search

nf-core / eager

A fully reproducible and state-of-the-art ancient DNA analysis pipeline
https://nf-co.re/eager
MIT License
134 stars 79 forks source link

Failing adapter_removal task for benchmarking_vikingfish profile when running on AWS #469

Closed pditommaso closed 4 years ago

pditommaso commented 4 years ago

The adapter_removal task terminates in an unexpected manner: 

Error executing process > 'adapter_removal (COD092E1bL1i69_L7)'

Caused by:
  Process `adapter_removal (COD092E1bL1i69_L7)` terminated with an error exit status (1)

Command executed:

  mkdir -p output
  AdapterRemoval --file1 ERR1943608_1.fastq.gz --file2 ERR1943608_2.fastq.gz --basename ERR1943608_1.fastq_L7.pe --trimns --trimqualities --adapter1 AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC --adapter2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA --minlength 30 --minquality 20 --minadapteroverlap 1 --gzip --threads 8 --collapse 

  #Combine files
  if [   = "--preserve5p" ] && [ N = "N" ]; then 
    cat *.collapsed.gz *.singleton.truncated.gz *.pair1.truncated.gz *.pair2.truncated.gz > output/ERR1943608_1.fastq_L7.pe.combined.fq.gz
  elif [   = "--preserve5p" ] && [ N = "Y" ] ; then
    cat *.collapsed.gz > output/ERR1943608_1.fastq_L7.pe.combined.fq.gz
  elif [ N = "Y" ] ; then
    cat *.collapsed.gz *.collapsed.truncated.gz > output/ERR1943608_1.fastq_L7.pe.combined.fq.gz
  else
    cat *.collapsed.gz *.collapsed.truncated.gz *.singleton.truncated.gz *.pair1.truncated.gz *.pair2.truncated.gz > output/ERR1943608_1.fastq_L7.pe.combined.fq.gz
  fi

  mv *.settings output/

Command exit status:
  1

Command output:
  (empty)

Command error:
  Trimming paired end reads ...
  Opening FASTQ file 'ERR1943608_1.fastq.gz', line numbers start at 1
  Opening FASTQ file 'ERR1943608_2.fastq.gz', line numbers start at 1

  Processed 1,001,222 reads in 4.0s; 250,000 reads per second ...
  Processed 2,004,094 reads in 7.9s; 252,000 reads per second ...
  Processed 3,004,801 reads in 11.8s; 253,000 reads per second ...
  Processed 4,006,702 reads in 16.0s; 251,000 reads per second ...
  Processed 5,007,676 reads in 19.5s; 256,000 reads per second ...
  Processed 6,008,488 reads in 23.2s; 258,000 reads per second ...
  Processed 7,010,958 reads in 26.9s; 260,000 reads per second ...
  Processed 8,013,476 reads in 30.7s; 260,000 reads per second ...
  Processed 9,015,627 reads in 34.8s; 259,000 reads per second ...
  Processed 10,017,107 reads in 38.6s; 259,000 reads per second ...
  Processed 11,018,811 reads in 42.4s; 260,000 reads per second ...
  Processed 12,022,922 reads in 46.3s; 261,000 reads per second ...
  Processed 13,024,917 reads in 50.1s; 261,000 reads per second ...
  Processed 14,026,966 reads in 54.0s; 263,000 reads per second ...
  Processed 15,027,940 reads in 57.9s; 261,000 reads per second ...
  Processed 16,028,215 reads in 1:01.8s; 259,000 reads per second ...
  Processed 17,030,277 reads in 1:05.7s; 258,000 reads per second ...
  Error reading FASTQ record at line 36097233; aborting:
      partial FASTQ record; cut off after header
  Aborting thread due to error.
  ERROR: AdapterRemoval did not run to completion;
         do NOT make use of resulting trimmed reads!

Work dir:
  s3://nextflow-ci/scratch/vQZ2yYQK/a6/5a82d2311a734c827c24bfa0cd4223

Launch command line 

nextflow run nf-core/eager -name astonishing_northcutt -with-tower -r dev -profile benchmarking_vikingfish

Resolved config

params {
   input = 'https://raw.githubusercontent.com/jfy133/test-datasets/eager/testdata/Benchmarking/benchmarking_vikingfish.tsv'
   colour_chemistry = 4
   single_stranded = false
   single_end = false
   bam = false
   fasta = 'https://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_other/Gadus_morhua/representative/GCF_902167405.1_gadMor3.0/GCF_902167405.1_gadMor3.0_genomic.fna.gz'
   large_ref = false
   save_reference = false
   saveTrimmed = true
   saveAlignedIntermediates = false
   genome = false
   fasta_index = ''
   bwa_index = false
   snpcapture = false
   bedfile = ''
   seq_dict = ''
   outdir = './results'
   skip_fastqc = false
   skip_preseq = false
   skip_damage_calculation = false
   skip_qualimap = false
   skip_deduplication = false
   run_convertinputbam = false
   skip_adapterremoval = false
   skip_trim = false
   complexity_filter_poly_g = false
   complexity_filter_poly_g_min = 10
   trim_bam = false
   clip_forward_adaptor = 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
   clip_reverse_adaptor = 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA'
   clip_readlength = 30
   clip_min_read_quality = 20
   min_adap_overlap = 1
   skip_collapse = false
   preserve5p = false
   mergedonly = false
   mapper = 'bwaaln'
   bwaalnn = 0.04
   bwaalnk = 2
   bwaalnl = 1024
   circularextension = 500
   circulartarget = 'MT'
   circularfilter = false
   run_bam_filtering = true
   bam_discard_unmapped = true
   bam_unmapped_type = 'discard'
   bam_mapping_quality_threshold = 25
   damageprofiler_length = 100
   damageprofiler_threshold = 15
   damageprofiler_yaxis = 0.30
   dedupper = 'dedup'
   dedup_all_merged = false
   preseq_step_size = 1000
   run_bedtools_coverage = false
   anno_file = ''
   run_pmdtools = false
   udg_type = 'none'
   pmdtools_range = 10
   pmdtools_threshold = 3
   pmdtools_reference_mask = ''
   pmdtools_max_reads = 10000
   run_trim_bam = false
   bamutils_clip_left = 1
   bamutils_clip_right = 1
   bamutils_softclip = false
   strip_input_fastq = false
   strip_mode = 'strip'
   run_genotyping = true
   genotyping_tool = 'hc'
   genotyping_source = 'raw'
   gatk_ug_jar = ''
   gatk_ug_genotype_model = 'SNP'
   gatk_hc_emitrefconf = 'GVCF'
   gatk_call_conf = '30'
   gatk_ploidy = 2
   gatk_downsample = '250'
   gatk_ug_out_mode = 'EMIT_VARIANTS_ONLY'
   gatk_hc_out_mode = 'EMIT_VARIANTS_ONLY'
   gatk_ug_keep_realign_bam = false
   gatk_dbsnp = ''
   gatk_ug_defaultbasequalities = ''
   freebayes_C = 1
   freebayes_g = 0
   freebayes_p = 2
   pileupcaller_snpfile = ''
   pileupcaller_bedfile = ''
   pileupcaller_method = 'randomHaploid'
   run_vcf2genome = false
   vcf2genome_outfile = ''
   vcf2genome_header = ''
   vcf2genome_minc = 5
   vcf2genome_minq = 30
   vcf2genome_minfreq = 0.8
   run_multivcfanalyzer = false
   write_allele_frequencies = false
   min_genotype_quality = 30
   min_base_coverage = 5
   min_allele_freq_hom = 0.9
   min_allele_freq_het = 0.9
   additional_vcf_files = ''
   reference_gff_annotations = 'NA'
   reference_gff_exclude = 'NA'
   snp_eff_results = 'NA'
   run_mtnucratio = false
   mtnucratio_header = 'MT'
   run_sexdeterrmine = false
   sexdeterrmine_bedfile = ''
   run_nuclear_contamination = false
   contamination_chrom_name = 'X'
   run_metagenomic_screening = false
   metagenomic_tool = 'malt'
   metagenomic_min_support_reads = 1
   database = ''
   percent_identity = 85
   malt_mode = 'BlastN'
   malt_alignment_mode = 'SemiGlobal'
   malt_top_percent = 1
   malt_min_support_mode = 'percent'
   malt_min_support_percent = 0.01
   malt_max_queries = 100
   malt_memory_mode = 'load'
   malt_weighted_lca = false
   run_maltextract = false
   maltextract_taxon_list = ''
   maltextract_ncbifiles = ''
   maltextract_filter = 'def_anc'
   maltextract_toppercent = 0.01
   maltextract_destackingoff = false
   maltextract_downsamplingoff = false
   maltextract_duplicateremovaloff = false
   maltextract_matches = false
   maltextract_megansummary = false
   maltextract_percentidentity = 85.0
   maltextract_topalignment = false
   maltextract_singlestranded = false
   name = false
   multiqc_config = false
   email = false
   email_on_fail = false
   max_multiqc_email_size = '25 MB'
   plaintext_email = false
   monochrome_logs = false
   help = false
   igenomes_base = 's3://ngi-igenomes/igenomes/'
   tracedir = './results/pipeline_info'
   awsqueue = '[secret]'
   awsregion = '[secret]'
   igenomes_ignore = false
   custom_config_version = 'master'
   custom_config_base = 'https://raw.githubusercontent.com/nf-core/configs/master'
   hostnames = [binac:['.binac.uni-tuebingen.de'], cbe:['.cbe.vbc.ac.at'], cfc:['.hpc.uni-tuebingen.de'], crick:['.thecrick.org'], icr_davros:['.davros.compute.estate'], genotoul:['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], genouest:['.genouest.org'], uppmax:['.uppmax.uu.se'], utd_ganymede:['ganymede.utdallas.edu']]
   config_profile_description = 'A \'fullsized\' benchmarking profile for deepish sequencing aDNA data'
   config_profile_contact = false
   config_profile_url = false
   max_memory = '128 GB'
   max_cpus = 16
   max_time = '10d'
   config_profile_name = 'nf-core/eager benchmarking - Viking Fish profile'
   genomes {
      GRCh37 {
         fasta = 's3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed'
         readme = 's3://ngi-igenomes/igenomes//Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt'
         mito_name = 'MT'
         macs_gsize = '2.7e9'
         blacklist = '/.nextflow/assets/nf-core/eager/assets/blacklists/GRCh37-blacklist.bed'
      }
      GRCh38 {
         fasta = 's3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed'
         mito_name = 'chrM'
         macs_gsize = '2.7e9'
         blacklist = '/.nextflow/assets/nf-core/eager/assets/blacklists/hg38-blacklist.bed'
      }
      GRCm38 {
         fasta = 's3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed'
         readme = 's3://ngi-igenomes/igenomes//Mus_musculus/Ensembl/GRCm38/Annotation/README.txt'
         mito_name = 'MT'
         macs_gsize = '1.87e9'
         blacklist = '/.nextflow/assets/nf-core/eager/assets/blacklists/GRCm38-blacklist.bed'
      }
      TAIR10 {
         fasta = 's3://ngi-igenomes/igenomes//Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed'
         readme = 's3://ngi-igenomes/igenomes//Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt'
         mito_name = 'Mt'
      }
      EB2 {
         fasta = 's3://ngi-igenomes/igenomes//Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed'
         readme = 's3://ngi-igenomes/igenomes//Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt'
      }
      'UMD3.1' {
         fasta = 's3://ngi-igenomes/igenomes//Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed'
         readme = 's3://ngi-igenomes/igenomes//Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt'
         mito_name = 'MT'
      }
      WBcel235 {
         fasta = 's3://ngi-igenomes/igenomes//Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed'
         mito_name = 'MtDNA'
         macs_gsize = '9e7'
      }
      'CanFam3.1' {
         fasta = 's3://ngi-igenomes/igenomes//Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed'
         readme = 's3://ngi-igenomes/igenomes//Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt'
         mito_name = 'MT'
      }
      GRCz10 {
         fasta = 's3://ngi-igenomes/igenomes//Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed'
         mito_name = 'MT'
      }
      BDGP6 {
         fasta = 's3://ngi-igenomes/igenomes//Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed'
         mito_name = 'M'
         macs_gsize = '1.2e8'
      }
      EquCab2 {
         fasta = 's3://ngi-igenomes/igenomes//Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed'
         readme = 's3://ngi-igenomes/igenomes//Equus_caballus/Ensembl/EquCab2/Annotation/README.txt'
         mito_name = 'MT'
      }
      EB1 {
         fasta = 's3://ngi-igenomes/igenomes//Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed'
         readme = 's3://ngi-igenomes/igenomes//Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt'
      }
      Galgal4 {
         fasta = 's3://ngi-igenomes/igenomes//Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed'
         mito_name = 'MT'
      }
      Gm01 {
         fasta = 's3://ngi-igenomes/igenomes//Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Glycine_max/Ensembl/Gm01/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed'
         readme = 's3://ngi-igenomes/igenomes//Glycine_max/Ensembl/Gm01/Annotation/README.txt'
      }
      Mmul_1 {
         fasta = 's3://ngi-igenomes/igenomes//Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed'
         readme = 's3://ngi-igenomes/igenomes//Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt'
         mito_name = 'MT'
      }
      'IRGSP-1.0' {
         fasta = 's3://ngi-igenomes/igenomes//Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed'
         mito_name = 'Mt'
      }
      'CHIMP2.1.4' {
         fasta = 's3://ngi-igenomes/igenomes//Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed'
         readme = 's3://ngi-igenomes/igenomes//Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt'
         mito_name = 'MT'
      }
      'Rnor_6.0' {
         fasta = 's3://ngi-igenomes/igenomes//Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed'
         mito_name = 'MT'
      }
      'R64-1-1' {
         fasta = 's3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed'
         mito_name = 'MT'
         macs_gsize = '1.2e7'
      }
      EF2 {
         fasta = 's3://ngi-igenomes/igenomes//Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed'
         readme = 's3://ngi-igenomes/igenomes//Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt'
         mito_name = 'MT'
         macs_gsize = '1.21e7'
      }
      Sbi1 {
         fasta = 's3://ngi-igenomes/igenomes//Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed'
         readme = 's3://ngi-igenomes/igenomes//Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt'
      }
      'Sscrofa10.2' {
         fasta = 's3://ngi-igenomes/igenomes//Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed'
         readme = 's3://ngi-igenomes/igenomes//Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt'
         mito_name = 'MT'
      }
      AGPv3 {
         fasta = 's3://ngi-igenomes/igenomes//Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed'
         mito_name = 'Mt'
      }
      hg38 {
         fasta = 's3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg38/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed'
         mito_name = 'chrM'
         macs_gsize = '2.7e9'
         blacklist = '/.nextflow/assets/nf-core/eager/assets/blacklists/hg38-blacklist.bed'
      }
      hg19 {
         fasta = 's3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg19/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed'
         readme = 's3://ngi-igenomes/igenomes//Homo_sapiens/UCSC/hg19/Annotation/README.txt'
         mito_name = 'chrM'
         macs_gsize = '2.7e9'
         blacklist = '/.nextflow/assets/nf-core/eager/assets/blacklists/hg19-blacklist.bed'
      }
      mm10 {
         fasta = 's3://ngi-igenomes/igenomes//Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Mus_musculus/UCSC/mm10/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Mus_musculus/UCSC/mm10/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed'
         readme = 's3://ngi-igenomes/igenomes//Mus_musculus/UCSC/mm10/Annotation/README.txt'
         mito_name = 'chrM'
         macs_gsize = '1.87e9'
         blacklist = '/.nextflow/assets/nf-core/eager/assets/blacklists/mm10-blacklist.bed'
      }
      bosTau8 {
         fasta = 's3://ngi-igenomes/igenomes//Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed'
         mito_name = 'chrM'
      }
      ce10 {
         fasta = 's3://ngi-igenomes/igenomes//Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed'
         readme = 's3://ngi-igenomes/igenomes//Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt'
         mito_name = 'chrM'
         macs_gsize = '9e7'
      }
      canFam3 {
         fasta = 's3://ngi-igenomes/igenomes//Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed'
         readme = 's3://ngi-igenomes/igenomes//Canis_familiaris/UCSC/canFam3/Annotation/README.txt'
         mito_name = 'chrM'
      }
      danRer10 {
         fasta = 's3://ngi-igenomes/igenomes//Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Danio_rerio/UCSC/danRer10/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed'
         mito_name = 'chrM'
      }
      dm6 {
         fasta = 's3://ngi-igenomes/igenomes//Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed'
         mito_name = 'chrM'
         macs_gsize = '1.2e8'
      }
      equCab2 {
         fasta = 's3://ngi-igenomes/igenomes//Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Equus_caballus/UCSC/equCab2/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed'
         readme = 's3://ngi-igenomes/igenomes//Equus_caballus/UCSC/equCab2/Annotation/README.txt'
         mito_name = 'chrM'
      }
      galGal4 {
         fasta = 's3://ngi-igenomes/igenomes//Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed'
         readme = 's3://ngi-igenomes/igenomes//Gallus_gallus/UCSC/galGal4/Annotation/README.txt'
         mito_name = 'chrM'
      }
      panTro4 {
         fasta = 's3://ngi-igenomes/igenomes//Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed'
         readme = 's3://ngi-igenomes/igenomes//Pan_troglodytes/UCSC/panTro4/Annotation/README.txt'
         mito_name = 'chrM'
      }
      rn6 {
         fasta = 's3://ngi-igenomes/igenomes//Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed'
         mito_name = 'chrM'
      }
      sacCer3 {
         fasta = 's3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/'
         readme = 's3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt'
         mito_name = 'chrM'
         macs_gsize = '1.2e7'
      }
      susScr3 {
         fasta = 's3://ngi-igenomes/igenomes//Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa'
         bwa = 's3://ngi-igenomes/igenomes//Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/genome.fa'
         bowtie2 = 's3://ngi-igenomes/igenomes//Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/'
         star = 's3://ngi-igenomes/igenomes//Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/'
         bismark = 's3://ngi-igenomes/igenomes//Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/'
         gtf = 's3://ngi-igenomes/igenomes//Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf'
         bed12 = 's3://ngi-igenomes/igenomes//Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed'
         readme = 's3://ngi-igenomes/igenomes//Sus_scrofa/UCSC/susScr3/Annotation/README.txt'
         mito_name = 'chrM'
      }
   }
}

process {
   container = 'nfcore/eager:dev'
   cpus = { check_max( 1 * task.attempt, 'cpus' ) }
   memory = { check_max( 7.GB * task.attempt, 'memory' ) }
   time = { check_max( 4.h * task.attempt, 'time' ) }
   errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
   maxRetries = 3
   maxErrors = '-1'
   withLabel:sc_tiny {
      cpus = { check_max( 1, 'cpus' ) }
      memory = { check_max( 1.GB * task.attempt, 'memory' ) }
      time = { check_max( 2.h * task.attempt, 'time' ) }
   }
   withLabel:sc_small {
      cpus = { check_max( 1, 'cpus' ) }
      memory = { check_max( 4.GB * task.attempt, 'memory' ) }
      time = { check_max( 2.h * task.attempt, 'time' ) }
   }
   withLabel:sc_medium {
      cpus = { check_max( 1, 'cpus' ) }
      memory = { check_max( 8.GB * task.attempt, 'memory' ) }
      time = { check_max( 2.h * task.attempt, 'time' ) }
   }
   withLabel:mc_small {
      cpus = { check_max( 2, 'cpus' ) }
      memory = { check_max( 4.GB * task.attempt, 'memory' ) }
      time = { check_max( 2.h * task.attempt, 'time' ) }
   }
   withLabel:mc_medium {
      cpus = { check_max( 4, 'cpus' ) }
      memory = { check_max( 8.GB * task.attempt, 'memory' ) }
      time = { check_max( 2.h * task.attempt, 'time' ) }
   }
   withLabel:mc_large {
      cpus = { check_max( 8, 'cpus' ) }
      memory = { check_max( 16.GB * task.attempt, 'memory' ) }
      time = { check_max( 2.h * task.attempt, 'time' ) }
   }
   withLabel:mc_huge {
      cpus = { check_max( 32, 'cpus' ) }
      memory = { check_max( 256.GB * task.attempt, 'memory' ) }
      time = { check_max( 2.h * task.attempt, 'time' ) }
   }
   withName:get_software_versions {
      memory = { check_max( 2.GB, 'memory' ) }
      cache = false
   }
   withName:qualimap {
      errorStrategy = 'ignore'
   }
   withName:preseq {
      errorStrategy = 'ignore'
   }
   withName:pmdtools {
      errorStrategy = { task.exitStatus in [141] ? 'ignore' : 'retry' }
   }
   withName:malt {
      errorStrategy = { task.exitStatus in [1] ? 'retry' : 'finish' } 
   }
   withName:multiqc {
      errorStrategy = { task.exitStatus in [143,137] ? 'retry' : 'ignore' }
   }
   withName:adapter_removal {
      cpus = { check_max( 8, 'cpus' ) }
      memory = { check_max( 16.GB * task.attempt, 'memory' ) }
      time = { check_max( 2.h * task.attempt, 'time' ) }
   }
   withName:bwa {
      cpus = { check_max( 8, 'cpus' ) }
      memory = { check_max( 16.GB * task.attempt, 'memory' ) }
      time = { check_max( 8.h * task.attempt, 'time' ) }
   }
   withName:dedup {
      cpus = { check_max( 8, 'cpus' ) }
      memory = { check_max( 16.GB * task.attempt, 'memory' ) }
      time = { check_max( 4.h * task.attempt, 'time' ) }
   }
   withName:genotyping_hc {
      cpus = { check_max( 8, 'cpus' ) }
      memory = { check_max( 16.GB * task.attempt, 'memory' ) }
      time = { check_max( 8.h * task.attempt, 'time' ) }
   }
   shell = ['/bin/bash', '-euo', 'pipefail']
   executor = 'awsbatch'
   queue = 'nextflow-ci'
}

env {
   PYTHONNOUSERSITE = 1
}

timeline {
   enabled = true
   file = './results/pipeline_info/execution_timeline.html'
}

report {
   enabled = true
   file = './results/pipeline_info/execution_report.html'
}

trace {
   enabled = true
   file = './results/pipeline_info/execution_trace.txt'
}

dag {
   enabled = true
   file = './results/pipeline_info/pipeline_dag.svg'
}

manifest {
   name = 'nf-core/eager'
   author = 'The nf-core/eager community'
   homePage = 'https://github.com/nf-core/eager'
   description = 'A fully reproducible ancient and modern DNA pipeline in Nextflow and with cloud support.'
   mainScript = 'main.nf'
   nextflowVersion = '!>=19.10.0'
   version = '2.2.0dev'
}

aws {
   region = 'eu-west-1'
   client {
      uploadChunkSize = 10485760
   }
   batch {
      cliPath = '/home/ec2-user/miniconda/bin/aws'
   }
}

workDir = 's3://nextflow-ci/scratch/vQZ2yYQK'
runName = 'astonishing_northcutt'

tower {
   enabled = true
   endpoint = '-'
}
jfy133 commented 4 years ago

Thanks @pditommaso Alex and I are investigating. Looks like the staging of the files download is resulting in corrupted FASTQs, dunno why.

jfy133 commented 4 years ago

Appears to be ENA instability. Running now!