Add fix to #626

Author: jfy133

CHANGELOG.md

@@ -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`
 

main.nf

@@ -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
@@ -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}"