search

nextflow-io / nf-prov

Apache License 2.0
23 stars 11 forks source link

Render nested params correctly #11

Closed bentsherman closed 11 months ago

bentsherman commented 11 months ago

The nf-core/rnaseq pipeline has a params section genomes which contains many nested params. Currently this param is rendered as follows in the BCO manifest:

        {
            "param": "genomes",
            "value": "[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/version0.6.0/, 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:/home/bent/.nextflow/assets/nf-core/rnaseq/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/version0.6.0/, 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:/home/bent/.nextflow/assets/nf-core/rnaseq/assets/blacklists/hg38-blacklist.bed], CHM13:[fasta:s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa, bwa:s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/, bwamem2:s3://ngi-igenomes/igenomes/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/, gtf:s3://ngi-igenomes/igenomes/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf, gff:ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz, mito_name:chrM], 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/version0.6.0/, 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:/home/bent/.nextflow/assets/nf-core/rnaseq/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/version0.6.0/, 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/version0.6.0/, 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/version0.6.0/, 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/version0.6.0/, 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/version0.6.0/, 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/version0.6.0/, 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/version0.6.0/, 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/version0.6.0/, 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/version0.6.0/, 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/version0.6.0/, 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/version0.6.0/, 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/version0.6.0/, 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/version0.6.0/, 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/version0.6.0/, 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_5.0:[fasta:s3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa, bwa:s3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/, bowtie2:s3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/Bowtie2Index/, star:s3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/STARIndex/, bismark:s3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BismarkIndex/, gtf:s3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.gtf, bed12:s3://ngi-igenomes/igenomes/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.bed, 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/version0.6.0/, 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/version0.6.0/, 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/version0.6.0/, 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/version0.6.0/, 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/version0.6.0/, 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/version0.6.0/, 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/version0.6.0/, 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:/home/bent/.nextflow/assets/nf-core/rnaseq/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/version0.6.0/, 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:/home/bent/.nextflow/assets/nf-core/rnaseq/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/version0.6.0/, 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:/home/bent/.nextflow/assets/nf-core/rnaseq/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/version0.6.0/, 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/version0.6.0/, 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/version0.6.0/, 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/version0.6.0/, 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, macs_gsize:1.37e9], 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/version0.6.0/, 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/version0.6.0/, 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/version0.6.0/, 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/version0.6.0/, 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/version0.6.0/, 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/version0.6.0/, 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/version0.6.0/, 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]]",
            "step": "0"
        }

These params should be flattened and rendered as separate params:

Should be enough to do params.flatten() (aka Bolts.flatten(params))