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change input type for finish_asm #9

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change input type for finish_asm #9

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scanon and others added 30 commits December 7, 2022 12:13
@scanon
change input type for finish_asm
846ebf0
add make_info_file task
95ae1f9
udpate README
2e334d2
fix missing make_info file direct
2729674
@scanon
Merge pull request #11 from microbiomedata/make_info
d1fb88e 
Werkflow to master for ASM
added release workflow for assembly
38eeedd
switched out uses for run
354e297
removed v from version bump
20ffb00
removed unused variables
1cedae9
added version.txt and upated create_release.yml to source from versio…
7f665b2 
…n.txt
remove unused input_file variable from finish_asm
57f3391
add jgi_meta_wdl submodules
484a137
@kaijli
changed wdl files to version 1.0
c2dc346
update jgi_meta_wdl submodules
ae28597
@kaijli
quick script to choose between long and short reads
468b75b
take one input either to long reads workflow or to short reads workflow
bcdc0e8
@kaijli
working on input dependencies
24e91ca
@kaijli
merged to include interleave
a784baa
@kaijli
having trouble importing jgi long reads
72e12ce
@kaijli
quick json to test choice wdl
47b758a
update jgi_meta_wdl submodules
713cf33
move make_interleaved_reads into shortReads condition, and add contai…
b40bae5 
…ner in interleaved_reads.wdl
@kaijli
working on file localization errors
fd3c145
@kaijli
added imports.zip for cromwell runs
696579e
@kaijli
Merge branch 'longreads' of https://github.com/microbiomedata/metaAss…
24db934 
…embly into longreads
@kaijli
merged import lines
f4e6db8
@kaijli
added test file
4b46283
@kaijli
changed folder paths for nmdc edge server
94da6eb
@kaijli
Merge branch 'longreads' of https://github.com/microbiomedata/metaAss…
1df1c4c 
…embly into longreads
@kaijli
container issue in interleaved fixed
7c7c4f8
kaijli and others added 30 commits October 15, 2024 10:01
@kaijli
bump version
547f3a8
@kaijli
add runtime mem for interleave
6c98933
@kaijli
remove extra comma
c8283f1
@kaijli
Merge pull request #24 from microbiomedata/23-update-to-spades-version-4
8d7df73 
removed unused git submodule, updated spades container
@vlilanl
fixed formatting and added in asmstats to metaflye.wdl
79635f1
@vlilanl
added stats.json as an output for task finish_lrasm
64f8467
@vlilanl
worflowmeta_contiainer -> workflowmeta_container
7766db8
@vlilanl
Updated bbtools container
d8b10a9
@vlilanl
reverted bbtools container for shortreads
f8dddd6
@vlilanl
Merge branch 'master' into 21-stats-file
ab0e5cc
@vlilanl
formatting issues
061e646
@vlilanl
Update index.rst
859c061
@vlilanl
Updated image for documentation
df5b86a
@vlilanl
Update version.txt
f47f965
@vlilanl
Update index.rst
86de934
@vlilanl
Update index.rst
0f47549
@vlilanl
Update index.rst
4676bf3
@vlilanl
Revert index.rst
34e83d1
@vlilanl
Merge pull request #25 from microbiomedata/21-stats-file
1274bc9 
21 Added in stats file for outputs
@vlilanl
Update index.rst
b2cf317
@vlilanl
Merge branch 'master' into documentation
dbbfc10
@vlilanl
Revert "Merge branch 'master' into documentation"
fdfb07d 
This reverts commit dbbfc10, reversing
changes made to b2cf317.

Formatting issues
@vlilanl
Update index.rst
7ffb200
@vlilanl
Update README.md
99241fb
@vlilanl
Update index.rst
28540ed
@vlilanl
Update bbtools container for short reads
85c2421
@vlilanl
Update version.txt
19d8b75
@vlilanl
Update workflow diagram
62593b2
@vlilanl
Update version.txt
76e2ad9
@vlilanl
Merge pull request #26 from microbiomedata/documentation
db80b0a 
Update Documentation and Update short reads bbtools container
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5 participants
@Michal-Babins @scanon @kaijli @vlilanl @aclum