Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

restruct DIA-NN step2 #178

Merged
merged 1 commit into from
May 8, 2022
Merged

restruct DIA-NN step2 #178

merged 1 commit into from
May 8, 2022

Conversation

daichengxin
Copy link
Collaborator

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/quantms 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).

@github-actions
Copy link

github-actions bot commented May 7, 2022 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 03f52b9

+| ✅ 143 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.3.2
  • Run at 2022-05-07 11:36:08

@daichengxin
Copy link
Collaborator Author

Full commands as follow:

diann   --lib ${predict_tsv} \\
           --f ${mzML} \\
           ${min_pr_mz} \\
           ${max_pr_mz} \\
           ${min_fr_mz} \\
           ${max_fr_mz} \\
           --threads ${task.cpus} \\
           --missed-cleavages $params.allowed_missed_cleavages \\
           --min-pep-len $params.min_peptide_length \\
           --max-pep-len $params.max_peptide_length \\
           --min-pr-charge $params.min_precursor_charge \\
           --max-pr-charge $params.max_precursor_charge \\
           --var-mods $params.max_mods \\
           --verbose $params.diann_debug \\
           --window $params.scan_window \\
            --cut ${enzyme from sdrf} \\
           --fixed-mod  ${diann_fixed_ptm from sdrf} \\
           --var-mod ${diann_var_ptm from sdrf} \\
           --mass_acc ${fragment tolerence from sdrf } \\
           --mass_acc_ms1 ${precursor tolerence from sdrf } \\
           --gen-spec-lib \\
           --out-lib ${mzML.baseName}_lib.tsv \\
           --temp ./ \\
           --min-corr $params.min_corr \\
           --corr-diff $params.corr_diff \\
           ${quick_mass_acc} \\
           ${time_corr_only} \\

@ypriverol ypriverol self-requested a review May 7, 2022 13:17
@jpfeuffer
Copy link
Collaborator

Feel free to merge

@ypriverol ypriverol merged commit d91599a into bigbio:diann May 8, 2022
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@ypriverol ypriverol ypriverol approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@daichengxin @jpfeuffer @ypriverol