--save_reference does not save bowtie2 index

[SuhasSrinivasan]

Description of the bug

Dear Authors,

Thank you for developing and maintaining this pipeline.

Using --save_reference does not save the bowtie2 computed index to ./results/genome/index.
This expectation is based on the same parameter behavior in the Nextflow ATAC-seq pipeline: https://nf-co.re/atacseq/2.1.2/parameters/

Please see two more comments below.

Command used and terminal output

$ nextflow run nf-core/cutandrun -profile docker --only-genome --save-reference 
--input ~/drive1/ubl/ubl_cnr/cnr_sample_sheet.csv 
--outdir ~/drive1/ubl/ubl_cnr/results/ 
--fasta ~/drive1/ubl/ubl_cnr/results/genome/Homo_sapiens.GRCh38.dna.primary_assembly.fa 
--gtf ~/drive1/ubl/ubl_cnr/results/genome/Homo_sapiens.GRCh38.111._ensembl.gtf 
--blacklist ~/drive1/ubl/ubl_cnr/results/genome/hg38-blacklist.v3.bed

[4a/b199cf] NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_BEDTOOLS_INTERSECT (blacklist)                             [100%] 1 of 1 ✔
[75/d636e1] NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_BEDTOOLS_SORT (blacklist)                                  [100%] 1 of 1 ✔
[e4/5dddd3] NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:BLACKLIST_BEDTOOLS_COMPLEMENT (blacklist)                            [100%] 1 of 1 ✔
[9f/e2b64f] NFCORE_CUTANDRUN:CUTANDRUN:INPUT_CHECK:SAMPLESHEET_CHECK (cnr_sample_sheet.csv)                                [100%] 1 of 1 ✔
[-        ] NFCORE_CUTANDRUN:CUTANDRUN:CAT_FASTQ                                                                           -
[98/6dfdd5] NFCORE_CUTANDRUN:CUTANDRUN:FASTQC_TRIMGALORE:FASTQC (K27me3_R2)                                                [100%] 8 of 8 ✔
[28/63dfc1] NFCORE_CUTANDRUN:CUTANDRUN:FASTQC_TRIMGALORE:TRIMGALORE (Beads_K27me3_R1)                                      [ 12%] 1 of 8

Relevant files

No response

System information

Version of nf-core/cutandrun: 3.2.2
Nextflow version: v24.10.3
Container engine: Docker 27.4.1
OS: Ubuntu 22.04.5 LTS x86_64
Executor: Local
Hardware: Desktop

[SuhasSrinivasan]

Also, it is unclear where the bowtie2 index is being saved. Can you please provide this information?

[SuhasSrinivasan]

This also does not work when using iGenomes

nextflow run nf-core/cutandrun -profile docker
--input ~/drive1/ubl/ubl_cnr/cnr_sample_sheet.csv
--outdir ~/drive1/ubl/ubl_cnr/results/
--genome GRCh38
--spikein_genome K12-MG1655
--save-reference
--remove_mitochondrial_reads
--blacklist ~/drive1/ubl/ubl_cnr/results/genome/hg38-blacklist.v3.bed