Missing barcodes from sample input break the pipeline

[ammaraziz]

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

v0.3.31-gcb0ad4a

Workflow Execution

Command line

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-artic -c covid.cfg --fastq data/ --out_dir results/ \
--custom_scheme .../custom_scheme/V1/ --sample_sheet data/barcodes.csv \
--update_data --normalise 400 --basecaller_cfg dna_r10.4.1_e8.2_400bps_hac \
--min_len 150 --max_len 1200

Sample sheet (example):

barcode	sample_id	alias	type
barcode1	X1	X1	test_sample
barcode9	X2	X2	test_sample
barcode12	X3	X3	test_sample
...

Note the barcode1 should be barcode01

Workflow Execution - CLI Execution Profile

None

What happened?

When running the pipeline with custom primers and a borked sample input sheet with missing barcode entries, the pipeline errors out. It seems like the missing barcode entries are causing issues in the pipeline at this part in the code:

https://github.com/epi2me-labs/wf-artic/blob/master/main.nf#L446C17-L446C103

Relevant log output

Checking fastq input.
executor >  local (124)
[01/340b8e] process > validate_sample_sheet                    [100%] 1 of 1 ✔
[14/e71e19] process > fastcat (86)                             [100%] 87 of 87 ✔
[7d/bbfcfe] process > pipeline:getVersions                     [100%] 1 of 1 ✔
[25/e6be23] process > pipeline:getParams                       [100%] 1 of 1 ✔
[4e/944042] process > pipeline:lookup_medaka_variant_model (1) [100%] 1 of 1 ✔
[ec/189333] process > pipeline:runArtic (32)                   [  0%] 0 of 87
[-        ] process > pipeline:combineDepth                    -
[-        ] process > pipeline:allConsensus                    -
[-        ] process > pipeline:allVariants                     -
[68/736f76] process > pipeline:prep_nextclade                  [100%] 1 of 1 ✔
[-        ] process > pipeline:nextclade                       -
[-        ] process > pipeline:pangolin                        -
[-        ] process > pipeline:report                          -
[-        ] process > output                                   -
WARN: Input directory 'barcode01' was found, but sample sheet 'data/tvr_barcodes.csv' has no such entry.
WARN: Input directory 'barcode06' was found, but sample sheet 'data/tvr_barcodes.csv' has no such entry.
WARN: Input directory 'barcode03' was found, but sample sheet 'data/tvr_barcodes.csv' has no such entry.
WARN: Input directory 'barcode05' was found, but sample sheet 'data/tvr_barcodes.csv' has no such entry.
WARN: Input directory 'barcode02' was found, but sample sheet 'data/tvr_barcodes.csv' has no such entry.
WARN: Input directory 'barcode08' was found, but sample sheet 'data/tvr_barcodes.csv' has no such entry.
WARN: Input directory 'barcode07' was found, but sample sheet 'data/tvr_barcodes.csv' has no such entry.
WARN: Input directory 'barcode04' was found, but sample sheet 'data/tvr_barcodes.csv' has no such entry.
WARN: Input directory 'barcode09' was found, but sample sheet 'data/tvr_barcodes.csv' has no such entry.

ERROR ~ Cannot invoke method resolve() on null object

 -- Check script '~epi2me-labs/wf-artic/main.nf' at line: 446 or see '.nextflow.log' file for more details

Application activity log entry

No response

[ammaraziz]

Related to this, the example sample_sheet.csv has the wrong header:
https://github.com/epi2me-labs/wf-artic/blob/master/test_data/sample_sheet.csv

sample_id should be sample_name

There's a possibility this is actually cause the above issue. Running the pipeline now to confirm.

[mattdmem]

Thanks for this - we'll take a look at both the issues you describe above.

Matt

[ammaraziz]

I think this issue is not related to the barcode.csv but to fastcat failing. I will investigate and open up an issue for fastcat.

Thanks for your support Matt.