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Merge pull request #1040 from nf-core/dev
Dev -> Master for 3.12.0 release
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| name: "Close user-tagged issues and PRs" | ||
| on: | ||
| schedule: | ||
| - cron: "0 0 * * 0" # Once a week | ||
|
|
||
| jobs: | ||
| clean-up: | ||
| runs-on: ubuntu-latest | ||
| permissions: | ||
| issues: write | ||
| pull-requests: write | ||
| steps: | ||
| - uses: actions/stale@v7 | ||
| with: | ||
| stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days." | ||
| stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful." | ||
| close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity." | ||
| days-before-stale: 30 | ||
| days-before-close: 20 | ||
| days-before-pr-close: -1 | ||
| any-of-labels: "awaiting-changes,awaiting-feedback" | ||
| exempt-issue-labels: "WIP" | ||
| exempt-pr-labels: "WIP" | ||
| repo-token: "${{ secrets.GITHUB_TOKEN }}" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,5 @@ | ||
| repos: | ||
| - repo: https://github.com/pre-commit/mirrors-prettier | ||
| rev: "v2.7.1" | ||
| hooks: | ||
| - id: prettier |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,72 @@ | ||
| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| AWS ECR Config | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Config to set public AWS ECR images wherever possible | ||
| This improves speed when running on AWS infrastructure. | ||
| Use this as an example template when using your own private registry. | ||
| ---------------------------------------------------------------------------------------- | ||
| */ | ||
|
|
||
| docker.registry = 'public.ecr.aws' | ||
| podman.registry = 'public.ecr.aws' | ||
|
|
||
| process { | ||
| withName: 'CAT_ADDITIONAL_FASTA' { | ||
| container = 'quay.io/biocontainers/python:3.9--1' | ||
| } | ||
| withName: 'CAT_FASTQ' { | ||
| container = 'quay.io/nf-core/ubuntu:20.04' | ||
| } | ||
| withName: 'DESEQ2_QC' { | ||
| container = 'quay.io/biocontainers/mulled-v2-8849acf39a43cdd6c839a369a74c0adc823e2f91:ab110436faf952a33575c64dd74615a84011450b-0' | ||
| } | ||
| withName: 'GTF2BED' { | ||
| container = 'quay.io/biocontainers/perl:5.26.2' | ||
| } | ||
| withName: 'GTF_GENE_FILTER' { | ||
| container = 'quay.io/biocontainers/python:3.9--1' | ||
| } | ||
| withName: 'GUNZIP' { | ||
| container = 'quay.io/nf-core/ubuntu:20.04' | ||
| } | ||
| withName: 'HISAT2_ALIGN' { | ||
| container = 'quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2cdf6bf1e92acbeb9b2834b1c58754167173a410-0' | ||
| } | ||
| withName: 'MULTIQC_CUSTOM_BIOTYPE' { | ||
| container = 'quay.io/biocontainers/python:3.9--1' | ||
| } | ||
| withName: 'PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' { | ||
| container = 'quay.io/nf-core/ubuntu:20.04' | ||
| } | ||
| withName: 'RSEM_CALCULATEEXPRESSION' { | ||
| container = 'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' | ||
| } | ||
| withName: 'RSEM_MERGE_COUNTS' { | ||
| container = 'quay.io/nf-core/ubuntu:20.04' | ||
| } | ||
| withName: 'RSEM_PREPAREREFERENCE' { | ||
| container = 'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' | ||
| } | ||
| withName: 'SALMON_TX2GENE' { | ||
| container = 'quay.io/biocontainers/python:3.9--1' | ||
| } | ||
| withName: 'SAMPLESHEET_CHECK' { | ||
| container = 'quay.io/biocontainers/python:3.9--1' | ||
| } | ||
| withName: 'STAR_ALIGN' { | ||
| container = 'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' | ||
| } | ||
| withName: 'STAR_ALIGN_IGENOMES' { | ||
| container = 'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' | ||
| } | ||
| withName: 'STAR_GENOMEGENERATE' { | ||
| container = 'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0' | ||
| } | ||
| withName: 'STAR_GENOMEGENERATE_IGENOMES' { | ||
| container = 'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' | ||
| } | ||
| withName: 'UNTAR' { | ||
| container = 'quay.io/nf-core/ubuntu:20.04' | ||
| } | ||
| } |
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