kevbrick
c29ad052bd
Revert "Add module: nf-core hackathon #207 : new module: msisensor/msi ( #343 )"
...
This reverts commit fead37d57a
2021-03-25 16:46:31 -04:00
kevbrick
fead37d57a
Add module: nf-core hackathon #207 : new module: msisensor/msi ( #343 )
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* Add module: nf-core hackathon #207 : new module: msisensor/msi
* Add module: nf-core hackathon #207 : new module: msisensor/msi
* Fix 4-spacing issues (caught in PR linting)
* Code review fixes & update configs
* Code review: remove stray echo
* Code review: Add msisensor modules
* Slashes to underscores to get tests to run on github
* Update software/msisensor/scan/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/msisensor/scan/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/msisensor/msi/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/msisensor/msi/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Add all outputs to meta.ymls
* Fixes from code review
* Fixes from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-25 16:46:00 -04:00
Batool
f90b8ecb24
Fix the test path salmon/index and quant after switching to config data ( #385 )
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* fix the test path in main.nf for salmon/index and quant
* fix typo
* Apply suggestions from code review
* Apply suggestions from code review
* Apply suggestions from code review
Mannnn, hopefully I finally got it right :)
* replaced /salmon/salmon/ with /index/salmon/
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-25 17:03:25 +00:00
Edmund Miller
6e4b23a1ca
ci: Upload work directory on failure ( #388 )
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Closes #374
2021-03-25 09:34:19 +00:00
FriederikeHanssen
555f1710e0
Update test paths in bwa mappers ( #387 )
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* Update test paths in bwa mappers
* Fix indentation
* indices pass lcoally now
* no idea how they could ever pass before, Tests pass locally no
* Update samtools and bwamem2 versions
* Correct mulled containers + md5
2021-03-25 09:24:21 +00:00
Kevin Menden
6973df628f
Fixing vcftools and bismark tests ( #383 )
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* fixed vcftools
* fixed genomepreparation, methylationextractor
* fixed deduplicate
2021-03-25 09:12:08 +00:00
Jose Espinosa-Carrasco
13bd67ed8a
Fix some module test after adapting test config approach ( #379 )
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* Fix paths for bowtie2/build_test
* Fix paths for bowtie2/align
* Fix paths for bwameth/index
* Fix paths for bwameth/align
* Fix paths for multiqc tests
2021-03-24 18:29:41 +00:00
Gregor Sturm
2dba72dd14
Fix a bunch of failing tests after switching to test config ( #378 )
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* Update test for trimgalore
* Fix picard markduplicate test
* Fix tests for picard mergesamfiles
* Fix checksum for markduplicates
* Fix multiplemetrics and wgsmetrics
* Fix checksum for mergesamfiles
2021-03-24 18:28:54 +00:00
Jose Espinosa-Carrasco
17fbdf96cb
Fix some module tests after switching to config data ( #386 )
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* Adding tar.gz kraken2 db to test data
* Update test path files for untar module
* Update test path files for kraken2/run module
* Update test path files for cat/fastq module
2021-03-24 18:28:07 +00:00
pericsson
1e4fa57139
Update restructured paths ( #380 )
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* dsh filterbed path updated
* dsh splitbed path updated
* adapterremoval path updated
2021-03-24 18:26:54 +00:00
Anthony Underwood
62775ea203
multi-tool instructions ( #376 )
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* multi-tool instructions
Add instructions on how to build a bespoke multi-tool Docker container and Singularity image
* fix linting issues
* Change bash to console
* Update README.md
* Update README.md
* Update README.md
* Update README.md
* Update README.md
Co-authored-by: Ramon Rivera <ramon.rivera10@upr.edu>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-24 18:18:38 +00:00
Anthony Fullam
c5a5e25129
Update test data paths. ( #375 )
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* Updata test data paths.
* Remove quote
* Revert quast
* Fix broken test
* Update md5
2021-03-24 18:18:01 +00:00
arontommi
d162f21ab3
Update samtools modules with config logic ( #381 )
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* fixing paths for test
* fixing paths for test
* fixing pats to tests
* fixing paths to tests
* fixing paths to tests
* fixing paths for tests
* fixing paths for tests
* fixing paths for tests
* fixing paths fro tests
* fixing paths for tests
* indentation fixes
* typo
* renaming test results according to new file name
* replacing the md5sums
* fixing brackets
* replacing md5sums
* fixing md5sums
* fixing md5sums'
* Update test.yml
* Update test.yml
* Update test.yml
* Update test.yml
* Update test.yml
* Update test.yml
* Update test.yml
* Update test.yml
Co-authored-by: Ramon Rivera <ramon.rivera10@upr.edu>
Co-authored-by: Ramon Rivera <riveravicens@gmail.com>
2021-03-24 18:15:30 +00:00
Mark-S-Hill
889465cb2b
update test data paths ( #373 )
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* update test data paths
* Update test md5sums
* gatk test fixes & update variantfiltration main
* few extra fixes after review
* fix suspected format error
* Update software/gatk4/variantfiltration/main.nf
* Update software/gatk4/variantfiltration/main.nf
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-24 18:14:11 +00:00
Kevin Menden
04c3684db7
Fixing a bunch of module tests ( #370 )
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* initial 'modules create' of minia
* fixed tests
* finished meta.yml
* fixed filters.yml
* resolved issues in pytest_software.yml
* add newline
* Update software/minia/main.nf
* fixing a bunch of module tests
* remove vscode
* fixed minia
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-24 17:36:29 +00:00
Alexander Peltzer
0337916f8a
Add YARA module ( #353 )
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* Initial work on yara module
* Adding in index basics
* Updated the index stuff
* Adding in proper tests
* Fix editorconfig
* Odd paths
* that should do it
* Fix tests
* Fix tests
* FFS
* Once more
* Mapping is not deterministic
2021-03-24 17:14:52 +01:00
Maxime Borry
cfc94b96dd
modify fastp tests ( #367 )
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Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-03-24 17:08:59 +01:00
FriederikeHanssen
86df111707
Seqkit/split2 test path update ( #372 )
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* Update test path
* Fix bracket
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-24 17:05:43 +01:00
Harshil Patel
c7155d023e
Update bedtools modules with config logic ( #369 )
2021-03-24 14:14:19 +00:00
Harshil Patel
83a500e6b0
Use a config containing all test data for module tests ( #365 )
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* Re-organise all test data
* Fix ECLint
* Fix ECLint agaaainn
* Now is not the time EClint
* Initial commit for test data config
* Rename test data
* Include test config
* Update indents
* Update test for FastQC via config
* Remove quotes of bottom-level variables
* Use underscores in key names
* Get tests working for fastp
* Remove whitespace at beginning of file
2021-03-24 13:07:37 +00:00
Gisela Gabernet
22eaefe583
Add module kallisto/index ( #357 )
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* add kallisto index module
* update kallisto module
* add kallisto module tests
* update kallisto index test.yml
* update test data paths
* fix version
* fix kallisto index test yml
* remove TODOs
* Update software/kallisto/index/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/kallisto/index/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* output folder instead
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-24 12:25:39 +00:00
Harshil Patel
acb1a12a56
Re-organise all test data ( #354 )
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* Re-organise all test data
* Fix ECLint
* Fix ECLint agaaainn
* Now is not the time EClint
2021-03-24 09:53:41 +00:00
Yuk Kei Wan
323856a9da
add nanopore 100-read test subset (fast5, fastq, and bam/bai) ( #344 )
2021-03-24 05:13:34 +00:00
arontommi
86bb832fae
Strelka germline ( #340 )
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* nf-core template created
* boilerplate and sarek_dsl2 code merged
* adding an option to give it args
* bai got away
* seperating vcf files and vcf index files into seperate streams
* some minor spacefixes
* adding standard information about the module
* removing typos
* some basic tests based on tiddit tests
* removed the bed parameter, should be provided via options.args instead
* removing typos
* adding indexed bam file instead
* Adding changing out fasta with reference to deal with empty fasta input
* adding the correct fasta
* removing the empty test
* adding the correct data to the testoutput and removing the md5sum since
it constantly changes
* adding target_bed to input
* adding info on target bed
* adding target bed to test
* adding more files to the test
* adding meta for target bed test
* adding a test for target_bed
* typo
* fixing pytest with master
2021-03-24 05:07:29 +00:00
Erkison Ewomazino Odih
67b3e00f58
add flash module ( #341 )
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* add flash module
* remove todo
* run tests
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-24 05:05:45 +00:00
Robert A. Petit III
6d14819859
Fix link describing process labels ( #349 )
2021-03-24 05:03:57 +00:00
Ravneet Bhuller
a70abc236b
PR for sequenzautils/gcwiggle ( #345 )
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* added files
* edited files
* edited files
* edited file
* test(sequenzautils): Remove md5sum
Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
2021-03-24 05:03:03 +00:00
Robert A. Petit III
3f14b1fabe
Update shovill module ( #337 )
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* add shovill module
* removed deprecated shovill module
* fix line ending in functions.nf
* fix yaml indentation
* reduce spades memory usage
* update md5sums
* remove non reproducible md5sum
* Update test.yml
Remove last non-reproducible md5sum.
* purely cosmetic order change
* proper process label, improve output readability
Co-authored-by: Florian Wuennemann <flowuenne@gmail.com>
2021-03-24 04:57:41 +00:00
Yuk Kei Wan
af3bc225c0
ucsc_bed12tobigbed (previous pull request had conflicts) ( #302 )
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* Add files via upload
* Add files via upload
* Add files via upload
* Add files via upload
* Update pytest_software.yml
* Update main.nf
* fix linting error
* Delete test.yml
* Create functions.nf
* Update main.nf
* change test data
* revert to !>=20.11.0-edge
2021-03-24 04:55:49 +00:00
Robert A. Petit III
a13d859c87
Add process label to prokka ( #350 )
2021-03-24 04:54:52 +00:00
Mark-S-Hill
399b58043d
add vcftools module ( #334 )
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* add vcftools module
* fix padding issue
* fix linting errors
2021-03-24 04:54:23 +00:00
Kevin Menden
fe8a783cef
Homer ( #330 )
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* started with homer
* added tests for homer annotatepeaks
* fix md5
* remove md5 sum
2021-03-23 11:24:54 -07:00
Gregor Sturm
e33860a2e8
Prodigal ( #333 )
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* WIP add prodigal
* Implement module and add tests
* Fix EC lint
2021-03-23 11:03:58 -07:00
Jose Espinosa-Carrasco
ee90e7af77
Add default output dir for modules that create indices, updated ( #336 )
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* Add default output dir for modules that create indices
* Change path for index module test output
* Fix bowtie2/align tests
* Fixing bowtie/align tests
* Fix genomegenerate test
* Fixing README linting
2021-03-23 17:55:01 +00:00
suzannejin
d6850f8312
modified the samtools/fastq module ( #339 )
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* new module: samtools/fastq
* solve conflict: pytest_software.yml
* solve linting conflicts
* solved EditorConfig linting problem
* Module samtools/fastq:
* output compressed fastq.gz file(s)
* add if conditionals for single/paired reads
* samtools/fastq: modified test.yml
* samtools/fastq: modified main.nf to avoid duplicated part of the script section
Co-authored-by: suzannejin <suzanne.jin@crg.eu>
2021-03-23 17:43:52 +00:00
yocra3
5e3c9dfbf0
Add gatk4/baserecalibrator ( #327 )
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* Add gatk4 BaseRecalibrator
* Solve format in main.nf
* Correct functions
* Add pytest
2021-03-23 18:32:37 +01:00
Alexander Peltzer
d13e22dcbe
Add in OptiType (configbuilder, type) module(s) ( #301 )
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* Adding in optitype prototype (To be worked on these days)
* I've tried my best 😆
* No idea
* Add in YML stuff
* Fix paths
* Ok, lets try this
* Adding proper options
* Replacec configbuilder thing
* Fix seq_type
* Adding human bam - sarscov doesnt work
* Fix a bunch of things
* -def
* Make this test run
* Fancy as fuck
* Update tests/software/optitype/test.yml
* Add proper tag
* Remove md5sums
Co-authored-by: Kevin Menden <kevin.menden@t-online.de>
2021-03-23 16:48:05 +01:00
Harshil Patel
246011f59b
Add docs for running tests locally with pytest ( #338 )
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* Add docs for running tests locally with pytest
* Add docs for tag
2021-03-23 15:29:52 +00:00
Anthony Fullam
3d720a24fd
Add alleleCounter module ( #313 )
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* Add allelecount module
* Add bed file input
* Added bai file
* Changed conda version
* Update main.nf
* Update pytest_software.yml
* Update pytest_software.yml
* Update pytest_software.yml
* Update pytest_software.yml
* Update pytest_software.yml
* Update pytest_software.yml
* Update pytest_software.yml
* Update pytest_software.yml
* Update pytest_software.yml
* Update pytest_software.yml
* Add allelecount module
* Add bed file input
* Added bai file
* Changed conda version
* Update main.nf
* Update pytest_software.yml
* Update pytest_software.yml
* Update pytest_software.yml
* Update pytest_software.yml
* Update pytest_software.yml
* Update pytest_software.yml
* Remove newline
* Fix pytest_software.yml
* Update pytest_software.yml
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
2021-03-23 14:37:53 +01:00
yocra3
614d61dc13
Add gatk4/applybqsr ( #331 )
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* Add applybqsr module
* Solve problem in functions.nf
* Add to pytest
2021-03-23 14:15:26 +01:00
suzannejin
9115c12f88
new module: samtools/fastq ( #316 )
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* new module: samtools/fastq
* solve conflict: pytest_software.yml
* solve linting conflicts
* solved EditorConfig linting problem
2021-03-23 12:13:07 +01:00
yocra3
569ff03af9
Add readgroup to bam files ( #324 )
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* Add readgroup to bam files
Add recalibration table
* Solve README.md issue
2021-03-23 11:59:49 +01:00
Robert A. Petit III
c2aa95cb6c
add prokka module ( #298 )
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* add prokka module
* adjust test outputs
* fix prokka command
* adjust test outputs
* handle optional input
* update pytest
* update pytest
* adjust test outputs
* adjust test outputs
* switch to lists for optional inputs, add md5sums for non-timestamped outputs
* add optional prodigal training file
* add optional prodigal training info to meta yaml
2021-03-23 02:51:23 -07:00
Edmund Miller
1fc4aa260d
ci: Add 21.03.0 version to matrix ( #317 )
2021-03-22 22:57:59 +00:00
Ravneet Bhuller
8a2a9f7e81
cnvkit module ( #173 )
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* Normal bam file added
* Normal bam.bai file added
* Tumour bam bai files added
* human dir added
* annotation dir added
* cnvkit dir added
* cnvkit dir added
* Update software/cnvkit/main.nf
Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>
* Update software/cnvkit/main.nf
Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>
* Update software/cnvkit/main.nf
Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>
* changed input filenames
* edited main.nf
* edited main.nf
* edited meta.nf
* edited test.yml
* filters.yml
* edited main
* edited main
* edited meta
* edited meta
* edited main
* removed unwanted lines
* edited the path to the main.nf
* removed function.nf
* added functions.nf
* deleted 2 workflows and craeted a common workflow
* deleted paths for 2 workflows and created paths for a common workflow
* Deleted annotation dir
* deleted params.modules
* Edited meta.with_normal
* deleted normal_280_sub_chr21.bam
* deleted normal_280_sub_chr21.bam.bai
* deleted tumour_278_sub_chr21.bam
* deleted tumour_278_sub_chr21.bam.bai
* Edited input and script parts
* Edited input part
* Added
* Edited args
* Edited script
* Edited input
* Changed annotation to annotationfile
* Changed description of the tool
* edited singularuty container
* edited input
* line 44 removed trailing whitespace
* Edited addParams
* Deleted pdf output
* Deleted pdf output
* edited the path to main.nf
* edited path to the main.nf
* Added docker image version
* Removed extra ../
* added md5sums
* added md5sums
* Update software/cnvkit/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Update software/cnvkit/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
* Edited the script
* Edited the input
* Edited main.nf
* Edited main.nf
* edited md5sum for reference.cnn
* removed human fasta
* removed human fasta.fai
* added GRCh38 fasta
* added GRCh38 fasta.fai
* added hg19 fasta.fai
* added hg19 fasta
* Edited fasta file name
* Edited bed file names and md5sums
* Edited md5sums
* edited the input and script section
* edited input section
* added targetfile
* changed the files
* changed the output files
* added bam files
* added bam files
* remove files
* added md5sums
* replace file
* added files
* edited tests/software/cnvkit files
* edited tests/software/cnvkit files
* edited authors list
* removed files
* added files
* added files
* added files
* added files
* added file
* added file
* added file
* added file
* edited files
* edited files
* edited files
* edited files
* edited files
* edited files
* added new module
* added new module
* edited files
* edited file
* edited file
* edited file
* removed files
Co-authored-by: kaurravneet4123 <kaurravneet4123@yahoo.com@users.noreply.github.com>
Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 15:27:30 -07:00
Nicholas Toda
53109d53c0
add gatk4/fastqtosam #198 ( #311 )
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* Inital nf-core create
* remove TODO comments, input and output files defined
* add get version in script
* added flow control for single/paired end data
* added script main commands
* removed completed TODO messages
* removed completed TODO messages
* added software info
* added input reads description
* added output description
* added description and keywords
* added single end test
* added paired end test
* fixed sample name flag
* fixed reverse read variable
* added test yaml
* update for pytest_software
* order in pytest_software was different
* replaced functions.nf with copy from another module
* simplify read command line
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Nicholas TODA <nicholas.toda@mnhn.fr>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 18:26:02 +00:00
Maxime Garcia
0a4fa5050a
Update main.nf ( #314 )
2021-03-22 17:16:43 +00:00
Maxime Borry
aa76c6d870
new module: AdapterRemoval ( #309 )
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* add adapterremoval module
* fix indentations
* switch to process_medium
* update docker tests
* remove duplicated entry
* fix line ending
* Update software/adapterremoval/main.nf
* Update software/adapterremoval/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-03-22 17:16:04 +00:00
Jose Espinosa-Carrasco
cfa8f64c4f
Adding unicycler module ( #307 )
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* Adding unicycler module
* Do not forget to change default keywords on meta.yml
2021-03-22 18:14:24 +01:00
Gregor Sturm
bed31cd9b4
Add link to issue in pull request template ( #312 )
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* Add link to issue in pull request template
* Update PULL_REQUEST_TEMPLATE.md
2021-03-22 10:04:20 -07:00
