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Merge v0.7.0 to main #111

Merged
merged 43 commits into from
Aug 11, 2023
Merged

Merge v0.7.0 to main #111

merged 43 commits into from
Aug 11, 2023

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rhysnewell
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rhysnewell and others added 30 commits July 26, 2023 14:42
@rhysnewell
Merge pull request #102 from rhysnewell/main
019a9bf 
Catch dev up to main
@AroneyS
add test for recover_mags_no_singlem workflow
1adb98a
@AroneyS
add refinery max iterations argument
705d970
@AroneyS
add test runner on pull_request
1c74d1d
@AroneyS
add bin check to checkm_metabat2 and checkm_semibin
de2b358
@AroneyS
skip checkm_{binner} rules when refinery iterations 0
f7cdfb4
@AroneyS
add note about iterations=0
a475904
@AroneyS
set max iterations type to int
cb0b0b6
@AroneyS
add more friendly message when skipping refinery
0ff4bc3
@AroneyS
Merge pull request #103 from AroneyS/add-refinery-max-iterations-arg
1a699ac 
Add refinery max iterations arg
@AroneyS
add refinery_max_iterations to checkm rules
f1cd6c5
@AroneyS
update to semibin2
79996a0
@AroneyS
ensure bins are copied when refinement is skipped
f5424ba
@AroneyS
rework skip binners test
43cd0ee
@AroneyS
fix short recovery only test
08f1def
@rhysnewell
Merge pull request #104 from rhysnewell/update-to-semibin2
520dedd 
Update to semibin2
@AroneyS
fix checkm subprocess
35cfd3f
@AroneyS
fix test
5857170
@AroneyS
revert shell=True and fix subprocess call
0749aa4
@rhysnewell
Merge pull request #105 from rhysnewell/fix-checkm-subprocess
aa90293 
Fix checkm subprocess
fix: removal of instances of shell=True
6b1abf7
put shell=True back into main process command to debug
e748b34
put shell=True back into main process command to debug
87e75c4
convert to run with no shell=True
3a05d71
convert to run with no shell=True
d3bd50c
fix: initial subprocess command, removed quotes around config.yaml path
b63a6b4
update complex piped subprocess commands, needs testing
8a50ac0
replace commands in polish.py, needs testing
6d77ed4
all relevant instances of shell=True converted
ee12734
fix #108 update concoct recipe to limit sklean version
87baa7e
rhysnewell and others added 13 commits August 8, 2023 22:54
fix: set TMPDIR env var before subprocess call. remove hardcoded cond…
54623cd 
…a paths in tests
fix: tests and graceful exits on singlem. Move finalise stats
6d9befd
revert: add conda-prefix to test commands
8ab73c7
fix: typo finalize -> finalise
a85d53d
@AroneyS
add long-read integration test
5975815 
long reads simulated with pbsim2 R95.model 23:31:46
filtered first 20 reads from each file and deduplicated
@AroneyS
cleanup pdb call
24d714e
@rhysnewell
fix: polish.py and pipeing commands
df84291
@rhysnewell
fix: add bam index creation in map_reads_ref rule
44d7ae8
@AroneyS
assembly not expected since it is input
8347dfd
@rhysnewell
fix: singlem script no longer uses glob
13d98fb
@rhysnewell
Merge pull request #107 from rhysnewell/sanitise_subprocess_calls
17f55db 
fix: removal of instances of shell=True
@rhysnewell
update: v0.7.0
75703f7
@rhysnewell
Merge pull request #110 from rhysnewell/v0.7.0
3061a2e 
update: v0.7.0
@rhysnewell rhysnewell merged commit ec56ef8 into main Aug 11, 2023
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2 participants
@rhysnewell @AroneyS