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Base container image update #315

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merged 5 commits into from
Jun 3, 2022
Merged

Base container image update #315

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a5dc5cc
Replace busybox with Ubuntu base image for GCP support
jfy133 Jun 3, 2022
c1a30cd
Update CHANGELOG.md
jfy133 Jun 3, 2022
152c1b0
Add missing file
jfy133 Jun 3, 2022
6e6e630
Merge branch 'base-container-image-update' of github.com:jfy133/nf-co…
jfy133 Jun 3, 2022
c666942
Update CHANGELOG.md
jfy133 Jun 3, 2022
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#286](https://github.com/nf-core/mag/pull/286) - Cite our publication instead of the preprint
- [#299](https://github.com/nf-core/mag/pull/299) - Add extra results folder `GenomeBinning/depths` for `[assembler]-[sample/group]-depth.txt.gz`, `bin_depths_summary.tsv` and `[assembler]-[binner]-[sample/group]-binDepths.heatmap.png`
- [#302](https://github.com/nf-core/mag/pull/302) - Update to nf-core 2.4 `TEMPLATE`
- [#315](https://github.com/nf-core/mag/pull/315) - Replace base container for standard shell tools to fix problems with running on Google Cloud

### `Fixed`

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2 changes: 1 addition & 1 deletion modules.json
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Expand Up @@ -34,7 +34,7 @@
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
},
"gunzip": {
"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
"git_sha": "9aadd9a6d3f5964476582319b3a1c54a3e3fe7c9"
},
"maxbin2": {
"git_sha": "b78a4a456762a4c59fd5023e70f36a27f76d4a97"
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4 changes: 2 additions & 2 deletions modules/local/busco_db_preparation.nf
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Expand Up @@ -3,8 +3,8 @@ process BUSCO_DB_PREPARATION {

conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
'biocontainers/biocontainers:v1.2.0_cv1' }"
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'ubuntu:20.04' }"

input:
path database
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4 changes: 2 additions & 2 deletions modules/local/busco_save_download.nf
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Expand Up @@ -4,8 +4,8 @@ process BUSCO_SAVE_DOWNLOAD {

conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
'biocontainers/biocontainers:v1.2.0_cv1' }"
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'ubuntu:20.04' }"

input:
path(busco_downloads)
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4 changes: 2 additions & 2 deletions modules/local/cat_db.nf
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Expand Up @@ -3,8 +3,8 @@ process CAT_DB {

conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
'biocontainers/biocontainers:v1.2.0_cv1' }"
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'ubuntu:20.04' }"

input:
path(database)
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4 changes: 2 additions & 2 deletions modules/local/centrifuge_db_preparation.nf
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Expand Up @@ -2,8 +2,8 @@ process CENTRIFUGE_DB_PREPARATION {

conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
'biocontainers/biocontainers:v1.2.0_cv1' }"
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'ubuntu:20.04' }"

input:
path db
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4 changes: 2 additions & 2 deletions modules/local/gtdbtk_db_preparation.nf
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Expand Up @@ -3,8 +3,8 @@ process GTDBTK_DB_PREPARATION {

conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
'biocontainers/biocontainers:v1.2.0_cv1' }"
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'ubuntu:20.04' }"

input:
path(database)
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4 changes: 2 additions & 2 deletions modules/local/kraken2_db_preparation.nf
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Expand Up @@ -2,8 +2,8 @@ process KRAKEN2_DB_PREPARATION {

conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
'biocontainers/biocontainers:v1.2.0_cv1' }"
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'ubuntu:20.04' }"

input:
path db
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4 changes: 2 additions & 2 deletions modules/local/pool_paired_reads.nf
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Expand Up @@ -3,8 +3,8 @@ process POOL_PAIRED_READS {

conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
'biocontainers/biocontainers:v1.2.0_cv1' }"
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'ubuntu:20.04' }"

input:
tuple val(meta), path(reads1), path(reads2)
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4 changes: 2 additions & 2 deletions modules/local/pool_single_reads.nf
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Expand Up @@ -3,8 +3,8 @@ process POOL_SINGLE_READS {

conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
'biocontainers/biocontainers:v1.2.0_cv1' }"
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'ubuntu:20.04' }"

input:
tuple val(meta), path(reads)
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4 changes: 2 additions & 2 deletions modules/local/quast_bins_summary.nf
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Expand Up @@ -2,8 +2,8 @@ process QUAST_BINS_SUMMARY {

conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
'biocontainers/biocontainers:v1.2.0_cv1' }"
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'ubuntu:20.04' }"

input:
path(summaries)
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4 changes: 2 additions & 2 deletions modules/nf-core/modules/gunzip/main.nf
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