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Develop #13

Merged
merged 68 commits into from
Nov 28, 2023
Merged

Develop #13

merged 68 commits into from
Nov 28, 2023

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gconcepcion
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Ready to merge develop into main

williamrowell and others added 30 commits May 19, 2023 17:24
@williamrowell
Added version print statements to all tasks.
edee46d 
- Also updated to parse_cohort:1.0.2 with an option to print version.
@williamrowell
CommandShellCheck, SC2046 Quote this to prevent word splitting.
74d14fa
@github-actions
update wdl-ci config file after successful tests
bc86fa6
@williamrowell
Fix htsbox version command.
c631102
@github-actions
update wdl-ci config file after successful tests
28d0011
@williamrowell
update submodule
052365f
@williamrowell
Create LICENSE
fcbd54c
@hkeward
Set max retries to 3 for HPC backend configuration
de2e218
@hkeward
Format docs; add backend-specific docs
0ba71f4
@hkeward
Update paths for AWS reference files
e1b4074
@hkeward
Allow user to override container registry
c7714fe
@williamrowell
Avoid underestimating disk size based on first element of array.
5d1299b
@github-actions
update wdl-ci config file after successful tests
cb9f17f
@williamrowell
Merge pull request #7 from PacificBiosciences/bugfix/disk-size-arrays
6ea580a 
Avoid underestimating disk size based on first element of array.
@gconcepcion
Calculate total bases input for each parent to set yak params on the fly
9c6c96e
@gconcepcion
less than not greater than
c9f7092
@hkeward
Document submitting the workflow directly to Cromwell using cURL
e873f20
@hkeward
Add dependencies.zip to gitignore
902f926
@hkeward
Merge pull request #8 from PacificBiosciences/docs/cromwell-curl-command
f1e76ea 
Document submitting workflow directly to Cromwell using cURL
@gconcepcion
Adding multi-reference alignment option
56833d4
@gconcepcion
add yak bloom filter condition
a40d2a2
@gconcepcion
fix coverage
fcf9ffe
@gconcepcion
determine yak settings for both parents rather than independently
d462924
@gconcepcion
fix tests and remove some debug comments I missed
af88a08
@github-actions
update wdl-ci config file after successful tests
137d6a9
@github-actions
update wdl-ci config file after successful tests
6c02327
@williamrowell
Take a stab at estimating depth based on filesize.
49acf5c 
- updated parameter_meta
- updated inputs.json
- cleaned up some whitespace
- added comments
- using fasta filesize to estimate depth rather than a separate task; based on Greg's experiments, an uncompressed 10x FASTA is ~60GB
@williamrowell
changed flag name and fixed my flipped logic
f24e1e6
@williamrowell
Adjusted tests.
42d0d84
@williamrowell
Memory is an int.
c8a9b8d
gconcepcion and others added 18 commits November 7, 2023 15:52
@gconcepcion
now that we are aligning haps separately, there is a single assembly …
150b4a4 
…input instead of a list
@gconcepcion
add double quotes and fix tests
58bdf47
@github-actions
update wdl-ci config file after successful tests
de6bf21
@gconcepcion
update wdl-ci json
cc5afcb
@gconcepcion
update wdl-common
fe8b97f
@gconcepcion
update tests for new wdl-common
b5b121e
@gconcepcion
fix tests
f2b175f
@github-actions
update wdl-ci config file after successful tests
2471441
@gconcepcion
attempt to fix tests
c434e7d
@gconcepcion
update test locaton and remove tests from non-humanassembly tasks
979ab48
@gconcepcion
update wdl config to reflect local HPC test running
22c3fc2
@gconcepcion
temporarily disable tests while troubleshooting
421fcc7
@gconcepcion
fix tests for CoA
013c77f
@gconcepcion
finally fixed?
51a53aa
@hkeward
Use latest version of wdl-ci
d1b2510
@gconcepcion
do not save haplotype bams and output trio merged bam
a88f0c2
@github-actions
update wdl-ci config file after successful tests
37b6ffb
@gconcepcion
shorten chm13 name
24cfc8d
williamrowell
williamrowell requested changes Nov 27, 2023
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Looks great, just some small changes.

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williamrowell
williamrowell reviewed Nov 28, 2023
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williamrowell
williamrowell reviewed Nov 28, 2023
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@gconcepcion gconcepcion merged commit 6011e32 into main Nov 28, 2023
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3 participants
@gconcepcion @williamrowell @hkeward