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Release PR v1.4.0
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name: release-announcements | ||
# Automatic release toot and tweet anouncements | ||
on: | ||
release: | ||
types: [published] | ||
workflow_dispatch: | ||
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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 | ||
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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 }} | ||
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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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sample,family,cram,crai,roi,ped,truth_vcf,truth_tbi,truth_bed | ||
DNA049572,Proband_12345,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test.cram,,,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-germline/dev/assets/test.ped,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/vcf/test.vcf.gz,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/vcf/test.vcf.gz.tbi,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/regions/roi.bed | ||
NA24385D2_NVQ_034,Proband_12345,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test2.cram,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test2.cram.crai,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/regions/roi.bed,,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/vcf/test2.vcf.gz,, | ||
sample,family,cram,crai,roi,ped,truth_vcf,truth_tbi,truth_bed,vardict_min_af | ||
DNA049572,Proband_12345,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test.cram,,,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-germline/dev/assets/test.ped,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/vcf/test.vcf.gz,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/vcf/test.vcf.gz.tbi,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/regions/roi.bed,0.01 | ||
NA24385D2_NVQ_034,Proband_12345,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test2.cram,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/cram/test2.cram.crai,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/regions/roi.bed,,https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-test-datasets/main/data/genomics/homo_sapiens/illumina/vcf/test2.vcf.gz,,, |
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/* | ||
======================================================================================== | ||
Nextflow config file for HyperCap runs | ||
======================================================================================== | ||
*/ | ||
|
||
params { | ||
callers = "vardict" | ||
filter = true | ||
normalize = true | ||
annotate = true | ||
vcfanno = true | ||
scatter_count = 5 | ||
vep_dbnsfp = true | ||
vep_spliceai = true | ||
vep_spliceregion = true | ||
vep_mastermind = true | ||
vep_maxentscan = true | ||
vep_eog = true | ||
} |
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/* | ||
======================================================================================== | ||
Nextflow config file for SeqCap runs | ||
======================================================================================== | ||
*/ | ||
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params { | ||
callers = "vardict" | ||
filter = true | ||
normalize = true | ||
scatter_count = 14 | ||
} |
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/* | ||
======================================================================================== | ||
Nextflow config file for WES runs | ||
======================================================================================== | ||
*/ | ||
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params { | ||
roi = "${params.genomes_base}/Hsapiens/GRCh38.p14/regions/CMGG_WES_analysis_ROI_v4.bed" | ||
scatter_count = 14 | ||
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} |
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/* | ||
======================================================================================== | ||
Nextflow config file for WGS runs | ||
======================================================================================== | ||
*/ | ||
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params { | ||
scatter_count = 30 | ||
} |
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/* | ||
======================================================================================== | ||
Nextflow config file for runs that need to be imported in seqplorer | ||
======================================================================================== | ||
*/ | ||
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params { | ||
filter = true | ||
decompose = true | ||
normalize = true | ||
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annotate = true | ||
vep_dbnsfp = true | ||
vep_spliceai = true | ||
vep_mastermind = true | ||
vep_eog = true | ||
vep_maxentscan = true | ||
vep_spliceregion = true | ||
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gemini = true | ||
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} |
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add_ped = true | ||
vep_chunk_size = 10000 | ||
project = "test" | ||
normalize = true | ||
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vep_merged = false | ||
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|
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class DynamicContainers { | ||
static String apiUrl = "https://api.biocontainers.pro/ga4gh/trs/v2" | ||
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public static String findLatest(String containerName, Double version, String type="docker") { | ||
this.findLatest(containerName, version as String, type) | ||
} | ||
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public static String findLatest(String containerName, Float version, String type="docker") { | ||
this.findLatest(containerName, version as String, type) | ||
} | ||
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public static String findLatest(String containerName, Integer version, String type="docker") { | ||
this.findLatest(containerName, version as String, type) | ||
} | ||
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public static String findLatest(String containerName, String version, String type="docker") { | ||
type = type ? type.toLowerCase() : "docker" | ||
def String url = "${this.apiUrl}/tools/${containerName}/versions/${containerName}-${version}" | ||
def biocontainersGet = new URL(url).openConnection() | ||
biocontainersGet.setRequestProperty("accept", "application/json") | ||
def getRC = biocontainersGet.getResponseCode() | ||
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if (getRC != 200) { return null } | ||
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def parser = new groovy.json.JsonSlurper() | ||
def jsonResponse = parser.parseText(biocontainersGet.getInputStream().getText()) | ||
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def ArrayList images = jsonResponse["images"].findAll { it["image_type"].toLowerCase() == type } | ||
if(images.size() > 1 && type != "conda") { | ||
return this.getLatestImage(images) | ||
} | ||
else if(images.size() == 0 && type == "singularity") { | ||
images = jsonResponse["images"].findAll { it["image_type"].toLowerCase() == "docker" } | ||
return this.getLatestImage(images) | ||
} | ||
else { | ||
return images[0]["image_name"] | ||
} | ||
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} | ||
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static String getLatestImage(ArrayList images) { | ||
def Date latestTime | ||
def String latestImage | ||
for(image : images) { | ||
def Integer year = image["updated"].split("-")[0] as Integer | ||
def Integer month = image["updated"].split("-")[1] as Integer | ||
def Integer day = image["updated"].split("-")[2].split("T")[0] as Integer | ||
def Integer hour = image["updated"].split("T")[1].split(":")[0] as Integer | ||
def Integer minutes = image["updated"].split("T")[1].split(":")[1] as Integer | ||
def Integer seconds = image["updated"].split("T")[1].split(":")[2].split("Z")[0] as Integer | ||
def Date time = new Date(year, month, day, hour, minutes, seconds) | ||
if (time > latestTime) { | ||
latestTime = time | ||
latestImage = image["image_name"] | ||
} | ||
} | ||
return latestImage | ||
} | ||
} |
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// A class that contains some variables that need to be globally accesible | ||
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class GlobalVariables { | ||
// The available callers | ||
public static List availableCallers = ["haplotypecaller", "vardict"] | ||
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public static List gvcfCallers = ["haplotypecaller"] | ||
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} |
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Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
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Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
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Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
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Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
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Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
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Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.
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