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Give informative error when empty tsv column #677

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Merged
apeltzer merged 3 commits into from
Feb 16, 2021
Merged

Give informative error when empty tsv column #677

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5669222
Add fix to #626
jfy133 Feb 4, 2021
bce3e37
Fix consistency
jfy133 Feb 4, 2021
f773b5c
Merge branch 'dev' into empty-tsv-column
apeltzer Feb 16, 2021
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7 changes: 4 additions & 3 deletions CHANGELOG.md
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Expand Up @@ -10,10 +10,11 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
### `Fixed`

- [#666](https://github.com/nf-core/eager/issues/666) - Fixed input file staging for `print_nuclear_contamination`
- [#631](https://github.com/nf-core/eager/issues/631): - Update minimum Nextflow version to 20.07.1, due to unfortunate bug in Nextflow 20.04.1 causing eager to crash if patch pulled
- [#631](https://github.com/nf-core/eager/issues/631) - Update minimum Nextflow version to 20.07.1, due to unfortunate bug in Nextflow 20.04.1 causing eager to crash if patch pulled
- Made MultiQC crash behaviour stricter when dealing with large datasets, as reported by @ashildv
- Added note to documentation that when using `--skip_collapse` this will use _paired-end_ alignment mode with mappers when using PE data. `
- [#673](https://github.com/nf-core/eager/pull/673): Fix Kraken database loading when loading from directory instead of compressed file.
- [#652](https://github.com/nf-core/eager/issues/652) Added note to documentation that when using `--skip_collapse` this will use _paired-end_ alignment mode with mappers when using PE data
- [#673](https://github.com/nf-core/eager/pull/673) - Fix Kraken database loading when loading from directory instead of compressed file
- [#626](https://github.com/nf-core/eager/issues/626) - Add additional checks to ensure pipeline will give useful error if cells of a TSV column are empty

### `Dependencies`

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16 changes: 14 additions & 2 deletions main.nf
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Expand Up @@ -3490,6 +3490,18 @@ def extract_data(tsvFile) {

checkNumberOfItem(row, 11)

if ( row.Sample_Name.isEmpty() ) exit 1, "[nf-core/eager] error: the Sample_Name column is empty. Ensure all cells are filled or contain 'NA' for optional fields. Check row:\n ${row}"
if ( row.Library_ID.isEmpty() ) exit 1, "[nf-core/eager] error: the Library_ID column is empty. Ensure all cells are filled or contain 'NA' for optional fields. Check row:\n ${row}"
if ( row.Lane.isEmpty() ) exit 1, "[nf-core/eager] error: the Lane column is empty. Ensure all cells are filled or contain 'NA' for optional fields. Check row:\n ${row}"
if ( row.Colour_Chemistry.isEmpty() ) exit 1, "[nf-core/eager] error: the Colour_Chemistry column is empty. Ensure all cells are filled or contain 'NA' for optional fields. Check row:\n ${row}"
if ( row.SeqType.isEmpty() ) exit 1, "[nf-core/eager] error: the SeqType column is empty. Ensure all cells are filled or contain 'NA' for optional fields. Check row:\n ${row}"
if ( row.Organism.isEmpty() ) exit 1, "[nf-core/eager] error: the Organism column is empty. Ensure all cells are filled or contain 'NA' for optional fields. Check row:\n ${row}"
if ( row.Strandedness.isEmpty() ) exit 1, "[nf-core/eager] error: the Strandedness column is empty. Ensure all cells are filled or contain 'NA' for optional fields. Check row:\n ${row}"
if ( row.UDG_Treatment.isEmpty() ) exit 1, "[nf-core/eager] error: the UDG_Treatment column is empty. Ensure all cells are filled or contain 'NA' for optional fields. Check row:\n ${row}"
if ( row.R1.isEmpty() ) exit 1, "[nf-core/eager] error: the R1 column is empty. Ensure all cells are filled or contain 'NA' for optional fields. Check row:\n ${row}"
if ( row.R2.isEmpty() ) exit 1, "[nf-core/eager] error: the R2 column is empty. Ensure all cells are filled or contain 'NA' for optional fields. Check row:\n ${row}"
if ( row.BAM.isEmpty() ) exit 1, "[nf-core/eager] error: the BAM column is empty. Ensure all cells are filled or contain 'NA' for optional fields. Check row:\n ${row}"

def samplename = row.Sample_Name
def libraryid = row.Library_ID
def lane = row.Lane
Expand All @@ -3503,10 +3515,10 @@ def extract_data(tsvFile) {
def bam = row.BAM.matches('NA') ? 'NA' : return_file(row.BAM)

// check no empty metadata fields
if (samplename == '' || libraryid == '' || lane == '' || colour == '' || seqtype == '' || seqtype == '' || udg == '' || r1 == '' || r2 == '') exit 1, "[nf-core/eager] error: a field does not contain any information. Ensure all cells are filled or contain 'NA' for optional fields. Check row:\n ${row}"
if (samplename == '' || libraryid == '' || lane == '' || colour == '' || seqtype == '' || organism == '' || strandedness == '' || udg == '' || r1 == '' || r2 == '' || bam == '') exit 1, "[nf-core/eager] error: a field/column does not contain any information. Ensure all cells are filled or contain 'NA' for optional fields. Check row:\n ${row}"

// Check no 'empty' rows
if (r1.matches('NA') && r2.matches('NA') && bam.matches('NA') && bai.matches('NA')) exit 1, "[nf-core/eager] error: A row in your TSV appears to have all files defined as NA. See '--help' flag and documentation under 'running the pipeline' for more information. Check row for: ${samplename}"
if (r1.matches('NA') && r2.matches('NA') && bam.matches('NA')) exit 1, "[nf-core/eager] error: A row in your TSV appears to have all files defined as NA. See '--help' flag and documentation under 'running the pipeline' for more information. Check row for: ${samplename}"

// Ensure BAMs aren't submitted with PE
if (!bam.matches('NA') && seqtype.matches('PE')) exit 1, "[nf-core/eager] error: BAM input rows in TSV cannot be set as PE, only SE. See '--help' flag and documentation under 'running the pipeline' for more information. Check row for: ${samplename}"
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