8000 Use script with echo + sed instead of exec with task.WorkDir for rMATS create_bamlist by olgabot · Pull Request #29 · nf-core/rnasplice · GitHub
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Use script with echo + sed instead of exec with task.WorkDir for rMATS create_bamlist #29

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Merged
merged 1 commit into from
Nov 23, 2022
Merged

Use script with echo + sed instead of exec with task.WorkDir for rMATS create_bamlist #29

merged 1 commit into from
Nov 23, 2022

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olgabot
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@olgabot olgabot commented Nov 16, 2022 •
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PR checklist

Hello,
Hope you are doing well. I was getting the error below with RMATs, which seems to be related to nextflow-io/nextflow#2706 where the script used native Nextflow code instead of a bash/python script. This PR changes the rMATS bamlist creation to use echo and sed.

Error executing process > 'NFCORE_RNASPLICE:RNASPLICE:RMATS:CREATE_BAMLIST_COND1'

Caused by:
  Process requirement exceeds available memory -- req: 36 GB; avail: 16 GB

Source block:
  task.workDir.resolve("${cond}_bamlist.txt").text = bam.join(',')

Work dir:
  s3://bbio-nextflow/work/d0/fe1f96c3edf9bbbafd3a078a20c75f

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`


Unexpected error [AbortedException]


[78/4b0361] Cached process > NFCORE_RNASPLICE:RNASPLICE:TX2GENE_TXIMPORT_SALMON:TXIMPORT (null)
A DataflowVariable can only be assigned once. Use bind() to allow for equal values to be passed into already-bound variables.


-[nf-core/rnasplice] Sent summary e-mail to olga.botvinnik@bridgebio.com (sendmail)-
-[nf-core/rnasplice] Pipeline completed with errors-
WARN: Killing running tasks (1)

make: *** [run1] Error 1
  • 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/rnasplice 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 --outdir <OUTDIR>).
  • 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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github-actions bot commented Nov 16, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9d2f8aa

+| ✅ 157 tests passed       |+
!| ❗  58 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required
  • schema_description - No description provided in schema for parameter: gff
  • schema_description - No description provided in schema for parameter: rmats
  • schema_description - No description provided in schema for parameter: rmats_splice_diff_cutoff
  • schema_description - No description provided in schema for parameter: rmats_paired_stats
  • schema_description - No description provided in schema for parameter: rmats_read_len
  • schema_description - No description provided in schema for parameter: rmats_novel_splice_site
  • schema_description - No description provided in schema for parameter: rmats_min_intron_len
  • schema_description - No description provided in schema for parameter: rmats_max_exon_len
  • schema_description - No description provided in schema for parameter: dexseq_exon
  • schema_description - No description provided in schema for parameter: gff_dexseq
  • schema_description - No description provided in schema for parameter: alignment_quality
  • schema_description - No description provided in schema for parameter: aggregation
  • schema_description - No description provided in schema for parameter: deu_lfc_denominator
  • schema_description - No description provided in schema for parameter: edger_exon
  • schema_description - No description provided in schema for parameter: dexseq_dtu
  • schema_description - No description provided in schema for parameter: dtu_txi
  • schema_description - No description provided in schema for parameter: dtu_lfc_denominator
  • schema_description - No description provided in schema for parameter: min_samps_feature_expr
  • schema_description - No description provided in schema for parameter: min_samps_feature_prop
  • schema_description - No description provided in schema for parameter: min_samps_gene_expr
  • schema_description - No description provided in schema for parameter: min_feature_expr
  • schema_description - No description provided in schema for parameter: min_feature_prop
  • schema_description - No description provided in schema for parameter: min_gene_expr
  • schema_description - No description provided in schema for parameter: suppa
  • schema_description - No description provided in schema for parameter: suppa_per_local_event
  • schema_description - No description provided in schema for parameter: suppa_per_isoform
  • schema_description - No description provided in schema for parameter: suppa_tpm
  • schema_description - No description provided in schema for parameter: generateevents_pool_genes
  • schema_description - No description provided in schema for parameter: generateevents_localevents
  • schema_description - No description provided in schema for parameter: generateevents_boundary
  • schema_description - No description provided in schema for parameter: generateevents_threshold
  • schema_description - No description provided in schema for parameter: generateevents_exon_length
  • schema_description - No description provided in schema for parameter: psiperevent_total_filter
  • schema_description - No description provided in schema for parameter: diffsplice_local_event
  • schema_description - No description provided in schema for parameter: diffsplice_isoform
  • schema_description - No description provided in schema for parameter: diffsplice_method
  • schema_description - No description provided in schema for parameter: diffsplice_area
  • schema_description - No description provided in schema for parameter: diffsplice_lower_bound
  • schema_description - No description provided in schema for parameter: diffsplice_gene_correction
  • schema_description - No description provided in schema for parameter: diffsplice_paired
  • schema_description - No description provided in schema for parameter: diffsplice_alpha
  • schema_description - No description provided in schema for parameter: diffsplice_median
  • schema_description - No description provided in schema for parameter: diffsplice_tpm_threshold
  • schema_description - No description provided in schema for parameter: diffsplice_nan_threshold
  • schema_description - No description provided in schema for parameter: clusterevents_local_event
  • schema_description - No description provided in schema for parameter: clusterevents_isoform
  • schema_description - No description provided in schema for parameter: clusterevents_sigthreshold
  • schema_description - No description provided in schema for parameter: clusterevents_dpsithreshold
  • schema_description - No description provided in schema for parameter: clusterevents_eps
  • schema_description - No description provided in schema for parameter: clusterevents_metric
  • schema_description - No description provided in schema for parameter: clusterevents_separation
  • schema_description - No description provided in schema for parameter: clusterevents_min_pts
  • schema_description - No description provided in schema for parameter: clusterevents_method

✅ Tests passed:

Run details

  • nf-core/tools version 2.6
  • Run at 2022-11-16 22:01:53

@olgabot
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olgabot commented Nov 18, 2022

Even with this fix, MATS is not producing any output of Psi or delta Psi across samples -- not sure how to interpret this. Thoughts?

==> tmp/JC_SE/rMATS_result_paired.txt <==
Loading required package: nloptr
Error in PAIRADISE::pairadise(data_frame, numCluster = number_of_threads) :
  is(pdat, "PDseDataSet") is not TRUE
Calls: <Anonymous> -> stopifnot
Execution halted

@bensouthgate
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Hi @olgabot thanks for spotting this. Using sed instead of task.WorkDir seems totally reasonable. The second issue sounds like it might be due to problems with the version of pairadise we have referenced for using rMATS with its paired stats model (https://groups.google.com/g/rmats-user-group/c/y-6SVjMaW0A). The google group thread seems to suggest that the only version that works is the latest version from github and not the bioconductor versions (I have tried the v1.14 from bioconductor and this still causes the same error). @jma1991 any thoughts?

@bensouthgate bensouthgate marked this pull request as ready for review November 23, 2022 15:25
@bensouthgate bensouthgate merged commit 68bb17c into nf-core:dev Nov 23, 2022
@jma1991
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jma1991 commented Nov 25, 2022

Hi @olgabot !

Thanks for contributing to the pipeline. We've discussed the issue and decided to open an issue on the bioconda-recipes repository. If we can fix the conda package, then BioContainers should automatically build the docker and singularity images as well.

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