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June 2, 2020 14:58
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| # Fastqs can be provided as: | |
| # -- a pairs of relative/absolute paths | |
| # -- sra:<SRA_NUMBER>, optionally followed by the indices of the first and | |
| # the last entry in the SRA in the form of "?start=<first>&end=<last> | |
| # [to implement] -- as a path to a folder with fastqs '<base_folder>', with the structure | |
| # <base_folder>/<library_name>/<run_name>/, with each folder containing only | |
| # two fastq.gz files | |
| input: | |
| raw_reads_paths: | |
| Schmitt2016_STL002_Adrenal-1: | |
| lane1: | |
| - sra:SRR4271980 | |
| lane2: | |
| - sra:SRR4271981 | |
| lane3: | |
| - sra:SRR4271982 | |
| lane4: | |
| - sra:SRR4271983 | |
| Schmitt2016_STL001_Bladder-1: | |
| lane1: | |
| - sra:SRR4271984 | |
| lane2: | |
| - sra:SRR4271985 | |
| lane3: | |
| - sra:SRR4271986 | |
| lane4: | |
| - sra:SRR4271987 | |
| Schmitt2016_STL001_Bladder-2: | |
| lane1: | |
| - sra:SRR4271988 | |
| lane2: | |
| - sra:SRR4271989 | |
| lane3: | |
| - sra:SRR4271990 | |
| lane4: | |
| - sra:SRR4271991 | |
| lane5: | |
| - sra:SRR4271992 | |
| Schmitt2016_Cortex-1: | |
| lane1: | |
| - sra:SRR4271993 | |
| lane2: | |
| - sra:SRR4271994 | |
| lane3: | |
| - sra:SRR4271995 | |
| lane4: | |
| - sra:SRR4271996 | |
| Schmitt2016_Hippocampus-1: | |
| lane1: | |
| - sra:SRR4271997 | |
| lane2: | |
| - sra:SRR4271998 | |
| lane3: | |
| - sra:SRR4271999 | |
| lane4: | |
| - sra:SRR4272000 | |
| Schmitt2016_STL002_Lung-1: | |
| lane1: | |
| - sra:SRR4272001 | |
| lane2: | |
| - sra:SRR4272002 | |
| lane3: | |
| - sra:SRR4272003 | |
| Schmitt2016_STL001_Lung-1: | |
| lane1: | |
| - sra:SRR4272004 | |
| lane2: | |
| - sra:SRR4272005 | |
| lane3: | |
| - sra:SRR4272006 | |
| Schmitt2016_STL002_Ovary-1: | |
| lane1: | |
| - sra:SRR4272007 | |
| lane2: | |
| - sra:SRR4272008 | |
| lane3: | |
| - sra:SRR4272009 | |
| lane4: | |
| - sra:SRR4272010 | |
| Schmitt2016_STL002_Pancreas-1: | |
| lane1: | |
| - sra:SRR4272011 | |
| lane2: | |
| - sra:SRR4272012 | |
| lane3: | |
| - sra:SRR4272013 | |
| Schmitt2016_STL003_Pancreas-1: | |
| lane1: | |
| - sra:SRR4272014 | |
| Schmitt2016_STL003_Pancreas-2: | |
| lane1: | |
| - sra:SRR4272015 | |
| lane2: | |
| - sra:SRR4272016 | |
| Schmitt2016_STL003_Pancreas-3: | |
| lane1: | |
| - sra:SRR4272017 | |
| Schmitt2016_STL003_Psoas-1: | |
| lane1: | |
| - sra:SRR4272018 | |
| lane2: | |
| - sra:SRR4272019 | |
| lane3: | |
| - sra:SRR4272020 | |
| Schmitt2016_STL001_Psoas-1: | |
| lane1: | |
| - sra:SRR4272021 | |
| lane2: | |
| - sra:SRR4272022 | |
| lane3: | |
| - sra:SRR4272023 | |
| Schmitt2016_STL001_Psoas-2: | |
| lane1: | |
| - sra:SRR4272024 | |
| Schmitt2016_STL003_RightVentricle-1: | |
| lane1: | |
| - sra:SRR4272025 | |
| lane2: | |
| - sra:SRR4272026 | |
| lane3: | |
| - sra:SRR4272027 | |
| lane4: | |
| - sra:SRR4272028 | |
| lane5: | |
| - sra:SRR4272029 | |
| lane6: | |
| - sra:SRR4272030 | |
| Schmitt2016_STL002_SmallBowel-1: | |
| lane1: | |
| - sra:SRR4272031 | |
| lane2: | |
| - sra:SRR4272032 | |
| lane3: | |
| - sra:SRR4272033 | |
| lane4: | |
| - sra:SRR4272034 | |
| Schmitt2016_STL003_Spleen-1: | |
| lane1: | |
| - sra:SRR4272035 | |
| lane2: | |
| - sra:SRR4272036 | |
| lane3: | |
| - sra:SRR4272037 | |
| Schmitt2016_STL001_Spleen-1: | |
| lane1: | |
| - sra:SRR4272038 | |
| lane2: | |
| - sra:SRR4272039 | |
| lane3: | |
| - sra:SRR4272040 | |
| lane4: | |
| - sra:SRR4272041 | |
| Leung2015_STL002_Aorta-1: | |
| lane1: | |
| - sra:SRR1501138 | |
| lane2: | |
| - sra:SRR1501139 | |
| lane3: | |
| - sra:SRR1501140 | |
| lane4: | |
| - sra:SRR1501141 | |
| Leung2015_STL003_LeftVentricle-1: | |
| lane1: | |
| - sra:SRR1501142 | |
| lane2: | |
| - sra:SRR1501143 | |
| lane3: | |
| - sra:SRR1501144 | |
| lane4: | |
| - sra:SRR1501145 | |
| lane5: | |
| - sra:SRR1501146 | |
| Leung2015_STL011_Liver-1: | |
| lane1: | |
| - sra:SRR1501147 | |
| lane2: | |
| - sra:SRR1501148 | |
| lane3: | |
| - sra:SRR1501149 | |
| lane4: | |
| - sra:SRR1501150 | |
| lane5: | |
| - sra:SRR1501151 | |
| library_groups: | |
| Schmitt2016_Adrenal: | |
| - Schmitt2016_STL002_Adrenal-1 | |
| Schmitt2016_Bladder: | |
| - Schmitt2016_STL001_Bladder-1 | |
| - Schmitt2016_STL001_Bladder-2 | |
| Schmitt2016_Cortex: | |
| - Schmitt2016_Cortex-1 | |
| Schmitt2016_Hippocampus: | |
| - Schmitt2016_Hippocampus-1 | |
| Schmitt2016_Lung: | |
| - Schmitt2016_STL002_Lung-1 | |
| - Schmitt2016_STL001_Lung-1 | |
| Schmitt2016_Ovary: | |
| - Schmitt2016_STL002_Ovary-1 | |
| Schmitt2016_Pancreas: | |
| - Schmitt2016_STL002_Pancreas-1 | |
| - Schmitt2016_STL003_Pancreas-1 | |
| - Schmitt2016_STL003_Pancreas-2 | |
| Schmitt2016_Psoas: | |
| - Schmitt2016_STL003_Psoas-1 | |
| - Schmitt2016_STL001_Psoas-1 | |
| - Schmitt2016_STL001_Psoas-2 | |
| Schmitt2016_RightVentricle: | |
| - Schmitt2016_STL003_RightVentricle-1 | |
| Schmitt2016_SmallBowel: | |
| - Schmitt2016_STL002_SmallBowel-1 | |
| Schmitt2016_Spleen: | |
| - Schmitt2016_STL003_Spleen-1 | |
| - Schmitt2016_STL001_Spleen-1 | |
| Leung2015_Aorta: | |
| - Leung2015_STL002_Aorta-1 | |
| Leung2015_LeftVentricle: | |
| - Leung2015_STL003_LeftVentricle-1 | |
| Leung2015_Liver: | |
| - Leung2015_STL011_Liver-1 | |
| truncate_fastq_reads: 0 | |
| genome: | |
| assembly_name: 'hg38' | |
| bwa_index_wildcard_path: '/exports/igmm/eddie/wendy-lab/ilia/genomes/hg38/bwaindex/hg38.fa*' | |
| chrom_sizes_path: '/exports/igmm/eddie/wendy-lab/ilia/genomes/hg38/chrfile.txt' | |
| do_fastqc: False | |
| map: | |
| chunksize: 10000000 | |
| mapping_options: '' | |
| parse: | |
| make_pairsam: False | |
| drop_readid: True | |
| drop_seq: True | |
| keep_unparsed_bams: False | |
| parsing_options: '--add-columns mapq' | |
| dedup: | |
| max_mismatch_bp: 0 | |
| bin: | |
| resolutions: | |
| - 10000000 | |
| - 5000000 | |
| - 2000000 | |
| - 1000000 | |
| - 500000 | |
| - 200000 | |
| - 100000 | |
| - 50000 | |
| - 20000 | |
| - 10000 | |
| - 5000 | |
| - 2000 | |
| - 1000 | |
| balance: True | |
| # balance_options: '--cis-only' | |
| filters: | |
| # no_filter: '' | |
| mapq_30: '(mapq1>=30) and (mapq2>=30)' | |
| output: | |
| dirs: | |
| processed_fastqs: './project/output/processed_fastqs/' | |
| mapped_parsed_sorted_chunks: './project/output/mapped_parsed_sorted_chunks' | |
| fastqc: './project/output/fastqc/' | |
| pairs_library: './project/output/pairs_library' | |
| coolers_library: './project/output/coolers_library/' | |
| coolers_library_group: './project/output/coolers_library_group/' | |
| stats_library_group: './project/output/stats_library_group/' |
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