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Alexander Peltzer apeltzer Boehringer Ingelheim Biberach an der Riss, Germany apeltzer.github.io Large-scale & cloud computing in the life sciences, ML & @nf-core . My private account.

apeltzer/CircularMapper 6

A method to improve mappings on circular genomes, using the BWA mapper

apeltzer/DeDup 5

A merged read deduplication tool capable to perform merged read deduplication on single end data.

alexhbnr/mitoBench-ancientMT 3

Pipeline for processing (non-)published ancient mtDNA genomes for mitoBench

apeltzer/action-nextflow 2

WIP / NOT WORKING YET: GitHub action for setting up Nextflow https://www.nextflow.io/

apeltzer/116117bot 0

A proof of concept bot, checking impfterminservice.de for available COVID-19 vaccination appointments.

apeltzer/AdapterContaminator 0

Small tool to simulate AdapterContamination of NGS reads and evaluate the findings afterwards.

apeltzer/AdapterRemovalFixPrefix 0

Fixes adapter removal prefixes to make sure no clashing read names are in the output.

apeltzer/admixr 0

An R package for running ADMIXTOOLS analyses directly within R. See the project website at https://bodkan.net/admixr.

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Pull request review commentnf-core/bacass

Fixes #69 nanoplot error

 process NANOPLOT {      output:     tuple val(meta), path("*.html"), emit: html-    tuple val(meta), path("*.png") , emit: png

One could also make that one optional ...? with optional: true ?

drchriscole

comment created time in 2 days

PR closed nf-core/bacass

Bugfixes + template

PR checklist

  • [x] This comment contains a description of changes (with reason)
  • [x] CHANGELOG.md is updated
  • [x] If you've fixed a bug or added code that should be tested, add tests!
  • [ ] Documentation in docs is updated
  • [ ] If necessary, also make a PR on the nf-core/bacass branch on the nf-core/test-datasets repo
+362 -117

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apeltzer

pr closed time in 2 days

push eventnf-core/rnafusion

Annick Renevey

commit sha 79a1d3c6372329c3b7104cb71524685fed35c0e2

publish star index results

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Annick Renevey

commit sha af1d897c33951ca16426175e69cbc4291c5e436f

Exchange gtf with chr.gtf

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Annick Renevey

commit sha bc026fd6df83b1ced14245b7235a2803af4a0a0a

publish fusioncatcher results

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Annick Renevey

commit sha dc72942960a30f36c7cd46e865583c83d7be181b

Change starfusion container and give absolute path to prep_genome_lib.pl

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Annick Renevey

commit sha 4ba72f4991dfce2078cd42c152392fe653b45394

modify genome dir tree as only GRCh38

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Annick Renevey

commit sha db427fab876a2fd1bd7ff7d9009f0247c5001d1d

--fasta is not required with --build_references

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Annick Renevey

commit sha 0f1b9a7ba18dc95d3228d57782720d4eb3a6ec0e

only specify publish_dir in the modules main.nf for now

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Annick Renevey

commit sha 6c19f547212c3194417305428db93bee478d4dcb

add build_reference param to main

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Annick Renevey

commit sha 80b35869d468cedb95147fdf2b30fd7ea11057fc

add build_reference param to nextflow.config

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Annick Renevey

commit sha e41c9e43016632aa645006d69a3eda7932246df9

Change publish_dir to publishDir, remove function.nf module files and make modules dsl2 friendly

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Annick Renevey

commit sha a4a4e096e4bf168ddd27a3e33dac78ed2fc740e3

option.args -> args and ext.args in modules.config

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Annick Renevey

commit sha 47ea7e766925254111242d89aa46bbde4b71830c

comment out the rnasusion workflow for now

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Annick Renevey

commit sha 880312c1c6186e0dc381c3141b30ec57a7cf430e

Increase cpu and time for high processes and set starfusion download as high + changed output for fusioncatcher

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Annick Renevey

commit sha 33184a3c1dab016033b595b40e6658e9cc3de07a

changed time and cpus allocated to starfusion don download and modification to fusioncatcher output

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Annick Renevey

commit sha 14b241ea41d7d79caa498c5e986974dceb239933

Merge branch 'dsl2_reference_building' of https://github.com/rannick/rnafusion into dsl2_reference_building

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Annick Renevey

commit sha 624ec946aef60dc8b4787fbb5f71095b274ffd97

back to standard process_high + typo fix

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Annick Renevey

commit sha d506476d7ab32d318e963ec860153ddc76bdf73e

small fixes

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rannick

commit sha 3fc794294ec513a0f87cc90decb09254f8e605b9

Update fastqc module

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rannick

commit sha a7c3a7313c323a0d621db8751fadd61ab8eb3f42

Update nf-core modules and nextflow_schema.json to include all arguments

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rannick

commit sha 5bcdc4b2656a12b549354d06d236709774522062

fix files_unchanged

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PR merged nf-core/rnafusion

reference building

nf-core/rnafusion pull request

DSL2 related changes:

  • publish_dir to publishDir
  • $software version.txt to versions.yml
  • removing module files: functions.nf
  • options.args to ext.args/args
  • update of template files
  • update modules from nf-core

Non-DSL2 related changes

  • replace gtf file with chr.gtf: Please confirm if this change is ok for the whole pipeline
  • remove subdirectory with params.genome as only GRCh38 is supported (not necessary but helped me see the output more clearly, can be reversed)
  • modification of output parameters to make sure every important file is published
  • additional build_references flag to trigger the workflow to build references
  • container for starfusion is changed and the absolute path to prep_genome_lib.pl is given --fasta argument is not required when executing the workflow to build references
  • increase cpu + memory for process STARFUSION_DOWNLOAD
  • ci test done on stubs of reference building subprocesses ensembl and arriba
  • For the moment, the rnafusion workflow (to analyse data and not build the references) is removed as dependencies and links would have to be fixed in the rnafusion workflow for execution of the build references otherwise

I am still optimising the cpu/memory allocation of STARFUSION_DOWNLOAD but building references should run with these changes

PR checklist

  • [ ] This comment contains a description of changes (with reason)
  • [x] If you've fixed a bug or added code that should be tested, add tests!
  • [x] If necessary, also make a PR on the nf-core/rnafusion branch on the nf-core/test-datasets repo
  • [ ] Ensure the test suite passes (nextflow run . -profile test,docker).
  • [ ] Make sure your code lints (nf-core lint .).
  • [ ] Documentation in docs is updated
  • [ ] CHANGELOG.md is updated
  • [x] README.md is updated

Learn more about contributing: CONTRIBUTING.md

+518 -1818

2 comments

74 changed files

maxulysse

pr closed time in 2 days

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startedtwpayne/chezmoi

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pull request commentnf-core/rnafusion

Dsl2 reference building

So if you want to give 195 a try, ping me on slack and I can review once you resolved the conflicts etc pp

rannick

comment created time in 10 days

pull request commentnf-core/rnafusion

Dsl2 reference building

Hi @rannick !

Yes, would be nicest if we can merge #195 into dev for the first try and then adding your changes to the pipeline itself on top. That way we're in sync with the latest DSLv2 template from nf-core AND have your working referencebuilder code in 👍🏻 Future proof ✅

rannick

comment created time in 10 days

Pull request review commentnf-core/rnafusion

Dsl2 reference building

 ======================================================================================== */ -// Don't overwrite global params.modules, create a copy instead and use that within the main script.-def modules = params.modules.clone()--include { ENSEMBL_DOWNLOAD }                from '../modules/local/ensembl/main'                    addParams( options: modules['ensembl_download'] )-include { ARRIBA_DOWNLOAD }                 from '../modules/local/arriba/download/main'            addParams( options: modules['arriba_download'] )-include { STAR_GENOMEGENERATE }             from '../modules/local/star/genomegenerate/main'        addParams( options: modules['star_index'] )-include { ERICSCRIPT_DOWNLOAD }             from '../modules/local/ericscript/download/main'        addParams( options: modules['ericscript_download'] )-include { FUSIONCATCHER_DOWNLOAD }          from '../modules/local/fusioncatcher/download/main'     addParams( options: modules['fusioncatcher_download'] )-include { KALLISTO_INDEX as PIZZLY_INDEX }  from '../modules/nf-core/modules/kallisto/index/main'   addParams( options: modules['pizzly_download'] )-include { STARFUSION_DOWNLOAD }             from '../modules/local/starfusion/download/main'        addParams( options: modules['starfusion_download'] )+include { ENSEMBL_DOWNLOAD }                from '../modules/local/ensembl/main'+include { ARRIBA_DOWNLOAD }                 from '../modules/local/arriba/download/main'+include { STAR_GENOMEGENERATE }             from '../modules/local/star/genomegenerate/main'

Agreed! The ones that only this pipeline will use can stay and should stay local, but everything else could be taken from nf-core/modules no?

rannick

comment created time in 10 days

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Pull request review commentnf-core/rnafusion

Dsl2 reference building

 ======================================================================================== */ -// Don't overwrite global params.modules, create a copy instead and use that within the main script.-def modules = params.modules.clone()--include { ENSEMBL_DOWNLOAD }                from '../modules/local/ensembl/main'                    addParams( options: modules['ensembl_download'] )-include { ARRIBA_DOWNLOAD }                 from '../modules/local/arriba/download/main'            addParams( options: modules['arriba_download'] )-include { STAR_GENOMEGENERATE }             from '../modules/local/star/genomegenerate/main'        addParams( options: modules['star_index'] )-include { ERICSCRIPT_DOWNLOAD }             from '../modules/local/ericscript/download/main'        addParams( options: modules['ericscript_download'] )-include { FUSIONCATCHER_DOWNLOAD }          from '../modules/local/fusioncatcher/download/main'     addParams( options: modules['fusioncatcher_download'] )-include { KALLISTO_INDEX as PIZZLY_INDEX }  from '../modules/nf-core/modules/kallisto/index/main'   addParams( options: modules['pizzly_download'] )-include { STARFUSION_DOWNLOAD }             from '../modules/local/starfusion/download/main'        addParams( options: modules['starfusion_download'] )+include { ENSEMBL_DOWNLOAD }                from '../modules/local/ensembl/main'+include { ARRIBA_DOWNLOAD }                 from '../modules/local/arriba/download/main'+include { STAR_GENOMEGENERATE }             from '../modules/local/star/genomegenerate/main'

That one could be a nf-core module no?

rannick

comment created time in 10 days

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Pull request review commentnf-core/rnafusion

Dsl2 reference building

 class NfcoreSchema {             else {                 def param = ex_json['pointerToViolation'] - ~/^#\//                 def param_val = params_json[param].toString()-                log.error "* --${param}: ${ex_json['message']} (${param_val})"+                if (enums.containsKey(param)) {

Hmm, we should stick to the template files strictly for these as they will receive updates from time to time and making such changes potentially causes more trouble than it helps.

Would also be good to merge in the template first and then applying your other changes on top of it?

rannick

comment created time in 10 days

issue commentnf-core/scrnaseq

Test with kallisto fails

Should be fine in dev now 👍🏻 Please reopen if not

dangeles

comment created time in 10 days

issue closednf-core/scrnaseq

Test with kallisto fails

I used the dev branch of this nextflow pipeline and ran the following command:

nextflow run ../scrnaseq -profile awsbatch,test --awsregion us-east-1 --awsqueue nextflow-default --aligner kallisto -w 's3://egenesis-data-processed/dangeles/tmp'

However, I got the following error:

Error executing process > 'bustools_correct_sort (S10_L001_bus_output)'

Caused by:
  Process `bustools_correct_sort (S10_L001_bus_output)` terminated with an error exit status (137)

Command executed:

  bustools correct -w 10x_V3_barcode_whitelist -o S10_L001_bus_output/output.corrected.bus S10_L001_bus_output/output.bus
  mkdir -p tmp
  bustools sort -T tmp/ -t 2 -m 6G -o S10_L001_bus_output/output.corrected.sort.bus S10_L001_bus_output/output.corrected.bus

Command exit status:
  137

Command output:
  (empty)

Command error:
  Found 6794880 barcodes in the whitelist
  Processed 0 bus records
  In whitelist = 0
  Corrected = 0
  Uncorrected = 0
  .command.sh: line 4:   520 Killed                  bustools sort -T tmp/ -t 2 -m 6G -o S10_L001_bus_output/output.corrected.sort.bus S10_L001_bus_output/output.corrected.bus

Work dir:
  s3://egenesis-data-processed/dangeles/tmp/c1/e3c21a3a97279df7ec1e6327202896

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

I also ran this using conda, with the same results.

Any help would be appreciated. I am having other issues with bustools_correct_sort, but it seems worthwhile to fix the test first and go from there.

Thank you very much!!!

closed time in 10 days

dangeles

issue closednf-core/scrnaseq

Kallistobustools subworkflow fails ("no such propery launchDir for class: java.lang.String")

Check Documentation

I have checked the following places for your error:

Description of the bug

Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:KALLISTO_BUSTOOLS:KALLISTOBUSTOOLS_REF (GRCm38.p6.genome.chr19.fa)'

Caused by:
  No such property: launchDir for class: java.lang.String

Source block:
  if (workflow == "standard") {
          """
          kb \\
              ref \\
              -i kb_ref_out.idx \\
              -g t2g.txt \\
              -f1 cdna.fa \\
              --workflow $workflow \\
              $fasta \\
              $gtf

          cat <<-END_VERSIONS > versions.yml
          ${getProcessName(task.process)}:
              ${getSoftwareName(task.process)}: \$(echo \$(kb --version 2>&1) | sed 's/^.*kb_python //;s/positional arguments.*\$//')
          END_VERSIONS
          """
      } else {
          """
          kb \\
              ref \\
              -i kb_ref_out.idx \\
              -g t2g.txt \\
              -f1 cdna.fa \\
              -f2 intron.fa \\
              -c1 cdna_t2c.txt \\
              -c2 intron_t2c.txt \\
              --workflow $workflow \\
              $fasta \\
              $gtf

          cat <<-END_VERSIONS > versions.yml
          ${getProcessName(task.process)}:
              ${getSoftwareName(task.process)}: \$(echo \$(kb --version 2>&1) | sed 's/^.*kb_python //;s/positional arguments.*\$//')
          END_VERSIONS
          """
      }

Work dir:

Steps to reproduce

nextflow run nf-core/scrnaseq -r dev -profile test,<docker/singularity/...>

Expected behaviour

Should not be triggering an error 👍🏻

Log files

Have you provided the following extra information/files:

  • [x] The command used to run the pipeline

Nextflow Installation

  • Version: 21.04.2

Container engine

  • Engine: Singularity

@alexblaessle initially found it, reproduced it with the test profile. Might also be that the module for kallistobustools is not function properly 🤔

closed time in 10 days

apeltzer

push eventnf-core/scrnaseq

nf-core-bot

commit sha ee073bebb491596fc0c75afd46222d3f01ae5b54

Template update for nf-core/tools version 2.2

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Gregor Sturm

commit sha 8f07c89e69d5b373b5fe188e6f95179df78a24b2

Merge branch 'dev' into nf-core-template-merge-2.2

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Gregor Sturm

commit sha 6b57e5c857f0e3e4023b6924e6b2d08cff48bd7a

nf-core modules update --all

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Gregor Sturm

commit sha 286ece1ddd5863c9dd0314a9a9ccfad9e07c5c6c

Fix some nf-core lint

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Gregor Sturm

commit sha 9ea336ea3314f08124ebdd005e0760d8c940f1a9

Temporarily re-add functions.nf for local modules

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Gregor Sturm

commit sha 23ac0a415b29d6a5c203e740822d2834681b39ea

Update pipeline to work with new nf-core modules

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Gregor Sturm

commit sha 8a4d4b7edf63c7704b170e40ace09f0a19d237e9

Update modules config to use new syntax

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Gregor Sturm

commit sha 6b109917aff4894e7dbb69e78d1aeda80424e320

Update local modules part 1

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Gregor Sturm

commit sha a1cab59ad976fef5f1a6242336e6a1bfc8e0cb56

Update modules container directive

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Gregor Sturm

commit sha 1222c9bbb204dd29c06ad1fd0f03e641dcb9d1a4

Remove addParams

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Gregor Sturm

commit sha cac6fea4a1bd393b6b43a381daadbed57f496416

Make process configuration conditional on aligner

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Gregor Sturm

commit sha c78b6d9ad9eb28cf4230280e27207e9942f9eaa6

Switch to cellranger modules from nf-core/modules

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Gregor Sturm

commit sha fc5c35c8dfa20d6cd7db28915f247d37b69ec766

Update local modules to versions.yml syntax

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Gregor Sturm

commit sha b9a2700077b5370338d71b55ab3b2d20d2151838

Fix channel names due to updated modules

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Gregor Sturm

commit sha f5f18bc852595c8b4f6ac8bb2de18d6fc270b6ac

Fix eclint

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Alexander Peltzer

commit sha bbec4cfa77d5cbc276958335bbeb5b80b5d17590

Add Zenodo DOI

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Alexander Peltzer

commit sha 21c56ac708902e3c74a064cbf47cf48866ffb86f

Remove todos for samplesheet py

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Alexander Peltzer

commit sha 931ee16a7f69d0acdf8703fd436343f2ec5d269c

Drop it like its hot

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Alexander Peltzer

commit sha 10221c0aba3bd5117708e6a0db868d3e8e148df7

Only lint warnings left

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Alexander Peltzer

commit sha ef3f49479f2e18810d75eb3b6bf4f5511404686f

Merge pull request #76 from nf-core/nf-core-template-merge-2.2 All green - lets go!

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delete branch nf-core/scrnaseq

delete branch : nf-core-template-merge-2.2

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PR merged nf-core/scrnaseq

Important! Template update for nf-core/tools v2.2

Version 2.2 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-2.2 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see https://nf-co.re/developers/sync.

For more information about this release of nf-core/tools, please see the v2.2 release page.

+915 -1650

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83 changed files

nf-core-bot

pr closed time in 10 days

pull request commentnf-core/scrnaseq

Important! Template update for nf-core/tools v2.2

Linting fixed now, remaining points could be adressed in separate PRs after this is merged to dev:

  • Reference genome loading
  • CellRanger stuff

Should we open extra issues for that one @grst ?

nf-core-bot

comment created time in 10 days

delete branch nf-core/scrnaseq

delete branch : fix-kbtools

delete time in 10 days

PR closed nf-core/scrnaseq

Fix issue #83 with kbtools

This fixes the issue @alexblaessle and i experienced when running the kallisto bustools subworkflow. Likely because the modules weren't following latest standards, so I just fixed this by upgrading to the latest nf-core modules and that resolved the issue.

+273 -849

1 comment

26 changed files

apeltzer

pr closed time in 10 days

pull request commentnf-core/scrnaseq

Fix issue #83 with kbtools

Please disregard, #76 with changes from Gregor is adressing all of this already.

apeltzer

comment created time in 10 days

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