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Fix processing of input parameter #133

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merged 3 commits into from
Nov 19, 2020
Merged

Fix processing of input parameter #133

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9a59db6
Fix processing of input parameter.
skrakau Nov 18, 2020
a6baf63
Initialize `input_paths` variable to avoid warning for users if not set
skrakau Nov 18, 2020
e07a04e
Update CHANGELOG
skrakau Nov 18, 2020
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -5,6 +5,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

## v1.2.0dev - [date]

### `Fixed`

- [#133](https://github.com/nf-core/mag/pull/133) - Fixed processing of `--input` parameter

## v1.1.1 - 2019/11/10

### `Added`
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4 changes: 2 additions & 2 deletions main.nf
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Expand Up @@ -280,8 +280,8 @@ if(params.manifest){
}
} else {
Channel
.fromFilePairs(params.reads, size: params.single_end ? 1 : 2)
.ifEmpty { exit 1, "Cannot find any reads matching: ${params.reads}\nNB: Path needs to be enclosed in quotes!\nIf this is single-end data, please specify --single_end on the command line." }
.fromFilePairs(params.input, size: params.single_end ? 1 : 2)
.ifEmpty { exit 1, "Cannot find any reads matching: ${params.input}\nNB: Path needs to be enclosed in quotes!\nIf this is single-end data, please specify --single_end on the command line." }
.into { read_files_fastqc; read_files_fastp }
files_long_raw = Channel.from()
}
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3 changes: 3 additions & 0 deletions nextflow.config
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Expand Up @@ -66,6 +66,9 @@ params {
spadeshybrid_fix_cpus = false
metabat_rng_seed = 1

// For testing
input_paths = false

// Boilerplate options
name = false
multiqc_config = false
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5 changes: 5 additions & 0 deletions nextflow_schema.json
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Expand Up @@ -22,6 +22,11 @@
"description": "Manifest file, required for hybrid assembly with metaSPAdes. Alternative to `--input`.",
"help_text": "Has 4 headerless columns (tab separated): Sample_Id, Long_Reads, Short_Reads_1, Short_Reads_2\n"
},
"input_paths": {
"type": "string",
"description": "Paths to input FastQ files for tests.",
"hidden": true
},
"single_end": {
"type": "boolean",
"description": "Specifies that the input is single-end reads.",
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