[ERROR] Please provide a valid value for --ena_metadata_fields!

[sirclockalot]

Description of the bug

Over the past few days I have encountered an issue when running nextflow run nf-core/fetchngsthat is related to the accepted values for --ena_metadata_fields. No changes were made in the script or parameter files between successful and incomplete runs.

It appears that the hard coded preset metadata fields are no longer found when referencing the list online. The current list of accepted values has possibly changed as quite a few of the preset metadata fields are no longer in the list. Accepted ena metadata values as defined in get_ena_fields().

Hard coded metadata from ra_ids_to_runinfo.py
ENA_METADATA_FIELDS = ( "run_accession", "experiment_accession", "sample_accession", "secondary_sample_accession", "study_accession", "secondary_study_accession", "submission_accession", "run_alias", "experiment_alias", "sample_alias", "study_alias", "library_layout", "library_selection", "library_source", "library_strategy", "library_name", "instrument_model", "instrument_platform", "base_count", "read_count", "tax_id", "scientific_name", "sample_title", "experiment_title", "study_title", "sample_description", "fastq_md5", "fastq_bytes", "fastq_ftp", "fastq_galaxy", "fastq_aspera", )

Command used and terminal output

$ nextflow run nf-core/fetchngs -r 1.9 --input data/acc/acc_all.csv --input_type 'sra' --outdir output/ -profile docker 


Caused by:
  Process `NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR13499410)` terminated with an error exit status (1)

Command executed:

  echo SRR13499410 > id.txt
  sra_ids_to_runinfo.py \
      id.txt \
      SRR13499410.runinfo.tsv \
  
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO":
      python: $(python --version | sed 's/Python //g')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
  [ERROR] Please provide a valid value for --ena_metadata_fields!
  Provided values = accession,run_accession,experiment_accession,sample_accession,secondary_sample_accession,study_accession,secondary_study_accession,parent_study,submission_accession,run_alias,experiment_alias,sample_alias,study_alias,library_layout,library_selection,library_source,library_strategy,library_name,instrument_model,instrument_platform,base_count,read_count,tax_id,scientific_name,sample_title,experiment_title,study_title,description,sample_description,fastq_md5,fastq_bytes,fastq_ftp,fastq_galaxy,fastq_aspera
  Accepted values = aligned,altitude,assembly_quality,assembly_software,bam_aspera,bam_bytes,bam_ftp,bam_galaxy,bam_md5,base_count,binning_software,bio_material,bisulfite_protocol,broad_scale_environmental_context,broker_name,cage_protocol,cell_line,cell_type,center_name,checklist,chip_ab_provider,chip_protocol,chip_target,collected_by,collection_date,completeness_score,contamination_score,control_experiment,country,cultivar,culture_collection,depth,dev_stage,dnase_protocol,ecotype,elevation,environment_biome,environment_feature,environment_material,environmental_medium,environmental_sample,experiment_accession,experiment_alias,experiment_target,experiment_title,experimental_factor,experimental_protocol,extraction_protocol,faang_library_selection,fastq_aspera,fastq_bytes,fastq_ftp,fastq_galaxy,fastq_md5,file_location,first_created,first_public,germline,hi_c_protocol,host,host_body_site,host_genotype,host_gravidity,host_growth_conditions,host_phenotype,host_sex,host_status,host_tax_id,identified_by,instrument_model,instrument_platform,investigation_type,isolate,isolation_source,last_updated,lat,library_construction_protocol,library_gen_protocol,library_layout,library_max_fragment_size,library_min_fragment_size,library_name,library_pcr_isolation_protocol,library_prep_date,library_prep_date_format,library_prep_latitude,library_prep_location,library_prep_longitude,library_selection,library_source,library_strategy,local_environmental_context,location,location_end,location_start,lon,marine_region,mating_type,ncbi_reporting_standard,nominal_length,nominal_sdev,pcr_isolation_protocol,ph,project,protocol_label,read_count,read_strand,restriction_enzyme,restriction_enzyme_target_sequence,restriction_site,rna_integrity_num,rna_prep_3_protocol,rna_prep_5_protocol,rna_purity_230_ratio,rna_purity_280_ratio,rt_prep_protocol,run_accession,run_alias,run_date,salinity,sample_accession,sample_alias,sample_capture_status,sample_collection,sample_description,sample_material,sample_prep_interval,sample_prep_interval_units,sample_storage,sample_storage_processing,sample_title,sampling_campaign,sampling_platform,sampling_site,scientific_name,secondary_project,secondary_sample_accession,secondary_study_accession,sequencing_date,sequencing_date_format,sequencing_location,sequencing_longitude,sequencing_method,sequencing_primer_catalog,sequencing_primer_lot,sequencing_primer_provider,serotype,serovar,sex,specimen_voucher,sra_aspera,sra_bytes,sra_ftp,sra_galaxy,sra_md5,status,strain,study_accession,study_alias,study_title,sub_species,sub_strain,submission_accession,submission_tool,submitted_aspera,submitted_bytes,submitted_format,submitted_ftp,submitted_galaxy,submitted_host_sex,submitted_md5,submitted_read_type,tag,target_gene,tax_id,taxonomic_classification,taxonomic_identity_marker,temperature,tissue_lib,tissue_type,transposase_protocol,variety

Relevant files

No response

System information

No response

[ejseqera]

There was an update to ENA API last week and the spec has changed in v2.0.0 of the API. It's fixed in the dev branch (see PR #148) and we should be making a release to 1.10 hopefully end of this week or early next week.

In the meanwhile, try nextflow run nf-core/fetchngs -r dev instead.

[sirclockalot]

Thank you for the reply. I will give it a try.

[drpatelh]

Closing as will be fixed in 1.10.0. Thanks for reporting!