Skip to content

Commit

Permalink
Replaced UNZIP with GUNZIP
Browse files Browse the repository at this point in the history
  • Loading branch information
nschcolnicov committed Mar 19, 2024
1 parent 07dee64 commit 83fef7b
Show file tree
Hide file tree
Showing 6 changed files with 145 additions and 154 deletions.
1 change: 1 addition & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#127](https://github.com/nf-core/rnavar/pull/127) - Fixed s3 bucket path in conditional statement for VEP cache
- [#130](https://github.com/nf-core/rnavar/pull/130) - Added missing "def" in local variables
- [#132](https://github.com/nf-core/rnavar/pull/132) - Added missing variantcaller key to meta map, to fix null value in publishDir
- [#134](https://github.com/nf-core/rnavar/pull/134) - Replaced unzip module with gunzip, removed unzip module

### Dependencies

Expand Down
186 changes: 137 additions & 49 deletions modules.json
Original file line number Diff line number Diff line change
Expand Up @@ -8,207 +8,289 @@
"bcftools/concat": {
"branch": "master",
"git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09",
"installed_by": ["vcf_annotate_ensemblvep_snpeff"]
"installed_by": [
"vcf_annotate_ensemblvep_snpeff"
]
},
"bcftools/pluginscatter": {
"branch": "master",
"git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09",
"installed_by": ["vcf_annotate_ensemblvep_snpeff"]
"installed_by": [
"vcf_annotate_ensemblvep_snpeff"
]
},
"bcftools/sort": {
"branch": "master",
"git_sha": "44096c08ffdbc694f5f92ae174ea0f7ba0f37e09",
"installed_by": ["vcf_annotate_ensemblvep_snpeff"]
"installed_by": [
"vcf_annotate_ensemblvep_snpeff"
]
},
"bedtools/merge": {
"branch": "master",
"git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"bedtools/sort": {
"branch": "master",
"git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"cat/fastq": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"custom/dumpsoftwareversions": {
"branch": "master",
"git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"ensemblvep/download": {
"branch": "master",
"git_sha": "214d575774c172062924ad3564b4f66655600730",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"ensemblvep/vep": {
"branch": "master",
"git_sha": "214d575774c172062924ad3564b4f66655600730",
"installed_by": ["modules", "vcf_annotate_ensemblvep", "vcf_annotate_ensemblvep_snpeff"]
"installed_by": [
"modules",
"vcf_annotate_ensemblvep",
"vcf_annotate_ensemblvep_snpeff"
]
},
"fastqc": {
"branch": "master",
"git_sha": "c9488585ce7bd35ccd2a30faa2371454c8112fb9",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"gatk4/applybqsr": {
"branch": "master",
"git_sha": "f1b92874e0de01dd82fe1bf7c6a7409673578065",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"gatk4/baserecalibrator": {
"branch": "master",
"git_sha": "85561f483acc3bc6a885667ea431b3bb3fccdecb",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"gatk4/bedtointervallist": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"gatk4/combinegvcfs": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"gatk4/createsequencedictionary": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"gatk4/haplotypecaller": {
"branch": "master",
"git_sha": "eab2bd29e589bd05da2b47c9bf95ef10b9508699",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"gatk4/indexfeaturefile": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"gatk4/intervallisttools": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"gatk4/markduplicates": {
"branch": "master",
"git_sha": "bc93a4b8904472ce64c6bb50b1fb0a1659b9cf78",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"gatk4/mergevcfs": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"gatk4/splitncigarreads": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"gatk4/variantfiltration": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"gffread": {
"branch": "master",
"git_sha": "a2d6c3082c5c44b4155a3246daff36701ee49af8",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"gunzip": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"mosdepth": {
"branch": "master",
"git_sha": "69e3eb17fb31b772b18f134d6e8f8b93ee980e65",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"multiqc": {
"branch": "master",
"git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"samtools/faidx": {
"branch": "master",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"samtools/flagstat": {
"branch": "master",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"samtools/idxstats": {
"branch": "master",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"samtools/index": {
"branch": "master",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"samtools/merge": {
"branch": "master",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"samtools/sort": {
"branch": "master",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"samtools/stats": {
"branch": "master",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"snpeff/download": {
"branch": "master",
"git_sha": "214d575774c172062924ad3564b4f66655600730",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"snpeff/snpeff": {
"branch": "master",
"git_sha": "214d575774c172062924ad3564b4f66655600730",
"installed_by": ["modules", "vcf_annotate_ensemblvep_snpeff", "vcf_annotate_snpeff"]
"installed_by": [
"modules",
"vcf_annotate_ensemblvep_snpeff",
"vcf_annotate_snpeff"
]
},
"star/align": {
"branch": "master",
"git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"star/genomegenerate": {
"branch": "master",
"git_sha": "d87a6e2156c2099c09280fa70776eaf0a824817a",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
},
"tabix/bgziptabix": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules", "vcf_annotate_snpeff"]
"installed_by": [
"modules",
"vcf_annotate_snpeff"
]
},
"tabix/tabix": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules", "vcf_annotate_ensemblvep", "vcf_annotate_ensemblvep_snpeff"]
"installed_by": [
"modules",
"vcf_annotate_ensemblvep",
"vcf_annotate_ensemblvep_snpeff"
]
},
"untar": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
},
"unzip": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"installed_by": ["modules"]
"installed_by": [
"modules"
]
}
}
},
Expand All @@ -217,20 +299,26 @@
"vcf_annotate_ensemblvep": {
"branch": "master",
"git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
"installed_by": ["subworkflows"]
"installed_by": [
"subworkflows"
]
},
"vcf_annotate_ensemblvep_snpeff": {
"branch": "master",
"git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
"installed_by": ["subworkflows"]
"installed_by": [
"subworkflows"
]
},
"vcf_annotate_snpeff": {
"branch": "master",
"git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
"installed_by": ["subworkflows"]
"installed_by": [
"subworkflows"
]
}
}
}
}
}
}
}
7 changes: 0 additions & 7 deletions modules/nf-core/unzip/environment.yml

This file was deleted.

Loading

0 comments on commit 83fef7b

Please sign in to comment.