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update all modules + fix schema_input #1695

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merged 11 commits into from
Oct 28, 2024
Merged

update all modules + fix schema_input #1695

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cd7b4c7
update all modules
maxulysse Oct 25, 2024
ee88b37
update CHANGELOG
maxulysse Oct 25, 2024
cb9f74f
validation with lenient mode
maxulysse Oct 25, 2024
2fbb8fa
update schema_input
maxulysse Oct 25, 2024
04b961f
sort inputs
maxulysse Oct 25, 2024
b14e9da
0 without quotes
maxulysse Oct 25, 2024
b739d5a
exclude test
maxulysse Oct 25, 2024
6b430fd
update md5sum
maxulysse Oct 25, 2024
dc30629
update CHANGELOG
maxulysse Oct 25, 2024
36110c3
fix output
maxulysse Oct 27, 2024
6079fcf
fix output
maxulysse Oct 27, 2024
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1 change: 1 addition & 0 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -279,6 +279,7 @@ jobs:
- tags: "strelka/germline"
- tags: "strelka/somatic"
- tags: "subworkflows/utils_nfvalidation_plugin"
- tags: "svdb/merge"
- tags: "tabix/bgziptabix"
- tags: "tabix/tabix"
- tags: "tiddit/sv"
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6 changes: 6 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -21,7 +21,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [1677](https://github.com/nf-core/sarek/pull/1677) - Migrate pytest aligner and pipeline default tests to nf-test
- [1680](https://github.com/nf-core/sarek/pull/1680) - Template update for nf-core/tools v3.0.0
- [1681](https://github.com/nf-core/sarek/pull/1681) - Template update for nf-core/tools v3.0.1
- [1686](https://github.com/nf-core/sarek/pull/1686) - Template update for nf-core/tools v3.0.2
- [1692](https://github.com/nf-core/sarek/pull/1692) - Update ensemblvep
- [1695](https://github.com/nf-core/sarek/pull/1695) - Update all modules

### Fixed

Expand All @@ -30,6 +32,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [1673](https://github.com/nf-core/sarek/pull/1673) - Print warning message instead of silent error with Nextflow versions prior to 24.08.0edge
- [1693](https://github.com/nf-core/sarek/pull/1693) - Fixes flowcell retrieval during samplesheet parsing
- [1694](https://github.com/nf-core/sarek/pull/1694) - Fix manifest DOI display on CLI
- [1695](https://github.com/nf-core/sarek/pull/1695) - Fix and update input_schema.json

### Removed

Expand All @@ -39,13 +42,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

| Dependency | Old version | New version |
| ------------- | ----------- | ----------- |
| `coreutils` | 8.30 | 9.5 |
| `deepvariant` | 1.5.0 | 1.6.1 |
| `ensemblvep` | 111.0 | 113.0 |
| `fgbio` | 2.0.2 | 2.1.2 |
| `htslib` | 1.20 | 1.21 |
| `lofreq` | | 2.1.5 |
| `multiqc` | 1.21 | 1.25.1 |
| `samtools` | 1.20 | 1.21 |
| `sentieon` | 202308.02 | 202308.03 |
| `svdb` | 2.8.1 | 2.8.2 |

### Parameters

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160 changes: 35 additions & 125 deletions assets/schema_input.json
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Expand Up @@ -23,22 +23,14 @@
"errorMessage": "Sex cannot contain spaces",
"meta": ["sex"],
"default": "NA",
"anyOf": [
{
"type": "string",
"pattern": "^\\S+$"
},
{
"type": "string",
"maxLength": 0
}
]
"type": "string",
"pattern": "^\\S+$"
},
"status": {
"type": "integer",
"errorMessage": "Status can only be 0 (normal) or 1 (tumor). Defaults to 0, if none is supplied.",
"meta": ["status"],
"default": "0",
"default": 0,
"minimum": 0,
"maximum": 1
},
Expand All @@ -48,183 +40,101 @@
"meta": ["lane"]
},
"fastq_1": {
"errorMessage": "Gzipped FastQ file for reads 1 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
"anyOf": [
{
"type": "string",
"pattern": "^\\S+\\.f(ast)?q\\.gz$"
},
{
"type": "string",
"maxLength": 0
}
],
"errorMessage": "FastQ file for reads 1 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
"type": "string",
"pattern": "^\\S+\\.f(ast)?q\\.gz$",
"format": "file-path",
"exists": true
},
"fastq_2": {
"errorMessage": "Gzipped FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
"anyOf": [
{
"type": "string",
"pattern": "^\\S+\\.f(ast)?q\\.gz$"
},
{
"type": "string",
"maxLength": 0
}
],
"errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
"type": "string",
"pattern": "^\\S+\\.f(ast)?q\\.gz$",
"format": "file-path",
"exists": true
},
"spring_1": {
"errorMessage": "Gzipped and spring-compressed FastQ file for reads 1 cannot contain spaces and must have extension '.fq.gz.spring' or '.fastq.gz.spring'",
"anyOf": [
{
"type": "string",
"pattern": "^\\S+\\.f(ast)?q\\.gz.spring$"
},
{
"type": "string",
"maxLength": 0
}
],
"type": "string",
"pattern": "^\\S+\\.f(ast)?q\\.gz.spring$",
"format": "file-path",
"exists": true
},
"spring_2": {
"errorMessage": "Gzipped and spring-compressed FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz.spring' or '.fastq.gz.spring'",
"anyOf": [
{
"type": "string",
"pattern": "^\\S+\\.f(ast)?q\\.gz.spring$"
},
{
"type": "string",
"maxLength": 0
}
],
"type": "string",
"pattern": "^\\S+\\.f(ast)?q\\.gz.spring$",
"format": "file-path",
"exists": true
},
"table": {
"errorMessage": "Recalibration table cannot contain spaces and must have extension '.table'",
"anyOf": [
{
"type": "string",
"pattern": "^\\S+\\.table$"
},
{
"type": "string",
"maxLength": 0
}
],
"type": "string",
"pattern": "^\\S+\\.table$",
"format": "file-path",
"exists": true
},
"cram": {
"errorMessage": "CRAM file cannot contain spaces and must have extension '.cram'",
"anyOf": [
{
"type": "string",
"pattern": "^\\S+\\.cram$"
},
{
"type": "string",
"maxLength": 0
}
],
"type": "string",
"pattern": "^\\S+\\.cram$",
"format": "file-path",
"exists": true
},
"crai": {
"errorMessage": "CRAM index file cannot contain spaces and must have extension '.crai'",
"anyOf": [
{
"type": "string",
"pattern": "^\\S+\\.crai$"
},
{
"type": "string",
"maxLength": 0
}
],
"type": "string",
"pattern": "^\\S+\\.crai$",
"format": "file-path",
"exists": true
},
"bam": {
"errorMessage": "BAM file cannot contain spaces and must have extension '.bam'",
"anyOf": [
{
"type": "string",
"pattern": "^\\S+\\.bam$"
},
{
"type": "string",
"maxLength": 0
}
],
"type": "string",
"pattern": "^\\S+\\.bam$",
"format": "file-path",
"exists": true
},
"bai": {
"errorMessage": "BAM index file cannot contain spaces and must have extension '.bai'",
"anyOf": [
{
"type": "string",
"pattern": "^\\S+\\.bai$"
},
{
"type": "string",
"maxLength": 0
}
],
"type": "string",
"pattern": "^\\S+\\.bai$",
"format": "file-path",
"exists": true
},
"vcf": {
"errorMessage": "VCF file for reads 1 cannot contain spaces and must have extension '.vcf' or '.vcf.gz'",
"anyOf": [
{
"type": "string",
"pattern": "^\\S+\\.vcf(\\.gz)?$"
},
{
"type": "string",
"maxLength": 0
}
],
"type": "string",
"pattern": "^\\S+\\.vcf(\\.gz)?$",
"format": "file-path",
"exists": true
},
"variantcaller": {
"type": "string"
}
},
"required": ["patient", "sample"],
"uniqueEntries": ["patient", "sample"],
"anyOf": [
{
"dependentRequired": {
"fastq_2": ["fastq_1"],
"spring_2": ["spring_1"],
"lane": ["bam"]
"lane": ["fastq_1"]
}
},
{
"dependentRequired": {
"fastq_2": ["fastq_1"],
"spring_2": ["spring_1"],
"lane": ["fastq_1"]
"lane": ["spring_1"]
}
},
{
"dependentRequired": {
"fastq_2": ["fastq_1"],
"spring_2": ["spring_1"],
"lane": ["spring_1"]
"lane": ["bam"]
}
}
]
],
"dependentRequired": {
"fastq_2": ["fastq_1"],
"spring_2": ["spring_1"]
},
"required": ["patient", "sample"],
"uniqueEntries": ["lane", "patient", "sample"]
}
}
1 change: 1 addition & 0 deletions conf/modules/tiddit.config
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Original file line number Diff line number Diff line change
Expand Up @@ -47,6 +47,7 @@ process {

// SVDB
withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_TIDDIT:SVDB_MERGE' {
ext.args2 = { '--output-type z' }
ext.prefix = { "${meta.id}.tiddit_sv_merge" }
publishDir = [
mode: params.publish_dir_mode,
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