try to bring in trackhubs - #10

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erikenbody wants to merge 270 commits into

ccgproject:mainfrom

harvardinformatics:main

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Commits on Jul 11, 2023

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
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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

add template module to provide scaffold for new modules
cademirch
committed
b28b3f4
add backwards compatibility for snakemake7
cademirch
committed
b67e24b
use pkg_resources.parse_version instead of distutils
cademirch
committed
2811618

Commits on Apr 10, 2024

Merge pull request #170 from harvardinformatics/snakemake8
tsackton
authored
730475f

Commits on Apr 12, 2024

add mark_duplicates option. defaults to true
cademirch
committed
896babb
add mark duplicates option
cademirch
committed
c6e8524
add bcftools norm
cademirch
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ff5aa05
update profiles
cademirch
committed
22f1a13

Commits on Apr 13, 2024

fix docs
cademirch
authored
c41f28a
add mark dups option
cademirch
authored
3391225

Commits on Apr 14, 2024

Commits on Apr 18, 2024

get rid of stray resource_config refs
cademirch
committed
d46220f
add mark_duplicates to config
cademirch
committed
f07c3fd
add sentieon test dryun
cademirch
committed
034a449
dont add mapfile to output if sentieon
cademirch
committed
e7456f9
Merge pull request #181 from harvardinformatics/fix-get-rid-of-resources_config-refs
cademirch
authored
a3aef31
use json summary from fastp to make sure all stdout/stderr goes to log
cademirch
committed
0c6fab0

Commits on Apr 19, 2024

Merge pull request #184 from harvardinformatics/fastp-use-json
tsackton
authored
7bad90d

Commits on Apr 29, 2024

Commits on Apr 30, 2024

fix QC html to correctly report the number of filtered SNPs
erikenbody
committed
a33a6be
remove unused diversity line
erikenbody
committed
570daa1

Commits on May 1, 2024

Merge pull request #189 from harvardinformatics/fix_SNP_summary
tsackton
authored
5dd2e7e

Commits on May 14, 2024

make gls work again. fix minor issues with non-intervals. update docs
cademirch
committed
064d665

Commits on May 15, 2024

Merge pull request #192 from harvardinformatics/testings-gls
cademirch
authored
91c8495
concat json fastp summary
cademirch
committed
2908f16

Commits on May 16, 2024

Merge pull request #194 from harvardinformatics/fix-json
tsackton
authored
abc9c68

Commits on Jun 6, 2024

typo
erikenbody
committed
92fbf1c
caluclate correctly
erikenbody
committed
f1f378e

Commits on Jun 10, 2024

Merge pull request #199 from harvardinformatics/postprocessing_update
tsackton
authored
72a482f

Commits on Jun 11, 2024

gnu parallel to sentieon filter_vcf
erikenbody
committed
17e9e7f
add shadow directive to cleanup
erikenbody
committed
489d24b

Commits on Jun 12, 2024

update docs about profiles
cademirch
authored
7fc229d
Merge pull request #205 from harvardinformatics/update-docs
tsackton
authored
857625c

Commits on Jun 17, 2024

Commits on Jun 18, 2024

fix issue with trackhub
erikenbody
committed
438547e

Commits on Jun 20, 2024

fix issue with trackhub

erikenbody
authored and
cademirch
committed
25864b7

Commits on Jun 21, 2024

add unzip as option to download ref
erikenbody
committed
192caad
Merge branch 'main' into ref_unzip_fix
erikenbody
committed
d214b65

Commits on Jun 24, 2024

Merge pull request #211 from harvardinformatics/ref_unzip_fix
tsackton
authored
0907afc

Commits on Aug 9, 2024

add logs for concat gvcf and normalise
cademirch
authored
b1b1f48

Commits on Aug 14, 2024

update docs typos
cademirch
authored
9f810b4

Commits on Aug 15, 2024

Commits on Oct 11, 2024

make local fastq bigger
cademirch
committed
0fe1e1b
Merge pull request #224 from harvardinformatics/fix-ecoli-test
tsackton
authored
88efde3

Commits on Oct 18, 2024

make sort reads its own rule
cademirch
committed
0219d75

Commits on Oct 28, 2024

fix window vis
cademirch
committed
3299670
new line for genome line
cademirch
committed
9d7ade7

Commits on Oct 30, 2024

Merge pull request #228 from harvardinformatics/trackhubs
tsackton
authored
76df953

Commits on Nov 22, 2024

Update modules.md
erikenbody
authored
817b8c0

Commits on Nov 25, 2024

Merge pull request #231 from harvardinformatics/erikenbody-patch-1
tsackton
authored
092a99c

Commits on Jan 29, 2025

add jvm heap options to interval rules
cademirch
committed
55ebb1a

Commits on Apr 1, 2025

fix: ncbi datasets
cademirch
committed
c1fddc5
Merge pull request #241 from harvardinformatics/fix-datasets
tsackton
authored
dea4f34
Merge pull request #235 from harvardinformatics/fix-picard-memory
tsackton
authored
5454fdf

Commits on Apr 9, 2025

Commits on Apr 30, 2025

remove unused shell scripts
cademirch
committed
3dccc43
update profiles
cademirch
committed
df3d756
update docs to reflect profile changes
cademirch
committed
259a4ee

Commits on May 1, 2025

update actions to use worklfow-profile
cademirch
committed
c1893ba

Commits on May 2, 2025

Merge pull request #246 from harvardinformatics/v1-dev
tsackton
authored
765d83a

Commits on May 14, 2025

docs: code block missing backticks
cademirch
authored
6ce7983
Merge pull request #253 from harvardinformatics/fix-docs-typo
tsackton
authored
84073f2

Commits on May 15, 2025

Commits on Jun 25, 2025

fix: use bedtk to merge clam callable bed b/c its more mem efficient than bedtools
cademirch
committed
4ceec5b
fix wildcards
cademirch
committed
2580aec
fix typo
cademirch
committed
b3720e7
log mv
cademirch
committed
5c23b77
cp not mv
cademirch
committed
54c0c1b

Commits on Jun 26, 2025

Merge pull request #262 from harvardinformatics/fix-clam-bed-file
erikenbody
authored
9967a06

Commits on Jul 7, 2025

Update executing.md
cademirch
authored
cb39172
Merge pull request #265 from harvardinformatics/cademirch-patch-1
tsackton
authored
048cd76

Commits on Aug 26, 2025

Update dataset link in documentation

tsackton
authored and
cademirch
committed
2fc5cb6

Commits on Nov 21, 2025

initial design for version2
tsackton
committed
7a39593

Commits on Jan 30, 2026

V2/config sample sheet (#276)
cademirch
authored
c647f18

Commits on Feb 5, 2026

Update gitignore
tsackton
committed
c05c2af

Commits on Feb 10, 2026

Codex/hotfix pkg resources main (#279)
tsackton
authored
d960d0f

Commits on Feb 19, 2026

v2: align config/tool contract, tmpdir defaults, and multi-row sample processing (#280)

authored
9ebe5a2

Commits on Feb 20, 2026

Implement staged interval concat for large VCF/gVCF merges
Tim Sackton
committed
f9ffc1d
Fix bcftools staged concat tmp prefix for macOS temp dirs
tsackton
committed
b914e7a
Add explicit multistage interval concat test coverage
tsackton
committed
02dd524
Update workflow/rules/variant_calling/gatk_intervals.smk

tsackton
and
Copilot
authored
f991c6e
Update workflow/rules/variant_calling/gatk_intervals.smk

tsackton
and
Copilot
authored
9a5183b
Update workflow/rules/variant_calling/gatk_intervals.smk

tsackton
and
Copilot
authored
f09d6c2
update final concat rule
tsackton
committed
f425cf0
Merge pull request #281 from harvardinformatics/codex/feat-codex-intervals
tsackton
authored
7d08ec1

Commits on Feb 21, 2026

add a doc that includes a methods section and refs
erikenbody
authored
0040d43

Commits on Feb 22, 2026

Merge pull request #282 from harvardinformatics/erikenbody-patch-1
tsackton
authored
2cb5481

Commits on Mar 6, 2026

Commits on Mar 13, 2026

Improve v2 config handling
Tim Sackton
committed
c17db19
Refresh ecoli smoke test dataset
Tim Sackton
committed
cdee345
Harden interval checkpoint manifest reads
Tim Sackton
committed
836702c
Warn on unsupported Snakemake versions
Tim Sackton
committed
daee422
remove defaults from glnexus and deepvariant conda envs
Tim Sackton
committed
2332f83
Merge pull request #289 from harvardinformatics/codex/config-compat-normalization
tsackton
authored
58d9c5b
Add standalone QC runner script
Tim Sackton
committed
23d287e
Merge pull request #290 from harvardinformatics/codex/qc-script
gwct
authored
aada999
Codex/v2 bugfix (#292)

tsackton
and
Tim Sackton
authored
ce69c74

Commits on Mar 24, 2026

Implement callable sites BED generation (#293)

authored
f061b98
add example dir; clean up old .test (#295)
cademirch
authored
1c9b194

Commits on Mar 25, 2026

docs: add config and sample-sheet field reference docs (#298)
tsackton
authored
16b410c

Commits on Mar 27, 2026

Support mixed SRA and FASTQ inputs per sample (#297)
tsackton
authored
2e5b2f5

Commits on Mar 30, 2026

docs: documentation links and add Snakemake version note (#300)
cademirch
authored
bfbe1a7

Commits on Apr 2, 2026

Remove retired modules and harden QC modules (#301)
tsackton
authored
5b5fa2c
Fix Snakemake version detection warning (#302)
tsackton
authored
d862843

Commits on Apr 6, 2026

Fix ffq fallback for SRA downloads (#305)

tsackton
and
Tim Sackton
authored
70bf1b5

Commits on Apr 7, 2026

Preserve numeric-like IDs in QC and add regression test (#307)
tsackton
authored
a39d44b

Commits on Apr 8, 2026

Fix default target selection when QC module is enabled (#310)
tsackton
authored
477ada6

Commits on Apr 13, 2026

Filter sparse QC samples before PLINK GRM (#312)

tsackton
and
Tim Sackton
authored
07df95b
Auto-tune GenMap indexing for large genomes (#313)

tsackton
and
Tim Sackton
authored
2579f63
add debug info (#311)

cademirch
and
Tim Sackton
authored
0cacaee

Commits on May 11, 2026

update QC module to be robust to snp caller annotation differences (#319)

tsackton
and
Tim Sackton
authored
f8ce723
Fix (some) coverage bed OOM errors (#320)

tsackton
and
Tim Sackton
authored
d516d4d

Commits on May 14, 2026

Add complexity-aware DB interval splitting (#321)

tsackton
and
Tim Sackton
authored
b4e5ee0

Commits on May 20, 2026

Disable coverage bed for mixed sample sheets (#324)
tsackton
authored
51d27e6
Move GATK memory resources into profile (#325)

tsackton
and
Tim Sackton
authored
33d6f30

Commits on May 21, 2026

Fix deepvariant (#323)

tsackton
and
Tim Sackton
authored
675dab0

Commits on Jun 4, 2026

bai -> csi migration (#326)

tsackton
and
Tim Sackton
authored
aaf7b2e

Commits on Jul 16, 2026

Commits on Jul 17, 2026

docs: sync v2 reference with current workflow (#336)
cademirch
authored
a1ba478

Commits on Jul 29, 2026

Refresh promoted variant output timestamps (#339)

tsackton
and
Tim Sackton
authored
6209bb5