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Pipeline Release Version 1.1.0 #64
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f250381
Updated Dockerfile
DSchreyer 2204d2e
Removed versions
DSchreyer 616e157
Updates - Unsure what they were
DSchreyer ef61377
doesnt work
DSchreyer fc81a30
Fixed collect issue -> Immediate release in new pull request
DSchreyer 1c9f798
test
DSchreyer 32c4798
Update, not working yet
DSchreyer 8ab10ae
updated to ampliconsuite-pipeline. Much work needed to finalise. Work…
DSchreyer 39306e4
Template update for nf-core/tools version 2.9
nf-core-bot 7c28c3c
Updated modules
DSchreyer 884c0db
Updated test configs
DSchreyer cd3381c
Updated parameter requirements
DSchreyer 3542830
Updated ampliconarchitect tools to amplicon-suite pipeline
DSchreyer f8a7ef6
Removed ampliconarchitect python scripts -> changed to ampliconsuite
DSchreyer c69d62d
Removed due to depracation
DSchreyer cd84761
Updates
DSchreyer f1e48a0
updates
DSchreyer 7483cbe
Updated Tag
DSchreyer 74cd8fe
Updated with new variables for ampliconarchitect modules
DSchreyer 032ea60
Fixes
DSchreyer d015b5e
Changed AA variable command
DSchreyer 982e234
Template update for nf-core/tools version 2.10
nf-core-bot 6c05cae
Template update for nf-core/tools version 2.11
nf-core-bot 294666e
Template update for nf-core/tools version 2.11.1
nf-core-bot 9f2330a
Updates
DSchreyer 9ee14eb
Updates on ampliconsuite, removed ampliconarchitect, not finished yet
DSchreyer 0419286
Template update for nf-core/tools v2.11.1
DSchreyer 4619740
modules and subworkflows update to 2.11.2
DSchreyer 79d9f03
lib update
DSchreyer 1657a11
updated gitignore
DSchreyer 06f0eb5
fix template change
DSchreyer 1e7c398
updateto 1.19
DSchreyer 327a531
removed redundant scripts
DSchreyer d64f0c7
removed redundant scripts
DSchreyer f85d6b2
added output directories and output for ampliconsuite
DSchreyer 2fcd72e
updated modules and multiqc
DSchreyer de09bcd
updated multiqc path
DSchreyer bb9c18e
remoced multiqc module
DSchreyer 138e458
Updated ampliconsuite docker file and environment.yml
DSchreyer 65bca09
updated ampliconsuite output
DSchreyer 47e4a88
Updated Dockerfile and github workflow version push
DSchreyer ec04c9f
Updated dockerfile with procps
DSchreyer d7286d3
updated build-docker image
DSchreyer c5c362c
updated ampliconsuite and implemented changes
DSchreyer cc888aa
Updated dockerfile for ampliconsutie
DSchreyer 7393761
singularity update dockerbuild
DSchreyer 6375272
update to fit singularity
DSchreyer f2fce80
Updated modules for ampliconclassifier
DSchreyer 18246fe
updated modules
DSchreyer cea7a6e
removed nf-core/multiqc
DSchreyer f9a0f03
updated ampliconsuite documentation
DSchreyer af32e8c
updated changelog
DSchreyer 4b58f64
updated ampliconsuite citations
DSchreyer d5f2995
prettier
DSchreyer 6b80d7b
updated dummy directory for test run
DSchreyer 0630570
update eclint check
DSchreyer a7ee658
Merge branch 'master' into dev
DSchreyer 70a5674
prettier
DSchreyer 65be064
update multiqc config to fit info
DSchreyer b037482
updated minimap2 fasta meta requirements
DSchreyer 3e44e07
Template update for nf-core/tools version 2.12
nf-core-bot 57f92a5
Updated Changelog
DSchreyer b04c482
Updated multiqc config to fit v1.1
DSchreyer f9987f8
removed dummy directory for aa_data_repo and mosek_license_dir
DSchreyer dfda421
updated version
DSchreyer 7373cbe
Removed todo
DSchreyer 04b9d30
Added better worfklow run description when using --help
DSchreyer d8cbf50
Updated Changelog.md to improve description and readability
DSchreyer c41ff3b
Removed multiqc from nf-core modules
DSchreyer 257de0b
prettier
DSchreyer 7600019
Merge branch 'dev' into nf-core-template-merge-2.12
DSchreyer 6a950be
nextflow config update
DSchreyer c86c82d
fixed issue with timestamp
DSchreyer 111c6a7
nf-core lint fixes
DSchreyer ea544ab
updated bam_markduplicates
DSchreyer f8805c3
files_unchanged fix
DSchreyer d7af74c
prettier
DSchreyer cfb463b
left-padding space fix
DSchreyer 1a3f5b1
replaced circdna logo with v2.12 version
DSchreyer c3f6f11
add linting test for test_AA
DSchreyer 5b17a74
Merge pull request #67 from nf-core/nf-core-template-merge-2.12
DSchreyer 7acfa77
--input_format is now a required parameter based on suggestion in htt…
DSchreyer 4deb7d4
prettier and added test_AA_local profile to test AA and AS locally wi…
DSchreyer 1f94fb6
Updated bwa_index parameter to accept only directories
DSchreyer e2bcc60
Changelog update to fit newest changes
DSchreyer 20e8d76
Updated readme
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Template update for nf-core/tools v2.11.1
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,68 @@ | ||
name: release-announcements | ||
# Automatic release toot and tweet anouncements | ||
on: | ||
release: | ||
types: [published] | ||
workflow_dispatch: | ||
|
||
jobs: | ||
toot: | ||
runs-on: ubuntu-latest | ||
steps: | ||
- uses: rzr/fediverse-action@master | ||
with: | ||
access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }} | ||
host: "mstdn.science" # custom host if not "mastodon.social" (default) | ||
# GitHub event payload | ||
# https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release | ||
message: | | ||
Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! | ||
|
||
Please see the changelog: ${{ github.event.release.html_url }} | ||
|
||
send-tweet: | ||
runs-on: ubuntu-latest | ||
|
||
steps: | ||
- uses: actions/setup-python@v4 | ||
with: | ||
python-version: "3.10" | ||
- name: Install dependencies | ||
run: pip install tweepy==4.14.0 | ||
- name: Send tweet | ||
shell: python | ||
run: | | ||
import os | ||
import tweepy | ||
|
||
client = tweepy.Client( | ||
access_token=os.getenv("TWITTER_ACCESS_TOKEN"), | ||
access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"), | ||
consumer_key=os.getenv("TWITTER_CONSUMER_KEY"), | ||
consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"), | ||
) | ||
tweet = os.getenv("TWEET") | ||
client.create_tweet(text=tweet) | ||
env: | ||
TWEET: | | ||
Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! | ||
|
||
Please see the changelog: ${{ github.event.release.html_url }} | ||
TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }} | ||
TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }} | ||
TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }} | ||
TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }} | ||
|
||
bsky-post: | ||
runs-on: ubuntu-latest | ||
steps: | ||
- uses: zentered/bluesky-post-action@v0.0.2 | ||
with: | ||
post: | | ||
Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! | ||
|
||
Please see the changelog: ${{ github.event.release.html_url }} | ||
env: | ||
BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }} | ||
BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }} | ||
# |
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If this is done you can remove the comment
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Removed. Good spot