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Pipeline Release Version 1.1.0 #64

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merged 86 commits into from
Feb 10, 2024
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f250381
Updated Dockerfile
DSchreyer Jun 20, 2023
2204d2e
Removed versions
DSchreyer Jun 20, 2023
616e157
Updates - Unsure what they were
DSchreyer Jun 20, 2023
ef61377
doesnt work
DSchreyer Jun 23, 2023
fc81a30
Fixed collect issue -> Immediate release in new pull request
DSchreyer Jun 26, 2023
1c9f798
test
DSchreyer Jun 26, 2023
32c4798
Update, not working yet
DSchreyer Jun 27, 2023
8ab10ae
updated to ampliconsuite-pipeline. Much work needed to finalise. Work…
DSchreyer Jun 28, 2023
39306e4
Template update for nf-core/tools version 2.9
nf-core-bot Jun 30, 2023
7c28c3c
Updated modules
DSchreyer Jul 3, 2023
884c0db
Updated test configs
DSchreyer Jul 3, 2023
cd3381c
Updated parameter requirements
DSchreyer Jul 3, 2023
3542830
Updated ampliconarchitect tools to amplicon-suite pipeline
DSchreyer Jul 3, 2023
f8a7ef6
Removed ampliconarchitect python scripts -> changed to ampliconsuite
DSchreyer Jul 3, 2023
c69d62d
Removed due to depracation
DSchreyer Jul 3, 2023
cd84761
Updates
DSchreyer Jul 3, 2023
f1e48a0
updates
DSchreyer Jul 3, 2023
7483cbe
Updated Tag
DSchreyer Jul 7, 2023
74cd8fe
Updated with new variables for ampliconarchitect modules
DSchreyer Jul 12, 2023
032ea60
Fixes
DSchreyer Jul 12, 2023
d015b5e
Changed AA variable command
DSchreyer Jul 12, 2023
982e234
Template update for nf-core/tools version 2.10
nf-core-bot Sep 25, 2023
6c05cae
Template update for nf-core/tools version 2.11
nf-core-bot Dec 19, 2023
294666e
Template update for nf-core/tools version 2.11.1
nf-core-bot Dec 20, 2023
9f2330a
Updates
DSchreyer Jan 5, 2024
9ee14eb
Updates on ampliconsuite, removed ampliconarchitect, not finished yet
DSchreyer Jan 6, 2024
0419286
Template update for nf-core/tools v2.11.1
DSchreyer Jan 6, 2024
4619740
modules and subworkflows update to 2.11.2
DSchreyer Jan 6, 2024
79d9f03
lib update
DSchreyer Jan 7, 2024
1657a11
updated gitignore
DSchreyer Jan 7, 2024
06f0eb5
fix template change
DSchreyer Jan 7, 2024
1e7c398
updateto 1.19
DSchreyer Jan 8, 2024
327a531
removed redundant scripts
DSchreyer Jan 8, 2024
d64f0c7
removed redundant scripts
DSchreyer Jan 8, 2024
f85d6b2
added output directories and output for ampliconsuite
DSchreyer Jan 8, 2024
2fcd72e
updated modules and multiqc
DSchreyer Jan 8, 2024
de09bcd
updated multiqc path
DSchreyer Jan 8, 2024
bb9c18e
remoced multiqc module
DSchreyer Jan 8, 2024
138e458
Updated ampliconsuite docker file and environment.yml
DSchreyer Jan 9, 2024
65bca09
updated ampliconsuite output
DSchreyer Jan 9, 2024
47e4a88
Updated Dockerfile and github workflow version push
DSchreyer Jan 9, 2024
ec04c9f
Updated dockerfile with procps
DSchreyer Jan 9, 2024
d7286d3
updated build-docker image
DSchreyer Jan 9, 2024
c5c362c
updated ampliconsuite and implemented changes
DSchreyer Jan 9, 2024
cc888aa
Updated dockerfile for ampliconsutie
DSchreyer Jan 9, 2024
7393761
singularity update dockerbuild
DSchreyer Jan 9, 2024
6375272
update to fit singularity
DSchreyer Jan 9, 2024
f2fce80
Updated modules for ampliconclassifier
DSchreyer Jan 9, 2024
18246fe
updated modules
DSchreyer Jan 9, 2024
cea7a6e
removed nf-core/multiqc
DSchreyer Jan 9, 2024
f9a0f03
updated ampliconsuite documentation
DSchreyer Jan 9, 2024
af32e8c
updated changelog
DSchreyer Jan 9, 2024
4b58f64
updated ampliconsuite citations
DSchreyer Jan 9, 2024
d5f2995
prettier
DSchreyer Jan 9, 2024
6b80d7b
updated dummy directory for test run
DSchreyer Jan 9, 2024
0630570
update eclint check
DSchreyer Jan 9, 2024
a7ee658
Merge branch 'master' into dev
DSchreyer Jan 9, 2024
70a5674
prettier
DSchreyer Jan 9, 2024
65be064
update multiqc config to fit info
DSchreyer Jan 9, 2024
b037482
updated minimap2 fasta meta requirements
DSchreyer Jan 10, 2024
3e44e07
Template update for nf-core/tools version 2.12
nf-core-bot Jan 29, 2024
57f92a5
Updated Changelog
DSchreyer Jan 30, 2024
b04c482
Updated multiqc config to fit v1.1
DSchreyer Jan 30, 2024
f9987f8
removed dummy directory for aa_data_repo and mosek_license_dir
DSchreyer Jan 30, 2024
dfda421
updated version
DSchreyer Jan 30, 2024
7373cbe
Removed todo
DSchreyer Jan 30, 2024
04b9d30
Added better worfklow run description when using --help
DSchreyer Jan 30, 2024
d8cbf50
Updated Changelog.md to improve description and readability
DSchreyer Jan 30, 2024
c41ff3b
Removed multiqc from nf-core modules
DSchreyer Jan 30, 2024
257de0b
prettier
DSchreyer Jan 30, 2024
7600019
Merge branch 'dev' into nf-core-template-merge-2.12
DSchreyer Jan 30, 2024
6a950be
nextflow config update
DSchreyer Jan 30, 2024
c86c82d
fixed issue with timestamp
DSchreyer Jan 30, 2024
111c6a7
nf-core lint fixes
DSchreyer Jan 30, 2024
ea544ab
updated bam_markduplicates
DSchreyer Jan 30, 2024
f8805c3
files_unchanged fix
DSchreyer Jan 30, 2024
d7af74c
prettier
DSchreyer Jan 30, 2024
cfb463b
left-padding space fix
DSchreyer Jan 30, 2024
1a3f5b1
replaced circdna logo with v2.12 version
DSchreyer Jan 31, 2024
c3f6f11
add linting test for test_AA
DSchreyer Jan 31, 2024
5b17a74
Merge pull request #67 from nf-core/nf-core-template-merge-2.12
DSchreyer Jan 31, 2024
7acfa77
--input_format is now a required parameter based on suggestion in htt…
DSchreyer Feb 3, 2024
4deb7d4
prettier and added test_AA_local profile to test AA and AS locally wi…
DSchreyer Feb 3, 2024
1f94fb6
Updated bwa_index parameter to accept only directories
DSchreyer Feb 4, 2024
e2bcc60
Changelog update to fit newest changes
DSchreyer Feb 4, 2024
20e8d76
Updated readme
DSchreyer Feb 8, 2024
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updated gitignore
  • Loading branch information
DSchreyer committed Jan 7, 2024
commit 1657a11b2db9c635a0c9ff4877857442acf3c1e1
1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -7,3 +7,4 @@ testing/
testing*
*.pyc
null
.vscode