tempo needed all container images

[ryao-mdanderson]

Dear TEMPO authors,

I am an HPC administrator for our institution research cluster. I help a research to set up tempo pipeline on our cluster.

I follow the instruction described https://github.com/mskcc/tempo/tree/develop, seems it is a develop release.

Our cluster has strict firewall rules to block external site, so I will use cache for the container images. How do I get all stable images that required to run Tempo nextflow pipeline?

Thank you,
Rong Yao

[ryao-mdanderson]

Dear authors, may any of you @Pamelanmrc @ckandoth @adamabeshouse @timosong please provide me suggestion?

Thank you!
Rong Yao

[ryao-mdanderson]

I followed https://github.com/mskcc/tempo/blob/develop/docs/juno-setup.md to test environment setting:

$ module list
Currently Loaded Modules:

1. openjdk/21.0.2+13 2) nextflow/24.10.1

[ryao@ldragon3 tempo]$ mkdir tmp
[ryao@ldragon3 tempo]$ export TMPDIR=/scratch/xxx/tempo/tmp
[ryao@ldragon3 tempo]$ nextflow run dsl2.nf \

--mapping test_inputs/local/full_test_mapping.tsv \
--pairing test_inputs/local/full_test_pairing.tsv \
-profile test_singularity \
--outDir results

Nextflow 25.10.4 is available - Please consider updating your version to it

N E X T F L O W ~ version 24.10.1

Launching dsl2.nf [reverent_galileo] DSL2 - revision: 6c3a8a75ad

WARN: Access to undefined parameter wallTimeExitCode -- Initialise it to a default value eg. params.wallTimeExitCode = some_value
ERROR ~ No such file or directory: /scratch/xxx/tempo/test-data/genome/dbsnp_138.b37.small.vcf

-- Check script './modules/function/define_maps.nf' at line: 5 or see '.nextflow.log' file for more detailse.fromCache(IndyInterface.java:321)
at nextflow.config.ConfigBuilder.buildConfig0(ConfigBuilder.groovy:375)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.config.ConfigBuilder.buildGivenFiles(ConfigBuilder.groovy:320)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.config.ConfigBuilder.buildConfigObject(ConfigBuilder.groovy:818)
at org.codehaus.groovy.vmplugin.v8.IndyInterface.fromCache(IndyInterface.java:321)
at nextflow.config.ConfigBuilder.build(ConfigBuilder.groovy:831)
at nextflow.cli.CmdRun.run(CmdRun.groovy:332)
at nextflow.cli.Launcher.run(Launcher.groovy:503)
at nextflow.cli.Launcher.main(Launcher.groovy:658)

I am sure /scratch/xxx/tempo/ is valid path, where tempo is a directory from  'git clone' command output.

May I know where is the test-data directory?

Thanks,
Rong

[johnoooh]

Hello Rong

Aaron let me know you needed some help.

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

The test-data you are looking for is here: https://docs.google.com/uc?export=download&id=10qEFp0KXY25hBdzykD-wHLFTMH--QloF

Let me know what else you need
John

[ryao-mdanderson]

Hello John,

Thank you for your reply. This helps!

Following https://github.com/mskcc/tempo/blob/develop/conf/containers.config, I am able to pull the first apptainer container using the command
$ apptainer pull docker://cmopipeline/fastp-bwa-samtools:2.0.0
this generates fastp-bwa-samtools_2.0.0.sif, will this .sif will be the exact container image name that be invoked by the workflow?

For the second image: I am seeing two versions of the gatk: broadinstitute/gatk:4.1.9.0 and broadinstitute/gatk:4.1.0.0 will both of them needed?

I have downloaded the test data from google.com.

Regards,
Rong

[johnoooh]

Usually our nextflow image names look like this: cmopipeline-fastp-bwa-samtools-2.0.0.img.

Nextflow pulls images with this name format: registry-org-image-tag.img or .sif depending on the NF version. Either sif or img should be okay.

I would use the exact versions stated in the container. Download both gatk images in case there are changes in the tools between the versions.

[ryao-mdanderson]

Hey John, Thank you. This helps!

[ryao-mdanderson]

Hey John, @johnoooh

Follow up, with your instruction, I am able to download 33 images from github, I stored them in a cluster accessible location.

I checked out the develop branch from github in this location /rsrch3/scratch/itops/ryao/tempo , downloaded test-data.tar.gz and decompressed. Seems I am ready for testing:)

On a compute node
[ryao@cdragon309 tempo]$ ls -l
total 9292
drwxr-xr-x 2 ryao rists 4096 Mar 18 12:21 aws_cf_scripts
drwxr-xr-x 2 ryao rists 4096 Mar 18 16:07 conf
drwxr-xr-x 30 ryao rists 4096 Mar 18 12:21 containers
drwxr-xr-x 3 ryao rists 4096 Mar 18 12:22 docs
-rw-r--r-- 1 ryao rists 13210 Mar 18 12:22 dsl2.nf
drwxr-xr-x 3 ryao rists 4096 Mar 18 12:22 lib
drwxr-xr-x 5 ryao rists 4096 Mar 18 12:22 modules
-rwxr-xr-x 1 ryao rists 4770 Mar 18 12:22 nextflow.config
-rw-r--r-- 1 ryao rists 158890 Mar 18 12:22 pipeline.nf
-rw-r--r-- 1 ryao rists 4010 Mar 18 12:21 README.md
drwxr-x--x 5 ryao rists 4096 Jul 12 2021 test-data
-rw-r--r-- 1 ryao rists 9097371 Apr 14 10:32 test-data.tar.gz
drwxr-xr-x 4 ryao rists 4096 Mar 18 12:22 test_inputs
drwxr-xr-x 2 ryao rists 4096 Mar 18 12:22 tests
drwxr-xr-x 6 ryao rists 4096 Apr 14 10:45 tmp
-rw-r--r-- 1 ryao rists 230 Mar 18 16:19 trace.txt
drwxr-xr-x 2 ryao rists 4096 Mar 18 15:43 work

I follow this link https://github.com/mskcc/tempo/blob/develop/docs/juno-setup.md

On a compute node cdragon309
[ryao@cdragon309 test-data]$ pwd
/rsrch3/scratch/itops/ryao/tempo/test-data

[ryao@cdragon309 testdata]$ module list
Currently Loaded Modules:

1. DefaultModules 2) openjdk/21.0.2+13 3) nextflow/25.10.4
   [ryao@cdragon309 test-data]$ export NXF_SINGULARITY_CACHEDIR=/risapps/apptainer/repo/tempo/1.4
   [ryao@cdragon309 test-data]$ export TMPDIR=/rsrch3/scratch/itops/ryao/tempo/tmp

I am a system admin, not a scientific staff, I appreciate your guidance to replace the files in this command from your test-data (I can't find the equivalent files). The command is from the above juno-setup.md

$ nextflow run dsl2.nf \

--mapping test_inputs/local/full_test_mapping.tsv \
--pairing test_inputs/local/full_test_pairing.tsv \
-profile test_singularity \
--outDir results

I am a system admin, not a scientific staff. As long as a test run works, I would pass this to the scientist to process further. Thank you very much for your help.
Rong

[ryao-mdanderson]

Hey John @johnoooh,

I may not explain clearly in my above question. With all the container images saved already, I try to run a test, where can I find the replacement files for test_inputs/local/full_test_mapping.tsv and test_inputs/local/full_test_pairing.tsv ? Might be it is a trivial question for you, forgive me I am not a scientific staff...

Thank you!
Rong

[johnoooh]

Oh sorry, I didnt understand the question. Use the input mapping and pairing files in the tests folder. They link to files in the test-data folder that you downloaded

[ryao-mdanderson]

Hi John, I got you. I find the mapping and pairing files in the tests folder.
However, when I tried this command under tempo check out directory.

$ nextflow run dsl2.nf --mapping tests/mapping.tsv --pairing tests/pairing.tsv -profile test_singularity --outDir .

Seeing the following output:
...
WARN: Access to undefined parameter wallTimeExitCode -- Initialise it to a default value eg. params.wallTimeExitCode = some_value
ERROR ~ No such file or directory: /rsrch3/scratch/itops/ryao/tempo/test-data/genome/dbsnp_138.b37.small.vcf

-- Check script 'modules/function/define_maps.nf' at line: 5 or see '.nextflow.log' file for more details

modules/function/define_maps.nf' at line: 5 has the content
return file(params."${item}", checkIfExists: true)

• not informative

I think the problem is .../tempo/test-data/genome/dbsnp_138.b37.small.vcf does not exist, instead, it is under .../tempo/test-data/reference/dbsnp_138.b37.small.vcf

Where Should I modify the path? Thank you!
Rong

[ryao-mdanderson]

Hi John @johnoooh,

I need a little help, the above test run error "No such file or directory: /rsrch3/scratch/itops/ryao/tempo/test-data/genome/dbsnp_138.b37.small.vcf" indicates it looks from the tempo installation test-data/genome directory, but actually, dbsnp_138.b37.small.vcf is under test-data/reference, how do I fix this by running the test command:
$ nextflow run dsl2.nf --mapping tests/mapping.tsv --pairing tests/pairing.tsv -profile test_singularity --outDir .

Thank you for your help!
Rong

[johnoooh]

Hey Rong,
You can point nextflow to the proper location of the dbsnp_138.b37.small.vcf by editing this line in the references.config

tempo/conf/references.config

Line 28 in ef39363

dbsnp = "${params.genome_base}/dbsnp_138.b37.small.vcf"

[ryao-mdanderson]

Hey John,

I tried but still not successful. I need further suggestion

I commented out the line in conf/reference.config
//dbsnp = "${params.genome_base}/dbsnp_138.b37.small.vcf"
and
dbsnpIndex = "${params.genome_base}/dbsnp_138.b37.small.vcf.idx"
...

and replaced with the line with the full path
dbsnp = "/rsrch3/scratch/itops/ryao/tempo/test-data/reference/dbsnp_138.b37.small.vcf"
dbsnpIndex = "/rsrch3/scratch/itops/ryao/tempo/test-data/reference/dbsnp_138.b37.small.vcf.idx"

I am sure these file exists.

But there are other lines need to be changed to the correct path as well, i.e. seems ${params.genome_base} need to be reflected to the correct path. How to?

Thank you for your help!
Rong

[johnoooh]

What other files are you having issues with?