Harvardinformatics snakemake7 - #12

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cademirch wants to merge 138 commits into

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harvardinformatics-snakemake7

Commits on May 9, 2023

fixes for checkpoints in the cloud
cademirch
committed
153c19b
make trackhubs prettier
cademirch
committed
5d9fff5

Commits on May 10, 2023

Merge pull request #105 from harvardinformatics/fix_cloud_checkpoints
tsackton
authored
4e0d845

Commits on May 30, 2023

bcftools v1.10
tsackton
committed
a0baaec

Commits on Jun 6, 2023

Merge pull request #108 from harvardinformatics/bugfix
cademirch
authored
a6c7e78

Commits on Jun 21, 2023

fix typo

erikenbody
authored and
cademirch
committed
777332b
Fix ncbi-ref error in write_samples.py

tsackton
authored and
cademirch
committed
9376375
update env spec
cademirch
committed
b170397
fix sort issue with chrom sizes
cademirch
committed
1ed52dd
remove organism from write_samples
cademirch
committed
e8ce330
fix logo and emoji
cademirch
authored
bcef46d
fix emoji
cademirch
authored
ce8b77f

Commits on Jun 22, 2023

Merge branch 'main' into trackhubs
cademirch
authored
d432b69
Merge pull request #111 from harvardinformatics/trackhubs
tsackton
authored
51941c2

Commits on Jul 11, 2023

Merge pull request #112 from harvardinformatics/main
cademirch
authored
e587af8
fix trackhub details
cademirch
authored
7abe165
reference html file in script
cademirch
authored
5c02b6d
fix copying html file
cademirch
committed
3d39cf5
put html in output
cademirch
committed
43b8b3b
fix output
cademirch
committed
2d608c4
fix hub script
cademirch
committed
f5070ef
fix html
cademirch
committed
cd6026d

Commits on Jul 15, 2023

Merge pull request #113 from harvardinformatics/trackhubs
erikenbody
authored
974caf8

Commits on Aug 7, 2023

Update resources.yaml
tsackton
authored
d85ce92
add resource spec for intervals #114
cademirch
authored
4846330
Merge pull request #115 from harvardinformatics/main
cademirch
authored
2a5992c

Commits on Aug 8, 2023

Fix mosdepth to 0.3.3
aewebb80
authored
caf1303
Merge pull request #116 from harvardinformatics/bugfix
tsackton
authored
f536114
Merge pull request #117 from aewebb80/main
tsackton
authored
a4849fa

Commits on Aug 9, 2023

Update path, enable conda
aewebb80
authored
c9f87ac
Merge pull request #118 from aewebb80/main
cademirch
authored
af8afd3

Commits on Sep 20, 2023

update read group naming in common.smk
erikenbody
authored
d00634d

Commits on Sep 21, 2023

Merge pull request #124 from harvardinformatics/erikenbody-regroups
cademirch
authored
5c42f3f

Commits on Sep 26, 2023

Update index.md
erikenbody
authored
0b0206b
Update setup.md
erikenbody
authored
d1f9eb8

Commits on Sep 27, 2023

Commits on Sep 29, 2023

Merge pull request #128 from aewebb80/main
tsackton
authored
753025d
Update README.md
tsackton
authored
c195291

Commits on Oct 2, 2023

Merge pull request #129 from harvardinformatics/update-readme
cademirch
authored
88b937f

Commits on Oct 3, 2023

Update common.smk
erikenbody
authored
8843afb

Commits on Oct 6, 2023

Update cov_filter.yml
tsackton
authored
95eeb86
Merge pull request #131 from harvardinformatics/pyd4-fix
cademirch
authored
8156efe
Merge pull request #130 from harvardinformatics/erikenbody-patch-4
cademirch
authored
adfcbe7

Commits on Oct 19, 2023

add ploidy options
cademirch
committed
d230125

Commits on Oct 20, 2023

add some doc stuff
cademirch
committed
62cb27a
Merge pull request #135 from harvardinformatics/update_docs
cademirch
authored
53109f8
Merge pull request #134 from harvardinformatics/ploidy
cademirch
authored
d5a37f5

Commits on Nov 2, 2023

update docs
cademirch
authored
930e0af
dont run ci tests on pr for docs/md files
cademirch
authored
6719c85

Commits on Nov 3, 2023

Commits on Nov 28, 2023

Update write_samples.py
tsackton
authored
aed98ce

Commits on Dec 12, 2023

Merge pull request #143 from harvardinformatics/tsackton-patch-1
cademirch
authored
1d0525e

Commits on Dec 15, 2023

add support for mixed local and sra fastqs
cademirch
committed
96b0b6b
handle sra only
cademirch
committed
a9d10ce

Commits on Dec 19, 2023

formatting
cademirch
committed
0b48783

Commits on Dec 29, 2023

Merge pull request #146 from harvardinformatics/local_and_sra
cademirch
authored
275de90
update citation
cademirch
authored
80e2105

Commits on Dec 30, 2023

Merge pull request #150 from harvardinformatics/cademirch-patch-1
tsackton
authored
1f3cb30

Commits on Jan 24, 2024

Fix typo in mk module
tsackton
authored
686be19

Commits on Feb 1, 2024

Update setup.md
cademirch
authored
042e64d
Merge pull request #152 from harvardinformatics/tsackton-patch-2
tsackton
authored
884d978
pin python versions
cademirch
committed
e62268b
try using my fork of snakemake actions
cademirch
committed
b355b09
remove version from gh action
cademirch
committed
fae8790
v1 action
cademirch
committed
e8055f2

Commits on Feb 6, 2024

Merge pull request #155 from harvardinformatics/cademirch-patch-1
tsackton
authored
bae8ec7

Commits on Feb 14, 2024

Update cov_filter.smk
tsackton
authored
fa49e7c
add resources to qc rules
tsackton
authored
8a671fa
Add resources to postprocess module
tsackton
authored
9c00331

Commits on Feb 15, 2024

Merge pull request #157 from harvardinformatics/tsackton-patch-2
cademirch
authored
5b479be

Commits on Mar 7, 2024

remove --overwrite from tar. incompatible with bsdtar, is default for gnutar anyway
cademirch
committed
b3c2025
Update setup.md
cademirch
authored
0464660
Update modules.md
cademirch
authored
c899806
Merge pull request #164 from harvardinformatics/cademirch-patch-1
tsackton
authored
c9971b8
Merge pull request #162 from harvardinformatics/osx-fixes
tsackton
authored
f0fe796

Commits on Mar 8, 2024

change file.rename to file.copy, then file.remove to deal with snparcher and results being on diff filesystems
cademirch
committed
39a899f

Commits on Mar 11, 2024

Merge pull request #167 from harvardinformatics/issue-166
tsackton
authored
a80e60a
improve admixture run contig names
erikenbody
committed
dd60dbb
remove comments
erikenbody
committed
74a649a
fix fai typo
erikenbody
committed
8e76407
trying to fix fai file path again
erikenbody
committed
fca158d

Commits on Mar 12, 2024

Merge pull request #168 from harvardinformatics/admixture_contig_names
tsackton
authored
ed43114

Commits on Mar 26, 2024

bump min snakemake version, update config for remote reads
cademirch
committed
a8bf7e8
change default_remote_prefix to new api
cademirch
committed
c38153e
missed a default prefix
cademirch
committed
be8b5b5

Commits on Mar 27, 2024

add copy_reference rule
cademirch
committed
fba5e97
add gz local genome test
cademirch
committed
fba55fe
update ecoli test case
cademirch
committed
5851c77
update reference stuff, replace default_remote_prefix
cademirch
committed
d6631a4
Merge pull request #169 from harvardinformatics/main
cademirch
authored
af48cee
revert gh actions to use snakemake's action
cademirch
committed
e3b081c
update ecoli csv
cademirch
committed
dc52a2f

Commits on Mar 28, 2024

add snparcher_utils to deal with samplesheet/config parsing for main workflow and modules
cademirch
committed
c47cf80
use snparcher utils, clean up some imports
cademirch
committed
ebc8992
move functions to init
cademirch
committed
bb66554
use snparcher_utils
cademirch
committed
3c117ed
clean up imports add snparcherutils, add logs
cademirch
committed
f4bc650
update postprocess and trackhub with utils
cademirch
committed
84516b6
update mk with utils
cademirch
committed
1855bef
update write samples and move it
cademirch
committed
bfd3c49
update git stuff
cademirch
committed
4bcf913
fix gh action syntax
cademirch
committed
36335d9
add config genome test case
cademirch
committed
ecb0fce
add refGenome and refPath to main config
cademirch
committed
58addff
clean up unused files
cademirch
committed
16b4548

Commits on Mar 29, 2024

moving resources to profile
cademirch
committed
94652dd
moving resources to profile
cademirch
committed
9fb2315
fix gh action workflow
cademirch
committed
05c0beb
fix gh action
cademirch
committed
b76aa92
add slurm profile
cademirch
committed
f8c3b2b

Commits on Mar 30, 2024

update profiles
cademirch
committed
9218196

Commits on Apr 2, 2024

update docs
cademirch
committed
5973c6f
update profiles
cademirch
committed
d27693d
initial example commit
cademirch
committed
0a41913
add example
cademirch
committed
956bad2

Commits on Apr 3, 2024

revert to old download ref behavior because of issue w/ ruleorder and checkpoints.
cademirch
committed
5adbcd9
Update main.yaml
cademirch
authored
9a37f6d
try again
cademirch
committed
c7bded4
switched to stable snakemake in gh action docker
cademirch
committed
44ae6b2
go back to snakemake gh action, use stagein to set python version
cademirch
committed
86ba347
update gh action version
cademirch
committed
0c99d0c
get rid of stagein
cademirch
committed
292795e

Commits on Apr 4, 2024

try pinning versions in cov filter
cademirch
authored
513b3d0
trying to get cov filter to build
cademirch
authored
c00f79f

Commits on Apr 5, 2024

add functions to create/modify curl rc, then undo at end of workflow
cademirch
committed
d506e27

Commits on Apr 8, 2024