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Update (almost) all modules #274

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merged 5 commits into from May 15, 2023
Merged

Update (almost) all modules #274

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a40a086
Pull all module updates + update local module
jasmezz May 12, 2023
02edf73
Update changelog
jasmezz May 12, 2023
efa9b5a
Update pyrodigal + respective AMP subworkflow
jasmezz May 12, 2023
c9b2bc6
Update combgc.nf
jasmezz May 12, 2023
930b091
Merge branch 'dev' into update-modules
jasmezz May 12, 2023
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -8,12 +8,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### `Added`

- [#270](https://github.com/nf-core/funcscan/pull/270) Merged pipeline template of nf-core/tools version 2.8 and updated modules accordingly. (by @jasmezz, @jfy133)
- [#274](https://github.com/nf-core/funcscan/pull/274) Update all modules: changed docker links according to the change of quay.io as default repository. (by @jasmezz)
- [#275](https://github.com/nf-core/funcscan/pull/275) Save DRAMP database in the common database directory if `--save_databases` is supplied. (by @jasmezz)

### `Fixed`

- [#272](https://github.com/nf-core/funcscan/pull/272) Fix typo in Prokka output path in modules.config. (by @jasmezz)
- [#237](https://github.com/nf-core/funcscan/pull/273) Update Ampir module after input bugfix in module (reported by @mathavanpu, fix by @louperelo)
- [#237](https://github.com/nf-core/funcscan/pull/273) Update Ampir module after input bugfix in module. (reported by @mathavanpu, fix by @louperelo)

### `Dependencies`

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68 changes: 34 additions & 34 deletions modules.json
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Expand Up @@ -7,12 +7,12 @@
"nf-core": {
"abricate/run": {
"branch": "master",
"git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"ampcombi": {
"branch": "master",
"git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"ampir": {
Expand All @@ -22,163 +22,163 @@
},
"amplify/predict": {
"branch": "master",
"git_sha": "5293fc55d4d645cf9daffad835bee270d328ce91",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"amrfinderplus/run": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"amrfinderplus/update": {
"branch": "master",
"git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"antismash/antismashlite": {
"branch": "master",
"git_sha": "3a8d2761600b789cbde3a7780a211a8328604af0",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"antismash/antismashlitedownloaddatabases": {
"branch": "master",
"git_sha": "ac07fba2543c5c9b6da9306c2d3ee58bdafb5262",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"bakta/bakta": {
"branch": "master",
"git_sha": "280c5c86b3da7dfcc92ebd5420584dd6ff26c4a8",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"bakta/baktadbdownload": {
"branch": "master",
"git_sha": "280c5c86b3da7dfcc92ebd5420584dd6ff26c4a8",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"bioawk": {
"branch": "master",
"git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"],
"patch": "modules/nf-core/bioawk/bioawk.diff"
},
"custom/dumpsoftwareversions": {
"branch": "master",
"git_sha": "76cc4938c1f6ea5c7d83fed1eeffc146787f9543",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"deeparg/downloaddata": {
"branch": "master",
"git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"deeparg/predict": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"deepbgc/download": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"deepbgc/pipeline": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"fargene": {
"branch": "master",
"git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"fastqc": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"gecco/run": {
"branch": "master",
"git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"gunzip": {
"branch": "master",
"git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71",
"git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
"installed_by": ["modules"]
},
"hamronization/abricate": {
"branch": "master",
"git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"hamronization/amrfinderplus": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"hamronization/deeparg": {
"branch": "master",
"git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"hamronization/fargene": {
"branch": "master",
"git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"hamronization/rgi": {
"branch": "master",
"git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"hamronization/summarize": {
"branch": "master",
"git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"hmmer/hmmsearch": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"macrel/contigs": {
"branch": "master",
"git_sha": "a5a5bb12e7cc25658fdc97d810f2d6688cdae169",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"multiqc": {
"branch": "master",
"git_sha": "f2d63bd5b68925f98f572eed70993d205cc694b7",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"prodigal": {
"branch": "master",
"git_sha": "8c4f2d2ceeb5e9cc4a49a91c0e9a675b6724c043",
"git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
"installed_by": ["modules"]
},
"prokka": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"pyrodigal": {
"branch": "master",
"git_sha": "93cca9af587f39eaaa357b9e589e3e657d8a0f75",
"git_sha": "1b91efd7ff7b2fb5fe0d78f0d2f6c728afc5e552",
"installed_by": ["modules"]
},
"rgi/main": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"tabix/bgzip": {
"branch": "master",
"git_sha": "90294980a903ecebd99ac31d8b6c66af48fa8259",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"untar": {
"branch": "master",
"git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71",
"git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
"installed_by": ["modules"]
}
}
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2 changes: 1 addition & 1 deletion modules/local/combgc.nf
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Expand Up @@ -5,7 +5,7 @@ process COMBGC {
conda "conda-forge::python=3.11.0 conda-forge::biopython=1.80 conda-forge::pandas=1.5.2"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-27978155697a3671f3ef9aead4b5c823a02cc0b7:548df772fe13c0232a7eab1bc1deb98b495a05ab-0' :
'quay.io/biocontainers/mulled-v2-27978155697a3671f3ef9aead4b5c823a02cc0b7:548df772fe13c0232a7eab1bc1deb98b495a05ab-0' }"
'biocontainers/mulled-v2-27978155697a3671f3ef9aead4b5c823a02cc0b7:548df772fe13c0232a7eab1bc1deb98b495a05ab-0' }"

input:
tuple val(meta), path(input_paths)
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2 changes: 1 addition & 1 deletion modules/local/dramp_download.nf
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Expand Up @@ -4,7 +4,7 @@ process DRAMP_DOWNLOAD {
conda "bioconda::ampcombi=0.1.7"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ampcombi:0.1.7--pyhdfd78af_0':
'quay.io/biocontainers/ampcombi:0.1.7--pyhdfd78af_0' }"
'biocontainers/ampcombi:0.1.7--pyhdfd78af_0' }"

output:
path "amp_ref_database/" , emit: db
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2 changes: 1 addition & 1 deletion modules/nf-core/abricate/run/main.nf
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2 changes: 1 addition & 1 deletion modules/nf-core/ampcombi/main.nf
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