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Change container for sra_ids_to_runinfo.nf process #14

Merged
merged 12 commits into from
Jun 22, 2021
Merged

Change container for sra_ids_to_runinfo.nf process #14

merged 12 commits into from
Jun 22, 2021

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drpatelh
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@drpatelh drpatelh commented Jun 21, 2021 •
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Closes #12

  • Update pipeline with current DSL2 template
  • Add --sample_mapping_fields parameter to create a separate mappings.tsv and multiqc_config.yml file with selected fields that can be used to rename samples in general and in MultiQC

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github-actions bot commented Jun 21, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 721621f

+| ✅ 105 tests passed       |+
#| ❔  18 tests were ignored |#
!| ❗  28 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
  • nextflow_config - Config manifest.version should end in dev: '1.1'
  • params_used - Config variable not found in main.nf: params.input
  • params_used - Config variable not found in main.nf: params.nf_core_pipeline
  • params_used - Config variable not found in main.nf: params.ena_metadata_fields
  • params_used - Config variable not found in main.nf: params.sample_mapping_fields
  • params_used - Config variable not found in main.nf: params.skip_fastq_download
  • params_used - Config variable not found in main.nf: params.outdir
  • params_used - Config variable not found in main.nf: params.tracedir
  • params_used - Config variable not found in main.nf: params.publish_dir_mode
  • 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.plaintext_email
  • params_used - Config variable not found in main.nf: params.monochrome_logs
  • params_used - Config variable not found in main.nf: params.help
  • params_used - Config variable not found in main.nf: params.validate_params
  • params_used - Config variable not found in main.nf: params.enable_conda
  • params_used - Config variable not found in main.nf: params.singularity_pull_docker_container
  • 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.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:

✅ Tests passed:

Run details

  • nf-core/tools version 1.14
  • Run at 2021-06-21 20:21:00

JoseEspinosa
JoseEspinosa approved these changes Jun 22, 2021
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LGTM 👍

modules/local/sra_ids_to_runinfo.nf
@@ -10,11 +10,11 @@ process SRA_IDS_TO_RUNINFO {
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }

conda (params.enable_conda ? "conda-forge::requests=2.24.0" : null)
conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
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Are these the same containers (conda vs. biocontainers) ? Couldn't we use the same container as in the multiqc process (quay.io/biocontainers/python:3.8.3)?
I guess that the answers is not but... 😜

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Nope, unfortunately not because it doesn't have requests installed 😏

@drpatelh drpatelh merged commit 3e06f50 into nf-core:dev Jun 22, 2021
@drpatelh drpatelh mentioned this pull request Jun 22, 2021
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@JoseEspinosa JoseEspinosa JoseEspinosa approved these changes

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@drpatelh @JoseEspinosa