diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0767506..0db15cf 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,15 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
-## v2.4.1-dev - [date]
+## Unreleased
+
+### `Added`
+- [#61](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/61) Add download VEP module form nf-core
+
+### `Changed`
+- [#59](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/59) Add ".snv" to VEP output filename prefix
+
+## v2.4.1-dev - 16/01/2025
## v2.4.0-dev
@@ -26,7 +34,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### `Changed`
- [#54](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/54) Standardize exomiser output filenames
-- [#59](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/59) Add ".snv" to VEP output filename prefix
### `Fixed`
- [#50](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/50) Use container tag 1.20 for splitMultiAllelics process
diff --git a/README.md b/README.md
index 805dd21..e1c98d8 100644
--- a/README.md
+++ b/README.md
@@ -22,7 +22,7 @@ It performs joint genotyping, tags low-quality variants, and optionally annotate
6. Tag false positive variants with either:
- For whole genome sequencing data: [Variant quality score recalibration (VQSR)](https://gatk.broadinstitute.org/hc/en-us/articles/360036510892-VariantRecalibrator)
- For whole exome sequencing data: [Hard-Filtering](https://gatk.broadinstitute.org/hc/en-us/articles/360036733451-VariantFiltration)
-7. Optionnally annotate variants with [Variant effect predictor (VEP)](https://useast.ensembl.org/info/docs/tools/vep/index.html)
+7. Optionnally annotate variants with [Variant effect predictor (VEP)](https://useast.ensembl.org/info/docs/tools/vep/index.html) and download reference cache (if not provided)
8. Optionnally integrate phenotype data to annotate, filter and prioritise variants likely to be disease-causing with [exomiser](https://www.sanger.ac.uk/tool/exomiser/)
@@ -76,7 +76,7 @@ See [docs/output.md](docs/output.md) for more details about pipeline outputs.
## Credits
-Ferlab-Ste-Justine/Post-processing-Pipeline was originally written by Damien Geneste, David Morais, Felix-Antoine Le Sieur, Jeremy Costanza, Lysiane Bouchard.
+Ferlab-Ste-Justine/Post-processing-Pipeline was originally written by Damien Geneste, David Morais, Felix-Antoine Le Sieur, Jeremy Costanza, Lysiane Bouchard, Georgette Femerling.
## Contributions and Support
diff --git a/conf/modules.config b/conf/modules.config
index 81fa961..72b8022 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -71,6 +71,18 @@ process {
ext.args = { "--output-filename=${meta.id}.exomiser" }
}
+ withName: ENSEMBLVEP_DOWNLOAD {
+ // Using the conda container as the official one from esemblorg does not have the download_vep function used in nf-core.
+ container = 'quay.io/biocontainers/ensembl-vep:111.0--pl5321h2a3209d_0'
+ ext.when = { params.tools && (params.tools.split(',').contains('vep')) }
+ ext.args = '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE'
+ ext.prefix = { "${params.vep_cache_version}_${params.vep_genome}" }
+ publishDir = [
+ mode: params.publish_dir_mode,
+ path: { params.outdir_cache ? "${params.outdir_cache}/": "${params.outdir}/cache/" }
+ ]
+ }
+
withName: ENSEMBLVEP_VEP {
container = 'ensemblorg/ensembl-vep:release_111.0' //sticking to v111 for now, but we should update this
def args_list = [
diff --git a/docs/reference_data.md b/docs/reference_data.md
index f4ab74f..4e4765e 100644
--- a/docs/reference_data.md
+++ b/docs/reference_data.md
@@ -46,7 +46,7 @@ For more details, see [Gatk documentation](https://gatk.broadinstitute.org/hc/en
## VEP Cache Directory
-The `vepCache` parameter specifies the directory for the vep cache. It is only required if `vep` is specified via the
+The `vep_cache` parameter specifies the directory for the vep cache. It is only required if `vep` is specified via the
`tools` parameter.
The vep cache is not automatically populated by the pipeline. It must be pre-downloaded. You can obtain a copy of the
diff --git a/docs/usage.md b/docs/usage.md
index 5abc755..86ae066 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -194,7 +194,11 @@ Parameters summary
| `broad` | _Optional_ | Path to the directory containing Broad reference data (for VQSR) |
| `intervalsFile` | _Optional_ | Path to the file containg the genome intervals list on which to operate |
| `tools` | _Optional_ | Additional tools to run separated by commas. Supported tools are `vep` and `exomiser` |
-| `vepCache` | _Optional_ | Path to the vep cache data directory |
+| `vep_cache` | _Optional_ | Path to the vep cache data directory |
+| `vep_cache_version` | _Optional_ | Version of the vep cache. e.g. `111` |
+| `vep_genome` | _Optional_ | Genome assembly version of the vep cache |
+| `download_cache` | _Optional_ | Download vep cache (default: false) |
+| `outdir_cache` | _Optional_ | Path to write the cache to. If not declared, cache will be written to `<outputdir>/cache/` |
| `exclude_mnps` | _Optional_ | Replace MNPs by individual SNPs (default: true). Must be true on whole genome data. |
| `exomiser_data_dir` | _Optional_ | Path to the exomiser reference data directory |
| `exomiser_genome` | _Optional_ | Genome assembly version to be used by exomiser(`hg19` or `hg38`) |
diff --git a/modules.json b/modules.json
index 4a574a5..48298c5 100644
--- a/modules.json
+++ b/modules.json
@@ -20,6 +20,11 @@
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
+ "ensemblvep/download": {
+ "branch": "master",
+ "git_sha": "6e3585d9ad20b41adc7d271009f8cb5e191ecab4",
+ "installed_by": ["modules"]
+ },
"ensemblvep/vep": {
"branch": "master",
"git_sha": "6e3585d9ad20b41adc7d271009f8cb5e191ecab4",
diff --git a/modules/nf-core/ensemblvep/download/environment.yml b/modules/nf-core/ensemblvep/download/environment.yml
new file mode 100644
index 0000000..3d36eb1
--- /dev/null
+++ b/modules/nf-core/ensemblvep/download/environment.yml
@@ -0,0 +1,5 @@
+channels:
+ - conda-forge
+ - bioconda
+dependencies:
+ - bioconda::ensembl-vep=113.0
diff --git a/modules/nf-core/ensemblvep/download/main.nf b/modules/nf-core/ensemblvep/download/main.nf
new file mode 100644
index 0000000..0664a2d
--- /dev/null
+++ b/modules/nf-core/ensemblvep/download/main.nf
@@ -0,0 +1,47 @@
+process ENSEMBLVEP_DOWNLOAD {
+ tag "$meta.id"
+ label 'process_medium'
+
+ conda "${moduleDir}/environment.yml"
+ container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+ 'https://depot.galaxyproject.org/singularity/ensembl-vep:113.0--pl5321h2a3209d_0' :
+ 'biocontainers/ensembl-vep:113.0--pl5321h2a3209d_0' }"
+
+ input:
+ tuple val(meta), val(assembly), val(species), val(cache_version)
+
+ output:
+ tuple val(meta), path(prefix), emit: cache
+ path "versions.yml" , emit: versions
+
+ when:
+ task.ext.when == null || task.ext.when
+
+ script:
+ def args = task.ext.args ?: ''
+ prefix = task.ext.prefix ?: 'vep_cache'
+ """
+ vep_install \\
+ --CACHEDIR $prefix \\
+ --SPECIES $species \\
+ --ASSEMBLY $assembly \\
+ --CACHE_VERSION $cache_version \\
+ $args
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//')
+ END_VERSIONS
+ """
+
+ stub:
+ prefix = task.ext.prefix ?: 'vep_cache'
+ """
+ mkdir $prefix
+
+ cat <<-END_VERSIONS > versions.yml
+ "${task.process}":
+ ensemblvep: \$( echo \$(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*\$//')
+ END_VERSIONS
+ """
+}
diff --git a/modules/nf-core/ensemblvep/download/meta.yml b/modules/nf-core/ensemblvep/download/meta.yml
new file mode 100644
index 0000000..8da9621
--- /dev/null
+++ b/modules/nf-core/ensemblvep/download/meta.yml
@@ -0,0 +1,53 @@
+name: ensemblvep_download
+description: Ensembl Variant Effect Predictor (VEP). The cache downloading options
+ are controlled through `task.ext.args`.
+keywords:
+ - annotation
+ - cache
+ - download
+tools:
+ - ensemblvep:
+ description: |
+ VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs
+ or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
+ homepage: https://www.ensembl.org/info/docs/tools/vep/index.html
+ documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html
+ licence: ["Apache-2.0"]
+ identifier: ""
+input:
+ - - meta:
+ type: map
+ description: |
+ Groovy Map containing sample information
+ e.g. [ id:'test', single_end:false ]
+ - assembly:
+ type: string
+ description: |
+ Genome assembly
+ - species:
+ type: string
+ description: |
+ Specie
+ - cache_version:
+ type: string
+ description: |
+ cache version
+output:
+ - cache:
+ - meta:
+ type: file
+ description: cache
+ pattern: "*"
+ - prefix:
+ type: file
+ description: cache
+ pattern: "*"
+ - versions:
+ - versions.yml:
+ type: file
+ description: File containing software versions
+ pattern: "versions.yml"
+authors:
+ - "@maxulysse"
+maintainers:
+ - "@maxulysse"
diff --git a/modules/nf-core/ensemblvep/download/tests/main.nf.test b/modules/nf-core/ensemblvep/download/tests/main.nf.test
new file mode 100644
index 0000000..a558599
--- /dev/null
+++ b/modules/nf-core/ensemblvep/download/tests/main.nf.test
@@ -0,0 +1,60 @@
+nextflow_process {
+
+ name "Test Process ENSEMBLVEP_DOWNLOAD"
+ script "../main.nf"
+ process "ENSEMBLVEP_DOWNLOAD"
+ config "./nextflow.config"
+
+ tag "modules"
+ tag "modules_nfcore"
+ tag "ensemblvep"
+ tag "ensemblvep/download"
+
+ test("celegans - download") {
+
+ when {
+ process {
+ """
+ input[0] = Channel.of([
+ [id:"113_WBcel235"],
+ params.vep_genome,
+ params.vep_species,
+ params.vep_cache_version
+ ])
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+
+ test("celegans - download - stub") {
+
+ options "-stub"
+
+ when {
+ process {
+ """
+ input[0] = Channel.of([
+ [id:"113_WBcel235"],
+ params.vep_genome,
+ params.vep_species,
+ params.vep_cache_version
+ ])
+ """
+ }
+ }
+
+ then {
+ assertAll(
+ { assert process.success },
+ { assert snapshot(process.out).match() }
+ )
+ }
+ }
+}
diff --git a/modules/nf-core/ensemblvep/download/tests/main.nf.test.snap b/modules/nf-core/ensemblvep/download/tests/main.nf.test.snap
new file mode 100644
index 0000000..706bd28
--- /dev/null
+++ b/modules/nf-core/ensemblvep/download/tests/main.nf.test.snap
@@ -0,0 +1,322 @@
+{
+ "celegans - download": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "113_WBcel235"
+ },
+ [
+ [
+ [
+ [
+ "1-1000000.gz:md5,cadcba92b0999210dd8d832505d2e4c4",
+ "10000001-11000000.gz:md5,998a75dd927d10d45f8eebeef5fc7a75",
+ "1000001-2000000.gz:md5,a5cb3adb1ec9f40eed6a355d1492ba9b",
+ "11000001-12000000.gz:md5,46e6917f51093e28cce061774b9ed158",
+ "12000001-13000000.gz:md5,0adffacf8482d6c224df27104f65c9d6",
+ "13000001-14000000.gz:md5,aee759d812fc900a980ab0c4c5bd0273",
+ "14000001-15000000.gz:md5,f65537a3f76c40e63b6deb0b6cdb09dc",
+ "15000001-16000000.gz:md5,379f092ad1afa888da1fc13e80535def",
+ "2000001-3000000.gz:md5,86839741524579fd089498d6bee44dff",
+ "3000001-4000000.gz:md5,509b28af3920427e951f00b6973b5df4",
+ "4000001-5000000.gz:md5,f606e69cf59b0bdf2b61653608d955a6",
+ "5000001-6000000.gz:md5,a14ce1e21856e4a77ed63c67cbdfb26a",
+ "6000001-7000000.gz:md5,e1a895d6e8b352182b53ed1d0ce6e24e",
+ "7000001-8000000.gz:md5,ddf91b60f636d26b68b6bab3520b6b32",
+ "8000001-9000000.gz:md5,57482b996f89e92bbd0196efa4915cd3",
+ "9000001-10000000.gz:md5,43b5d89f84236b49b384d7f37f928129"
+ ],
+ [
+ "1-1000000.gz:md5,d18811781848f70baef0b0348190d7ce",
+ "10000001-11000000.gz:md5,19011165abc56233ea0c5b0e6938d9c9",
+ "1000001-2000000.gz:md5,5e720fa191f3c9ac799b6a071bcc4332",
+ "11000001-12000000.gz:md5,b19c46fb00ca13a2a31128bd1829ddf5",
+ "12000001-13000000.gz:md5,54354b0870ca96641c51ed63382da007",
+ "13000001-14000000.gz:md5,6954fdc223f58eb406e602752ab7d139",
+ "14000001-15000000.gz:md5,929275a1cfea883999dddc20931a2e72",
+ "15000001-16000000.gz:md5,5f5b783a589a1fd80cc565e6f339c540",
+ "2000001-3000000.gz:md5,54e476e0e9f4a5d973ee710fd824abc7",
+ "3000001-4000000.gz:md5,d78d4a63165429fdb3a61b7cdbd3c43a",
+ "4000001-5000000.gz:md5,983f8efcebb7f62d7e7b1b3c0573d43e",
+ "5000001-6000000.gz:md5,e2cd03ed5b67b8ee123e4c4958508fe4",
+ "6000001-7000000.gz:md5,d04bc9335ba39ace20bce936e3a5cdeb",
+ "7000001-8000000.gz:md5,9354b26a9ba94aa5bc30f537c22382fb",
+ "8000001-9000000.gz:md5,b227c6ef81ab72d211d25dc4f44813b9",
+ "9000001-10000000.gz:md5,a6d7f29edd7c22139403a11cac989b7a"
+ ],
+ [
+ "1-1000000.gz:md5,2117acb322a117a9c5db85c072575331",
+ "10000001-11000000.gz:md5,646c9582b56eb12ddbb1dd35b25c3670",
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+ "11000001-12000000.gz:md5,962fd6e52046484b3b123f9380ed64e9",
+ "12000001-13000000.gz:md5,1abf2d695c829eb2c88e0d3dbc739a1c",
+ "13000001-14000000.gz:md5,a6e03bf867f5cc694174a230f1b13a6b",
+ "2000001-3000000.gz:md5,a5b250aa9e3ee8cecc23bea0e2fa19a1",
+ "3000001-4000000.gz:md5,1390a6d2a28a4861b282d36d0fb85660",
+ "4000001-5000000.gz:md5,4bc7106bb2661aea28613c31935a5c8f",
+ "5000001-6000000.gz:md5,7317d6fbb3c77d7cdd31e781afab8f7d",
+ "6000001-7000000.gz:md5,1a3b6fa586e570c16b4833e34b28751e",
+ "7000001-8000000.gz:md5,b7bcb06393682f621403afdf19bf87b4",
+ "8000001-9000000.gz:md5,0011675a8567d394da54a52480b35786",
+ "9000001-10000000.gz:md5,e4fa88e4ec57ed0c71fd21090d8aa17a"
+ ],
+ [
+ "1-1000000.gz:md5,a47af22d33275652036ddf7161699c7c",
+ "10000001-11000000.gz:md5,7fc129e7edbaa5be87306de417c2ef28",
+ "1000001-2000000.gz:md5,cbc12c339741df5ad06bf9a946be6c93",
+ "11000001-12000000.gz:md5,d1cc5e20e3d3402debdc102087a5407f",
+ "12000001-13000000.gz:md5,42c69c8e86d28151e9a8b1787dbee125",
+ "13000001-14000000.gz:md5,c7459d1789a833e8a898ebdbc607e7d8",
+ "14000001-15000000.gz:md5,5806b20108f56d9eeabcdd4f8450dca3",
+ "15000001-16000000.gz:md5,78e859f70026a05be43d48b9b272f287",
+ "16000001-17000000.gz:md5,539db7fc976bee4b6031f8dcb6a4641d",
+ "17000001-18000000.gz:md5,f3ea55e7552dc36734d6e8ba67d1e4c2",
+ "2000001-3000000.gz:md5,539013ecfdcd06eb653445f857265322",
+ "3000001-4000000.gz:md5,beb9701b402bd5ddc46a4da6e531f783",
+ "4000001-5000000.gz:md5,3f46efb2635850cc6c3d8ae51727a400",
+ "5000001-6000000.gz:md5,e11549bca12c5e2a7a208a997fda1c68",
+ "6000001-7000000.gz:md5,c0f3546c6859dc1a5fe9ff7f015ecd7e",
+ "7000001-8000000.gz:md5,344b72822f647819f4ee6b5afa9d7701",
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+ "9000001-10000000.gz:md5,79140e754039c6d6fc6eeecddcf2aa8e"
+ ],
+ [
+ "1-1000000.gz:md5,40ef48190d3269cd4112450bc717b1ef"
+ ],
+ [
+ "1-1000000.gz:md5,1a8739457c429931923ed77596a9ee54",
+ "10000001-11000000.gz:md5,316fa1d06fc1878b6a5995f4aee3e49d",
+ "1000001-2000000.gz:md5,3926c03a091850c909bd0ccfc7133c0b",
+ "11000001-12000000.gz:md5,29ca11d2f05051cc439a0d24a9db134c",
+ "12000001-13000000.gz:md5,a46f648554e91999652019516c933754",
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+ "16000001-17000000.gz:md5,07e1750d1c95a61e96774d2cf3da4d89",
+ "17000001-18000000.gz:md5,59d084309f6a975ec1066a828b5845ba",
+ "18000001-19000000.gz:md5,868c12d305dbd4d04399ec7848804328",
+ "19000001-20000000.gz:md5,6de03a00061f6a88dcbbb8ed5fc0b8dc",
+ "20000001-21000000.gz:md5,732b956f13da9ef01f9de3355d12e28b",
+ "2000001-3000000.gz:md5,7c7528266c523cad419ea25e75d9566e",
+ "3000001-4000000.gz:md5,bb2283c0cfb0e4601fc535a4d51e6f2d",
+ "4000001-5000000.gz:md5,64c7f28f554414a88c886b0bcadb3c39",
+ "5000001-6000000.gz:md5,58e7106fe577a8b5e5c698445b4f0c33",
+ "6000001-7000000.gz:md5,2e309d12cf1c1c6276585f457ceeacc2",
+ "7000001-8000000.gz:md5,08cb0600f7806608f0103187a6c9c64e",
+ "8000001-9000000.gz:md5,869333c2615f714860d17d794640d4ad",
+ "9000001-10000000.gz:md5,b85cc861c6a3b30cf6f06c8af136b383"
+ ],
+ [
+ "1-1000000.gz:md5,c8d97b084c159c3cb5be1fff4637dfce",
+ "10000001-11000000.gz:md5,f441f2af06fd4973749dfbfbef40fe1b",
+ "1000001-2000000.gz:md5,c42a1526a836cfacefb67e9217f648aa",
+ "11000001-12000000.gz:md5,264421c249c696b45c92e2611285fee7",
+ "12000001-13000000.gz:md5,e673d1fdbe7dc0d09bea3d11a5797d6a",
+ "13000001-14000000.gz:md5,88f4f84e63b362f1b4f800c48b37e82c",
+ "14000001-15000000.gz:md5,26282f2b305ed82fb9f8875e97361105",
+ "15000001-16000000.gz:md5,30b9132c2610d42919ba231d1adbef2a",
+ "16000001-17000000.gz:md5,3d0e975ccd1ae4e92bf1d9d915ed293f",
+ "17000001-18000000.gz:md5,7db5b3819da3df1e47fe757dc9c6f2ba",
+ "2000001-3000000.gz:md5,55f6130a8d5872bdc9f8eed231ad0f65",
+ "3000001-4000000.gz:md5,402b826dbf6993c207ad15483a44182b",
+ "4000001-5000000.gz:md5,43cf926d43db25af5724fb5077edfee1",
+ "5000001-6000000.gz:md5,f40276dbea3f6f9a75f9301d1253eb09",
+ "6000001-7000000.gz:md5,df0d2d38060d4e7c606072ae814b1f38",
+ "7000001-8000000.gz:md5,c4117cc51255c0a91c51ff43403f00f7",
+ "8000001-9000000.gz:md5,59a4ebadca27041634c58652c544c8dd",
+ "9000001-10000000.gz:md5,c54510616273a4d1bfa9d525dbbbca40"
+ ],
+ "chr_synonyms.txt:md5,d390f0bcc6fec9786bc66b75f2d4390b",
+ "info.txt:md5,249c88c7a71464e048cca0c4b2a21198"
+ ]
+ ]
+ ]
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,25f0fd61e1a90ecec5427a9400ad6bc9"
+ ],
+ "cache": [
+ [
+ {
+ "id": "113_WBcel235"
+ },
+ [
+ [
+ [
+ [
+ "1-1000000.gz:md5,cadcba92b0999210dd8d832505d2e4c4",
+ "10000001-11000000.gz:md5,998a75dd927d10d45f8eebeef5fc7a75",
+ "1000001-2000000.gz:md5,a5cb3adb1ec9f40eed6a355d1492ba9b",
+ "11000001-12000000.gz:md5,46e6917f51093e28cce061774b9ed158",
+ "12000001-13000000.gz:md5,0adffacf8482d6c224df27104f65c9d6",
+ "13000001-14000000.gz:md5,aee759d812fc900a980ab0c4c5bd0273",
+ "14000001-15000000.gz:md5,f65537a3f76c40e63b6deb0b6cdb09dc",
+ "15000001-16000000.gz:md5,379f092ad1afa888da1fc13e80535def",
+ "2000001-3000000.gz:md5,86839741524579fd089498d6bee44dff",
+ "3000001-4000000.gz:md5,509b28af3920427e951f00b6973b5df4",
+ "4000001-5000000.gz:md5,f606e69cf59b0bdf2b61653608d955a6",
+ "5000001-6000000.gz:md5,a14ce1e21856e4a77ed63c67cbdfb26a",
+ "6000001-7000000.gz:md5,e1a895d6e8b352182b53ed1d0ce6e24e",
+ "7000001-8000000.gz:md5,ddf91b60f636d26b68b6bab3520b6b32",
+ "8000001-9000000.gz:md5,57482b996f89e92bbd0196efa4915cd3",
+ "9000001-10000000.gz:md5,43b5d89f84236b49b384d7f37f928129"
+ ],
+ [
+ "1-1000000.gz:md5,d18811781848f70baef0b0348190d7ce",
+ "10000001-11000000.gz:md5,19011165abc56233ea0c5b0e6938d9c9",
+ "1000001-2000000.gz:md5,5e720fa191f3c9ac799b6a071bcc4332",
+ "11000001-12000000.gz:md5,b19c46fb00ca13a2a31128bd1829ddf5",
+ "12000001-13000000.gz:md5,54354b0870ca96641c51ed63382da007",
+ "13000001-14000000.gz:md5,6954fdc223f58eb406e602752ab7d139",
+ "14000001-15000000.gz:md5,929275a1cfea883999dddc20931a2e72",
+ "15000001-16000000.gz:md5,5f5b783a589a1fd80cc565e6f339c540",
+ "2000001-3000000.gz:md5,54e476e0e9f4a5d973ee710fd824abc7",
+ "3000001-4000000.gz:md5,d78d4a63165429fdb3a61b7cdbd3c43a",
+ "4000001-5000000.gz:md5,983f8efcebb7f62d7e7b1b3c0573d43e",
+ "5000001-6000000.gz:md5,e2cd03ed5b67b8ee123e4c4958508fe4",
+ "6000001-7000000.gz:md5,d04bc9335ba39ace20bce936e3a5cdeb",
+ "7000001-8000000.gz:md5,9354b26a9ba94aa5bc30f537c22382fb",
+ "8000001-9000000.gz:md5,b227c6ef81ab72d211d25dc4f44813b9",
+ "9000001-10000000.gz:md5,a6d7f29edd7c22139403a11cac989b7a"
+ ],
+ [
+ "1-1000000.gz:md5,2117acb322a117a9c5db85c072575331",
+ "10000001-11000000.gz:md5,646c9582b56eb12ddbb1dd35b25c3670",
+ "1000001-2000000.gz:md5,ee433e4e5e37b2d008c43e1af4be0f8d",
+ "11000001-12000000.gz:md5,962fd6e52046484b3b123f9380ed64e9",
+ "12000001-13000000.gz:md5,1abf2d695c829eb2c88e0d3dbc739a1c",
+ "13000001-14000000.gz:md5,a6e03bf867f5cc694174a230f1b13a6b",
+ "2000001-3000000.gz:md5,a5b250aa9e3ee8cecc23bea0e2fa19a1",
+ "3000001-4000000.gz:md5,1390a6d2a28a4861b282d36d0fb85660",
+ "4000001-5000000.gz:md5,4bc7106bb2661aea28613c31935a5c8f",
+ "5000001-6000000.gz:md5,7317d6fbb3c77d7cdd31e781afab8f7d",
+ "6000001-7000000.gz:md5,1a3b6fa586e570c16b4833e34b28751e",
+ "7000001-8000000.gz:md5,b7bcb06393682f621403afdf19bf87b4",
+ "8000001-9000000.gz:md5,0011675a8567d394da54a52480b35786",
+ "9000001-10000000.gz:md5,e4fa88e4ec57ed0c71fd21090d8aa17a"
+ ],
+ [
+ "1-1000000.gz:md5,a47af22d33275652036ddf7161699c7c",
+ "10000001-11000000.gz:md5,7fc129e7edbaa5be87306de417c2ef28",
+ "1000001-2000000.gz:md5,cbc12c339741df5ad06bf9a946be6c93",
+ "11000001-12000000.gz:md5,d1cc5e20e3d3402debdc102087a5407f",
+ "12000001-13000000.gz:md5,42c69c8e86d28151e9a8b1787dbee125",
+ "13000001-14000000.gz:md5,c7459d1789a833e8a898ebdbc607e7d8",
+ "14000001-15000000.gz:md5,5806b20108f56d9eeabcdd4f8450dca3",
+ "15000001-16000000.gz:md5,78e859f70026a05be43d48b9b272f287",
+ "16000001-17000000.gz:md5,539db7fc976bee4b6031f8dcb6a4641d",
+ "17000001-18000000.gz:md5,f3ea55e7552dc36734d6e8ba67d1e4c2",
+ "2000001-3000000.gz:md5,539013ecfdcd06eb653445f857265322",
+ "3000001-4000000.gz:md5,beb9701b402bd5ddc46a4da6e531f783",
+ "4000001-5000000.gz:md5,3f46efb2635850cc6c3d8ae51727a400",
+ "5000001-6000000.gz:md5,e11549bca12c5e2a7a208a997fda1c68",
+ "6000001-7000000.gz:md5,c0f3546c6859dc1a5fe9ff7f015ecd7e",
+ "7000001-8000000.gz:md5,344b72822f647819f4ee6b5afa9d7701",
+ "8000001-9000000.gz:md5,1c06d285ff5c53f89f073212343902b7",
+ "9000001-10000000.gz:md5,79140e754039c6d6fc6eeecddcf2aa8e"
+ ],
+ [
+ "1-1000000.gz:md5,40ef48190d3269cd4112450bc717b1ef"
+ ],
+ [
+ "1-1000000.gz:md5,1a8739457c429931923ed77596a9ee54",
+ "10000001-11000000.gz:md5,316fa1d06fc1878b6a5995f4aee3e49d",
+ "1000001-2000000.gz:md5,3926c03a091850c909bd0ccfc7133c0b",
+ "11000001-12000000.gz:md5,29ca11d2f05051cc439a0d24a9db134c",
+ "12000001-13000000.gz:md5,a46f648554e91999652019516c933754",
+ "13000001-14000000.gz:md5,167b126d1c690a0e7e25fc5ccd09fb7c",
+ "14000001-15000000.gz:md5,645554c896133c476c3083302371bcf8",
+ "15000001-16000000.gz:md5,60fc48d9a7aff6286fc6630c46bcfebc",
+ "16000001-17000000.gz:md5,07e1750d1c95a61e96774d2cf3da4d89",
+ "17000001-18000000.gz:md5,59d084309f6a975ec1066a828b5845ba",
+ "18000001-19000000.gz:md5,868c12d305dbd4d04399ec7848804328",
+ "19000001-20000000.gz:md5,6de03a00061f6a88dcbbb8ed5fc0b8dc",
+ "20000001-21000000.gz:md5,732b956f13da9ef01f9de3355d12e28b",
+ "2000001-3000000.gz:md5,7c7528266c523cad419ea25e75d9566e",
+ "3000001-4000000.gz:md5,bb2283c0cfb0e4601fc535a4d51e6f2d",
+ "4000001-5000000.gz:md5,64c7f28f554414a88c886b0bcadb3c39",
+ "5000001-6000000.gz:md5,58e7106fe577a8b5e5c698445b4f0c33",
+ "6000001-7000000.gz:md5,2e309d12cf1c1c6276585f457ceeacc2",
+ "7000001-8000000.gz:md5,08cb0600f7806608f0103187a6c9c64e",
+ "8000001-9000000.gz:md5,869333c2615f714860d17d794640d4ad",
+ "9000001-10000000.gz:md5,b85cc861c6a3b30cf6f06c8af136b383"
+ ],
+ [
+ "1-1000000.gz:md5,c8d97b084c159c3cb5be1fff4637dfce",
+ "10000001-11000000.gz:md5,f441f2af06fd4973749dfbfbef40fe1b",
+ "1000001-2000000.gz:md5,c42a1526a836cfacefb67e9217f648aa",
+ "11000001-12000000.gz:md5,264421c249c696b45c92e2611285fee7",
+ "12000001-13000000.gz:md5,e673d1fdbe7dc0d09bea3d11a5797d6a",
+ "13000001-14000000.gz:md5,88f4f84e63b362f1b4f800c48b37e82c",
+ "14000001-15000000.gz:md5,26282f2b305ed82fb9f8875e97361105",
+ "15000001-16000000.gz:md5,30b9132c2610d42919ba231d1adbef2a",
+ "16000001-17000000.gz:md5,3d0e975ccd1ae4e92bf1d9d915ed293f",
+ "17000001-18000000.gz:md5,7db5b3819da3df1e47fe757dc9c6f2ba",
+ "2000001-3000000.gz:md5,55f6130a8d5872bdc9f8eed231ad0f65",
+ "3000001-4000000.gz:md5,402b826dbf6993c207ad15483a44182b",
+ "4000001-5000000.gz:md5,43cf926d43db25af5724fb5077edfee1",
+ "5000001-6000000.gz:md5,f40276dbea3f6f9a75f9301d1253eb09",
+ "6000001-7000000.gz:md5,df0d2d38060d4e7c606072ae814b1f38",
+ "7000001-8000000.gz:md5,c4117cc51255c0a91c51ff43403f00f7",
+ "8000001-9000000.gz:md5,59a4ebadca27041634c58652c544c8dd",
+ "9000001-10000000.gz:md5,c54510616273a4d1bfa9d525dbbbca40"
+ ],
+ "chr_synonyms.txt:md5,d390f0bcc6fec9786bc66b75f2d4390b",
+ "info.txt:md5,249c88c7a71464e048cca0c4b2a21198"
+ ]
+ ]
+ ]
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,25f0fd61e1a90ecec5427a9400ad6bc9"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-10-21T09:09:48.574969389"
+ },
+ "celegans - download - stub": {
+ "content": [
+ {
+ "0": [
+ [
+ {
+ "id": "113_WBcel235"
+ },
+ [
+
+ ]
+ ]
+ ],
+ "1": [
+ "versions.yml:md5,25f0fd61e1a90ecec5427a9400ad6bc9"
+ ],
+ "cache": [
+ [
+ {
+ "id": "113_WBcel235"
+ },
+ [
+
+ ]
+ ]
+ ],
+ "versions": [
+ "versions.yml:md5,25f0fd61e1a90ecec5427a9400ad6bc9"
+ ]
+ }
+ ],
+ "meta": {
+ "nf-test": "0.9.0",
+ "nextflow": "24.04.4"
+ },
+ "timestamp": "2024-10-21T09:10:03.728940123"
+ }
+}
\ No newline at end of file
diff --git a/modules/nf-core/ensemblvep/download/tests/nextflow.config b/modules/nf-core/ensemblvep/download/tests/nextflow.config
new file mode 100644
index 0000000..0a4ae1a
--- /dev/null
+++ b/modules/nf-core/ensemblvep/download/tests/nextflow.config
@@ -0,0 +1,12 @@
+params {
+ vep_cache_version = "113"
+ vep_genome = "WBcel235"
+ vep_species = "caenorhabditis_elegans"
+}
+
+process {
+ withName: ENSEMBLVEP_DOWNLOAD {
+ ext.args = '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE'
+ ext.prefix = { "${params.vep_cache_version}_${params.vep_genome}" }
+ }
+}
diff --git a/modules/nf-core/ensemblvep/download/tests/tags.yml b/modules/nf-core/ensemblvep/download/tests/tags.yml
new file mode 100644
index 0000000..26671f3
--- /dev/null
+++ b/modules/nf-core/ensemblvep/download/tests/tags.yml
@@ -0,0 +1,2 @@
+ensemblvep/download:
+ - "modules/nf-core/ensemblvep/download/**"
diff --git a/nextflow.config b/nextflow.config
index cd044df..9a723fe 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -26,6 +26,8 @@ params {
vep_cache = null
vep_cache_version = null
vep_genome = null
+ download_cache = false
+ outdir_cache = null
exomiser_genome = null
exomiser_data_dir = null
exomiser_data_version = null
@@ -44,15 +46,17 @@ params {
exclude_mnps = true
TSfilterSNP = '99'
TSfilterINDEL = '99'
- hardFilters = [[name: 'QD2', expression: 'QD < 2.0'],
- [name: 'QD1', expression: 'QD < 1.0'],
- [name: 'QUAL30', expression: 'QUAL < 30.0'],
- [name: 'SOR3', expression: 'SOR > 3.0'],
- [name: 'FS60', expression: 'FS > 60.0'],
- [name: 'MQ40', expression: 'MQ < 40.0'],
- [name: 'MQRankSum-12.5', expression: 'MQRankSum < -12.5'],
- [name: 'ReadPosRankSum-8', expression: 'ReadPosRankSum < -8.0']]
-
+ hardFilters = [
+ [name: 'QD2', expression: 'QD < 2.0'],
+ [name: 'QD1', expression: 'QD < 1.0'],
+ [name: 'QUAL30', expression: 'QUAL < 30.0'],
+ [name: 'SOR3', expression: 'SOR > 3.0'],
+ [name: 'FS60', expression: 'FS > 60.0'],
+ [name: 'MQ40', expression: 'MQ < 40.0'],
+ [name: 'MQRankSum-12.5', expression: 'MQRankSum < -12.5'],
+ [name: 'ReadPosRankSum-8', expression: 'ReadPosRankSum < -8.0']
+ ]
+
allow_old_gatk_data = false
@@ -270,7 +274,7 @@ process {
disk = { check_max( 30.GB * task.attempt, 'disk' ) }
time = { check_max( 10.h * task.attempt, 'time' ) }
}
- withName: 'GATK4_VARIANTFILTRATION' {
+ withName: 'GATK4_VARIANTFILTRATION' {
errorStrategy = 'retry'
maxRetries = 2
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
@@ -286,6 +290,14 @@ process {
disk = { check_max( 30.GB * task.attempt, 'disk' ) }
time = { check_max( 10.h * task.attempt, 'time' ) }
}
+ withName: 'ENSEMBLVEP_DOWNLOAD' {
+ errorStrategy = 'retry'
+ maxRetries = 2
+ cpus = { check_max( 4 * task.attempt, 'cpus' ) }
+ memory = { check_max( 36.GB * task.attempt, 'memory' ) }
+ disk = { check_max( 140.GB * task.attempt, 'disk' ) }
+ time = { check_max( 8.h * task.attempt, 'time' ) }
+ }
withName: 'ENSEMBLVEP_VEP' {
errorStrategy = 'retry'
maxRetries = 2
@@ -294,7 +306,7 @@ process {
disk = { check_max( 80.GB * task.attempt, 'disk' ) }
time = { check_max( 10.h * task.attempt, 'time' ) }
}
- withName: 'EXOMISER' {
+ withName: 'EXOMISER' {
errorStrategy = 'retry'
maxRetries = 2
cpus = { check_max( 6 * task.attempt, 'cpus' ) }
@@ -302,7 +314,7 @@ process {
disk = { check_max( 150.GB * task.attempt, 'disk' ) }
time = { check_max( 10.h * task.attempt, 'time' ) }
}
- withName: 'writemeta' {
+ withName: 'writemeta' {
container = 'ubuntu:24.10'
}
}
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 3da8249..2f260ad 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -88,10 +88,7 @@
"format": "file-path"
}
},
- "required": [
- "referenceGenome",
- "referenceGenomeFasta"
- ],
+ "required": ["referenceGenome", "referenceGenomeFasta"],
"if": {
"required": ["dbsnpFile"]
},
@@ -227,7 +224,6 @@
"type": "boolean",
"description": "Boolean whether to validate parameters against the schema at runtime",
"default": true,
-
"hidden": true
},
"validationShowHiddenParams": {
@@ -272,6 +268,18 @@
},
"hardFilters": {
"type": "array",
+ "items": {
+ "type": "object",
+ "properties": {
+ "name": {
+ "type": "string"
+ },
+ "expression": {
+ "type": "string"
+ }
+ },
+ "required": ["name", "expression"]
+ },
"description": "Parameters for Hard-Filtering",
"help_text": "Parameters for Hard-Filtering. Must be an array containing each desired filter. Each filter must be formatted with the desired name and expression, for example\\n[[name: 'QD1', expression: 'QD < 1.0'],[name: 'QD2', expression: 'QD < 2.0]]"
},
@@ -289,7 +297,7 @@
"type": "boolean",
"description": "If true, exclude MNPs from the VEP annotation",
"help_text": "If true (default), exclude MNPs from the VEP annotation. Must be true on whole genome data.",
- "default": true
+ "default": true
}
}
},
@@ -314,6 +322,16 @@
"type": "string",
"description": "Will be used by vep to find the assembly version in the cache",
"help text": "Ex: GRCh38"
+ },
+ "download_cache": {
+ "type": "boolean",
+ "description": "Whether to download the vep cache or not"
+ },
+ "outdir_cache": {
+ "type": "string",
+ "description": "Path where vep cache will be downloaded",
+ "default": "${outdir}/cache",
+ "format": "directory-path"
}
},
"if": {
@@ -404,8 +422,7 @@
},
"exomiser_start_from_vep": {
"type": "boolean",
- "description": "If true, run the exomiser analysis on the VEP annotated VCF file",
- "default": false
+ "description": "If true, run the exomiser analysis on the VEP annotated VCF file"
}
},
"allOf": [
diff --git a/workflows/postprocessing.nf b/workflows/postprocessing.nf
index c9b5c06..15570c5 100644
--- a/workflows/postprocessing.nf
+++ b/workflows/postprocessing.nf
@@ -17,18 +17,18 @@ include { VCF_ANNOTATE_ENSEMBLVEP } from '../subworkflows/nf-core/vcf_annotate_e
include { COMBINEGVCFS } from '../modules/local/combine_gvcfs'
include { GATK4_GENOTYPEGVCFS } from '../modules/nf-core/gatk4/genotypegvcfs'
include { GATK4_VARIANTFILTRATION } from '../modules/nf-core/gatk4/variantfiltration'
+include { ENSEMBLVEP_DOWNLOAD } from '../modules/nf-core/ensemblvep/download/main'
//functions
include { isExomiserToolIncluded } from '../subworkflows/local/utils_nfcore_postprocessing_pipeline/utils'
include { isVepToolIncluded } from '../subworkflows/local/utils_nfcore_postprocessing_pipeline/utils'
-def HOMO_SAPIENS_SPECIES = "homo_sapiens"
-
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
RUN MAIN WORKFLOW
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
+
/**
Tag variants that are probable artifacts
In the case of whole genome sequencing data, we use the vqsr procedure.
@@ -48,7 +48,7 @@ def tagArtifacts(ch_artifact_input, hardFilters, pathFasta, pathFai, pathDict) {
[[:], pathDict])
def ch_variantfiltration_output = ch_gatk4_variantfiltration_output.vcf.join(ch_gatk4_variantfiltration_output.tbi)
- .map{ meta, vcf, tbi -> [meta, [vcf,tbi]]}
+ .map{ meta, vcf, tbi -> [meta, [vcf,tbi]]}
return ch_vqsr_output.concat(ch_variantfiltration_output)
}
@@ -144,9 +144,9 @@ def handle_mnps(input_channel, do_exclude_mnps) {
/*
- Deal with variations in input file formats, extensions, and the presence or absence of index files.
- input: [meta, vcf]
- output: [meta, vcf, tbi]
+Deal with variations in input file formats, extensions, and the presence or absence of index files.
+input: [meta, vcf]
+output: [meta, vcf, tbi]
*/
def standardize_input_vcf_files(input_channel) {
def view_input = input_channel.map{meta, vcf ->
@@ -158,6 +158,11 @@ def standardize_input_vcf_files(input_channel) {
}
workflow POSTPROCESSING {
+
+ take:
+ ch_samplesheet
+
+ main:
//Local Temp Params
def referenceGenome = file(params.referenceGenome)
def pathReferenceGenomeFasta = file(params.referenceGenome + "/" + params.referenceGenomeFasta)
@@ -168,13 +173,10 @@ workflow POSTPROCESSING {
def dbsnpFileIndex = params.dbsnpFileIndex? file(params.dbsnpFileIndex) : []
def exomiserLocalFrequencyFile = params.exomiser_local_frequency_path? file(params.exomiser_local_frequency_path) : []
def exomiserLocalFrequencyIndexFile = params.exomiser_local_frequency_index_path? file(params.exomiser_local_frequency_index_path) : []
-
- file(params.outdir).mkdirs()
- take:
- ch_samplesheet
-
- main:
+ def HOMO_SAPIENS_SPECIES = "homo_sapiens"
+
+ file(params.outdir).mkdirs()
ch_versions = Channel.empty()
@@ -227,7 +229,16 @@ workflow POSTPROCESSING {
def ch_output_from_vep //declaring vep output channel early so that it can be accessed outside the if block
//Annotating variants with VEP
if (isVepToolIncluded()) {
- def vep_cache = file(params.vep_cache)
+
+ // Download VEP cache if download = true. Assuming we want to download even if cache provided.
+ if (params.download_cache) {
+ ensemblvep_info = Channel.of([ [ id:"${params.vep_cache_version}_${params.vep_genome}" ], params.vep_genome, HOMO_SAPIENS_SPECIES, params.vep_cache_version ])
+ ENSEMBLVEP_DOWNLOAD(ensemblvep_info)
+ vep_cache = ENSEMBLVEP_DOWNLOAD.out.cache.collect().map{ _meta, cache -> [ cache ] }
+ ch_versions = ch_versions.mix(ENSEMBLVEP_DOWNLOAD.out.versions.first())
+ } else {
+ vep_cache = file(params.vep_cache)
+ }
ch_output_from_vep = vep(
ch_output_from_splitMultiAllelics,