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Merged
jfy133 merged 2 commits into from
Mar 17, 2022
Merged

Improve error message for metagenomic classification incorrect parameters #842

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99ae64d
Improve error message
jfy133 Mar 10, 2022
d889512
Merge branch 'dev' into metascreen-message
jfy133 Mar 17, 2022
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.

### `Fixed`

- [#828](https://github.com/nf-core/eager/issues/828) Improved error message if required metagenomic screening parameters not set correctly

### `Dependencies`

### `Deprecated`
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9 changes: 5 additions & 4 deletions main.nf
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Expand Up @@ -107,12 +107,13 @@ if (params.run_multivcfanalyzer) {
}

if (params.run_metagenomic_screening) {
if ( params.bam_unmapped_type == "discard" ) {
exit 1, "[nf-core/eager] error: metagenomic classification can only run on unmapped reads. Please supply --bam_unmapped_type 'fastq'. Supplied: --bam_unmapped_type '${params.bam_unmapped_type}'."

if ( !params.run_bam_filtering ) {
exit 1, "[nf-core/eager] error: metagenomic classification can only run on unmapped reads. Please supply --run_bam_filtering --bam_unmapped_type 'fastq'."
}

if (params.bam_unmapped_type != 'fastq' ) {
exit 1, "[nf-core/eager] error: metagenomic classification can only run on unmapped reads in FASTQ format. Please supply --bam_unmapped_type 'fastq'. Found parameter: --bam_unmapped_type '${params.bam_unmapped_type}'."
if ( params.bam_unmapped_type != "fastq" ) {
exit 1, "[nf-core/eager] error: metagenomic classification can only run on unmapped reads. Please supply --bam_unmapped_type 'fastq'. Supplied: --bam_unmapped_type '${params.bam_unmapped_type}'."
}

if (!params.database) {
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