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* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
261 lines
16 KiB
YAML
261 lines
16 KiB
YAML
- name: artic minion
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command: nextflow run tests/modules/artic/minion -entry test_artic_minion -c tests/config/nextflow.config
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tags:
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- artic
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- artic/minion
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files:
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- path: output/artic/test.1.vcf
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md5sum: f0278719cbb853addcad74b73d810a24
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- path: output/artic/test.2.vcf
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md5sum: f0278719cbb853addcad74b73d810a24
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- path: output/artic/test.alignreport.er
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md5sum: ddfff35c7ebc9837530c78f7a213cea0
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- path: output/artic/test.alignreport.txt
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md5sum: 0fcadf1467ac253476b2d43bbfa36616
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- path: output/artic/test.consensus.fasta
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md5sum: 60ace9fea33aca4c13f3502e330bff85
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- path: output/artic/test.coverage_mask.txt
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md5sum: 7abd414756c444c86766123a60687ed1
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- path: output/artic/test.coverage_mask.txt.1.depths
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md5sum: d4170a48491e12f34b0a15a336bdf5e6
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- path: output/artic/test.coverage_mask.txt.2.depths
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md5sum: 130f85d80c22fccc3e0bbd9de12d310d
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- path: output/artic/test.fail.vcf
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md5sum: e6e184f1fa153868e3acea0eab42e484
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- path: output/artic/test.fastq.gz.index
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md5sum: eaa2b34db5a53fb2d410c5b3bf857fd9
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- path: output/artic/test.fastq.gz.index.fai
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md5sum: 81d718eeaaaae68cb33003f56194e956
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- path: output/artic/test.fastq.gz.index.gzi
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md5sum: 7dea362b3fac8e00956a4952a3d4f474
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- path: output/artic/test.fastq.gz.index.readdb
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md5sum: 3c6296842e91578db93688b4021c8947
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- path: output/artic/test.merged.vcf
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md5sum: e6e184f1fa153868e3acea0eab42e484
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- path: output/artic/test.minion.log.txt
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contains:
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- 'artic_vcf_merge'
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- path: output/artic/test.muscle.in.fasta
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md5sum: 40ae4c89de797d1548c642f0da7a86cc
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- path: output/artic/test.muscle.out.fasta
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md5sum: 40ae4c89de797d1548c642f0da7a86cc
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- path: output/artic/test.pass.vcf.gz
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md5sum: baeafcfc2f738cce771ba895d66e9e01
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- path: output/artic/test.pass.vcf.gz.tbi
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md5sum: 4cb176febbc8c26d717a6c6e67b9c905
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- path: output/artic/test.preconsensus.fasta
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md5sum: 12b16397bae7c68d38150571a6ac6185
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- path: output/artic/test.primers.vcf
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md5sum: e6e184f1fa153868e3acea0eab42e484
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- path: output/artic/test.primersitereport.txt
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md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/artic/test.primertrimmed.rg.sorted.bam
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- path: output/artic/test.primertrimmed.rg.sorted.bam.bai
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md5sum: 0d76977b2e36046cc176112776c5fa4e
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- path: output/artic/test.sorted.bam
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md5sum: 292611ae9885df12575b80853cb5508b
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- path: output/artic/test.sorted.bam.bai
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md5sum: 0d76977b2e36046cc176112776c5fa4e
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- path: output/artic/test.trimmed.rg.sorted.bam
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- path: output/artic/test.trimmed.rg.sorted.bam.bai
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md5sum: 0d76977b2e36046cc176112776c5fa4e
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- path: output/untar/fast5/100read_fast5/00068f7a-51b3-4933-8fc6-7d6e29181ff9.fast5
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md5sum: b7aeb3cc877d858f97144d45551264bc
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- path: output/untar/fast5/100read_fast5/001ed67f-906f-4f37-9770-85d40f5ffee6.fast5
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md5sum: add9b8658095173f7cef6fc23236d913
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- path: output/untar/fast5/100read_fast5/0043238c-3a78-48f1-a8ec-d492280da6e4.fast5
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md5sum: 11d83db48d3b284017b919d476e44294
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- path: output/untar/fast5/100read_fast5/004a65aa-6700-4ad7-9550-dc59f8708908.fast5
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md5sum: fb9f124a05af59ea3ede371cd48e404c
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- path: output/untar/fast5/100read_fast5/00c6481f-9022-4173-9b74-f375c34b9a9b.fast5
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md5sum: c186053a4fee2d509e1d108be8e131e1
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- path: output/untar/fast5/100read_fast5/00da3999-12fd-449d-bd07-32a879667a3d.fast5
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md5sum: ec051e5ce357d632ff740a88087a08fd
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- path: output/untar/fast5/100read_fast5/018c4b52-48fa-4cc8-a7b4-500f41420279.fast5
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md5sum: 9d5bae9c9df0105b3b329777977d6f34
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- path: output/untar/fast5/100read_fast5/01faaaa1-eca2-4bcd-8666-b4d69497107e.fast5
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md5sum: 5855c80a192a242f03a93b74f12dfa46
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- path: output/untar/fast5/100read_fast5/02085a68-dc6e-4275-bd1e-f112fed3bd83.fast5
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md5sum: 6b30e06080aab94b6fa8f476e537f3d2
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- path: output/untar/fast5/100read_fast5/022647b9-0e16-4318-a794-c5749705b67d.fast5
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md5sum: 6606f2661a5463772f4ee30a3dba520e
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md5sum: 53d611cf6465ef914392c11b88339ba0
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- path: output/untar/fast5/100read_fast5/02445dc2-39ee-49f1-8a42-51ebfea52c33.fast5
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md5sum: f7c5844165cbc0566ce1569184fc4213
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- path: output/untar/fast5/100read_fast5/031ff99b-b11f-40dc-9258-273ec97683f8.fast5
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md5sum: e78faae6230537a20497d3114cffcafd
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- path: output/untar/fast5/100read_fast5/03e0e732-cb7a-4084-8fc9-303180c83786.fast5
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md5sum: 27c8ce19a0955d045053a6925e249ae4
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- path: output/untar/fast5/100read_fast5/0457184e-6e09-4883-baf3-824d11101c43.fast5
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md5sum: 7a89c45ae6b360bc585c8b14196ab3f7
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- path: output/untar/fast5/100read_fast5/045f1e6a-9b5d-4840-bad9-c4b738b61267.fast5
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md5sum: ee0c3e5fa1f6820968482594f45e8948
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- path: output/untar/fast5/100read_fast5/046258fa-b951-43a1-bbed-66cdbeac8e71.fast5
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md5sum: 262d3ee396bab6014505b25ba88cea90
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- path: output/untar/fast5/100read_fast5/048d5d3a-16ed-4f36-aeb9-3311dd9dc593.fast5
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md5sum: deea9c03b10aa287f873779baea2a649
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- path: output/untar/fast5/100read_fast5/04a0ee1e-0406-4394-87ba-a67344318a5d.fast5
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md5sum: 7f43a0e0de0053a63a28e36374ec20b4
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md5sum: d607992919072ddb025d766d8ba1a465
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md5sum: 22ccc03bee288edfc589d5f4b11cb70d
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md5sum: 1668668f2d0658a6e3417b08ea093c43
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md5sum: 649ff949e10052b877d9ddb7d6a19009
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md5sum: 5bddb9c020ddd233adc399c806186af6
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md5sum: 4f0d1d5400caa14c376c5c2ba5cf4e90
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md5sum: e8420b20501c06a31223204611aacd44
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md5sum: f703f4942aaa470e2d00706687cea430
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- path: output/untar/fast5/100read_fast5/069ce6e7-41b9-41b2-a6d8-8d39c16dbaa2.fast5
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md5sum: 4ef4d47bf346c9cca805e991a6f5400b
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md5sum: 163a97396e5cf91c40fab7432f52d101
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md5sum: da9798ae314dca12f69ef45c10c8a5a7
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md5sum: 58da6a195dad9cb15fb5ebb76f9ecd19
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md5sum: adfb65496a10bae743e3f0e144220b43
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- path: output/untar/fast5/100read_fast5/1783d96c-3955-4405-b765-472c6286be46.fast5
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md5sum: 6bcbda04b219c8bf971253cc2423a527
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- path: output/untar/fast5/100read_fast5/180da5c9-4574-48ab-8e6a-8f8a73767e30.fast5
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md5sum: 8ef4d3255d87a6fb0fa24b621b72e75a
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- path: output/untar/fast5/100read_fast5/1870a88c-439f-4125-a06c-38b1bf4416e4.fast5
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md5sum: 62db261bbc152a16b0d910680202ba8a
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- path: output/untar/fast5/100read_fast5/188b5eae-fce2-439c-b490-aff6c4327499.fast5
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md5sum: c3157f03f56d03820726ff8ff981b8c9
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- path: output/untar/fast5/100read_fast5/18cef30b-9fe5-40b4-9094-0389bb5aeb8e.fast5
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md5sum: 9fc63db9ca59ac6ff6fa15cfe55b3106
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- path: output/untar/fast5/100read_fast5/18ee103f-1cf8-4694-b2e7-ac228fe70ccd.fast5
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md5sum: 24dc02b54e6712c583f5977bce1d3cd3
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- path: output/untar/fast5/100read_fast5/190a9ebe-4d5f-43c0-a495-82ff58944d07.fast5
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md5sum: 489aa874a1c7c0603076f7ef359d6ace
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- path: output/untar/fast5/100read_fast5/190c4417-c4cf-40fe-a0df-db4b495a3f77.fast5
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md5sum: 997a74664ddab756907435890465d554
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- path: output/untar/fast5/100read_fast5/1a0c9927-e355-49c3-877a-e6b95bc1a402.fast5
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md5sum: fdc9f5f461d0e30ad29cf84e03b6c18d
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- path: output/untar/fast5/100read_fast5/1a276f1c-5a5b-4ed2-b071-87f59f7c5233.fast5
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md5sum: 6269d04009267b7e0df724d7ce355346
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- path: output/untar/fast5/100read_fast5/1a5c9192-aded-4e94-8dcb-9c04a402978e.fast5
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md5sum: 78ce5c5d770d7905bc1986203d69ed49
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- path: output/untar/fast5/100read_fast5/1af84d7e-8fc6-4dba-8750-a0d701f36d1d.fast5
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md5sum: ed5970f92ecdcce95f84dbb1bd275b8e
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- path: output/untar/fast5/100read_fast5/1b753736-87b1-4753-ab1d-bfd7e2d94e9e.fast5
|
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md5sum: 6b5a2fd8b445d4e43eef6d8597932d88
|
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- path: output/untar/fast5/100read_fast5/1b760e8d-7b17-47e0-ba96-5755fc4ddd63.fast5
|
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md5sum: 43eb9e8276e9d0870a4c74882d42e5a0
|
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- path: output/untar/fast5/100read_fast5/1b86544f-8075-46a2-91f4-baac36216ac2.fast5
|
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md5sum: d6266147405391c00aa4dc0ad6797532
|
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- path: output/untar/fast5/100read_fast5/1bd0dad7-1600-44a2-90b8-d5cd7b7caa6d.fast5
|
|
md5sum: 863226172b856834a779eb2013c3a765
|
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- path: output/untar/fast5/100read_fast5/1d568051-bdd6-4204-ac34-97b5a3f7375c.fast5
|
|
md5sum: 7d4cdf29110898e5f6a3288a0a2b9342
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- path: output/untar/fast5/100read_fast5/1d650a9e-4e67-456a-9abe-bd34b238abe4.fast5
|
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md5sum: 3fac1d13ed49703e33e92b8aaab3dac6
|
|
- path: output/untar/fast5/100read_fast5/1d86c2b3-c2c6-43a1-97ed-8c1f0cbf6476.fast5
|
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md5sum: 2eed32c760d94aac2dce49c2364f6cd9
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|
- path: output/untar/fast5/100read_fast5/20586d1a-2cd0-45aa-abc2-04ac66d8ea46.fast5
|
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md5sum: d89ef1d32a52fc5d45a17d7682e4de22
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|
- path: output/untar/fast5/100read_fast5/206626c5-ccf2-4927-9987-164f627bdede.fast5
|
|
md5sum: 045d9fdb48f0b58456c7012b735c8101
|
|
- path: output/untar/fast5/100read_fast5/2109d790-67ec-4fd1-8931-6c7e61908ff3.fast5
|
|
md5sum: 623d2e3213f0423e33b7993d803e4ae5
|
|
- path: output/untar/fast5/100read_fast5/2166cca5-c0ab-49eb-aec1-fec09bdfbd83.fast5
|
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md5sum: 54ac4ec12232104381d2dcd619c9b4be
|