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Re-write SRA download workflow to accept --ena_metadata_fields parameter #648

Merged
merged 12 commits into from
Jun 1, 2021
Merged

Re-write SRA download workflow to accept --ena_metadata_fields parameter #648

merged 12 commits into from
Jun 1, 2021

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drpatelh
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@drpatelh drpatelh commented Jun 1, 2021

Closes #646

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github-actions bot commented Jun 1, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit eb32d11

+| ✅ 116 tests passed       |+
#| ❔  17 tests were ignored |#
!| ❗  78 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.skip_sra_fastq_download
  • params_used - Config variable not found in main.nf: params.ena_metadata_fields
  • params_used - Config variable not found in main.nf: params.genome
  • params_used - Config variable not found in main.nf: params.transcript_fasta
  • params_used - Config variable not found in main.nf: params.additional_fasta
  • params_used - Config variable not found in main.nf: params.splicesites
  • params_used - Config variable not found in main.nf: params.gtf_extra_attributes
  • params_used - Config variable not found in main.nf: params.gtf_group_features
  • params_used - Config variable not found in main.nf: params.featurecounts_feature_type
  • params_used - Config variable not found in main.nf: params.featurecounts_group_type
  • params_used - Config variable not found in main.nf: params.gencode
  • params_used - Config variable not found in main.nf: params.save_reference
  • params_used - Config variable not found in main.nf: params.with_umi
  • params_used - Config variable not found in main.nf: params.umitools_extract_method
  • params_used - Config variable not found in main.nf: params.umitools_bc_pattern
  • params_used - Config variable not found in main.nf: params.save_umi_intermeds
  • params_used - Config variable not found in main.nf: params.clip_r1
  • params_used - Config variable not found in main.nf: params.clip_r2
  • params_used - Config variable not found in main.nf: params.three_prime_clip_r1
  • params_used - Config variable not found in main.nf: params.three_prime_clip_r2
  • params_used - Config variable not found in main.nf: params.trim_nextseq
  • params_used - Config variable not found in main.nf: params.save_trimmed
  • params_used - Config variable not found in main.nf: params.skip_trimming
  • params_used - Config variable not found in main.nf: params.remove_ribo_rna
  • params_used - Config variable not found in main.nf: params.save_non_ribo_reads
  • params_used - Config variable not found in main.nf: params.ribo_database_manifest
  • params_used - Config variable not found in main.nf: params.aligner
  • params_used - Config variable not found in main.nf: params.pseudo_aligner
  • params_used - Config variable not found in main.nf: params.seq_center
  • params_used - Config variable not found in main.nf: params.bam_csi_index
  • params_used - Config variable not found in main.nf: params.star_ignore_sjdbgtf
  • params_used - Config variable not found in main.nf: params.hisat2_build_memory
  • params_used - Config variable not found in main.nf: params.stringtie_ignore_gtf
  • params_used - Config variable not found in main.nf: params.min_mapped_reads
  • params_used - Config variable not found in main.nf: params.save_merged_fastq
  • params_used - Config variable not found in main.nf: params.save_unaligned
  • params_used - Config variable not found in main.nf: params.save_align_intermeds
  • params_used - Config variable not found in main.nf: params.skip_markduplicates
  • params_used - Config variable not found in main.nf: params.skip_alignment
  • params_used - Config variable not found in main.nf: params.skip_qc
  • params_used - Config variable not found in main.nf: params.skip_bigwig
  • params_used - Config variable not found in main.nf: params.skip_stringtie
  • params_used - Config variable not found in main.nf: params.skip_fastqc
  • params_used - Config variable not found in main.nf: params.skip_preseq
  • params_used - Config variable not found in main.nf: params.skip_dupradar
  • params_used - Config variable not found in main.nf: params.skip_qualimap
  • params_used - Config variable not found in main.nf: params.skip_rseqc
  • params_used - Config variable not found in main.nf: params.skip_biotype_qc
  • params_used - Config variable not found in main.nf: params.skip_deseq2_qc
  • params_used - Config variable not found in main.nf: params.skip_multiqc
  • params_used - Config variable not found in main.nf: params.deseq2_vst
  • params_used - Config variable not found in main.nf: params.rseqc_modules
  • params_used - Config variable not found in main.nf: params.outdir
  • params_used - Config variable not found in main.nf: params.publish_dir_mode
  • 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.monochrome_logs
  • params_used - Config variable not found in main.nf: params.help
  • params_used - Config variable not found in main.nf: params.tracedir
  • 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 2021-06-01 16:46:45

JoseEspinosa
JoseEspinosa approved these changes Jun 1, 2021
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LGTM 😄
Just a small question that probably is something I misunderstood.

workflows/sra_download.nf
@@ -4,6 +4,16 @@
========================================================================================
*/

def valid_params = [
ena_metadata_fields : ['run_accession', 'experiment_accession', 'library_layout', 'fastq_ftp', 'fastq_md5']
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I got lost here, this means that only these 5 fields can be retrieved?

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Nope. The code here just checks that --ena_metadata_fields contains those 5 fields as a minimum but it can contain as many others as long as they exist here

Was tricky figuring out how best to do this because if --ena_metadata_fields is not specified then by default the fields here will be used but I didn't want to specify a long list list that in the nextflow_schema.json so this was the workaround I came up with. I also manually curated the default list to remove any blank metadata fields so that accessions etc are next to each other in the final samplesheet so makes it easier to organise and visualise.

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Makes a lot of sense! Thanks for the explanation 😄

@drpatelh drpatelh merged commit b0ff698 into nf-core:dev Jun 1, 2021
@drpatelh drpatelh mentioned this pull request Jun 2, 2021
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@JoseEspinosa JoseEspinosa JoseEspinosa approved these changes

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@drpatelh @JoseEspinosa