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Merge pull request #208 from nf-cmgg/bump-modules
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Bump modules
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@nvnieuwk
nvnieuwk authored Oct 11, 2024
2 parents b3f88cd + 43c27bf commit 6d33f7e
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Showing 76 changed files with 2,501 additions and 1,608 deletions.
2 changes: 1 addition & 1 deletion .github/workflows/template_version_comment.yml
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Expand Up @@ -12,7 +12,7 @@ jobs:
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

- name: Read template version from .nf-core.yml
uses: pietrobolcato/action-read-yaml@1.0.0
uses: pietrobolcato/action-read-yaml@1.1.0
id: read_yml
with:
config: ${{ github.workspace }}/.nf-core.yml
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2 changes: 2 additions & 0 deletions .nf-core.yml
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Expand Up @@ -25,6 +25,8 @@ lint:
- custom_config
- manifest.name
- manifest.homePage
- validation.help.afterText
- validation.summary.afterText
nf_core_version: 3.0.1
repository_type: pipeline
template:
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1 change: 0 additions & 1 deletion conf/base.config
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Expand Up @@ -10,7 +10,6 @@

process {

// TODO nf-core: Check the defaults for all processes
cpus = { 1 * task.attempt }
memory = { 8.GB * task.attempt }
time = { 4.h * task.attempt }
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74 changes: 37 additions & 37 deletions modules.json
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Expand Up @@ -7,7 +7,7 @@
"nf-core": {
"bcftools/annotate": {
"branch": "master",
"git_sha": "88ae68490e8f2478a1e1bbeedac970fd7cc73022",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"],
"patch": "modules/nf-core/bcftools/annotate/bcftools-annotate.diff"
},
Expand All @@ -23,99 +23,99 @@
},
"bcftools/norm": {
"branch": "master",
"git_sha": "f6cc00f107826cfaf1c933297b10ed1757b41479",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"bcftools/pluginscatter": {
"branch": "master",
"git_sha": "33ef773a7ea36e88323902f63662aa53c9b88988",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["vcf_annotate_ensemblvep_snpeff"]
},
"bcftools/query": {
"branch": "master",
"git_sha": "34ac993e081b32d2170ab790d0386b74122f9d36",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"bcftools/reheader": {
"branch": "master",
"git_sha": "c32611ac6813055b9321d2827678e2f8aebcb394",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"bcftools/sort": {
"branch": "master",
"git_sha": "cdf83b18471db290a28fe98c2a0852cb05864890",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["vcf_annotate_ensemblvep_snpeff"]
},
"bcftools/stats": {
"branch": "master",
"git_sha": "a5ba4d59c2b248c0379b0f8aeb4e7e754566cd1f",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"bedtools/intersect": {
"branch": "master",
"git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"bedtools/merge": {
"branch": "master",
"git_sha": "a3d614e4a7b8691a259bcfe33ad80903217d6215",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"bedtools/split": {
"branch": "master",
"git_sha": "6dc8a32e32158bb4d3f9af92c802233b5d4f8e4d",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"ensemblvep/download": {
"branch": "master",
"git_sha": "54c183cba37cac58860d9967feaae54acf9cc3e0",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"],
"patch": "modules/nf-core/ensemblvep/download/ensemblvep-download.diff"
},
"ensemblvep/vep": {
"branch": "master",
"git_sha": "54c183cba37cac58860d9967feaae54acf9cc3e0",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["vcf_annotate_ensemblvep_snpeff"],
"patch": "modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff"
},
"gatk4/calibratedragstrmodel": {
"branch": "master",
"git_sha": "3f42e07a1133064c569b0dbe182979527bca9e59",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"gatk4/composestrtablefile": {
"branch": "master",
"git_sha": "926e2f394d01c71d3abbdbca9c588630bfe51abf",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"gatk4/createsequencedictionary": {
"branch": "master",
"git_sha": "e6fe277739f5894711405af3e717b2470bd956b5",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"gatk4/genomicsdbimport": {
"branch": "master",
"git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"gatk4/genotypegvcfs": {
"branch": "master",
"git_sha": "8b74c800af3d91e0d7bfbecb902308dc4369071c",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"gatk4/haplotypecaller": {
"branch": "master",
"git_sha": "c332ea831f95f750be962c4b5de655f7a1e6e245",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"gawk": {
"branch": "master",
"git_sha": "cf3ed075695639b0a0924eb0901146df1996dc08",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"mosdepth": {
"branch": "master",
"git_sha": "9bfc81874554e87740bcb3e5e07acf0a153c9ecb",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"multiqc": {
Expand All @@ -125,18 +125,18 @@
},
"rtgtools/format": {
"branch": "master",
"git_sha": "e743b2dea725bcfc4b76a209981808987332013a",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"rtgtools/pedfilter": {
"branch": "master",
"git_sha": "c1c2a770cfb0bfbf093a2434a27f091ebbc65987",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"],
"patch": "modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff"
},
"rtgtools/rocplot": {
"branch": "master",
"git_sha": "64770369d851c45c364e410e052ef9a6c3a7d2bb",
"git_sha": "83e2df1e4ec594beb8a575b4db0b4197900f4ebd",
"installed_by": ["modules"]
},
"rtgtools/vcfeval": {
Expand All @@ -146,73 +146,73 @@
},
"samtools/convert": {
"branch": "master",
"git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
"installed_by": ["modules"]
},
"samtools/faidx": {
"branch": "master",
"git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
"installed_by": ["modules"]
},
"samtools/index": {
"branch": "master",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
"installed_by": ["modules"]
},
"samtools/merge": {
"branch": "master",
"git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
"git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
"installed_by": ["modules"]
},
"snpeff/snpeff": {
"branch": "master",
"git_sha": "3ad7292d9b8da881386e9d5b58364d7da489b38b",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["vcf_annotate_ensemblvep_snpeff"]
},
"somalier/extract": {
"branch": "master",
"git_sha": "458c882987320e27fc90723ec96c127a243a5497",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"somalier/relate": {
"branch": "master",
"git_sha": "458c882987320e27fc90723ec96c127a243a5497",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"],
"patch": "modules/nf-core/somalier/relate/somalier-relate.diff"
},
"tabix/bgzip": {
"branch": "master",
"git_sha": "b20be35facfc5acdc1259f132ed79339d79e989f",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"tabix/bgziptabix": {
"branch": "master",
"git_sha": "0840b387799172e77510393ed09e4d4ec1bc6d7c",
"git_sha": "f448e846bdadd80fc8be31fbbc78d9f5b5131a45",
"installed_by": ["modules"]
},
"tabix/tabix": {
"branch": "master",
"git_sha": "0840b387799172e77510393ed09e4d4ec1bc6d7c",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules", "vcf_annotate_ensemblvep_snpeff"]
},
"untar": {
"branch": "master",
"git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"vardictjava": {
"branch": "master",
"git_sha": "e61e5a13ef49c5595986bd31efb85c3f0709a282",
"git_sha": "f85452fcbebab5dfd77c0752236f6f86e9a03b32",
"installed_by": ["modules"]
},
"vcf2db": {
"branch": "master",
"git_sha": "730f3aee80d5f8d0b5fc532202ac59361414d006",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"vcfanno": {
"branch": "master",
"git_sha": "9a8bba5910982ae637dedb8664e3121db77e173f",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
}
}
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91 changes: 53 additions & 38 deletions modules/nf-core/bcftools/annotate/meta.yml
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