8000 Docker/podman registry hotfix by jfy133 · Pull Request #305 · nf-core/taxprofiler · GitHub
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Docker/podman registry hotfix #305

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Merged
merged 1 commit into from
Jun 7, 2023
Merged

Docker/podman registry hotfix #305

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19 changes: 10 additions & 9 deletions CHANGELOG.md
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Expand Up @@ -12,15 +12,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Fixed`

- [#271](https://github.com/nf-core/taxprofiler/pull/271/files) Improved standardised table generation documentation nd mOTUs manual database download tutorial (♥ to @prototaxites for reporting, fix by @jfy133)
- [#269](https://github.com/nf-core/taxprofiler/pull/269/files) Reduced output files in AWS full test output due to very large files
- [#270](https://github.com/nf-core/taxprofiler/pull/270/files) Fixed warning for host removal index parameter, and improved index checks (♥ to @prototaxites for reporting, fix by @jfy133)
- [#274](https://github.com/nf-core/taxprofiler/pull/274/files) Substituted the samtools/bam2fq module with samtools/fastq module (fix by @sofstam)
- [#275](https://github.com/nf-core/taxprofiler/pull/275/files) Replaced function used for error reporting to more Nextflow friendly method (fix by @jfy133)
- [#285](https://github.com/nf-core/taxprofiler/pull/285/files) Fixed overly large log files in Kraken2 output (♥ to @prototaxites for reporting, fix by @Midnighter & @jfy133)
- [#286](https://github.com/nf-core/taxprofiler/pull/286/files) Runtime optimisation of MultiQC step via improved log file processing (fix by @Midnighter & @jfy133)
- [#289](https://github.com/nf-core/taxprofiler/pull/289/files) Pipeline updated to nf-core template 2.8 (fix by @Midnighter & @jfy133)
- [#290](https://github.com/nf-core/taxprofiler/pull/286/files) Minor database input documentation improvements (♥ to @alneberg for reporting, fix by @jfy133)
- [#271](https://github.com/nf-core/taxprofiler/pull/271) Improved standardised table generation documentation nd mOTUs manual database download tutorial (♥ to @prototaxites for reporting, fix by @jfy133)
- [#269](https://github.com/nf-core/taxprofiler/pull/269) Reduced output files in AWS full test output due to very large files
- [#270](https://github.com/nf-core/taxprofiler/pull/270) Fixed warning for host removal index parameter, and improved index checks (♥ to @prototaxites for reporting, fix by @jfy133)
- [#274](https://github.com/nf-core/taxprofiler/pull/274) Substituted the samtools/bam2fq module with samtools/fastq module (fix by @sofstam)
- [#275](https://github.com/nf-core/taxprofiler/pull/275) Replaced function used for error reporting to more Nextflow friendly method (fix by @jfy133)
- [#285](https://github.com/nf-core/taxprofiler/pull/285) Fixed overly large log files in Kraken2 output (♥ to @prototaxites for reporting, fix by @Midnighter & @jfy133)
- [#286](https://github.com/nf-core/taxprofiler/pull/286) Runtime optimisation of MultiQC step via improved log file processing (fix by @Midnighter & @jfy133)
- [#289](https://github.com/nf-core/taxprofiler/pull/289) Pipeline updated to nf-core template 2.8 (fix by @Midnighter & @jfy133)
- [#290](https://github.com/nf-core/taxprofiler/pull/290) Minor database input documentation improvements (♥ to @alneberg for reporting, fix by @jfy133)
- [#305](https://github.com/nf-core/taxprofiler/pull/305) Fix docker/podman registry definition for tower compatibility (fix by @adamrtalbot, @jfy133)

### `Dependencies`

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8 changes: 6 additions & 2 deletions nextflow.config
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Expand Up @@ -213,7 +213,6 @@ profiles {
}
docker {
docker.enabled = true
docker.registry = 'quay.io'
docker.userEmulation = true
conda.enabled = false
singularity.enabled = false
Expand All @@ -237,7 +236,6 @@ profiles {
}
podman {
podman.enabled = true
podman.registry = 'quay.io'
conda.enabled = false
docker.enabled = false
singularity.enabled = false
Expand Down Expand Up @@ -310,6 +308,12 @@ env {
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']

// Set default registry for Docker and Podman independent of -profile
// Will not be used unless Docker / Podman are enabled
// Set to your registry if you have a mirror of containers
docker.registry = 'quay.io'
podman.registry = 'quay.io'

def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
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