input file name collision

[vivischuch]

Description of the bug

ERROR ~ Error executing process > 'NFCORE_RNAVAR:RNAVAR:SPLITNCIGAR:SAMTOOLS_MERGE (15)'

Caused by:
Process NFCORE_RNAVAR:RNAVAR:SPLITNCIGAR:SAMTOOLS_MERGE input file name collision -- There are multiple input files for each of the following file names: Non-hypertensive_Control_SRR16505214.bam

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

-- Check '.nextflow.log' file for details
Execution cancelled -- Finishing pending tasks before exit

Command used and terminal output

$ nextflow run nf-core/rnavar -profile docker -c custom.comfig --genome GRCh38 --read_length 151 --fasta GRCh38.primary_assembly.genome.fa --dbsnp All_20180418.vcf.gz  --dbsnp_tbi All_20180418.vcf.gz.tbi --known_indels Homo_sapiens_assembly38.known_indels.vcf.gz --known_indels_tbi Homo_sapiens_assembly38.known_indels.vcf.gz.tbi --input Samplesheet.csv --outdir /home/vivischuch/fastq/output_rnavar --star_index /home/vivischuch/fastq/star_files -bg -resume

Relevant files

Samplesheet.csv

System information

N E X T F L O W ~ version 23.04.4
Launching https://github.com/nf-core/rnavar [disturbed_murdock] DSL2 - revision: 222d7a1 [master]

---

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nf-core/rnavar v1.0.0

Core Nextflow options
revision : master
runName : disturbed_murdock
containerEngine : docker
launchDir : /home/vivischuch/fastq
workDir : /home/vivischuch/fastq/work
projectDir : /home/vivischuch/.nextflow/assets/nf-core/rnavar
userName : vivischuch
profile : docker
configFiles : /home/vivischuch/.nextflow/assets/nf-core/rnavar/nextflow.config, /home/vivischuch/fastq/custom.comfig

Input/output options
input : Samplesheet.csv
outdir : /home/vivischuch/fastq/output_rnavar

Reference genome options
genome : GRCh38
fasta : GRCh38.primary_assembly.genome.fa
gtf : s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf
known_indels : Homo_sapiens_assembly38.known_indels.vcf.gz
known_indels_tbi: Homo_sapiens_assembly38.known_indels.vcf.gz.tbi
dbsnp : All_20180418.vcf.gz
dbsnp_tbi : All_20180418.vcf.gz.tbi

Alignment options
star_index : /home/vivischuch/fastq/star_files
star_twopass : true

!! Only displaying parameters that differ from the pipeline defaults !!

[maxulysse]

Can you share your samplesheet?

[maxulysse]

Nevermind, saw it

[maxulysse]

Can you try with that?
Samplesheet.csv
I'm not sure about the space in the sample id

[vivischuch]

I'll try. I didn't realize there was space in my sample id. Thank you so much!

[maxulysse]

I'll try. I didn't realize there was space in my sample id. Thank you so much!

there should be an error for that anyway, so thanks for finding out

[nvnieuwk]

Error message for this issue seems to be working in the dev branch:

        -> Entry 1: Error for field 'sample' (Severe preeclampsia_SRR16505203): "Severe preeclampsia_SRR16505203" does not match regular expression [^\S+$] (Sample name must be provided and cannot contain spaces)