When I ran the nfcore/ nascent pipeline for PRO-seq data using the default aligner in dev mode I ran into this issue.
I used 2 commands for 2 different runs, and both yielded the same Error message in the end.
Command used and terminal output
nextflow run nf-core/nascent -r dev --input samplesheet.csv --outdir nascentoutput --fasta hg38_noalt/fasta/genome_noalt.fa --gtf hg38_annotations/ucsc/hg38.ncbiRefSeq.gtf --bwa_index BWA_Human/bwa_hg38_noalt_index/ --assay_type PROseq --max_cpus 10 -profile singularity
nextflow run nf-core/nascent -r dev --input samplesheet.csv --outdir nascentoutput --genome hg38 --assay_type PROseq --max_cpus 10 -profile singularity
Error executing process > 'NFCORE_NASCENT:NASCENT:ALIGN_BWA:BWA_MEM (1)'
Caused by:
Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null)
Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
Relevant files
No response
System information
Nextflow Version: 21.10.6
Hardware Desktop
Executor Slurm
Container Engine Singularity
OS Linux
Description of the bug
When I ran the nfcore/ nascent pipeline for PRO-seq data using the default aligner in dev mode I ran into this issue.
I used 2 commands for 2 different runs, and both yielded the same Error message in the end.
Command used and terminal output
Relevant files
No response
System information
Nextflow Version: 21.10.6 Hardware Desktop Executor Slurm Container Engine Singularity OS Linux