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ASCC multi-assembly re-write #65

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merged 126 commits into from
Jan 17, 2025
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4403b94
Updates as part of Version 1 rewrite
DLBPointon Nov 12, 2024
4589922
Updates as part of Version 1 rewrite
DLBPointon Nov 12, 2024
e2dfd3a
Updates as part of Version 1 rewrite
DLBPointon Nov 12, 2024
79f36bf
Updates from rewrite to main repo
DLBPointon Nov 13, 2024
fd29a3d
Updates from rewite
DLBPointon Nov 13, 2024
1366293
Updating test case and CICD
DLBPointon Nov 13, 2024
9bd0beb
Updates from Eeriks docs branch
DLBPointon Nov 13, 2024
0a8d370
Roll back a couple of things
DLBPointon Nov 13, 2024
2c810e9
Formatting updates
DLBPointon Nov 13, 2024
6c49224
Newline
DLBPointon Nov 13, 2024
68f7521
Updates for CICD - addition of the modules.json
DLBPointon Nov 13, 2024
c009601
Updates for CICD
DLBPointon Nov 13, 2024
fdd1b02
Updates for CICD
DLBPointon Nov 13, 2024
91cd465
Updates for CICD
DLBPointon Nov 13, 2024
735c78a
Adding a test function to parse nextflow version and resouce requirem…
DLBPointon Nov 14, 2024
834ceb0
Adding a test function to parse nextflow version and resouce requirem…
DLBPointon Nov 14, 2024
cb574c7
Adding a test function to parse nextflow version and resouce requirem…
DLBPointon Nov 14, 2024
dff1b55
Adding a test function to parse nextflow version and resouce requirem…
DLBPointon Nov 14, 2024
6dd6867
Adding a test function to parse nextflow version and resouce requirem…
DLBPointon Nov 14, 2024
27b9129
Adding a test function to parse nextflow version and resouce requirem…
DLBPointon Nov 14, 2024
fd521dc
Updates
DLBPointon Nov 14, 2024
0612a44
Updates
DLBPointon Nov 14, 2024
a4e87aa
Adding a GitHub test yaml
DLBPointon Nov 14, 2024
5a092d7
Pinning verison of nf-core and bug fixes
DLBPointon Nov 15, 2024
e5024e7
Pinning verison of nf-core and bug fixes
DLBPointon Nov 15, 2024
44c8bd6
Update min nextflow version to test on
DLBPointon Nov 18, 2024
cee7a3c
updates
DLBPointon Nov 20, 2024
fa27ff0
Updating modules and fixing blast_lineage bug
DLBPointon Nov 21, 2024
568d701
Updating modules and fixing blast_lineage bug
DLBPointon Nov 21, 2024
fd00d0f
Fixing CI data
DLBPointon Nov 21, 2024
a89bd83
Fixing CI data
DLBPointon Nov 21, 2024
048671a
Fixing CI data
DLBPointon Nov 21, 2024
2334287
Fixing CI data
DLBPointon Nov 21, 2024
7aac083
Fixing CI data
DLBPointon Nov 21, 2024
302c18e
Updating biopython+numpy images built with anaconda to biopython wo a…
DLBPointon Nov 26, 2024
a28e957
Linting YML was broken
DLBPointon Nov 26, 2024
88d7423
Pre Commit linting
DLBPointon Nov 26, 2024
4f717cd
Pre Commit linting
DLBPointon Nov 26, 2024
6cc000f
Pre Commit linting
DLBPointon Nov 26, 2024
35703e4
Pre Commit linting
DLBPointon Nov 26, 2024
62552c6
Pre Commit linting
DLBPointon Nov 26, 2024
03f6ead
Re-add pipeline download
DLBPointon Nov 26, 2024
7e5f64d
Re-add pipeline download
DLBPointon Nov 26, 2024
f5f2e92
Forgot to point it to the github_testing folder
DLBPointon Nov 26, 2024
c7dd1a9
Forgot to point it to the github_testing folder
DLBPointon Nov 26, 2024
5dd28da
Updating notes in the pipeline and removed the BTK_YAML arg from the …
DLBPointon Nov 27, 2024
3d24a42
Using realpath so we don't have to pass the bam around like a wally
DLBPointon Nov 28, 2024
3b8d923
Updates to pipeline
DLBPointon Nov 29, 2024
0fb7342
Uncomment out the organellar workflow
DLBPointon Nov 29, 2024
d2dbd4a
Lint
DLBPointon Nov 29, 2024
0e6d799
revert blast makeblastdb to original
DLBPointon Nov 29, 2024
8e2ec15
Updated to fix organellar BTK issue
DLBPointon Nov 29, 2024
b05a4a6
Removing local busco dataset call
DLBPointon Dec 2, 2024
e35a762
Updates
DLBPointon Dec 5, 2024
aa241a9
Updating setup-nextflow from 1 to 2
DLBPointon Dec 5, 2024
ca770c9
Updates
DLBPointon Dec 9, 2024
f432b42
Adding functionality for gzipped input
DLBPointon Dec 12, 2024
fa7ebf2
Adding functionality for gzipped input
DLBPointon Dec 12, 2024
8afa3ec
Updates
DLBPointon Dec 12, 2024
4d3f395
Citation for sanger-tol-btk
DLBPointon Dec 12, 2024
4335b1e
Note for further updates
DLBPointon Dec 12, 2024
0ab38a2
Adding Unzip function
DLBPointon Jan 10, 2025
f46593a
Update linting workflow
DLBPointon Jan 10, 2025
9240924
Updating CICD and modules
DLBPointon Jan 10, 2025
0133d38
Fix to control race conditions in runs with larger genomes
DLBPointon Jan 13, 2025
cf731f0
Making sure that the barcodes subworkflow works
DLBPointon Jan 13, 2025
5889ef7
Adding test file
DLBPointon Jan 13, 2025
175bda7
Correcting cicd
DLBPointon Jan 13, 2025
aa1f2f7
Correcting path for pacbio_adaptors.fa
DLBPointon Jan 13, 2025
2a1d77b
Debugging the tests
DLBPointon Jan 13, 2025
be818e5
Debugging the test - Adding artifacts
DLBPointon Jan 13, 2025
20f98f3
Correcting use of channel.of to channel.frompath where appropriate
DLBPointon Jan 14, 2025
534cd52
resourceParams is for overriding hpc configs!
DLBPointon Jan 15, 2025
7e3264f
Updating resource requirements in test.config
DLBPointon Jan 15, 2025
257b961
Trying to pin down a GitHub actions error
DLBPointon Jan 15, 2025
9184890
Trying to pin down a GitHub actions error
DLBPointon Jan 15, 2025
211422a
Trying to pin down a GitHub actions error
DLBPointon Jan 15, 2025
53fac50
Truncating pipeline to ID failure
DLBPointon Jan 15, 2025
70d26e9
Truncating pipeline to ID failure
DLBPointon Jan 15, 2025
625289e
Truncating pipeline to ID failure
DLBPointon Jan 15, 2025
5c328b4
Truncating pipeline to ID failure
DLBPointon Jan 15, 2025
bde73bf
Truncating pipeline to ID failure
DLBPointon Jan 15, 2025
49a0c5a
Truncating pipeline to ID failure
DLBPointon Jan 15, 2025
606d5d1
Truncating pipeline to ID failure
DLBPointon Jan 15, 2025
f5d37eb
Truncating pipeline to ID failure
DLBPointon Jan 15, 2025
aef2a6b
Truncating pipeline to ID failure
DLBPointon Jan 15, 2025
c981dfa
Truncating pipeline to ID failure
DLBPointon Jan 15, 2025
b175f2e
Truncating pipeline to ID failure
DLBPointon Jan 15, 2025
1723360
Truncating pipeline to ID failure
DLBPointon Jan 15, 2025
59cb0a7
Truncating pipeline to ID failure
DLBPointon Jan 15, 2025
2a6442e
Truncating pipeline to ID failure
DLBPointon Jan 15, 2025
a9b81c7
Truncating pipeline to ID failure
DLBPointon Jan 15, 2025
b646131
Truncating pipeline to ID failure
DLBPointon Jan 15, 2025
3c4f86b
Wrong
DLBPointon Jan 15, 2025
13eb878
Uncommenting subworkflows to test and correcting multiple downloads f…
DLBPointon Jan 15, 2025
798e358
Uncommenting subworkflows to test and correcting multiple downloads f…
DLBPointon Jan 15, 2025
a34a036
Uncommenting subworkflows to test and correcting multiple downloads f…
DLBPointon Jan 15, 2025
5fedf9f
Uncommenting subworkflows to test and correcting multiple downloads f…
DLBPointon Jan 15, 2025
6e1b628
Uncommenting subworkflows to test and correcting multiple downloads f…
DLBPointon Jan 15, 2025
ed613ed
Uncommenting subworkflows to test and correcting multiple downloads f…
DLBPointon Jan 15, 2025
86b4b9d
Uncommenting subworkflows to test and correcting multiple downloads f…
DLBPointon Jan 15, 2025
05316cf
Uncommenting subworkflows to test and correcting multiple downloads f…
DLBPointon Jan 15, 2025
5124b2a
Uncommenting subworkflows to test and correcting multiple downloads f…
DLBPointon Jan 15, 2025
19b356d
Uncommenting subworkflows to test and correcting multiple downloads f…
DLBPointon Jan 15, 2025
7534063
Uncommenting subworkflows to test and correcting multiple downloads f…
DLBPointon Jan 15, 2025
35eaa38
Fixed the blast issue locally
DLBPointon Jan 16, 2025
48cb3b9
Fixed the blast issue locally
DLBPointon Jan 16, 2025
9c92d51
Fixed the blast issue locally
DLBPointon Jan 16, 2025
8b5d01f
Linting NF-CORE
DLBPointon Jan 16, 2025
3ad3938
Changes to allow genomic_only runs
DLBPointon Jan 16, 2025
8b3543f
Adding new param
DLBPointon Jan 16, 2025
8903c1c
Adding VecScreen file
DLBPointon Jan 16, 2025
ea2ca34
Changes to control EVERY subworklow and skip essentials if needed in …
DLBPointon Jan 17, 2025
ad2514c
Changes to control EVERY subworklow and skip essentials if needed in …
DLBPointon Jan 17, 2025
7b9757c
Changes to control EVERY subworklow and skip essentials if needed in …
DLBPointon Jan 17, 2025
4ccb8a1
If your running without essentials, then don't do it on the organelles
DLBPointon Jan 17, 2025
01d9afb
Adding the paper
DLBPointon Jan 17, 2025
536a71c
Adding the paper
DLBPointon Jan 17, 2025
df7c41c
Adding the paper - linting riles
DLBPointon Jan 17, 2025
cfa6c42
Adding the paper - linting rules
DLBPointon Jan 17, 2025
bf581e3
Adding Eeriks changes to Usage
DLBPointon Jan 17, 2025
d38d062
Template rules
DLBPointon Jan 17, 2025
0de2a7b
Changes requested by Eerik
DLBPointon Jan 17, 2025
2d22fca
Changes requested by Eerik
DLBPointon Jan 17, 2025
e44c736
Usage.md now properly updates
DLBPointon Jan 17, 2025
b3a0f45
LINTING
DLBPointon Jan 17, 2025
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Updates
DLBPointon committed Nov 14, 2024
commit fd521dcbc356a60e5907bb6d67419bccc48058ce
4 changes: 2 additions & 2 deletions conf/test.config
Original file line number Diff line number Diff line change
@@ -12,8 +12,8 @@

process {
resourceLimits = [
cpus = 4
memory = '8.GB'
cpus = 4,
memory = '8.GB',
time = '6.h'
]
}