TEMPO container images

[Ani6]

Dear team,
I am trying to implement the pipeline, by cloning the github repo & using the instructions for installing & running tempo.

I run into errors regarding various dependencies.
(gatk4-4.6.2.0) [xxx@ldragon3 pipeline]$ # 2. Run with the microsatellite path override
(gatk4-4.6.2.0) [xxx@ldragon3 pipeline]$ ./nextflow-22.10.8-all run pipeline.nf \

  --mapping test_inputs/local/full_test_mapping.tsv \
  --pairing test_inputs/local/full_test_pairing.tsv \
  -profile test_singularity \
  --igenomes_base /rsrch3/scratch/reflib/REFLIB_data/AWS-iGenomes/ \
  --genome_base /rsrch3/scratch/reflib/REFLIB_data/AWS-iGenomes/Homo_sapiens/GATK/GRCh37/ \
  --microsatellites /rsrch3/scratch/reflib/REFLIB_data/AWS-iGenomes/Homo_sapiens/GATK/GRCh37/Annotation/GATKBundle/human_g1k_v37_decoy.microsatellites.list \
  --outDir results

N E X T F L O W ~ version 22.10.8
Launching pipeline.nf [jovial_albattani] DSL1 - revision: 874d5607be
No such file: /rsrch3/scratch/reflib/REFLIB_data/AWS-iGenomes/Homo_sapiens/GATK/GRCh37/Sequence/WholeGenomeFasta/human_g1k_v37_decoy.fasta.microsatellites.list

-- Check script 'pipeline.nf' at line: 3777 or see '.nextflow.log' file for more details

Can I request all the dependencies files, and also the container images (.img files) which are required to run the script locally( as the Institutional HPC is closed with firewalls).

Thank you!

[johnoooh]

Hello,
I responded to Rong in the other thread as well.

First, you should be using the develop branch and dsl2.nf as the entrypoint.

For the container images it is likely easier for you to download them from dockerhub yourself than having me send them over. All of the images are versioned and you should be able to download them to a local machine then upload them to your HPC.
This config file has all of the needed the containers: https://github.com/mskcc/tempo/blob/develop/conf/containers.config
Everything should be on dockerhub.

For the dependency files, all of the references can be seen here. You should be using GRCh37. You are setting igenomes_base amd genome_base so thats good. Are you only having an issue with the microsatellies file? Or do you not have the other reference files either? I'll try to get you what you need.

One thing I wont be able to give you is the gnomad file, it's way too big. You will need to download that yourself. Also, we use VEP version 88 so you will need to get that yourself since that is also pretty big.

Finally, You wont be able to run oncokb annotation, which is fine. It happens here. Add your profile name here and in line 68 and you will be able to skip it.

Let me know what else you need.

[Ani6]

Thank you John; I am using the develop branch and using the dsl2.nf script. I downloaded the container image, and few issues during initialisation failures, due to hardcoded subdirectory structure. Currently, I am encountering a blocking initialization error where the pipeline fails to launch due to a missing reference file: human_g1k_v37_decoy.fasta.microsatellites.list. May I request that?

[johnoooh]

I have your email from Aaron, I'll email you there.

[Ani6]

Hi John, The pipeline is failing because it expects the following files to exist in the ${params.genome_base} or ${params.reference_base} paths, which are not included in the repository or standard iGenomes bundles
Can you point me to where i can find it:
Category | File Name Expected in genome_base | Status in Folder

1. GATK / Core | dbsnp_138.b37.vcf (and .idx) | Present
2. GATK / Core | human_g1k_v37_decoy.fasta (and indices) | Present
3. GATK / Core | human.b37.genome.bed | Missing
4. Facets/ASCAT | dbsnp_137.b37__RmDupsClean__plusPseudo50__DROP_SORT.vcf | Missing (Current Error)
5. Facets/ASCAT | 1000G_phase3_20130502_SNP_maf0.3.loci (and .gc) | Missing
6. Annotation | rmsk_mod.bed.gz (and .tbi) | Missing
7. Annotation | wgEncodeDacMapabilityConsensusExcludable.bed.gz | Missing
8. Annotation | isoforms | Missing
9. Annotation | wes.pon.vcf.gz (or wgs.pon.vcf.gz) | Missing
10. Annotation | abc_complete.fasta and hla.dat | Missing
11. SV Calling | human.hg19.excl.tsv | Missing
12. SV Calling | b37.minusDellyExclude.bed.gz | Missing

Thank you!

[johnoooh]

There are some you can download or build yourself:
rmsk, isoform, wgEncodeDacMapabilityConsensusExcludable, structural variant exclusion files, are all available if you follow the instructions here : https://github.com/mskcc/tempo/blob/develop/docs/reference-files.md

The hla.dat can be downloaded from this repo: https://github.com/ANHIG/IMGTHLA

I'll send you
1000G_phase3_20130502_SNP_maf0.3.loci
dbsnp_137.b37__RmDupsClean__plusPseudo50__DROP_SORT.vcf
human.b37.genome.bed
abc_complete.fasta

I'm trying to figure out how to send these large files to you. I'll try email first but I think they are too big for that.