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Upgrade modules accordingly
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@apeltzer
apeltzer committed Feb 14, 2024
1 parent 18ae224 commit ab52f26
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4 changes: 2 additions & 2 deletions CHANGELOG.md
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Expand Up @@ -34,14 +34,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

| Dependency | Old version | New version |
| ------------- | ----------- | ----------- |
| `multiqc` | 1.15 | 1.19 |
| `multiqc` | 1.15 | 1.20 |
| `edgeR` | 3.36.0 | 4.0.2 |
| `limma` | 3.50.0 | 3.58.1 |
| `bioconvert` | 0.4.3 | 1.1.1 |
| `mirdeep` | 2.0.1 | 2.0.1.3 |
| `seqkit` | 2.3.1 | 2.6.1 |
| `fastqc` | 0.11.4 | 0.12.1 |
| `samtools` | 1.17 | 1.18 |
| `samtools` | 1.17 | 1.19.2 |
| `umitools` | <none> | 1.1.4 |
| `umicollapse` | <none> | 1.0.0 |

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22 changes: 11 additions & 11 deletions modules.json
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Expand Up @@ -22,7 +22,7 @@
},
"fastp": {
"branch": "master",
"git_sha": "c9488585ce7bd35ccd2a30faa2371454c8112fb9",
"git_sha": "003920c7f9a8ae19b69a97171922880220bedf56",
"installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
},
"fastqc": {
Expand All @@ -32,32 +32,32 @@
},
"multiqc": {
"branch": "master",
"git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
"git_sha": "ccacf6f5de6df3bc6d73b665c1fd2933d8bbc290",
"installed_by": ["modules"]
},
"samtools/flagstat": {
"branch": "master",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["bam_stats_samtools", "modules"]
},
"samtools/idxstats": {
"branch": "master",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["bam_stats_samtools", "modules"]
},
"samtools/index": {
"branch": "master",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["bam_sort_stats_samtools", "modules"]
},
"samtools/sort": {
"branch": "master",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["bam_sort_stats_samtools", "modules"]
},
"samtools/stats": {
"branch": "master",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["bam_stats_samtools", "modules"]
},
"umicollapse": {
Expand All @@ -67,7 +67,7 @@
},
"umitools/extract": {
"branch": "master",
"git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53",
"git_sha": "9e56d7a647fbf6f7e45ef123bc916ad66b6f7c9d",
"installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
}
}
Expand All @@ -76,17 +76,17 @@
"nf-core": {
"bam_sort_stats_samtools": {
"branch": "master",
"git_sha": "0c38be7e652a0b2f3a37681ee4c0dbdf85677647",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["subworkflows"]
},
"bam_stats_samtools": {
"branch": "master",
"git_sha": "0c38be7e652a0b2f3a37681ee4c0dbdf85677647",
"git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
"installed_by": ["bam_sort_stats_samtools", "subworkflows"]
},
"fastq_fastqc_umitools_fastp": {
"branch": "master",
"git_sha": "a4bceac1aecee5aa0a5dbc601baf0e2e61013fb2",
"git_sha": "003920c7f9a8ae19b69a97171922880220bedf56",
"installed_by": ["subworkflows"]
}
}
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30 changes: 15 additions & 15 deletions modules/nf-core/fastp/tests/main.nf.test
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