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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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