Unset conflicting Singularity environment variables

[j23414]

Copying @vsatheesh's message from slack and #16 (comment) to a separate Issue, since this is unrelated to the SNPeff PR.

After adding these two lines to the slurm script, the pipeline completed successfully.

# Unset conflicting Singularity environment variables
unset SINGULARITYENV_TMPDIR
unset SINGULARITYENV_NXF_DEBUG

[9a/4915ee] process > DNA_VARIANT_CALLING:FastqTo... [100%] 27 of 27 ✔
[42/490b61] process > DNA_VARIANT_CALLING:MarkIll... [100%] 27 of 27 ✔
[e2/5c9a78] process > DNA_VARIANT_CALLING:SamToFa... [100%] 27 of 27 ✔
[18/a33d64] process > DNA_VARIANT_CALLING:bwamem2... [100%] 1 of 1 ✔
[d8/d501c2] process > DNA_VARIANT_CALLING:bwamem2... [100%] 27 of 27 ✔
[53/1155e9] process > DNA_VARIANT_CALLING:CreateS... [100%] 1 of 1 ✔
[f8/969de5] process > DNA_VARIANT_CALLING:samtool... [100%] 1 of 1 ✔
[0f/a92e33] process > DNA_VARIANT_CALLING:MergeBa... [100%] 27 of 27 ✔
[1c/6ebcc7] process > DNA_VARIANT_CALLING:MarkDup... [100%] 27 of 27 ✔
[86/d10967] process > DNA_VARIANT_CALLING:SortAnd... [100%] 27 of 27 ✔
[2d/7fd6ba] process > DNA_VARIANT_CALLING:bedtool... [100%] 1 of 1 ✔
[ae/f93ecc] process > DNA_VARIANT_CALLING:gatk_Ha... [100%] 10 of 10 ✔
[02/d68957] process > DNA_VARIANT_CALLING:merge_vcf  [100%] 1 of 1 ✔
[b5/0f8110] process > DNA_VARIANT_CALLING:vcftool... [100%] 1 of 1 ✔
[39/b07f21] process > DNA_VARIANT_CALLING:SortVcf... [100%] 1 of 1 ✔
[be/9ac910] process > DNA_VARIANT_CALLING:calc_DP... [100%] 1 of 1 ✔
[19/d72b93] process > DNA_VARIANT_CALLING:Variant... [100%] 1 of 1 ✔
[17/563fc9] process > DNA_VARIANT_CALLING:keep_on... [100%] 1 of 1 ✔
Completed at: 13-Jun-2024 00:22:28
Duration    : 35m 53s
CPU hours   : 2.4
Succeeded   : 209

There has been an update of the server and I will have to check the pipeline again.

[j23414]

@vsatheesh I haven't dived into nextflow in a while; but, I think you have a couple options for fixing this:

• Option A: Unset those variables in the slurm script:

  GATK-flow/submit_nf.slurm

  Lines 19 to 30 in 73bfc89

  	# == Atlas HPC (will need a local install of nextflow)
  	# module load singularity
  	# NEXTFLOW=/project/isu_gif_vrsc/programs/nextflow
  	# == Ceres HPC
  	# module load nextflow
  	# NEXTFLOW=nextflow
  	# == Nova HPC
  	module load gcc/7.3.0-xegsmw4 nextflow
  	module load singularity
  	NEXTFLOW=nextflow

• Option B: Create a custom config for your HPC of interest: duplicate and modify https://github.com/isugifNF/GATK-flow/blob/master/configs/custom.config
• Option C: Refactor the config to support Apptainer (was singularity) which may or may not bypass the issue:

  GATK-flow/nextflow.config

  Lines 115 to 118 in 73bfc89

  	singularity {
  	includeConfig 'configs/container.config'
  	singularity.enabled = true
  	}

  
  perhaps taking inspiration from other nf-core pipelines: https://github.com/nf-core/rnaseq/blob/b89fac32650aacc86fcda9ee77e00612a1d77066/nextflow.config#L232-L241

Let me know if you want to check-in on any of this