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jasmezzjasmezz
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Merge pull request #322 from nf-core/modules-update
Update all modules
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‎CHANGELOG.md

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@@ -7,10 +7,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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### `Added`
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- [#322](https://github.com/nf-core/funcscan/pull/322) Updated all modules: introduce environment.yml files. (by @jasmezz)
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### `Fixed`
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### `Dependencies`
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| Tool | Previous version | New version |
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| ------- | ---------------- | ----------- |
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| MultiQC | 1.15 | 1.17 |
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### `Deprecated`
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## v1.1.4 - [2023-11-07]

‎modules.json

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"nf-core": {
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"abricate/run": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"ampcombi": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"ampir": {
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"branch": "master",
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"git_sha": "6ac776f62fad7360685a87680c5f57f74c3682dc",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"amplify/predict": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"amrfinderplus/run": {
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"branch": "master",
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"git_sha": "016547e536216e0e839eb8ec678d13b25211c174",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"amrfinderplus/update": {
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"branch": "master",
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"git_sha": "868d4c3dc7a3db39d36184173e4fe3484499396e",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"antismash/antismashlite": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"antismash/antismashlitedownloaddatabases": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"bakta/bakta": {
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"branch": "master",
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"git_sha": "f05fa7c6753f92be861d606378860dcd5c828880",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"bakta/baktadbdownload": {
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"branch": "master",
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"git_sha": "f05fa7c6753f92be861d606378860dcd5c828880",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"bioawk": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"],
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"patch": "modules/nf-core/bioawk/bioawk.diff"
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},
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"custom/dumpsoftwareversions": {
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"branch": "master",
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"git_sha": "1b372269755a5c4a13c23bc130ebada8cb9d4cd0",
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"git_sha": "fc6caedab1c71113aa440900e5989dd1c03ec58f",
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"installed_by": ["modules"]
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},
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"deeparg/downloaddata": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"deeparg/predict": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"deepbgc/download": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"deepbgc/pipeline": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"fargene": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"gecco/run": {
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"branch": "master",
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"git_sha": "8c029dd8e67754d937fb6b6814e568f1decb2fea",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"gunzip": {
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"branch": "master",
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"git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"hamronization/abricate": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"hamronization/amrfinderplus": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"hamronization/deeparg": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"hamronization/fargene": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"hamronization/rgi": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"hamronization/summarize": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"hmmer/hmmsearch": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"macrel/contigs": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"multiqc": {
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"branch": "master",
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"git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"prodigal": {
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"branch": "master",
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"git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"prokka": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"pyrodigal": {
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"branch": "master",
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"git_sha": "dd3ed02ddb21363b1892e4705c164aa4cf945435",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"rgi/main": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"tabix/bgzip": {
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"branch": "master",
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"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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},
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"untar": {
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"branch": "master",
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"git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8",
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"git_sha": "8fc1d24c710ebe1d5de0f2447ec9439fd3d9d66a",
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"installed_by": ["modules"]
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}
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}

‎modules/nf-core/abricate/run/environment.yml

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‎modules/nf-core/abricate/run/main.nf

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‎modules/nf-core/abricate/run/meta.yml

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‎modules/nf-core/ampcombi/environment.yml

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‎modules/nf-core/ampcombi/main.nf

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‎modules/nf-core/ampcombi/meta.yml

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‎modules/nf-core/ampir/environment.yml

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‎modules/nf-core/ampir/main.nf

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‎modules/nf-core/ampir/meta.yml

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‎modules/nf-core/amplify/predict/environment.yml

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‎modules/nf-core/amplify/predict/main.nf

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‎modules/nf-core/amplify/predict/meta.yml

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