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Prototype implementation for new Nextflow native DSL2 syntax on nf-core #701

Merged
merged 16 commits into from
Oct 29, 2021
Merged

Prototype implementation for new Nextflow native DSL2 syntax on nf-core #701

merged 16 commits into from
Oct 29, 2021

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mahesh-panchal
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@mahesh-panchal mahesh-panchal commented Sep 27, 2021 •
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Suggestion

Swap from the current method of publishing to the using publishDir directly in configs.

Benefits:

  • Separate configuration from workflow.
  • Configuration is in one file. Currently it's in at least three places ( module/main.nf, within workflow itself, and from the modules.config).
  • Using process selectors allows better identification of which configuration goes to which process. It's difficult to trace options in large workflows, and has the potential for error during the propagation via options.
  • Process selectors can be more generalized to a group of methods than the current method
  • labels can also be supported.

Additionally, use the process.ext directive to pass custom tool parameters and suffixes to processes.
Code snippet also added to allow this to be updated via params. e.g., --process.FASTQC.args '--quiet'.

Also suggest removing functions.nf in every module and either replacing with

include { getProcessName, getSoftwareName } from "$projectDir/lib/functions.nf"

Or removing entirely.
getSoftwareName seems to be only really needed for the default publishing directory, and getProcessName could be included at the bottom of a module main.nf as it's such as a small function.

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
    • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
    • If necessary, also make a PR on the nf-core/rnaseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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Tested with:

nextflow run -profile test,uppmax main.nf --outdir '/proj/snic2018-8-34/rnaseq-test' --project 'snic2018-8-34'

Directory tree is exactly the same as nextflow run -profile test,uppmax nf-core/rnaseq --outdir '/proj/snic2018-8-34/rnaseq-nf-core-test' --project 'snic2018-8-34'

Major changes to remember/check for rebasing:

  • Move inclusion of modules until after institute configs are loaded.
  • Update test.config with new way of passing tools args.
  • module.config updated to use process selectors and not pass using params.
  • Remove all configuration setting and passing in rnaseq.nf workflow and subworkflows too (addParams not needed in most cases)
  • Remove options and publishDir from all module files.
  • All modules should check if task.ext.args is initialized.
  • Will need to change saveAs: case to check for versions.yml instead of *versions.txt.

Additional suggestion.

  • Can move functions.nf to libs folder and all modules then load file from "$projectDir/libs/functions.nf". Only getProcessName and getSoftwareName functions needed. Technically getSoftwareName only really needed for generic case.

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Ready for review.

@drpatelh
Merge pull request #707 from nf-core/dev
964425e 
Dev -> Master for 3.4 release
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Updates from 3.4 incorporated.
nextflow run -profile test,uppmax rnaseq/main.nf --outdir '/proj/snic2018-8-34/rnaseq-nf-core-test' --project 'snic2018-8-34' on branch use_publishDir produces the same output as
nextflow run -profile test,uppmax nf-core/rnaseq --outdir '/proj/snic2018-8-34/rnaseq-nf-core-test' --project 'snic2018-8-34'

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github-actions bot commented Oct 8, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0ad0307

+| ✅ 129 tests passed       |+
#| ❔   8 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version mentioned in Quick Start section.

❔ Tests ignored:

  • files_exist - File is ignored: bin/scrape_software_versions.py
  • files_exist - File is ignored: modules/local/get_software_versions.nf
  • files_unchanged - File ignored due to lint config: .markdownlint.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File does not exist: bin/scrape_software_versions.py
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: assets/multiqc_config.yaml

✅ Tests passed:

Run details

  • nf-core/tools version 2.1
  • Run at 2021-10-18 18:11:13

@grst grst self-requested a review October 8, 2021 14:29
@heuermh heuermh self-requested a review October 8, 2021 14:43
@mahesh-panchal mahesh-panchal marked this pull request as ready for review October 8, 2021 17:43
drpatelh
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drpatelh commented Oct 10, 2021 •
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WARN: There's no process matching config selector: NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK
WARN: There's no process matching config selector: .*:PREPARE_GENOME:BBMAP_BBSPLIT
WARN: There's no process matching config selector: .*:QUANTIFY_RSEM:RSEM_CALCULATEEXPRESSION
WARN: There's no process matching config selector: .*:QUANTIFY_RSEM:RSEM_MERGE_COUNTS
WARN: There's no process matching config selector: NFCORE_RNASEQ:RNASEQ:.*:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT
<TRUNCATED>

Mannn all of these WARN messages have started to prop up now with the new syntax 🤦🏽

Related to nextflow-io/nextflow#2072

drpatelh
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Having now looked at it properly. This really looks awesome @mahesh-panchal 🤩 Let's wait for some more opinions. Maybe we can get this PR as it is into a separate branch on this repo? Seeing the diff with stuff commented out may be useful for others that want to switch.

Once this PR is in then we can systematically strip out all of the comments and tidy stuff up to get it release ready. I don't see any limitations at the moment providing we have ticked all of the boxes with the older implementation in terms of publishing files and passing options around. You also mentioned that the tree looks the same before and after so that suggests we are on the right track.

Lemme know what you think. I am feeling optimistic that we may even be able to start the proess of converting modules/pipelines to this format during the Hackathon.

grst
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@mahesh-panchal, you're a genius!

This addresses most of the points I raised in nf-core/tools#1163.

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Awesome @mahesh-panchal ! 😍
I really think this PR fits perfectly Nextflow philosophy of keeping separated configuration from the workflow code which is one of the reasons that makes Nextflow so powerful. I agree that we should move to this new implementation 🚀

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Lemme know what you think. I am feeling optimistic that we may even be able to start the process of converting modules/pipelines to this format during the Hackathon.

The only thing left we need to decide is whether to use the getProcessName and getSoftwareName in the modules code now I think

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@mahesh-panchal are we able to dump the more "controversial" aspects of this implementation that have been raised here somewhere so we can maybe have more focussed discussions around those? e.g. this, this, this etc.

A TODO list of things we need to get sorted to implement it would be useful too (e.g. updating nf-core/modules, module template, pipeline template, lib/, linter etc). We can update this collectively as we go along. I am trying to assess whether it is something we can get done before the Hackathon (but in any case I think it would be useful either way I think).

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I got an idea that we can keep passing opts using params too if we like:

main.nf:

nextflow.enable.dsl = 2

workflow {

    FOO(params.name)
}

process FOO {

    input:
    val name

    script:
    def message = task.ext.message ?: 'Hello'
    """
    echo $message $name
    """
}

nextflow.config:

params.name = 'J.A.R.V.I.S'
params.process = [:]

process.echo = true
process.'withName:FOO'.ext.message = 'Welcome'

if ( params.process ){
    params.process.each { selector ->
        process."withName:${selector.key}".ext.message = selector.value.message
    }
}

Example:

nextflow run main.nf --process.FOO.message 'Good day'

output:

N E X T F L O W  ~  version 21.04.0
Launching `main.nf` [big_poisson] - revision: ecbd9202f8
executor >  local (1)
[c0/ad0122] process > FOO [100%] 1 of 1 ✔
Good day J.A.R.V.I.S

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Can someone check the json schema please for the params.process. Is the type correct ?

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mahesh-panchal commented Oct 18, 2021
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New bug. Not sure if it's my fault in configuration.

Error executing process > 'NFCORE_RNASEQ:RNASEQ:BBMAP_BBSPLIT (1)'

Caused by:
  Process `NFCORE_RNASEQ:RNASEQ:BBMAP_BBSPLIT (1)` terminated with an error exit status (1)

Command executed:

  bbsplit.sh \
      -Xmx6g \
      path=bbsplit \
      threads=2 \
      in=RAP1_IAA_30M_REP1_1_val_1.fq.gz in2=RAP1_IAA_30M_REP1_2_val_2.fq.gz \
      basename=RAP1_IAA_30M_REP1_%_#.fastq.gz \
      refstats=RAP1_IAA_30M_REP1.stats.txt \
      build=1 ambiguous2=all maxindel=150000
  
  cat <<-END_VERSIONS > versions.yml
  BBMAP_BBSPLIT:
      bbmap: $(bbversion.sh 2>&1)
  END_VERSIONS

Command exit status:
  1
Command output:
  (empty)

Command error:
  java -ea -Xmx6g -Xms6g -cp /usr/local/opt/bbmap-38.93-0/current/ align2.BBSplitter ow=t fastareadlen=500 minhits=1 minratio=0.56 maxindel=20 qtrim=rl untrim=t trimq=6 -Xmx6g path=bbsplit threads=2 in=RAP1_IAA_30M_REP1_1_val_1.fq.gz in2=RAP1_IAA_30M_REP1_2_val_2.fq.gz basename=RAP1_IAA_30M_REP1_%_#.fastq.gz refstats=RAP1_IAA_30M_REP1.stats.txt build=1 ambiguous2=all maxindel=150000
  Executing align2.BBSplitter [ow=t, fastareadlen=500, minhits=1, minratio=0.56, maxindel=20, qtrim=rl, untrim=t, trimq=6, -Xmx6g, path=bbsplit, threads=2, in=RAP1_IAA_30M_REP1_1_val_1.fq.gz, in2=RAP1_IAA_30M_REP1_2_val_2.fq.gz, basename=RAP1_IAA_30M_REP1_%_#.fastq.gz, refstats=RAP1_IAA_30M_REP1.stats.txt, build=1, ambiguous2=all, maxindel=150000]
  
  Merged reference file bbsplit/ref/genome/1/merged_ref_8374379829187813017.fa.gz already exists; skipping merge.
  Ref merge time:       0.191 seconds.
  Executing align2.BBMap [ow=t, fastareadlen=500, minhits=1, minratio=0.56, maxindel=20, qtrim=rl, untrim=t, trimq=6, threads=2, in=RAP1_IAA_30M_REP1_1_val_1.fq.gz, in2=RAP1_IAA_30M_REP1_2_val_2.fq.gz, refstats=RAP1_IAA_30M_REP1.stats.txt, build=1, ambiguous2=all, maxindel=150000, ref=bbsplit/ref/genome/1/merged_ref_8374379829187813017.fa.gz, out_primary=RAP1_IAA_30M_REP1_primary_#.fastq.gz, out_sarscov2=RAP1_IAA_30M_REP1_sarscov2_#.fastq.gz, out_human=RAP1_IAA_30M_REP1_human_#.fastq.gz]
  Version 38.93
  
  Set MINIMUM_ALIGNMENT_SCORE_RATIO to 0.560
  Set threads to 2
  Reference set statistics will be written to RAP1_IAA_30M_REP1.stats.txt
  Retaining first best site only for ambiguous mappings.
  NOTE: Ignoring reference file because it already appears to have been processed.
  NOTE: If you wish to regenerate the index, please manually delete bbsplit/ref/genome/1/summary.txt
  Set genome to 1
  
  Loaded Reference:     0.126 seconds.
  Loading index for chunk 1-1, build 1
  Exception in thread "Thread-0" java.lang.RuntimeException: java.util.zip.ZipException: too many length or distance symbols
        at fileIO.ReadWrite.readObject(ReadWrite.java:823)
        at fileIO.ReadWrite.read(ReadWrite.java:1282)
        at align2.Block.read(Block.java:132)
        at align2.IndexMaker4$BlockMaker.makeArrays(IndexMaker4.java:140)
        at align2.IndexMaker4$BlockMaker.run(IndexMaker4.java:128)
  Caused by: java.util.zip.ZipException: too many length or distance symbols
        at java.base/java.util.zip.InflaterInputStream.read(InflaterInputStream.java:165)
        at java.base/java.util.zip.GZIPInputStream.read(GZIPInputStream.java:118)
        at java.base/java.io.ObjectInputStream$PeekInputStream.read(ObjectInputStream.java:2854)
        at java.base/java.io.ObjectInputStream$PeekInputStream.readFully(ObjectInputStream.java:2870)
        at java.base/java.io.ObjectInputStream$BlockDataInputStream.readInts(ObjectInputStream.java:3523)
        at java.base/java.io.ObjectInputStream.readArray(ObjectInputStream.java:2081)
        at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1667)
        at java.base/java.io.ObjectInputStream.readObject(ObjectInputStream.java:493)
        at java.base/java.io.ObjectInputStream.readObject(ObjectInputStream.java:451)
        at fileIO.ReadWrite.readObject(ReadWrite.java:819)
        ... 4 more
  Generated Index:      0.642 seconds.
  Exception in thread "main" java.lang.NullPointerException
        at align2.BBIndex.analyzeIndex(BBIndex.java:115)
        at align2.BBMap.loadIndex(BBMap.java:420)
        at align2.BBMap.main(BBMap.java:32)
        at align2.BBSplitter.main(BBSplitter.java:48)

Run with:

#! /usr/bin/env nextflow

NXF_VER=21.10.0-SNAPSHOT \
nextflow run rnaseq/main.nf \
    --outdir "$PWD/pubdir_results" \
    --project 'snic2018-8-34' \
    -profile test,uppmax \
    -resume \
    -w "$PWD/work"

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mahesh-panchal commented Oct 28, 2021 •
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Test profile still throws these warnings with the fix in 21.10.0-SNAPSHOT

WARN: There's no process matching config selector: .*:QUANTIFY_RSEM:RSEM_CALCULATEEXPRESSION
WARN: There's no process matching config selector: .*:QUANTIFY_RSEM:RSEM_MERGE_COUNTS
WARN: There's no process matching config selector: .*:QUANTIFY_STAR_SALMON:SALMON_MERGE_COUNTS
WARN: There's no process matching config selector: .*:QUANTIFY_SALMON:SALMON_MERGE_COUNTS
WARN: There's no process matching config selector: NFCORE_RNASEQ:RNASEQ:SAMTOOLS_SORT
WARN: There's no process matching config selector: .*:FASTQC_UMITOOLS_TRIMGALORE:UMITOOLS_EXTRACT
WARN: There's no process matching config selector: .*:ALIGN_HISAT2:HISAT2_ALIGN
WARN: There's no process matching config selector: NFCORE_RNASEQ:RNASEQ:BAM_SORT_SAMTOOLS:SAMTOOLS_SORT
WARN: There's no process matching config selector: NFCORE_RNASEQ:RNASEQ:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX
WARN: There's no process matching config selector: NFCORE_RNASEQ:RNASEQ:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:.*
WARN: There's no process matching config selector: .*:DEDUP_UMI_UMITOOLS_GENOME:UMITOOLS_DEDUP
WARN: There's no process matching config selector: .*:DEDUP_UMI_UMITOOLS_GENOME:SAMTOOLS_INDEX
WARN: There's no process matching config selector: .*:DEDUP_UMI_UMITOOLS_GENOME:BAM_STATS_SAMTOOLS:.*
WARN: There's no process matching config selector: .*:DEDUP_UMI_UMITOOLS_TRANSCRIPTOME:UMITOOLS_DEDUP
WARN: There's no process matching config selector: .*:DEDUP_UMI_UMITOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX
WARN: There's no process matching config selector: .*:DEDUP_UMI_UMITOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:.*

These process are not run in the test profile, but there is configuration for them.

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What if we use conditional process selectors? 🤔 Is that even possible in a config file? So for example, withName for certain processes are only used if a particular params is set. I realise the code below won't work but something along those lines?

if (params.aligner == 'star_rsem') {
    withName: ......

}

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Yes. That's possible. That's effectively how we're allowing args from the command line:

if ( params.process ){
    params.process.each { selector ->
        selector.value.each { extension ->
            process."withName:${selector.key}".ext."${extension.key}" = selector.value."${extension.key}"
        }
    }
}

I need to take a closer look at the code to see what conditionals are needed though.

@drpatelh drpatelh changed the base branch from dev to dsl2 October 29, 2021 07:39
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Absolutely fantastic effort @mahesh-panchal ! 👏🏽

@drpatelh drpatelh merged commit 0ecc9a1 into nf-core:dsl2 Oct 29, 2021
@drpatelh drpatelh changed the title Proposal: Use publishDir from config instead of current method Prototype implementation for new Nextflow native DSL2 syntax on nf-core Oct 29, 2021
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New bug. Not sure if it's my fault in configuration.

Error executing process > 'NFCORE_RNASEQ:RNASEQ:BBMAP_BBSPLIT (1)'

Caused by:
  Process `NFCORE_RNASEQ:RNASEQ:BBMAP_BBSPLIT (1)` terminated with an error exit status (1)

Command executed:

  bbsplit.sh \
      -Xmx6g \
      path=bbsplit \
      threads=2 \
      in=RAP1_IAA_30M_REP1_1_val_1.fq.gz in2=RAP1_IAA_30M_REP1_2_val_2.fq.gz \
      basename=RAP1_IAA_30M_REP1_%_#.fastq.gz \
      refstats=RAP1_IAA_30M_REP1.stats.txt \
      build=1 ambiguous2=all maxindel=150000
  
  cat <<-END_VERSIONS > versions.yml
  BBMAP_BBSPLIT:
      bbmap: $(bbversion.sh 2>&1)
  END_VERSIONS

Command exit status:
  1
Command output:
  (empty)

Command error:
  java -ea -Xmx6g -Xms6g -cp /usr/local/opt/bbmap-38.93-0/current/ align2.BBSplitter ow=t fastareadlen=500 minhits=1 minratio=0.56 maxindel=20 qtrim=rl untrim=t trimq=6 -Xmx6g path=bbsplit threads=2 in=RAP1_IAA_30M_REP1_1_val_1.fq.gz in2=RAP1_IAA_30M_REP1_2_val_2.fq.gz basename=RAP1_IAA_30M_REP1_%_#.fastq.gz refstats=RAP1_IAA_30M_REP1.stats.txt build=1 ambiguous2=all maxindel=150000
  Executing align2.BBSplitter [ow=t, fastareadlen=500, minhits=1, minratio=0.56, maxindel=20, qtrim=rl, untrim=t, trimq=6, -Xmx6g, path=bbsplit, threads=2, in=RAP1_IAA_30M_REP1_1_val_1.fq.gz, in2=RAP1_IAA_30M_REP1_2_val_2.fq.gz, basename=RAP1_IAA_30M_REP1_%_#.fastq.gz, refstats=RAP1_IAA_30M_REP1.stats.txt, build=1, ambiguous2=all, maxindel=150000]
  
  Merged reference file bbsplit/ref/genome/1/merged_ref_8374379829187813017.fa.gz already exists; skipping merge.
  Ref merge time:       0.191 seconds.
  Executing align2.BBMap [ow=t, fastareadlen=500, minhits=1, minratio=0.56, maxindel=20, qtrim=rl, untrim=t, trimq=6, threads=2, in=RAP1_IAA_30M_REP1_1_val_1.fq.gz, in2=RAP1_IAA_30M_REP1_2_val_2.fq.gz, refstats=RAP1_IAA_30M_REP1.stats.txt, build=1, ambiguous2=all, maxindel=150000, ref=bbsplit/ref/genome/1/merged_ref_8374379829187813017.fa.gz, out_primary=RAP1_IAA_30M_REP1_primary_#.fastq.gz, out_sarscov2=RAP1_IAA_30M_REP1_sarscov2_#.fastq.gz, out_human=RAP1_IAA_30M_REP1_human_#.fastq.gz]
  Version 38.93
  
  Set MINIMUM_ALIGNMENT_SCORE_RATIO to 0.560
  Set threads to 2
  Reference set statistics will be written to RAP1_IAA_30M_REP1.stats.txt
  Retaining first best site only for ambiguous mappings.
  NOTE: Ignoring reference file because it already appears to have been processed.
  NOTE: If you wish to regenerate the index, please manually delete bbsplit/ref/genome/1/summary.txt
  Set genome to 1
  
  Loaded Reference:     0.126 seconds.
  Loading index for chunk 1-1, build 1
  Exception in thread "Thread-0" java.lang.RuntimeException: java.util.zip.ZipException: too many length or distance symbols
        at fileIO.ReadWrite.readObject(ReadWrite.java:823)
        at fileIO.ReadWrite.read(ReadWrite.java:1282)
        at align2.Block.read(Block.java:132)
        at align2.IndexMaker4$BlockMaker.makeArrays(IndexMaker4.java:140)
        at align2.IndexMaker4$BlockMaker.run(IndexMaker4.java:128)
  Caused by: java.util.zip.ZipException: too many length or distance symbols
        at java.base/java.util.zip.InflaterInputStream.read(InflaterInputStream.java:165)
        at java.base/java.util.zip.GZIPInputStream.read(GZIPInputStream.java:118)
        at java.base/java.io.ObjectInputStream$PeekInputStream.read(ObjectInputStream.java:2854)
        at java.base/java.io.ObjectInputStream$PeekInputStream.readFully(ObjectInputStream.java:2870)
        at java.base/java.io.ObjectInputStream$BlockDataInputStream.readInts(ObjectInputStream.java:3523)
        at java.base/java.io.ObjectInputStream.readArray(ObjectInputStream.java:2081)
        at java.base/java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1667)
        at java.base/java.io.ObjectInputStream.readObject(ObjectInputStream.java:493)
        at java.base/java.io.ObjectInputStream.readObject(ObjectInputStream.java:451)
        at fileIO.ReadWrite.readObject(ReadWrite.java:819)
        ... 4 more
  Generated Index:      0.642 seconds.
  Exception in thread "main" java.lang.NullPointerException
        at align2.BBIndex.analyzeIndex(BBIndex.java:115)
        at align2.BBMap.loadIndex(BBMap.java:420)
        at align2.BBMap.main(BBMap.java:32)
        at align2.BBSplitter.main(BBSplitter.java:48)

Run with:

#! /usr/bin/env nextflow

NXF_VER=21.10.0-SNAPSHOT \
nextflow run rnaseq/main.nf \
    --outdir "$PWD/pubdir_results" \
    --project 'snic2018-8-34' \
    -profile test,uppmax \
    -resume \
    -w "$PWD/work"

Looks like this may have been a one-off fluke. I haven't been able to reproduce.

@drpatelh drpatelh mentioned this pull request Oct 29, 2021
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@grst grst mentioned this pull request Nov 11, 2021
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@JoseEspinosa JoseEspinosa mentioned this pull request Nov 22, 2021
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@alnfedorov alnfedorov mentioned this pull request Jan 20, 2022
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@mahesh-panchal mahesh-panchal mentioned this pull request Apr 25, 2024
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@heuermh heuermh Awaiting requested review from heuermh

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@mahesh-panchal @drpatelh @JoseEspinosa @grst