NF core rna-seq pipeline

Question

[rajdeepboral00]

I have been trying to use the nf rna seq pipeline but everytime i use it i withstand such errors when i ran this command

 nf-core/rnaseq   -profile conda   --input samplesheet_mouse_rnaseq.csv   --outdir results   --gtf /data/sata_data/home/rajdeep/TrimGalore/STAR/gencode.vM37.basic.annotation.gtf   --fasta /data/sata_data/home/rajdeep/TrimGalore/STAR/GRCm39.genome.fa   --star_index false   --save_reference   -resume**


> Blockquote

**Execution cancelled -- Finishing pending tasks before exit
-[nf-core/rnaseq] Pipeline completed with errors-
WARN: Directive `process.shell` cannot contain new-line characters - offending value: [bash
set -e # Exit if a tool returns a non-zero status/exit code
set -u # Treat unset variables and parameters as an error
set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
]
ERROR ~ Error executing process > 'NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (GRCm39.genome.fa)'
Caused by:
  Process `NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (GRCm39.genome.fa)` terminated with an error exit status (126)
Command executed:
  samtools faidx GRCm39.genome.fa
  cut -f 1,2 GRCm39.genome.fa.fai > GRCm39.genome.fa.sizes

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES":
      getchromsizes: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
  END_VERSIONS
Command exit status:
  126
Command output:
  (empty)
Command error:
  .command.run: line 301: .command.run: Permission denied
Work dir:
  /data/sata_data/home/rajdeep/NF/work/6b/4895e66914ebeee4d0803301ac0432
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
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
 -- Check '.nextflow.log' file for details**

How will i overcome this error?

[Pierre Lindenbaum]

.command.run permission denied in 3.16.1, 3.17.0, 3.18.0 #1554

https://github.com/nf-core/rnaseq/issues/1554