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Build branch main with version main (73b07a9)

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Build pipeline: vsh-ci-template-xxl9g

Source commit: 73b07a96e0

Source message: Fix quotes in test (#4)

* Fix quotes in test

* query the first output file to pick up the 'name' value again and output it

grep with start and end position constaints
This commit is contained in:
CI
2024-06-25 12:38:48 +00:00
parent b533a32bc8
commit f1307f7487
15 changed files with 2 additions and 106 deletions
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50
.nextflow.log
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Jun-25 12:24:34.214 [main] DEBUG nextflow.cli.Launcher - $> nextflow -q run /opt/viash_tools/target/native/nextflow/generate_schema_v9/main.nf --resourcesDir /opt/viash_tools/target/native/nextflow/generate_schema_v9 --input /workdir/root/repo/src/yq/config.vsh.yaml --output target/nextflow/yq/nextflow_schema.json --add_global_params true --enable_dataset_input false
Jun-25 12:24:34.429 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 24.04.2
Jun-25 12:24:34.493 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/.nextflow/plugins; core-plugins: nf-amazon@2.5.2,nf-azure@1.6.0,nf-cloudcache@0.4.1,nf-codecommit@0.2.0,nf-console@1.1.3,nf-ga4gh@1.3.0,nf-google@1.13.2,nf-tower@1.9.1,nf-wave@1.4.2
Jun-25 12:24:34.534 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jun-25 12:24:34.535 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jun-25 12:24:34.542 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.10.0 in 'deployment' mode
Jun-25 12:24:34.596 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Jun-25 12:24:34.693 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /workdir/root/repo/nextflow.config
Jun-25 12:24:34.704 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /workdir/root/repo/nextflow.config
Jun-25 12:24:34.760 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /.nextflow/secrets/store.json
Jun-25 12:24:34.767 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@2e647e59] - activable => nextflow.secret.LocalSecretsProvider@2e647e59
Jun-25 12:24:34.800 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Jun-25 12:24:36.250 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Jun-25 12:24:36.293 [main] INFO nextflow.cli.CmdRun - Launching `/opt/viash_tools/target/native/nextflow/generate_schema_v9/main.nf` [cheeky_lavoisier] DSL2 - revision: 513aeab0c0
Jun-25 12:24:36.308 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jun-25 12:24:36.309 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Jun-25 12:24:36.533 [main] DEBUG nextflow.Session - Session UUID: 8c0657a5-f61b-4b51-b7dc-a023ac27ee7c
Jun-25 12:24:36.534 [main] DEBUG nextflow.Session - Run name: cheeky_lavoisier
Jun-25 12:24:36.535 [main] DEBUG nextflow.Session - Executor pool size: 4
Jun-25 12:24:36.561 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Jun-25 12:24:36.592 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=12; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jun-25 12:24:36.654 [main] DEBUG nextflow.cli.CmdRun -
Version: 24.04.2 build 5914
Created: 29-05-2024 06:19 UTC
System: Linux 6.1.85+
Runtime: Groovy 4.0.21 on OpenJDK 64-Bit Server VM 17.0.10+7-LTS
Encoding: UTF-8 (UTF-8)
Process: 239@vsh-ci-template-7m7cc-nxf-generate-schemas-382080591 [10.48.2.43]
CPUs: 4 - Mem: 15.6 GB (838.7 MB) - Swap: 0 (0)
Jun-25 12:24:36.744 [main] DEBUG nextflow.Session - Work-dir: /workdir/root/repo/work [ext2/ext3]
Jun-25 12:24:36.745 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /opt/viash_tools/target/native/nextflow/generate_schema_v9/bin
Jun-25 12:24:36.769 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jun-25 12:24:36.807 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jun-25 12:24:36.905 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jun-25 12:24:36.947 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 5; maxThreads: 1000
Jun-25 12:24:37.183 [main] DEBUG nextflow.Session - Session start
Jun-25 12:24:38.920 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jun-25 12:24:41.528 [main] DEBUG nextflow.Session - Workflow process names [dsl2]:
Jun-25 12:24:41.529 [main] DEBUG nextflow.Session - Igniting dataflow network (0)
Jun-25 12:24:41.529 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_85cbbb9c9058ccbe: /opt/viash_tools/target/native/nextflow/generate_schema_v9/main.nf
Script_a1b09e222ee37273: /opt/viash_tools/target/native/nextflow/generate_schema_v9/WorkflowHelper_v9.nf
Jun-25 12:24:41.529 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Jun-25 12:24:41.529 [main] DEBUG nextflow.Session - Session await
Jun-25 12:24:41.529 [main] DEBUG nextflow.Session - Session await > all processes finished
Jun-25 12:24:41.529 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jun-25 12:24:41.543 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=0; peakCpus=0; peakMemory=0; ]
Jun-25 12:24:41.569 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Jun-25 12:24:41.601 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Jun-25 12:24:41.601 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

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Jun-25 12:24:34.172 [main] DEBUG nextflow.cli.Launcher - $> nextflow -q run /opt/viash_tools/target/native/nextflow/generate_schema_v9/main.nf --resourcesDir /opt/viash_tools/target/native/nextflow/generate_schema_v9 --input /workdir/root/repo/src/bgzip/config.vsh.yaml --output target/nextflow/bgzip/nextflow_schema.json --add_global_params true --enable_dataset_input false
Jun-25 12:24:34.364 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 24.04.2
Jun-25 12:24:34.407 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/.nextflow/plugins; core-plugins: nf-amazon@2.5.2,nf-azure@1.6.0,nf-cloudcache@0.4.1,nf-codecommit@0.2.0,nf-console@1.1.3,nf-ga4gh@1.3.0,nf-google@1.13.2,nf-tower@1.9.1,nf-wave@1.4.2
Jun-25 12:24:34.444 [main] INFO o.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Jun-25 12:24:34.445 [main] INFO o.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Jun-25 12:24:34.450 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.10.0 in 'deployment' mode
Jun-25 12:24:34.500 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Jun-25 12:24:34.614 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /workdir/root/repo/nextflow.config
Jun-25 12:24:34.623 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /workdir/root/repo/nextflow.config
Jun-25 12:24:34.733 [main] DEBUG n.secret.LocalSecretsProvider - Secrets store: /.nextflow/secrets/store.json
Jun-25 12:24:34.748 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@3249a1ce] - activable => nextflow.secret.LocalSecretsProvider@3249a1ce
Jun-25 12:24:34.857 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `standard`
Jun-25 12:24:36.315 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declaration
Jun-25 12:24:36.366 [main] INFO nextflow.cli.CmdRun - Launching `/opt/viash_tools/target/native/nextflow/generate_schema_v9/main.nf` [amazing_cantor] DSL2 - revision: 513aeab0c0
Jun-25 12:24:36.370 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Jun-25 12:24:36.371 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Jun-25 12:24:36.494 [main] DEBUG nextflow.Session - Session UUID: 60a82ca9-724b-4668-b35b-d10f456b1562
Jun-25 12:24:36.495 [main] DEBUG nextflow.Session - Run name: amazing_cantor
Jun-25 12:24:36.497 [main] DEBUG nextflow.Session - Executor pool size: 4
Jun-25 12:24:36.511 [main] DEBUG nextflow.file.FilePorter - File porter settings maxRetries=3; maxTransfers=50; pollTimeout=null
Jun-25 12:24:36.526 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=12; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Jun-25 12:24:36.567 [main] DEBUG nextflow.cli.CmdRun -
Version: 24.04.2 build 5914
Created: 29-05-2024 06:19 UTC
System: Linux 6.1.85+
Runtime: Groovy 4.0.21 on OpenJDK 64-Bit Server VM 17.0.10+7-LTS
Encoding: UTF-8 (UTF-8)
Process: 238@vsh-ci-template-7m7cc-nxf-generate-schemas-382080591 [10.48.2.43]
CPUs: 4 - Mem: 15.6 GB (845.9 MB) - Swap: 0 (0)
Jun-25 12:24:36.660 [main] DEBUG nextflow.Session - Work-dir: /workdir/root/repo/work [ext2/ext3]
Jun-25 12:24:36.661 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /opt/viash_tools/target/native/nextflow/generate_schema_v9/bin
Jun-25 12:24:36.681 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Jun-25 12:24:36.718 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Jun-25 12:24:36.839 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Jun-25 12:24:36.872 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 5; maxThreads: 1000
Jun-25 12:24:37.090 [main] DEBUG nextflow.Session - Session start
Jun-25 12:24:38.850 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Jun-25 12:24:41.267 [main] DEBUG nextflow.Session - Workflow process names [dsl2]:
Jun-25 12:24:41.268 [main] DEBUG nextflow.Session - Igniting dataflow network (0)
Jun-25 12:24:41.270 [main] DEBUG nextflow.script.ScriptRunner - Parsed script files:
Script_85cbbb9c9058ccbe: /opt/viash_tools/target/native/nextflow/generate_schema_v9/main.nf
Script_a1b09e222ee37273: /opt/viash_tools/target/native/nextflow/generate_schema_v9/WorkflowHelper_v9.nf
Jun-25 12:24:41.271 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
Jun-25 12:24:41.271 [main] DEBUG nextflow.Session - Session await
Jun-25 12:24:41.271 [main] DEBUG nextflow.Session - Session await > all processes finished
Jun-25 12:24:41.271 [main] DEBUG nextflow.Session - Session await > all barriers passed
Jun-25 12:24:41.301 [main] DEBUG n.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=0; failedCount=0; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=0ms; failedDuration=0ms; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=0; peakCpus=0; peakMemory=0; ]
Jun-25 12:24:41.361 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Jun-25 12:24:41.406 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Jun-25 12:24:41.407 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

0
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MANIFEST-000002

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MANIFEST-000002

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2024-06-25 12:24:36 5.4s amazing_cantor OK 513aeab0c0380e607d62198f977630e1 60a82ca9-724b-4668-b35b-d10f456b1562 nextflow -q run /opt/viash_tools/target/native/nextflow/generate_schema_v9/main.nf --resourcesDir /opt/viash_tools/target/native/nextflow/generate_schema_v9 --input /workdir/root/repo/src/bgzip/config.vsh.yaml --output target/nextflow/bgzip/nextflow_schema.json --add_global_params true --enable_dataset_input false
2024-06-25 12:24:36 5.6s cheeky_lavoisier OK 513aeab0c0380e607d62198f977630e1 8c0657a5-f61b-4b51-b7dc-a023ac27ee7c nextflow -q run /opt/viash_tools/target/native/nextflow/generate_schema_v9/main.nf --resourcesDir /opt/viash_tools/target/native/nextflow/generate_schema_v9 --input /workdir/root/repo/src/yq/config.vsh.yaml --output target/nextflow/yq/nextflow_schema.json --add_global_params true --enable_dataset_input false

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target/executable/bgzip/bgzip
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@@ -508,7 +508,7 @@ ENTRYPOINT []
RUN bgzip -h | grep 'Version:' 2>&1 | sed 's/Version:\s\(.*\)/bgzip: "\1"/' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component bgzip"
LABEL org.opencontainers.image.created="2024-06-25T12:22:13Z"
LABEL org.opencontainers.image.created="2024-06-25T12:35:57Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/htslib"
LABEL org.opencontainers.image.revision="73b07a96e07de3b4429499795ef9fee678a96366"
LABEL org.opencontainers.image.version="main"

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target/executable/yq/yq
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@@ -490,7 +490,7 @@ RUN apk add --no-cache bash yq-go
RUN /usr/bin/yq --version | sed 's/.*version\sv\(.*\)/yq: "\1"/' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component yq"
LABEL org.opencontainers.image.created="2024-06-25T12:22:14Z"
LABEL org.opencontainers.image.created="2024-06-25T12:35:58Z"
LABEL org.opencontainers.image.source="https://github.com/mikefarah/yq"
LABEL org.opencontainers.image.revision="73b07a96e07de3b4429499795ef9fee678a96366"
LABEL org.opencontainers.image.version="main"