Pipeline succeeded only for the first sample in the sample sheet

[leurwu]

Description of the bug

I’m trying out the dev version on my sample sets and encountered a problem. My sample sheet has 20 samples and the pipeline only ran the whole process on the first sample, for the remaining 19 samples they only finished the FastQC step. The pipeline was still reported as completed successfully.

nextflow.log

Command used and terminal output

nextflow run nf-core/rnavar -r dev \
                --input /home/hpcngoc1/storage/gatk_rnaseq/samplesheet_batch1.csv \
                --fasta /rds/project/who1000-1/rds-who1000-cbrc/data/NBR-RNAseq/software/reference_files/ensembl/fasta_genome/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa \
                --gtf /rds/project/who1000-1/rds-who1000-cbrc/data/NBR-RNAseq/software/reference_files/ensembl/gtf/Homo_sapiens.GRCh38.112.gtf \
                --star_index /rds/project/who1000-1/rds-who1000-cbrc/data/NBR-RNAseq/software/reference_files//ensembl/genome_indexed_star2.7.4a \
                --dict /rds/project/who1000-1/rds-who1000-cbrc/data/NBR-RNAseq/software/reference_files/ensembl/genome_indexed_star2.7.4a/genome/Homo_sapiens.GRCh38.dna_sm.primary_assembly.dict \
                --fasta_fai /rds/project/who1000-1/rds-who1000-cbrc/data/NBR-RNAseq/software/reference_files//ensembl/genome_indexed_star2.7.4a/genome/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.fai \
                --read_length 100 --dbsnp /rds/project/who1000-1/rds-who1000-cbrc/data/NBR-RNAseq/software/reference_files//rnavar/dbsnp_00-common_all.vcf.gz \
                --dbsnp_tbi /rds/project/who1000-1/rds-who1000-cbrc/data/NBR-RNAseq/software/reference_files//rnavar/dbsnp_00-common_all.vcf.gz.tbi \
                --skip_variantannotation \
                --outdir /home/hpcngoc1/storage/gatk_rnaseq/out_batch1 \
                --partition cclake --project BRIDGE-OLD-SL2-CPU \
                -work-dir /home/hpcngoc1/storage/gatk_rnaseq/work -profile cambridge -resume

Relevant files

No response

System information

No response

[maxulysse]

@leurwu can you try with -r dev -latest