Failure parsing sample sheet, FASTA is null

[johncthomas]

Description of the bug

I get the error

ERROR ~ Cannot invoke method endsWith() on null object                                                                     
                                                                                                                           
 -- Check script '/home/username/.nextflow/assets/nf-core/methylseq/./subworkflows/local/prepare_genome/main.nf' at line: 26...

Looking at prepare_genome/main.nf it's because fasta is null. I suspect it shouldn't be trying to prepare a genome at all because I'm supplying --bismark_index DIR, but I'm not sure.

I don't get this error when running with 2.6.0. Didn't try 2.7.0.

Command used and terminal output

nextflow run nf-core/methylseq \
	--input nf_methylseq_samplesheet.2.csv \
	-w ~/project/tmp/methylseq/work/20241111-canary \
	--outdir /rds/project/rds-nutgKVmnlpI/CM1014_Canary/data/methylseq/2024-11-11 \
	--save_reference \
	--non_directional \
	--num_mismatches 0 \
	--bismark_index /rds/project/rds-nutgKVmnlpI/Ref/GRCh38/ \
	--aligner bismark \
	 -c /rds/project/rds-nutgKVmnlpI/tools/nfcore_configs/cambridge_icelake_himem.config


With a sample sheet that looks like 


sample,fastq_1,fastq_2
name,fastq.r_1.fq.gz,fastq.r_2.fq.gz


or 


sample,fastq_1,fastq_2,genome
name,fastq.r_1.fq.gz,fastq.r_2.fq.gz,

Relevant files

No response

System information

nf-core/methylseq: 2.7.1
nextflow: 24.10.0

[sateeshperi]

@johncthomas This is not a bug! You will need to provide the --fasta file along with the bismark index. This change was introduced in 2.7.1to avoid nested symlinks in the index folder, you will now have to provide the fasta file which is later symlinked into the index folder. Do try providing fasta file and plz report back if any issues

[johncthomas]

Ah fair enough! Thanks for the fast response. Yes it does work when given the fasta.

Catching this earlier and giving a clearer error message would be nice, like "--fasta must also be given when an index is supplied".

[sateeshperi]

good point! I will see if I can add a warn message. will update back