Module	Section	Sample Name	Source
Samtools	stats	SRR7062655.recal	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/SamToolsStats/SRR7062655.recal.bam.samtools.stats.out
Samtools	stats	SRR7062654.recal	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/SamToolsStats/SRR7062654.recal.bam.samtools.stats.out
FastQC	all_sections	SRR7062654_1_R1	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/FastQC/SRR7062654_1_R1_fastqc.zip
FastQC	all_sections	SRR7062655_1_R1	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/FastQC/SRR7062655_1_R1_fastqc.zip
FastQC	all_sections	SRR7062655_1_R2	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/FastQC/SRR7062655_1_R2_fastqc.zip
FastQC	all_sections	SRR7062654_1_R2	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/FastQC/SRR7062654_1_R2_fastqc.zip
Picard	DuplicationMetrics	SRR7062655	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/MarkDuplicates/SRR7062655.bam.metrics
Picard	DuplicationMetrics	SRR7062654	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/MarkDuplicates/SRR7062654.bam.metrics
GATK	base_recalibrator	1.recal.table	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/DuplicatesMarked/1.recal.table
GATK	base_recalibrator	2.recal.table	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/DuplicatesMarked/2.recal.table
QualiMap	mapped_gc_distribution	SRR7062655.recal	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/bamQC/SRR7062655.recal/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt
QualiMap	mapped_gc_distribution	SRR7062654.recal	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/bamQC/SRR7062654.recal/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt
QualiMap	mapped_gc_distribution	SRR7062655_1	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/bamQC/SRR7062655_1/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt
QualiMap	mapped_gc_distribution	SRR7062654_1	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/bamQC/SRR7062654_1/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt
QualiMap	insert_size_histogram	SRR7062655.recal	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/bamQC/SRR7062655.recal/raw_data_qualimapReport/insert_size_histogram.txt
QualiMap	insert_size_histogram	SRR7062654.recal	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/bamQC/SRR7062654.recal/raw_data_qualimapReport/insert_size_histogram.txt
QualiMap	insert_size_histogram	SRR7062655_1	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/bamQC/SRR7062655_1/raw_data_qualimapReport/insert_size_histogram.txt
QualiMap	insert_size_histogram	SRR7062654_1	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/bamQC/SRR7062654_1/raw_data_qualimapReport/insert_size_histogram.txt
QualiMap	genome_results	SRR7062655.recal	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/bamQC/SRR7062655.recal/genome_results.txt
QualiMap	genome_results	SRR7062654.recal	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/bamQC/SRR7062654.recal/genome_results.txt
QualiMap	genome_results	SRR7062655_1	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/bamQC/SRR7062655_1/genome_results.txt
QualiMap	genome_results	SRR7062654_1	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/bamQC/SRR7062654_1/genome_results.txt
QualiMap	coverage_histogram	SRR7062655.recal	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/bamQC/SRR7062655.recal/raw_data_qualimapReport/coverage_histogram.txt
QualiMap	coverage_histogram	SRR7062654.recal	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/bamQC/SRR7062654.recal/raw_data_qualimapReport/coverage_histogram.txt
QualiMap	coverage_histogram	SRR7062655_1	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/bamQC/SRR7062655_1/raw_data_qualimapReport/coverage_histogram.txt
QualiMap	coverage_histogram	SRR7062654_1	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/bamQC/SRR7062654_1/raw_data_qualimapReport/coverage_histogram.txt
Bcftools	stats	HaplotypeCaller_SRR7062655	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/BCFToolsStats/HaplotypeCaller_SRR7062655.bcf.tools.stats.out
Bcftools	stats	HaplotypeCaller_SRR7062654	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/BCFToolsStats/HaplotypeCaller_SRR7062654.bcf.tools.stats.out
Bcftools	stats	HaplotypeCaller_SRR7062654.g	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/BCFToolsStats/HaplotypeCaller_SRR7062654.g.bcf.tools.stats.out
Bcftools	stats	FreeBayes_SRR7062654	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/BCFToolsStats/FreeBayes_SRR7062654.bcf.tools.stats.out
Bcftools	stats	FreeBayes_SRR7062655	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/BCFToolsStats/FreeBayes_SRR7062655.bcf.tools.stats.out
Bcftools	stats	HaplotypeCaller_SRR7062655.g	/work2/project/sigenae/Philippe/NextFlow/Chicken_Test_2_Full_Samples/work/e1/1f5c959f975c7715dd3e1931b053e0/BCFToolsStats/HaplotypeCaller_SRR7062655.g.bcf.tools.stats.out