update how PipeVal is being used to validate input and output files #240

jarbet · 2022-08-31T20:55:11Z

Description

Replace blcdsdockerregistry/validate:2.1.5 (out of date) with the version from pipeline-Nextflow-module.

Closes #239

Testing Results

/hot/software/pipeline/pipeline-align-DNA/Nextflow/development/unreleased/jarbet-validate

BWA-MEM2
- input csv: /hot/software/pipeline/pipeline-align-DNA/Nextflow/development/input/csv/a_mini_n1_standardized
- config: /hot/software/pipeline/pipeline-align-DNA/Nextflow/development/unreleased/jarbet-validate/BWA-MEM2-a_mini_n1.config
- output: /hot/software/pipeline/pipeline-align-DNA/Nextflow/development/unreleased/jarbet-validate/align-DNA-8.1.0

Checklist

I have read the code review guidelines and the code review best practice on GitHub check-list.
I have reviewed the Nextflow pipeline standards.
The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].
I have set up the branch protection rule following the github standards before opening this pull request, or the branch protection rule has already been set up.
I have added my name to the contributors listings in the manifest block in the nextflow.config as part of this pull request, am listed
already, or do not wish to be listed. (This acknowledgement is optional.)
I have added the changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.
I have updated the version number in the metadata.yaml and manifest block of the nextflow.config file following semver, or the version number has already been updated. (Leave it unchecked if you are unsure about new version number and discuss it with the infrastructure team in this PR.)
I have tested the pipeline on at least one A-mini sample with aligner setting to BWA-MEM2, HISAT2, and both. The paths to the test config files and output directories were attached in the Testing Results section.

tyamaguchi-ucla · 2022-08-31T22:01:29Z

config/default.config

@@ -14,12 +14,13 @@ params {
    // tools and their versions
    bwa_version = "BWA-MEM2-2.2.1"
    hisat2_version = "HISAT2-2.2.1"
+    pipeval_version = "2.1.6"


3.0.0 is available :)

https://github.com/uclahs-cds/public-tool-PipeVal

https://github.com/uclahs-cds/pipeline-Nextflow-module/tree/main/modules/PipeVal/validate

jarbet · 2022-08-31T23:29:00Z

@aybeshlikyan, @yashpatel6 : I'm having trouble figuring out how to switch to PipeVal/validate. Any suggestions on how to modify my code?

Here is the error I'm currently getting:

WARN: Input tuple does not match input set cardinality declared by process align_DNA_BWA_MEM2_workflow:validate_output_file -- offending value: /scratch
WARN: Input tuple does not match input set cardinality declared by process align_DNA_BWA_MEM2_workflow:run_validate_PipeVal -- offending value: /hot/ref/tool-specific-input/BWA-MEM2-2.2.1/GRCh38-BI-20160721/index/genome.fa.bwt.2bit.64
Error executing process > 'align_DNA_BWA_MEM2_workflow:run_validate_PipeVal (6)'

Caused by:
Not a valid path value type: org.codehaus.groovy.runtime.NullObject (null)

Yash mentioned I might need to first process the input files using a line similar to here. I'm not sure what this line is doing, and I noticed align-RNA does not include a similar step, so I'm not sure if this line is needed?

aybeshlikyan · 2022-09-01T20:08:05Z

@jarbet For the first warning/error, it seems like it's caused by lines 134-137 in "module/align_DNA_BWA_MEM2.nf" ; the function validate_output_file (AKA run_validate_PipeVal from the submodule) is expecting a channel with 2 items: the mode of the file to validate (in this case it would be 'file-bam') and the file to be validated (i.e. och_bam), but it's getting a channel with the items och_bam, och_bam_index, params.work_dir (i.e. "/scratch"), and params.output_dir. That's why it's complaining about the input set cardinality-- it's expecting 2 items but getting 4. The old run_validate_PipeVal in "validate.nf" took in the output log dir as an input, but the submodule handles that with the options passed into "addParams" with the include statement at the top of the file.

For the second warning/error, it's caused by lines 91-94 in the same file. It seems like it's complaining about the cardinality again, but also the index file (I think it's talking about ich_reference_index_files?); PipeVal can't handle that type of file.

The line that Yash linked in call-gSNP basically sets up a channel with the correct cardinality, mapping the unique BAM files from the input csv into items that are tuples of the form [<PipeVal file type>, <path to BAM file>] (i.e. ['file-input', it]).

I think setting up both validate_output_file and run_validate_PipeVal to take in channels with the correct number/type of items should fix it or at least get it closer to running. However I might not be understanding what's going on fully because I'm confused about how/why the index files are passed into run_validate_PipeVal, because I thought PipeVal couldn't run on those; maybe @yashpatel6 can make sure everything I said is accurate and give more insight if I misunderstood anything.

aybeshlikyan · 2022-09-01T20:24:42Z

I noticed align-RNA does not include a similar step, so I'm not sure if this line is needed?

@jarbet Align-RNA doesn't use that exact way to set up the channel but it does something similar here, here, and here.

aybeshlikyan · 2022-09-01T20:26:20Z

@jarbet Also a couple other things I noticed:

the pipeval_version variable in "default.config" is set to 3.0.0 but the submodule is still the version of the repo that's using 2.1.6; you can run git submodule update --remote external/nextflow-modules/ from the root of the align-DNA repo to pull the latest version of the submodule
You can change docker_image_validate_params = "blcdsdockerregistry/validate:2.1.6" to docker_image_validate_params = "blcdsdockerregistry/pipeval:3.0.0" in the default.config.

yashpatel6 · 2022-09-02T18:58:24Z

@jarbet For the first warning/error, it seems like it's caused by lines 134-137 in "module/align_DNA_BWA_MEM2.nf" ; the function validate_output_file (AKA run_validate_PipeVal from the submodule) is expecting a channel with 2 items: the mode of the file to validate (in this case it would be 'file-bam') and the file to be validated (i.e. och_bam), but it's getting a channel with the items och_bam, och_bam_index, params.work_dir (i.e. "/scratch"), and params.output_dir. That's why it's complaining about the input set cardinality-- it's expecting 2 items but getting 4. The old run_validate_PipeVal in "validate.nf" took in the output log dir as an input, but the submodule handles that with the options passed into "addParams" with the include statement at the top of the file.

For the second warning/error, it's caused by lines 91-94 in the same file. It seems like it's complaining about the cardinality again, but also the index file (I think it's talking about ich_reference_index_files?); PipeVal can't handle that type of file.

The line that Yash linked in call-gSNP basically sets up a channel with the correct cardinality, mapping the unique BAM files from the input csv into items that are tuples of the form [<PipeVal file type>, <path to BAM file>] (i.e. ['file-input', it]).

I think setting up both validate_output_file and run_validate_PipeVal to take in channels with the correct number/type of items should fix it or at least get it closer to running. However I might not be understanding what's going on fully because I'm confused about how/why the index files are passed into run_validate_PipeVal, because I thought PipeVal couldn't run on those; maybe @yashpatel6 can make sure everything I said is accurate and give more insight if I misunderstood anything.

Generally, you're correct! Some minor clarifications:

The process does expect each input to be a tuple with cardinality 2. So each emission in the input channel to the process must be a tuple of cardinality 2. The channel itself can contain as many emissions as you want. The cause for the error is that the input channel contains 4 emissions that each have a single item (cardinality 1). So the problem isn't that there are 4 items but that these 4 items have cardinality 1 when they need to have cardinality 2.

The second error/warning is actually caused because the input only had cardinality 1 so the second expected item (the actual path to the file for validating) is null and so you get that error.

PipeVal doesn't have explicit validation for index files but it is still able to verify that the file actually exists I believe. So passing ['file-input', <index_file>] should still work fine as a basic check that the file exists and if there's a checksum, I believe PipeVal will validate that (I could be wrong on the checksum part).

jarbet · 2022-09-02T22:07:03Z

@aybeshlikyan , @yashpatel6 : thanks for the help so far. I understand the new run_validate_PipeVal requires 2 parameters, although Yash mentioned it can take a channel/set of many inputs, as long as each has the 2 required parameters. I don't know how to setup the inputs/channel to do this, but I'm reading more of the Nextflow documentation to try and figure it out.

Conceptually, I think I need something like the following:

For the input validation:

run_validate_PipeVal(
         // This needs to be a vector containing 'file-input' (or 'file-fasta'?), repeated X times, where X is the number of fasta files to validate
         [ file-input, file-input, ...., file-input]
         // I think this is a vector of paths to multiple fasta files? 
         ich_samples_validate.mix(.
         ich_reference_index_files
         )
         )

For the output validation:

validate_output_file(
         // This needs to be a vector containing 'file-input' (or 'file-bam'?), repeated X times, where X is the number of bam files to validate
         [ file-input, file-input, ...., file-input]
         // I think this is a vector of paths to multiple bam files?
         och_bam.mix(
            och_bam_index,
            Channel.from(params.work_dir, params.output_dir)
            )
         )

I don't know how to do this in groovy but here is a very rough guess based on here:

For the input validation:

ich_samples_validate.mix(.
         ich_reference_index_files
         ).flatMap{it -> ['file-input', it}.set{pipeval_input}
         // this assumes 'it' is every element of the ich_samples_validate.mix channel vector?

For the output validation:

och_bam.mix(
            och_bam_index,
            Channel.from(params.work_dir, params.output_dir)
            ).flatMap{it -> ['file-input', it}.set{pipeval_output}

Then somehow I would have to send the pipeval_input and pipeval_output stuff to the corresponding calls to run_validate_PipeVal and validate_output_file ?

yashpatel6 · 2022-09-06T22:01:52Z

Generally, that's correct. You'll want to use map instead of flatMap though. flatMap is meant for doing a mapping operation on a channel and then flattening the result so if you use that, you'll end up with with each emission being a single element rather than a tuple of size 2. The reason there's a flatMap in call-gSNP is that the input channel contained values that didn't need to be validated so we map to keep only the things we want to validate -> flatten the result so each file to validate is a single emission -> map to ['file-input', it] to get it to the required input format. The flatMap operator handles the first two steps and the map handles the last step.

jarbet · 2022-09-20T22:42:00Z

@yashpatel6 @aybeshlikyan : I think I fixed the input cardinality problem when validating the input files and output files, since I am no longer getting the cardinality warnings.

However, I am now getting the following error:
/hot/software/pipeline/pipeline-align-DNA/Nextflow/development/unreleased/jarbet-validate/BWA-MEM2-a_mini_n2.log

Error executing process > 'align_DNA_BWA_MEM2_workflow:run_validate_PipeVal (1)'

Caused by:
  Process `align_DNA_BWA_MEM2_workflow:run_validate_PipeVal (1)` terminated with an error exit status (1)

Command executed:

  set -euo pipefail
  validate -t file-input genome.fa > 'validation.txt'

Command exit status:
  1

Command output:
  (empty)

Work dir:
  /scratch/0a/231f887f90535270d8b01aa4749ea5

Although the cardinality is correct now, I think the contents of what is being passed to PipeVal seems wrong:

/hot/software/pipeline/pipeline-align-DNA/Nextflow/development/unreleased/jarbet-validate/align-DNA-8.1.0/a_mini_n2/BWA-MEM2-2.2.1/validation:

[[email protected] validation]$ cat input_validation.txt 
Input: HG002.N-n2_R2.fq.gz is valid file-fastq
Input: genome.fa.0123 is valid file-unknown
Input: genome.fa.fai is valid file-unknown
Input: genome.fa.bwt.2bit.64 is valid file-unknown
Input: genome.fa.ann is valid file-unknown

[[email protected] validation]$ cat output_validation.txt 
Input: scratch is valid file-unknown
Input: jarbet-validate is valid file-unknown

Any thoughts on how to fix this?
I'm guessing this line is no longer needed, but I don't understand the error from run_validate_PipeVal.

yashpatel6 · 2022-09-20T23:20:04Z

This seems to be because PipeVal got updated to throw an error for any file type that's not BAM, VCF, or FASTQ. Previous versions of PipeVal used to allow for other extensions and would check checksums if available and otherwise just pass the validation. @aybeshlikyan @tyamaguchi-ucla Any reason PipeVal was set up to only accept BAM, VCF, and FASTQ files in 3.0.0?

tyamaguchi-ucla · 2022-09-20T23:21:26Z

@aybeshlikyan @tyamaguchi-ucla Any reason PipeVal was set up to only accept BAM, VCF, and FASTQ files in 3.0.0?

I wasn't aware of the change. @aybeshlikyan thoughts?

yashpatel6 · 2022-09-27T01:22:22Z

CHANGELOG.md

@@ -10,6 +10,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ## [Unreleased]

 ### Changed
+- Replace `blcdsdockerregistry/validate:2.1.5` (out of date) with the version from [pipeline-Nextflow-module](https://github.com/uclahs-cds/pipeline-Nextflow-module/tree/main/modules/PipeVal/validate).


We might want to specify that we're using v3.0.0; the module might get updated to newer versions but the version used by the pipeline is still dictated by in default.config

yashpatel6 · 2022-09-27T01:23:06Z

config/default.config


    docker_image_bwa_and_samtools = "blcdsdockerregistry/bwa-mem2_samtools-1.12:2.2.1"
    docker_image_hisat2_and_samtools = "blcdsdockerregistry/hisat2_samtools-1.12:2.2.1"
    docker_image_picardtools = "blcdsdockerregistry/picard:2.26.10"
    docker_image_sha512sum = "blcdsdockerregistry/align-dna:sha512sum-1.0"
-    docker_image_validate_params = "blcdsdockerregistry/validate:2.1.5"    
+    docker_image_validate_params = "blcdsdockerregistry/pipeval:3.0.0"


Suggested change

docker_image_validate_params = "blcdsdockerregistry/pipeval:3.0.0"

docker_image_validate_params = "blcdsdockerregistry/pipeval:${pipeval_version}"

To avoid hard-coding and duplication

yashpatel6 · 2022-09-27T01:23:51Z

module/align_DNA_BWA_MEM2.nf

@@ -3,7 +3,15 @@
 // here it actually saves cost, time, and memory to directly pipe the output into 
 // samtools due to the large size of the uncompressed SAM files.
 include { run_sort_SAMtools ; run_merge_SAMtools } from './samtools.nf'
-include { run_validate_PipeVal; run_validate_PipeVal as validate_output_file } from './validation.nf'
+
+// need to rename run_validate_PipeVal since using twice.  Use run_validate_PipeVal for input validation; validate_output_file for output validation


Suggested change

// need to rename run_validate_PipeVal since using twice. Use run_validate_PipeVal for input validation; validate_output_file for output validation

// Use run_validate_PipeVal for input validation; validate_output_file for output validation

The first part of the comment is unnecessary for the actual pipeline I think

yashpatel6 · 2022-09-27T01:25:06Z

module/align_DNA_BWA_MEM2.nf

@@ -80,16 +88,20 @@ workflow align_DNA_BWA_MEM2_workflow {
      ich_reference_fasta
      ich_reference_index_files
   main:
-      run_validate_PipeVal(ich_samples_validate.mix(
+
+      run_validate_PipeVal_inputs = ich_samples_validate.mix( //


Suggested change

run_validate_PipeVal_inputs = ich_samples_validate.mix( //

run_validate_PipeVal_inputs = ich_samples_validate.mix(

Empty comment

yashpatel6 · 2022-09-27T01:26:36Z

module/align_DNA_BWA_MEM2.nf

@@ -80,16 +88,20 @@ workflow align_DNA_BWA_MEM2_workflow {
      ich_reference_fasta
      ich_reference_index_files
   main:
-      run_validate_PipeVal(ich_samples_validate.mix(
+
+      run_validate_PipeVal_inputs = ich_samples_validate.mix( //


Also, generally for input channels, we want to use input_ch_*

yashpatel6 · 2022-09-27T01:28:45Z

module/align_DNA_HISAT2.nf

@@ -4,7 +4,7 @@
 // samtools due to the large size of the uncompressed SAM files.

 include { run_sort_SAMtools ; run_merge_SAMtools} from './samtools.nf'
-include { run_validate_PipeVal; run_validate_PipeVal as validate_output_file } from './validation.nf'
+include { run_validate_PipeVal; run_validate_PipeVal as validate_output_file } from '../external/nextflow-modules/modules/PipeVal/validate/main.nf'


Does the workflow for HISAT2 not require updates like the ones with BWA-MEM2?

The HISAT2 workflow needs to get the same updates. However, I cannot get PipeVal to work in the BWA-MEM2 workflow (see previous comments), so I am waiting to update HISAT2.

I don't understand what PipeVal is doing on the current main branch (ignoring changes from this PR), and I think there might be some issues. For example, here is A-mini-n1 testing output that uses the main branch (so no changes to PipeVal code):

/hot/software/pipeline/pipeline-align-DNA/Nextflow/development/unreleased/jarbet-filename-standardized/align-DNA-8.1.0/a_mini_n1_standardized

BWA-MEM2:

cat input_validation.txt Input: genome.fa is valid file-fasta Input: HG002.N-n1_R1.fq.gz is valid file-unknown Input: genome.fa.bwt.2bit.64 is valid file-unknown Input: genome.fa.0123 is valid file-unknown Input: genome.fa.fai is valid file-unknown Input: genome.fa.ann is valid file-unknown Input: genome.fa.amb is valid file-unknown Input: HG002.N-n1_R2.fq.gz is valid file-unknown Input: genome.fa.pac is valid file-unknown

cat output_validation.txt Input: BWA-MEM2-2.2.1_000000_a-mini-n1-standardized.bam is valid file-unknown Input: BWA-MEM2-2.2.1_000000_a-mini-n1-standardized.bam.bai is valid file-unknown Input: jarbet-filename-standardized is valid file-unknown Input: scratch is valid file-unknown

HISAT2:

cat input_validation.txt Input: Homo_sapiens_assembly38.7.ht2 is valid file-unknown Input: Homo_sapiens_assembly38.5.ht2 is valid file-unknown Input: Homo_sapiens_assembly38.2.ht2 is valid file-unknown Input: Homo_sapiens_assembly38.6.ht2 is valid file-unknown Input: HG002.N-n1_R2.fq.gz is valid file-unknown Input: Homo_sapiens_assembly38.1.ht2 is valid file-unknown Input: Homo_sapiens_assembly38.fasta is valid file-fasta Input: Homo_sapiens_assembly38.8.ht2 is valid file-unknown Input: Homo_sapiens_assembly38.3.ht2 is valid file-unknown Input: HG002.N-n1_R1.fq.gz is valid file-unknown Input: Homo_sapiens_assembly38.4.ht2 is valid file-unknown

cat output_validation.txt Input: HISAT2-2.2.1_000000_a-mini-n1-standardized.bam.bai is valid file-unknown Input: scratch is valid file-unknown Input: HISAT2-2.2.1_000000_a-mini-n1-standardized.bam is valid file-unknown Input: jarbet-filename-standardized is valid file-unknown

Nearly all files are valid file-unknown and it looks like the github branch name, as well as scratch are also passed to PipeVal in output_validation.txt? Does this output look correct to you?

Most of the files are file-unknown because they don't have an expected file extension, which is fine. Also, the main branch uses v2.1.5 of pipeval, which had issues detecting multiple extensions like fq.gz so those also got marked as file-unknown.

Align-DNA also tries to validate the work_dir and output_dir but it looks like they tried to validate them as file-input even though they're directories, leading to that statement. So with v3.0.0, these two would need to be validated as directories rather than as files.

We may need to wait for pipeval to get updated before we can proceed with this PR.

yashpatel6 · 2023-05-15T19:59:55Z

Closing this PR as it's old and will be handled in a different PR

Jaron Arbet added 7 commits August 31, 2022 11:23

attempt switching to common validate module

aba8443

external filepath

d677182

dont remove docker_image_validate_params

d5bcc29

validate v2.1.6

ea041df

validate_output_file should only take 1 input

75529bb

dont rename run_validate_PipeVal

e4677fd

run_validate_PipeVal.out.validation_result

73f9547

tyamaguchi-ucla reviewed Aug 31, 2022

View reviewed changes

Jaron Arbet added 3 commits August 31, 2022 15:15

pipeval v 3.0.0

26a09f4

cant call run-validate_PipeVal twice, need to rename

41b0380

cant call run_validate_PipeVal twice, need to rename

6e155a8

jarbet requested review from aybeshlikyan and yashpatel6 August 31, 2022 22:40

Jaron Arbet added 2 commits September 2, 2022 14:24

docker validate params v 3.0.0

6ffaa50

docker_image_validate_params: replace validate with pipeval

920b132

format

b0ae698

jarbet mentioned this pull request Sep 14, 2022

Make input type optional uclahs-cds/package-PipeVal#52

Merged

11 tasks

Jaron Arbet added 2 commits September 20, 2022 14:54

setup run_validate_PipeVal input to be tuple cardinality 2

34cf06a

setup validate_output_file process inputs to be tuple cardinality 2

27f641a

jarbet changed the title ~~Replace docker validate with pipeline-Nextflow-module validate~~ update how PipeVal is being used to validate input and output files Sep 20, 2022

jarbet marked this pull request as ready for review September 26, 2022 21:38

jarbet requested a review from a team as a code owner September 26, 2022 21:38

yashpatel6 reviewed Sep 27, 2022

View reviewed changes

yashpatel6 closed this May 15, 2023

yashpatel6 deleted the jarbet-validate branch March 30, 2024 00:25

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update how PipeVal is being used to validate input and output files #240

update how PipeVal is being used to validate input and output files #240

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yashpatel6 commented May 15, 2023

	docker_image_validate_params = "blcdsdockerregistry/pipeval:3.0.0"
	docker_image_validate_params = "blcdsdockerregistry/pipeval:${pipeval_version}"

	// need to rename run_validate_PipeVal since using twice. Use run_validate_PipeVal for input validation; validate_output_file for output validation
	// Use run_validate_PipeVal for input validation; validate_output_file for output validation

	run_validate_PipeVal_inputs = ich_samples_validate.mix( //
	run_validate_PipeVal_inputs = ich_samples_validate.mix(

update how PipeVal is being used to validate input and output files #240

update how PipeVal is being used to validate input and output files #240

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Description

Closes #239

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