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Support for IonTorrent data #280

Merged
merged 8 commits into from Jun 17, 2021
Merged

Support for IonTorrent data #280

merged 8 commits into from Jun 17, 2021

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jtangrot
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Added support for (single-ended) IonTorrent reads. Parameters changed compared to Illumina are dada(..., HOMOPOLYMER_GAP_PENALTY=-1, BAND_SIZE=32) and filterAndTrim(..., trimLeft=15) - all according to recommendations at https://benjjneb.github.io/dada2/faq.html#can-i-use-dada2-with-my-454-or-ion-torrent-data
I'm not quite sure where to document this.

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 necessary, also make a PR on the nf-core/ampliseq 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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github-actions bot commented Jun 14, 2021 •
edited

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 6eeb884

+| ✅ 125 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗  59 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: environment.yml
  • files_exist - File not found: Dockerfile
  • nextflow_config - Config variable not found: process.container
  • params_used - Config variable not found in main.nf: params.input
  • params_used - Config variable not found in main.nf: params.pacbio
  • params_used - Config variable not found in main.nf: params.iontorrent
  • params_used - Config variable not found in main.nf: params.FW_primer
  • params_used - Config variable not found in main.nf: params.RV_primer
  • params_used - Config variable not found in main.nf: params.classifier
  • params_used - Config variable not found in main.nf: params.metadata
  • params_used - Config variable not found in main.nf: params.extension
  • params_used - Config variable not found in main.nf: params.publish_dir_mode
  • params_used - Config variable not found in main.nf: params.trunc_qmin
  • params_used - Config variable not found in main.nf: params.trunc_rmin
  • params_used - Config variable not found in main.nf: params.trunclenf
  • params_used - Config variable not found in main.nf: params.trunclenr
  • params_used - Config variable not found in main.nf: params.max_ee
  • params_used - Config variable not found in main.nf: params.max_len
  • params_used - Config variable not found in main.nf: params.min_len
  • params_used - Config variable not found in main.nf: params.metadata_category
  • params_used - Config variable not found in main.nf: params.double_primer
  • params_used - Config variable not found in main.nf: params.retain_untrimmed
  • params_used - Config variable not found in main.nf: params.exclude_taxa
  • params_used - Config variable not found in main.nf: params.min_frequency
  • params_used - Config variable not found in main.nf: params.min_samples
  • params_used - Config variable not found in main.nf: params.multiple_sequencing_runs
  • params_used - Config variable not found in main.nf: params.single_end
  • params_used - Config variable not found in main.nf: params.sample_inference
  • params_used - Config variable not found in main.nf: params.illumina_pe_its
  • params_used - Config variable not found in main.nf: params.concatenate_reads
  • params_used - Config variable not found in main.nf: params.cut_its
  • params_used - Config variable not found in main.nf: params.skip_qiime
  • params_used - Config variable not found in main.nf: params.skip_fastqc
  • params_used - Config variable not found in main.nf: params.skip_alpha_rarefaction
  • params_used - Config variable not found in main.nf: params.skip_abundance_tables
  • params_used - Config variable not found in main.nf: params.skip_barplot
  • params_used - Config variable not found in main.nf: params.skip_taxonomy
  • params_used - Config variable not found in main.nf: params.skip_diversity_indices
  • params_used - Config variable not found in main.nf: params.skip_ancom
  • params_used - Config variable not found in main.nf: params.skip_multiqc
  • params_used - Config variable not found in main.nf: params.dada_ref_taxonomy
  • params_used - Config variable not found in main.nf: params.qiime_ref_taxonomy
  • params_used - Config variable not found in main.nf: params.outdir
  • params_used - Config variable not found in main.nf: params.multiqc_config
  • params_used - Config variable not found in main.nf: params.multiqc_title
  • params_used - Config variable not found in main.nf: params.email
  • params_used - Config variable not found in main.nf: params.email_on_fail
  • params_used - Config variable not found in main.nf: params.max_multiqc_email_size
  • params_used - Config variable not found in main.nf: params.plaintext_email
  • params_used - Config variable not found in main.nf: params.tracedir
  • params_used - Config variable not found in main.nf: params.hostnames
  • params_used - Config variable not found in main.nf: params.config_profile_description
  • params_used - Config variable not found in main.nf: params.config_profile_contact
  • params_used - Config variable not found in main.nf: params.config_profile_url
  • params_used - Config variable not found in main.nf: params.singularity_pull_docker_container
  • params_used - Config variable not found in main.nf: params.max_memory
  • params_used - Config variable not found in main.nf: params.max_cpus
  • params_used - Config variable not found in main.nf: params.max_time
  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

  • files_unchanged - File does not exist: .github/workflows/push_dockerhub_dev.yml
  • files_unchanged - File does not exist: .github/workflows/push_dockerhub_release.yml
  • conda_env_yaml - No environment.yml file found - skipping conda_env_yaml test
  • conda_dockerfile - No environment.yml / Dockerfile file found - skipping conda_dockerfile test

✅ Tests passed:

Run details

  • nf-core/tools version 1.14
  • Run at 2021-06-15 11:09:56

d4straub
d4straub reviewed Jun 14, 2021
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d4straub
d4straub requested changes Jun 15, 2021
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Looks pretty good!

Could you please add test_iontorrent to the ci.yml line 53 so that the test is automatically started on PRs.

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@d4straub
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Added support for (single-ended) IonTorrent reads. Parameters changed [...]
I'm not quite sure where to document this.

All parameters/options for dada2_filtntrim and dada2_denoising are captured in files (1,2) and published in results/dada2/args/ also described in the docs as

dada2/args/: Directory containing all parameters for DADA2 steps.

d4straub
d4straub approved these changes Jun 15, 2021
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Great!

Edit: Uh, just saw in the README.md:

Supported is single-end or paired-end Illumina and PacBio data.

This would be good to change as well!

@jtangrot jtangrot merged commit 0d74db9 into nf-core:dev Jun 17, 2021
@jtangrot jtangrot deleted the iontorrent branch June 17, 2021 07:03
@d4straub d4straub mentioned this pull request Jun 23, 2021
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@d4straub d4straub d4straub approved these changes

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