuplicationMetrics	multiqc_data_1 | multiqc_data.json	/data/m/multiqc_data_1/multiqc_data.json
Picard	DuplicationMetrics	tsb2 | map | 5TSB_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-s.bam	/data/m/tsb2/map/5TSB_L7_R1_001_dedup.fastq.gz/bowtie2/asm_pair-smd.metrics
Picard	DuplicationMetrics	tsb1 | map | 2TSB_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-s.bam	/data/m/tsb1/map/2TSB_L7_R1_001_dedup.fastq.gz/bowtie2/asm_pair-smd.metrics
Picard	DuplicationMetrics	tsb2 | map | 6TSB_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-s.bam	/data/m/tsb2/map/6TSB_L7_R1_001_dedup.fastq.gz/bowtie2/asm_pair-smd.metrics
Picard	DuplicationMetrics	ea1 | map | 1EA_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-s.bam	/data/m/ea1/map/1EA_L7_R1_001_dedup.fastq.gz/bowtie2/asm_pair-smd.metrics
Picard	DuplicationMetrics	ea1 | multiqc_data_1 | multiqc_data.json	/data/m/ea1/multiqc_data_1/multiqc_data.json
Picard	DuplicationMetrics	tsb2 | map | 4TSB_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-s.bam	/data/m/tsb2/map/4TSB_L7_R1_001_dedup.fastq.gz/bowtie2/asm_pair-smd.metrics
Picard	DuplicationMetrics	ea2 | map | 4EA_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-s.bam	/data/m/ea2/map/4EA_L7_R1_001_dedup.fastq.gz/bowtie2/asm_pair-smd.metrics
Picard	DuplicationMetrics	ea2 | map | 6EA_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-s.bam	/data/m/ea2/map/6EA_L7_R1_001_dedup.fastq.gz/bowtie2/asm_pair-smd.metrics
Picard	DuplicationMetrics	ea2 | map | 5EA_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-s.bam	/data/m/ea2/map/5EA_L7_R1_001_dedup.fastq.gz/bowtie2/asm_pair-smd.metrics
Picard	DuplicationMetrics	ea1 | map | 2EA_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-s.bam	/data/m/ea1/map/2EA_L7_R1_001_dedup.fastq.gz/bowtie2/asm_pair-smd.metrics
Picard	DuplicationMetrics	tsb1 | map | 1TSB_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-s.bam	/data/m/tsb1/map/1TSB_L7_R1_001_dedup.fastq.gz/bowtie2/asm_pair-smd.metrics
Picard	DuplicationMetrics	tsb1 | map | 3TSB_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-s.bam	/data/m/tsb1/map/3TSB_L7_R1_001_dedup.fastq.gz/bowtie2/asm_pair-smd.metrics
Picard	DuplicationMetrics	ea1 | map | 3EA_L7_R1_001_dedup.fastq.gz | bowtie2 | asm_pair-s.bam	/data/m/ea1/map/3EA_L7_R1_001_dedup.fastq.gz/bowtie2/asm_pair-smd.metrics
Prokka	all_sections	tsb2 | prokka | strain	/data/m/tsb2/prokka/PROKKA_12222018.txt
Prokka	all_sections	tsb1 | prokka | strain	/data/m/tsb1/prokka/PROKKA_12222018.txt
Prokka	all_sections	ea1 | prokka | strain	/data/m/ea1/prokka/PROKKA_12222018.txt
Prokka	all_sections	ea2 | prokka_old | strain	/data/m/ea2/prokka_old/PROKKA_12222018.txt
Prokka	all_sections	ea2 | prokka | strain	/data/m/ea2/prokka/PROKKA_12232018.txt
FastQC	all_sections	ea2 | 5EA_L7_R1_001.fastq.gz	/data/m/ea2/5EA_L7_R1_001_fastqc.zip
FastQC	all_sections	tsb2 | 4TSB_L7_R1_001.fastq.gz	/data/m/tsb2/4TSB_L7_R1_001_fastqc.zip
FastQC	all_sections	tsb1 | 3TSB_L7_R1_001.fastq.gz	/data/m/tsb1/3TSB_L7_R1_001_fastqc.zip
FastQC	all_sections	tsb1 | 2TSB_L7_R2_001.fastq.gz	/data/m/tsb1/2TSB_L7_R2_001_fastqc.zip
FastQC	all_sections	tsb1 | 3TSB_L7_R2_001.fastq.gz	/data/m/tsb1/3TSB_L7_R2_001_fastqc.zip
FastQC	all_sections	tsb1 | 1TSB_L7_R1_001.fastq.gz	/data/m/tsb1/1TSB_L7_R1_001_fastqc.zip
FastQC	all_sections	ea2 | 5EA_L7_R2_001.fastq.gz	/data/m/ea2/5EA_L7_R2_001_fastqc.zip
FastQC	all_sections	ea2 | 4EA_L7_R2_001.fastq.gz	/data/m/ea2/4EA_L7_R2_001_fastqc.zip
FastQC	all_sections	ea2 | 6EA_L7_R2_001.fastq.gz	/data/m/ea2/6EA_L7_R2_001_fastqc.zip
FastQC	all_sections	tsb2 | 6TSB_L7_R1_001.fastq.gz	/data/m/tsb2/6TSB_L7_R1_001_fastqc.zip
FastQC	all_sections	ea1 | 2EA_L7_R2_001.fastq.gz	/data/m/ea1/2EA_L7_R2_001_fastqc.zip
FastQC	all_sections	ea1 | 3EA_L7_R2_001.fastq.gz	/data/m/ea1/3EA_L7_R2_001_fastqc.zip
FastQC	all_sections	ea2 | 6EA_L7_R1_001.fastq.gz	/data/m/ea2/6EA_L7_R1_001_fastqc.zip
FastQC	all_sections	ea1 | 2EA_L7_R1_001.fastq.gz	/data/m/ea1/2EA_L7_R1_001_fastqc.zip
FastQC	all_sections	tsb2 | 6TSB_L7_R2_001.fastq.gz	/data/m/tsb2/6TSB_L7_R2_001_fastqc.zip
FastQC	all_sections	tsb2 | 4TSB_L7_R2_001.fastq.gz	/data/m/tsb2/4TSB_L7_R2_001_fastqc.zip
FastQC	all_sections	ea2 | 4EA_L7_R1_001.fastq.gz	/data/m/ea2/4EA_L7_R1_001_fastqc.zip
FastQC	all_sections	ea1 | 3EA_L7_R1_001.fastq.gz	/data/m/ea1/3EA_L7_R1_001_fastqc.zip
FastQC	all_sections	ea1 | 1EA_L7_R1_001.fastq.gz	/data/m/ea1/1EA_L7_R1_001_fastqc.zip
FastQC	all_sections	tsb2 | 5TSB_L7_R2_001.fastq.gz	/data/m/tsb2/5TSB_L7_R2_001_fastqc.zip
FastQC	all_sections	tsb2 | 5TSB_L7_R1_001.fastq.gz	/data/m/tsb2/5TSB_L7_R1_001_fastqc.zip
FastQC	all_sections	tsb1 | 2TSB_L7_R1_001.fastq.gz	/data/m/tsb1/2TSB_L7_R1_001_fastqc.zip
FastQC	all_sections	tsb1 | 1TSB_L7_R2_001.fastq.gz	/data/m/tsb1/1TSB_L7_R2_001_fastqc.zip
FastQC	all_sections	ea1 | 1EA_L7_R2_001.fastq.gz	/data/m/ea1/1EA_L7_R2_001_fastqc.zip
