8000 Update modules by LilyAnderssonLee · Pull Request #372 · nf-core/taxprofiler · GitHub
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Merged
merged 12 commits into from
Sep 15, 2023
Merged

Update modules #372

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459199c
update modules
LilyAnderssonLee Sep 13, 2023
441ca8a
correct reference channel in SAMTOOLS_STATS
LilyAnderssonLee Sep 13, 2023
4205136
update the change
LilyAnderssonLee Sep 13, 2023
59af4ba
Simplified the mapping operation.
LilyAnderssonLee Sep 14, 2023
d8f7896
Update CHANGELOG.md
LilyAnderssonLee Sep 14, 2023
076f0e2
Update subworkflows/local/longread_hostremoval.nf
LilyAnderssonLee Sep 14, 2023
d12e8cb
Update subworkflows/local/shortread_hostremoval.nf
LilyAnderssonLee Sep 14, 2023
34960d6
update the reference channel to SAMTOOLS_STATS
LilyAnderssonLee Sep 14, 2023
2f577b0
Update longread_hostremoval.nf
LilyAnderssonLee Sep 15, 2023
9312882
Update shortread_hostremoval.nf
LilyAnderssonLee Sep 15, 2023
a87af16
Update longread_hostremoval.nf
LilyAnderssonLee Sep 15, 2023
5a1999c
Skip taxpasta meta.tools check for metaphlan
LilyAnderssonLee Sep 15, 2023
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5 changes: 4 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -43,14 +43,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#342](https://github.com/nf-core/taxprofiler/pull/342) Fixed docs/usage to correctly list the required database files for Bracken and tips to obtain Kraken2 databases (fix by @husensofteng)
- [#350](https://github.com/nf-core/taxprofiler/pull/350) Reorganize the CI tests into separate profiles in preparation for implementation of nf-test (fix by @LilyAnderssonLee)
- [#364](https://github.com/nf-core/taxprofiler/pull/364) Add autoMounts to apptainer profile in nextflow.config (♥ to @hkaspersento for reporting, fix by @LilyAnderssonLee)
- [#372](https://github.com/nf-core/taxprofiler/pull/372) Update modules to use quay.io nf-core mirrored containers (♥ to @maxulysse for pointing out, fix by @LilyAnderssonLee and @jfy133)

### `Dependencies`

| Tool | Previous version | New version |
| --------- | ---------------- | ----------- |
| MultiQC | 1.13 | 1.14 |
| MultiQC | 1.13 | 1.15 |
| TAXPASTA | 0.2.3 | 0.6.0 |
| MetaPhlAn | 3.0.12 | 4.0.6 |
| fastp | 0.23.2 | 0.23.4 |
| samtools | 1.16.1 | 1.17 |

### `Deprecated`

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78 changes: 39 additions & 39 deletions modules.json
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Expand Up @@ -7,37 +7,37 @@
"nf-core": {
"adapterremoval": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"bbmap/bbduk": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"bowtie2/align": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "fe54581f8bed20e4c4a51c616c93fd3379d89820",
"installed_by": ["modules"]
},
"bowtie2/build": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "6a24fbe314bb2e6fe6306c29a63076ea87e8eb3c",
"installed_by": ["modules"]
},
"bracken/bracken": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"bracken/combinebrackenoutputs": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"cat/fastq": {
"branch": "master",
"git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71",
"git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
"installed_by": ["modules"]
},
"centrifuge/centrifuge": {
Expand All @@ -47,38 +47,38 @@
},
"centrifuge/kreport": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"custom/dumpsoftwareversions": {
"branch": "master",
"git_sha": "76cc4938c1f6ea5c7d83fed1eeffc146787f9543",
"git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4",
"installed_by": ["modules"]
},
"diamond/blastx": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"falco": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"],
"patch": "modules/nf-core/falco/falco.diff"
},
"fastp": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "d497a4868ace3302016ea8ed4b395072d5e833cd",
"installed_by": ["modules"]
},
"fastqc": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "9a4517e720bc812e95b56d23d15a1653b6db4f53",
"installed_by": ["modules"]
},
"filtlong": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"ganon/classify": {
Expand All @@ -98,22 +98,22 @@
},
"gunzip": {
"branch": "master",
"git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71",
"git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57",
"installed_by": ["modules"]
},
"kaiju/kaiju": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"kaiju/kaiju2krona": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"kaiju/kaiju2table": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
&quo 8000 t;kmcp/profile": {
Expand All @@ -128,47 +128,47 @@
},
"kraken2/kraken2": {
"branch": "master",
"git_sha": "7c695e0147df1157413e06246d9b0094617d3e6b",
"git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
"installed_by": ["modules"]
},
"krakentools/combinekreports": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"krakentools/kreport2krona": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"krakenuniq/preloadedkrakenuniq": {
"branch": "master",
"git_sha": "a6eb17f65b3ee5761c25c075a6166c9f76733cee",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"krona/ktimporttaxonomy": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"krona/ktimporttext": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"malt/run": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"megan/rma2info": {
"branch": "master&q 8000 uot;,
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"metaphlan/mergemetaphlantables": {
"branch": "master",
"git_sha": "9aa59197c0fb35c29e315bcd10c0fc9e1afc70a8",
"git_sha": "efae1c431e539d6a6d323ee2e9223c4b81a152ce",
"installed_by": ["modules"]
},
"metaphlan/metaphlan": {
Expand All @@ -178,58 +178,58 @@
},
"minimap2/align": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
"installed_by": ["modules"]
},
"minimap2/index": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"motus/merge": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"motus/profile": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"multiqc": {
"branch": "master",
"git_sha": "f2d63bd5b68925f98f572eed70993d205cc694b7",
"git_sha": "a6e11ac655e744f7ebc724be669dd568ffdc0e80",
"installed_by": ["modules"]
},
"porechop/porechop": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"],
"patch": "modules/nf-core/porechop/porechop/porechop-porechop.diff"
},
"prinseqplusplus": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"samtools/fastq": {
"branch": "master",
"git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"samtools/index": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
"installed_by": ["modules"]
},
"samtools/stats": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
"git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
"installed_by": ["modules"]
},
"samtools/view": {
"branch": "master",
"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c&qu B943 ot;,
"git_sha": "3ffae3598260a99e8db3207dead9f73f87f90d1f",
"installed_by": ["modules"]
},
"taxpasta/merge": {
Expand All @@ -244,7 +244,7 @@
},
"untar": {
"branch": "master",
"git_sha": "b9829e1064382745d8dff7f1d74d2138d2864f71",
"git_sha": "d0b4fc03af52a1cc8c6fb4493b921b57352b1dd8",
"installed_by": ["modules"]
}
}
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2 changes: 1 addition & 1 deletion modules/local/kraken2_standard_report.nf
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Expand Up @@ -5,7 +5,7 @@ process KRAKEN2_STANDARD_REPORT {
conda "conda-forge::sed=4.7"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'docker.io/ubuntu:20.04' }"
'nf-core/ubuntu:20.04' }"

input:
tuple val(meta), path(report)
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2 changes: 1 addition & 1 deletion modules/local/krona_cleanup.nf
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Expand Up @@ -5,7 +5,7 @@ process KRONA_CLEANUP {
conda "conda-forge::sed=4.7"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
'docker.io/ubuntu:20.04' }"
'nf-core/ubuntu:20.04' }"

input:
tuple val(meta), path(krona, stageAs: 'uncleaned.krona.txt')
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2 changes: 1 addition & 1 deletion modules/nf-core/adapterremoval/main.nf
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2 changes: 1 addition & 1 deletion modules/nf-core/bbmap/bbduk/main.nf
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3 changes: 1 addition & 2 deletions modules/nf-core/bbmap/bbduk/meta.yml
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35 changes: 29 additions & 6 deletions modules/nf-core/bowtie2/align/main.nf
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