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Fix checking whether input files exist #67

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merged 3 commits into from
Apr 5, 2024
Merged

Fix checking whether input files exist #67

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3976fc5
Add back files exist check, and fromSamplesheet
fellen31 Apr 4, 2024
89cbcc4
add params to config
fellen31 Apr 4, 2024
b20b0bb
Update CHANGELOG
fellen31 Apr 4, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -18,6 +18,7 @@ Initial release of genomic-medicine-sweden/skierfe, created with the [nf-core](h

### `Fixed`

- Fix input file validation [#67](https://github.com/genomic-medicine-sweden/skierfe/pull/67)
- Fix BCFTools merge module inputs [#43](https://github.com/genomic-medicine-sweden/skierfe/pull/43)

### `Dependencies`
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3 changes: 3 additions & 0 deletions nextflow.config
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Expand Up @@ -88,6 +88,9 @@ params {
validationSchemaIgnoreParams = 'genomes,igenomes_base'
validationShowHiddenParams = false
validate_params = true
validationSkipDuplicateCheck = false
validationS3PathCheck = false
monochromeLogs = false
}
// Load nf-core custom profiles from different Institutions
try {
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55 changes: 42 additions & 13 deletions nextflow_schema.json
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Expand Up @@ -105,7 +105,8 @@
"type": "string",
"description": "Reference genome",
"pattern": "^.*\\.(fasta|fa|fna)(\\.gz)?$",
"format": "file-path"
"format": "file-path",
"exists": true
},
"genome": {
"type": "string",
Expand Down Expand Up @@ -273,7 +274,8 @@
"format": "file-path",
"description": "Custom config file to supply to MultiQC.",
"fa_icon": "fas fa-cog",
"hidden": true
"hidden": true,
"exists": true
},
"multiqc_logo": {
"type": "string",
Expand All @@ -299,6 +301,21 @@
"description": "Show all params when using `--help`",
"hidden": true,
"help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
},
"validationSkipDuplicateCheck": {
"type": "boolean",
"hidden": true,
"description": "nf-validation related parameter"
},
"validationS3PathCheck": {
"type": "boolean",
"hidden": true,
"description": "Boolean whether to validate validate AWS S3 paths"
},
"monochromeLogs": {
"type": "boolean",
"hidden": true,
"description": "Boolean whether to color nf-validation logs"
}
}
},
Expand Down Expand Up @@ -351,63 +368,75 @@
"dipcall_par": {
"type": "string",
"description": "Provide a bed file of chrX PAR regions for dipcall",
"format": "file-path"
"format": "file-path",
"exists": true
},
"extra_gvcfs": {
"type": "string",
"description": "Extra input files for GLNexus",
"pattern": "^\\S+\\.csv$",
"format": "file-path",
"schema": "assets/schema_gvcfs.json"
"schema": "assets/schema_gvcfs.json",
"exists": true
},
"extra_snfs": {
"type": "string",
"description": "Extra input files for Sniffles",
"pattern": "^\\S+\\.csv$",
"format": "file-path",
"schema": "assets/schema_snfs.json"
"schema": "assets/schema_snfs.json",
"exists": true
},
"tandem_repeats": {
"type": "string",
"format": "file-path",
"description": "Tandem repeat BED-file for sniffles",
"pattern": "^\\S+\\.bed$"
"pattern": "^\\S+\\.bed$",
"exists": true
},
"trgt_repeats": {
"type": "string",
"description": "BED-file for repeats to be genotyped",
"format": "file-path"
"format": "file-path",
"exists": true
},
"snp_db": {
"type": "string",
"pattern": "^\\S+\\.csv$",
"format": "file-path",
"mimetype": "text/csv",
"schema": "/assets/schema_snpdb.json",
"description": "Extra echtvar-databases to annotate SNVs with"
"description": "Extra echtvar-databases to annotate SNVs with",
"exists": true
},
"vep_cache": {
"type": "string",
"description": "Path to directory of vep_cache",
"format": "directory-path"
"format": "directory-path",
"exists": true
},
"bed": {
"type": "string",
"pattern": "^\\S+\\.bed$",
"format": "file-path",
"description": "BED file with regions of interest"
"description": "BED file with regions of interest",
"exists": true
},
"hificnv_xy": {
"type": "string",
"format": "file-path"
"format": "file-path",
"exists": true
},
"hificnv_xx": {
"type": "string",
"format": "file-path"
"format": "file-path",
"exists": true
},
"hificnv_exclude": {
"type": "string",
"description": "HiFiCNV BED file specifying regions to exclude"
"format": "file-path",
"description": "HiFiCNV BED file specifying regions to exclude",
"exists": true
},
"validationFailUnrecognisedParams": {
"type": "boolean",
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2 changes: 2 additions & 0 deletions workflows/skierfe.nf
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Expand Up @@ -4,6 +4,8 @@
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

include { fromSamplesheet } from 'plugin/nf-validation'

// Check mandatory input files
ch_fasta = Channel.fromPath(params.fasta).map { it -> [it.simpleName, it] }.collect()

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