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Merge branch 'dev' into fresh-nf-test
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@maxulysse
maxulysse committed Oct 28, 2024
2 parents 04dca87 + c2bb706 commit acfec84
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6 changes: 6 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -22,7 +22,9 @@ 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 @@ -31,6 +33,7 @@ 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 @@ -40,13 +43,16 @@ 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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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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8 changes: 4 additions & 4 deletions modules.json
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Expand Up @@ -12,7 +12,7 @@
},
"bcftools/annotate": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "cb08035150685b11d890d90c9534d4f16869eaec",
"installed_by": ["modules"],
"patch": "modules/nf-core/bcftools/annotate/bcftools-annotate.diff"
},
Expand Down Expand Up @@ -63,7 +63,7 @@
},
"cat/fastq": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "a1abf90966a2a4016d3c3e41e228bfcbd4811ccc",
"installed_by": ["modules"]
},
"cnvkit/antitarget": {
Expand Down Expand Up @@ -306,7 +306,7 @@
},
"gawk": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "97321eded31a12598837a476d3615300af413bb7",
"installed_by": ["modules"]
},
"lofreq/callparallel": {
Expand Down Expand Up @@ -471,7 +471,7 @@
},
"svdb/merge": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "eb2c3f7ee2c938ab1a49764bdb1319adaa35492c",
"installed_by": ["modules"]
},
"tabix/bgziptabix": {
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10 changes: 5 additions & 5 deletions modules/nf-core/bcftools/annotate/main.nf
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2 changes: 1 addition & 1 deletion modules/nf-core/cat/fastq/environment.yml
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4 changes: 2 additions & 2 deletions modules/nf-core/cat/fastq/main.nf
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