New tool: biobambam/bamsormadup #1478

matthdsm · 2022-04-01T13:13:55Z

Add biobambam/bamsormadup
fixes #1479

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 module conventions in the contribution docs
If necessary, include test data in your PR.
Remove all TODO statements.
Emit the versions.yml file.
Follow the naming conventions.
Follow the parameters requirements.
Follow the input/output options guidelines.
Add a resource label
Use BioConda and BioContainers if possible to fulfil software requirements.
Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
- PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
- PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
- PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

matthdsm · 2022-04-01T14:21:08Z

I'm trying to run the tests locally, but keep running into errors with both docker and conda.
AFAIK everything should be ok, but I suppose I'm still missing something.

Some help would be much appreciated
M

edmundmiller · 2022-04-01T16:06:49Z

I ran it with manually with conda and got the error:
PROFILE=conda nextflow run tests/modules/biobambam/bamsormadup -entry test_biobambam_bamsormadup -c tests/config/nextflow.config

Command error:
  libmaus2::bambam::parallel::GenericInputControlReadWorkPackageDispatcher: Invalid empty stream is invalid bgzf/BAM

  /usr/local/bin/../lib/./libmaus2_stacktrace.so.2(libmaus2::stacktrace::StackTrace::StackTrace()+0x67)[0x7f4181dcce37]
  /usr/local/bin/../lib/libmaus2_exception.so.2(libmaus2::exception::LibMausException::LibMausException()+0x2c)[0x7f418247ea7c]
  bamsormadup(+0x648a1)[0x555ad5f518a1]
  bamsormadup(+0x9a4a8)[0x555ad5f874a8]
  bamsormadup(+0x4a565)[0x555ad5f37565]                                                                      /usr/local/bin/../lib/libstdc++.so.6(+0xcc9d4)[0x7f41823579d4]
  /lib/x86_64-linux-gnu/libpthread.so.0(+0x7fa3)[0x7f41820a0fa3]
  /lib/x86_64-linux-gnu/libc.so.6(clone+0x3f)[0x7f4181fd14cf]

  libmaus2::bambam::parallel::GenericInputControlReadWorkPackageDispatcher: Invalid empty stream is invalid bgzf/BAM

  /usr/local/bin/../lib/./libmaus2_stacktrace.so.2(libmaus2::stacktrace::StackTrace::StackTrace()+0x67)[0x7f4181dcce37]
  /usr/local/bin/../lib/libmaus2_exception.so.2(libmaus2::exception::LibMausException::LibMausException()+0x2c)[0x7f418247ea7c]
  bamsormadup(+0x648a1)[0x555ad5f518a1]
  bamsormadup(+0x9a4a8)[0x555ad5f874a8]
  bamsormadup(+0x4a565)[0x555ad5f37565]
  /usr/local/bin/../lib/libstdc++.so.6(+0xcc9d4)[0x7f41823579d4]
  /lib/x86_64-linux-gnu/libpthread.so.0(+0x7fa3)[0x7f41820a0fa3]
  /lib/x86_64-linux-gnu/libc.so.6(clone+0x3f)[0x7f4181fd14cf]

jfy133

overall pretty good, just a few requests/suggestions

modules/biobambam/bamsormadup/main.nf

tests/modules/biobambam/bamsormadup/test.yml

Co-authored-by: James A. Fellows Yates <[email protected]>

matthdsm · 2022-04-04T07:45:18Z

Awesome, thanks for the review. I'll get to it right away!

jfy133

Oops something went funky in last review and missed a bunch of comments..

Also tests were failing previously

jfy133 · 2022-04-04T07:45:16Z

modules/biobambam/bamsormadup/main.nf

+ $args \\
+ I=$bam \\
+ O=${prefix}.bam \\
+ M=${prefix}.metrics.txt \\


Please remove metrics, file naming should be up to the pipeline developer ¹

Footnotes

https://nf-co.re/developers/modules#naming-conventions point 5 ↩

how would you suggest differentiating the filename? Or do you mean remove M=xxx and moving it to $args?

Just I mean just specify as {prefix}.txt, unless the tool can also produce other .txt files? Otherwise .txt should be enough to differentiate - and a pipeline developer can add metrics themselves if they want.

Allright, thanks. This is resolved than.

I see you reverted back to metrics, is that required by the tool in the end?

- add (optional) reference input - add bam index ouput - add cram output option - make metrics output: more general

matthdsm · 2022-04-04T09:01:28Z

Is there a common way to check the args for errors?
e.g. If the output is a cram file, and reference is not defined we should get an error.

Also, is there a way to set the output extension based on a (possibly undefined) arg (outputformat) in $args?

jfy133 · 2022-04-04T11:18:28Z

Is there a common way to check the args for errors? e.g. If the output is a cram file, and reference is not defined we should get an error.

Also, is there a way to set the output extension based on a (possibly undefined) arg (outputformat) in $args?

It's generally OK to add some checks in the script block with the other process variable definitions. You can see an example of an error check at the bottom of point 5 here: https://nf-co.re/developers/modules#naming-conventions.

and like wise for the variable extension, you are welcome to write a internal conditional variable to adust this

…files

matthdsm · 2022-04-04T11:44:25Z

Most comments are fixed! Now we just need to get the tests to work...

modules/biobambam/bamsormadup/main.nf

Co-authored-by: James A. Fellows Yates <[email protected]>

jfy133 · 2022-04-04T12:02:19Z

For the failng tests, have you tried running locally?

https://nf-co.re/developers/modules#running-tests-manually

matthdsm · 2022-04-04T12:10:29Z

Yeah, but I keep having some issues with the versions.yml file it seems:

 NF_CORE_MODULES_TEST=1 TMPDIR=~ PROFILE=docker pytest --tag biobambam/bamsormadup --symlink --keep-workflow-wd
============================================================= test session starts ==============================================================
platform darwin -- Python 3.10.4, pytest-7.1.1, pluggy-0.12.0
rootdir: /Users/matdsmet/Projects/nf-core-modules, configfile: pytest.ini
plugins: datafiles-2.0, workflow-1.6.0, cov-3.0.0
collecting ... 
collected 732 items                                                                                                                            

biobambam/bamsormadup test_biobambam_bamsormadup:
        command:   nextflow run tests/modules/biobambam/bamsormadup -entry test_biobambam_bamsormadup -c tests/config/nextflow.config
        directory: /Users/matdsmet/pytest_workflow_gqwmex1a/biobambam/bamsormadup_test_biobambam_bamsormadup
        stdout:    /Users/matdsmet/pytest_workflow_gqwmex1a/biobambam/bamsormadup_test_biobambam_bamsormadup/log.out
        stderr:    /Users/matdsmet/pytest_workflow_gqwmex1a/biobambam/bamsormadup_test_biobambam_bamsormadup/log.err
'biobambam/bamsormadup test_biobambam_bamsormadup' done.

tests/test_versions_yml.py sssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss [ 14%]
sssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssFssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss [ 33%]
ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss [ 52%]
ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss [ 70%]
ssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss [ 89%]
sssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssssss                                                              [ 99%]
tests/modules/biobambam/bamsormadup/test.yml FFFF                                                                                        [100%] Keeping temporary directories and logs. Use '--kwd' or '--keep-workflow-wd' to disable this behaviour.


=================================================================== FAILURES ===================================================================
_______________________________ test_ensure_valid_version_yml[biobambam/bamsormadup test_biobambam_bamsormadup] ________________________________

workflow_dir = PosixPath('/Users/matdsmet/pytest_workflow_gqwmex1a/biobambam/bamsormadup_test_biobambam_bamsormadup')

    @pytest.mark.workflow(*_get_workflow_names())
    def test_ensure_valid_version_yml(workflow_dir):
        workflow_dir = Path(workflow_dir)
        software_name = workflow_dir.name.split("_")[0].lower()
        try:
            versions_yml_file = workflow_dir / f"output/{software_name}/versions.yml"
>           versions_yml = versions_yml_file.read_text()

tests/test_versions_yml.py:31: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = PosixPath('/Users/matdsmet/pytest_workflow_gqwmex1a/biobambam/bamsormadup_test_biobambam_bamsormadup/output/bamsormadup/versions.yml')
encoding = 'locale', errors = None

    def read_text(self, encoding=None, errors=None):
        """
        Open the file in text mode, read it, and close the file.
        """
        encoding = io.text_encoding(encoding)
>       with self.open(mode='r', encoding=encoding, errors=errors) as f:

../../miniconda3/lib/python3.10/pathlib.py:1132: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = PosixPath('/Users/matdsmet/pytest_workflow_gqwmex1a/biobambam/bamsormadup_test_biobambam_bamsormadup/output/bamsormadup/versions.yml')
mode = 'r', buffering = -1, encoding = 'locale', errors = None, newline = None

    def open(self, mode='r', buffering=-1, encoding=None,
             errors=None, newline=None):
        """
        Open the file pointed by this path and return a file object, as
        the built-in open() function does.
        """
        if "b" not in mode:
            encoding = io.text_encoding(encoding)
>       return self._accessor.open(self, mode, buffering, encoding, errors,
                                   newline)
E       FileNotFoundError: [Errno 2] No such file or directory: '/Users/matdsmet/pytest_workflow_gqwmex1a/biobambam/bamsormadup_test_biobambam_bamsormadup/output/bamsormadup/versions.yml'

../../miniconda3/lib/python3.10/pathlib.py:1117: FileNotFoundError

During handling of the above exception, another exception occurred:

workflow_dir = PosixPath('/Users/matdsmet/pytest_workflow_gqwmex1a/biobambam/bamsormadup_test_biobambam_bamsormadup')

    @pytest.mark.workflow(*_get_workflow_names())
    def test_ensure_valid_version_yml(workflow_dir):
        workflow_dir = Path(workflow_dir)
        software_name = workflow_dir.name.split("_")[0].lower()
        try:
            versions_yml_file = workflow_dir / f"output/{software_name}/versions.yml"
            versions_yml = versions_yml_file.read_text()
        except FileNotFoundError:
>           raise AssertionError(
                dedent(
                    f"""\
                    `versions.yml` not found in the output directory.
                    Expected path: `{versions_yml_file}`
    
                    This can have multiple reasons:
                    * The test-workflow failed before a `versions.yml` could be generated.
                    * The workflow name in `test.yml` does not start with the tool name.
                    """
                )
            )
E           AssertionError: `versions.yml` not found in the output directory.
E           Expected path: `/Users/matdsmet/pytest_workflow_gqwmex1a/biobambam/bamsormadup_test_biobambam_bamsormadup/output/bamsormadup/versions.yml`
E           
E           This can have multiple reasons:
E           * The test-workflow failed before a `versions.yml` could be generated.
E           * The workflow name in `test.yml` does not start with the tool name.

tests/test_versions_yml.py:33: AssertionError
_________________________________________________________________ test session _________________________________________________________________
'/Users/matdsmet/pytest_workflow_gqwmex1a/biobambam/bamsormadup_test_biobambam_bamsormadup/output/biobambam/test.bam' does not exist while it should
_________________________________________________________________ test session _________________________________________________________________
'/Users/matdsmet/pytest_workflow_gqwmex1a/biobambam/bamsormadup_test_biobambam_bamsormadup/output/biobambam/test.metrics.txt' does not exist while it should
_________________________________________________________________ test session _________________________________________________________________
'/Users/matdsmet/pytest_workflow_gqwmex1a/biobambam/bamsormadup_test_biobambam_bamsormadup/output/biobambam/versions.yml' does not exist while it should
_________________________________________________________________ test session _________________________________________________________________
'biobambam/bamsormadup test_biobambam_bamsormadup' exited with exit code '1' instead of '0'.
=============================================================== warnings summary ===============================================================
../../miniconda3/lib/python3.10/site-packages/pytest_workflow/plugin.py:391
  /Users/matdsmet/miniconda3/lib/python3.10/site-packages/pytest_workflow/plugin.py:391: UserWarning: .git dir detected: /Users/matdsmet/Projects/nf-core-modules/.git. pytest-workflow will copy the entire .git directory and all files ignored by git. It is recommended to use the --git-aware option.
    warnings.warn(

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================================================== short test summary info ============================================================
FAILED tests/test_versions_yml.py::test_ensure_valid_version_yml[biobambam/bamsormadup test_biobambam_bamsormadup] - AssertionError: `version...
FAILED tests/modules/biobambam/bamsormadup/test.yml::biobambam/bamsormadup test_biobambam_bamsormadup::output/biobambam/test.bam::should exist
FAILED tests/modules/biobambam/bamsormadup/test.yml::biobambam/bamsormadup test_biobambam_bamsormadup::output/biobambam/test.metrics.txt::should exist
FAILED tests/modules/biobambam/bamsormadup/test.yml::biobambam/bamsormadup test_biobambam_bamsormadup::output/biobambam/versions.yml::should exist
FAILED tests/modules/biobambam/bamsormadup/test.yml::biobambam/bamsormadup test_biobambam_bamsormadup::exit code should be 0
================================================== 5 failed, 727 skipped, 1 warning in 11.81s ==================================================

jfy133 · 2022-04-04T12:17:48Z

Yeah, but I keep having some issues with the versions.yml file it seems:

This is an unfortunate misdirection , you need to check the actual working directory or the .nexflow.log of the test to see what the error is (I hate python traceback sometimes ;) ) . I suspect the process is failing too early so it doesn't generate the versions.yml and but for whatever reason that specific check is the one that makes the largest error...

matthdsm · 2022-04-04T12:24:09Z

Ok, looks like a syntax error, altough I'm not really sure what's wrong...

N E X T F L O W  ~  version 21.10.6
Launching `tests/modules/biobambam/bamsormadup/main.nf` [berserk_meucci] - revision: 1a1ee0d1f7
Module compilation error
- file : /Users/matdsmet/pytest_workflow_pfgis0rq/biobambam/bamsormadup_test_biobambam_bamsormadup/tests/modules/biobambam/bamsormadup/../../../../modules/biobambam/bamsormadup/main.nf
- cause: Unexpected input: '{' @ line 1, column 31.
   process BIOBAMBAM_BAMSORMADUP {
                                 ^

1 error

jfy133 · 2022-04-04T18:27:45Z

The other option is to pick other BAM files from the nf-core test/datasets and see if the ywork! There are quite a few now.

matthdsm · 2022-04-05T04:24:51Z

I've tried using params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], but still no luck. samtools view of the test data seems to yield a valid result, so it must be something inside the docker image

matthdsm · 2022-04-05T04:28:46Z

The issue must be somewhere in the module, because when I update biobambam/bammarkduplicates to the latest version (so same docker image), the tests do work.

matthdsm · 2022-04-05T04:30:49Z

Downgrading the version of biobambam/bamsormadup doesn't help either

…bammarkduplicates2

jfy133 · 2022-04-05T09:07:40Z

@matthdsm if you go into the work directory of the process (after a failing test), and try manually running bash .command.sh does it work for you? Can be on any of docker/singularity/conda

matthdsm · 2022-04-05T09:15:21Z

I can't run any of the commands locally, the conda recipe isn't built for ARM, so not available on my computer

jfy133 · 2022-04-05T09:27:34Z

Ah I see... will need to get more input else where, I thikn it best to post the problem on slack and get some other people to try too... I still can't get it to run. Just hangs...

matthdsm · 2022-04-05T09:28:45Z

Turns out I'm actually an idiot and got the command line all wrong 🤦🏻 fixing right now

matthdsm · 2022-04-05T09:33:07Z

So I added the bamcat command in front of bamsormadup, since bamsormadup takes it's input from stdin.
bamcat is part of the biobambam suite, so actually the same tool, which is why I could do this without issue.

matthdsm · 2022-04-05T09:36:42Z

bamcat can take multiple inputs, making this chain also suitable to merge several bam files while simultaneously sorting/markdup.

I'm still new to nextflow. How would I define multiple bam inputs? I imagine would then be able to do something like "-I ".join([bam1,bam2,...])

EDIT: nvm, figured it out! I think this is good to go!

jfy133

Couple of comments but looking pretty ready for me now!

modules/biobambam/bamsormadup/meta.yml

jfy133 · 2022-04-05T19:04:34Z

modules/biobambam/bamsormadup/main.nf

+ $args \\
+ I=$bam \\
+ O=${prefix}.bam \\
+ M=${prefix}.metrics.txt \\


I see you reverted back to metrics, is that required by the tool in the end?

tests/modules/biobambam/bamsormadup/test.yml

Co-authored-by: James A. Fellows Yates <[email protected]>

matthdsm · 2022-04-06T05:51:41Z

I see you reverted back to metrics, is that required by the tool in the end?

Not required, but I noticed some other tools used for marking duplicates (picard, bammarkduplicates2) use the same convention, so I decided to stick with it for the sake of continuity

matthdsm · 2022-04-06T05:52:21Z

Feel free to merge if everything looks ok to you!

jfy133 · 2022-04-06T06:18:19Z

I see you reverted back to metrics, is that required by the tool in the end?

Not required, but I noticed some other tools used for marking duplicates (picard, bammarkduplicates2) use the same convention, so I decided to stick with it for the sake of continuity

Oh really? they were early tools so maybe that was before the guidlines were confirmed...

Hm ok. Fair enough then!

matthdsm · 2022-04-06T06:19:45Z

Thanks for the help and review. Lots more to come!

matthdsm added 2 commits April 1, 2022 15:12

add bamsormadup

453a13c

fix yaml

7fc5834

matthdsm self-assigned this Apr 1, 2022

matthdsm mentioned this pull request Apr 1, 2022

new module: biobambam/bamsormadup #1479

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Update tests/modules/biobambam/bamsormadup/test.yml

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Co-authored-by: James A. Fellows Yates <[email protected]>

Merge branch 'master' into tool/bamsormadup

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matthdsm added 2 commits April 4, 2022 09:50

test meta.yaml: remove md5sums

1e3ee75

Tool bamsormadup:

4908f1e

- add (optional) reference input - add bam index ouput - add cram output option - make metrics output: more general

matthdsm added 3 commits April 4, 2022 11:01

Merge branch 'master' into tool/bamsormadup

4b1d7cb

fix input and output formats

6c338a1

update input file description

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matthdsm added 3 commits April 4, 2022 13:34

drop sam output, goes against nf-core regs; add input check for cram …

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…files

fix typo

b936a5d

Merge branch 'master' into tool/bamsormadup

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Update modules/biobambam/bamsormadup/main.nf

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Co-authored-by: James A. Fellows Yates <[email protected]>

Merge branch 'master' into tool/bamsormadup

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set fixed suffix for metrics file to keep it in line with picard and …

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…bammarkduplicates2

matthdsm added the help wanted Extra attention is needed label Apr 5, 2022

Merge branch 'master' into tool/bamsormadup

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fix command line

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matthdsm added 2 commits April 5, 2022 11:46

update test.yml

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add support for multiple input bams

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matthdsm and others added 3 commits April 6, 2022 07:47

Update modules/biobambam/bamsormadup/meta.yml

a788720

Co-authored-by: James A. Fellows Yates <[email protected]>

Update modules/biobambam/bamsormadup/meta.yml

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Co-authored-by: James A. Fellows Yates <[email protected]>

Update tests/modules/biobambam/bamsormadup/test.yml

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Co-authored-by: James A. Fellows Yates <[email protected]>

jfy133 merged commit dc95e67 into master Apr 6, 2022

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New tool: biobambam/bamsormadup #1478

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New tool: biobambam/bamsormadup #1478

New tool: biobambam/bamsormadup #1478

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