Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

"exclude" samples aren't respected in SHINYNGS_STATICEXPLORATORY - Error in cor(matrices[[g]]) : supply both 'x' and 'y' or a matrix-like 'x' #196

Open
olgabot opened this issue Nov 8, 2023 · 5 comments · Fixed by #221
Open

"exclude" samples aren't respected in SHINYNGS_STATICEXPLORATORY - Error in cor(matrices[[g]]) : supply both 'x' and 'y' or a matrix-like 'x' #196

olgabot opened this issue Nov 8, 2023 · 5 comments · Fixed by #221
Assignees
@pinin4fjords
Labels
bug Something isn't working

Comments

@olgabot
Copy link

olgabot commented Nov 8, 2023 •
edited

Description of the bug

Hello,
I'm running this pipeline on the star_salmon/salmon.merged.gene_counts.tsv output from nf-core/rnaseq and am having an issue with the PLOT_EXPLORATORY step, which fails with a final error message of:

  [1] "Writing sample dendrogram..."
  null device
            1
  Error in cor(matrices[[g]]) :
    supply both 'x' and 'y' or a matrix-like 'x'
  Calls: madScore -> do.call -> lapply -> FUN -> cor -> cor
  Execution halted

Do you know what may be going on?

Below are the redacted parameters

Redacted parameters 
exploratory_final_assay = variance_stabilised
custom_config_base = https://raw.githubusercontent.com/nf-core/configs/master
monochrome-logs = false
validation-S3Path-check = false
affy_build_annotation = true
plaintext_email = false
features_metadata_cols = gene_id,gene_name,gene_biotype
gsea_rnd_type = no_balance
exploratory_cor_method = spearman
deseq2_min_replicates_for_replace = 7
affy_bgversion = 2
limma_p_value = 1
css_file = /.nextflow/assets/nf-core/differentialabundance/assets/nf-core_style.css
filtering_min_samples = 1
proteus_plotmv_loess = true
gsea_order = descending
proteus_round_digits = -1
features_id_col = gene_id
gsea_median = false
exploratory_clustering_method = ward.D2
exploratory_palette_name = Set1
version = false
publish_dir_mode = copy
input = [samplesheet.csv](https://api.tower.nf/workspaces/REDACTED/samplesheet.csv)
affy_background = true
gsea_zip_report = false
study_type = rnaseq
filtering_min_abundance = 1
validationSkipDuplicateCheck = false
gsea_plot_top_x = 20
validationSchemaIgnoreParams = genomes,igenomes_base
differential_subset_to_contrast_samples = false
features_gtf_feature_type = transcript
limma_block = None
gsea_set_min = 15
gsea_rnd_seed = timestamp
validation-skip-duplicate-check = false
report_description = None
deseq2_independent_filtering = true
limma_correlation = None
querygse = None
proteus_palette_name = Set1
gsea_save_rnd_lists = false
limma_lfc = 0
matrix = s3://REDACTED/star_salmon/salmon.merged.gene_counts.tsv
observations_name_col = sample
limma_trend = false
shinyngs_build_app = true
shinyngs_shinyapps_account = None
custom_config_version = master
study_abundance_type = counts
proteus_measurecol_prefix = LFQ intensity
proteus_norm_function = normalizeMedian
gsea_set_max = 500
affy_file_name_col = file
deseq2_vst_nsub = 1000
citations_file = /.nextflow/assets/nf-core/differentialabundance/CITATIONS.md
differential_feature_name_column = gene_name
limma_proportion = 0.01
gsea_nperm = 1000
differential_max_pval = 1
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/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 = /.nextflow/assets/nf-core/differentialabundance/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 = /.nextflow/assets/nf-core/differentialabundance/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 = /.nextflow/assets/nf-core/differentialabundance/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 = /.nextflow/assets/nf-core/differentialabundance/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 = /.nextflow/assets/nf-core/differentialabundance/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 = /.nextflow/assets/nf-core/differentialabundance/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
logo_file = /.nextflow/assets/nf-core/differentialabundance/docs/images/nf-core-differentialabundance_logo_light.png
affy_rm_mask = false
exploratory_main_variable = auto_pca
exploratory_n_features = 500
deseq2_minmu = 0.5
limma_adjust_method = BH
gsea_gene_sets = None
affy_rm_extra = false
gsea_norm = meandiv
differential_palette_name = Set1
outdir = s3://REDACTED
limma_winsor_tail_p = 0.05,0.1
help = false
shinyngs_deploy_to_shinyapps_io = false
deseq2_alt_hypothesis = greaterAbs
differential_foldchanges_logged = true
deseq2_test = Wald
limma_spacing = None
study_name = RNA-Seq_Project
report_author = None
monochrome_logs = false
deseq2_alpha = 0.1
max_cpus = 16
differential_qval_column = padj
gsea_sort = real
limma_robust = false
limma_stdev_coef_lim = 0.1,4
validationFailUnrecognisedParams = false
differential_min_fold_change = 2
gsea_make_sets = true
features_gtf_table_first_field = gene_id
exploratory_whisker_distance = 1.5
max_time = 240.h
sizefactors_from_controls = false
differential_feature_id_column = gene_id
deseq2_lfc_threshold = 0
validate_params = true
validationShowHiddenParams = false
differential_pval_column = pvalue
exploratory_mad_threshold = -5
affy_destructive = false
gsea_num = 100
validationS3PathCheck = false
affy_cdfname = None
deseq2_fit_type = parametric
exploratory_assay_names = raw,normalised,variance_stabilised
igenomes_base = s3://ngi-igenomes/igenomes
features_type = gene
gsea_run = false
validation-show-hidden-params = false
validation-lenient-mode = false
differential_file_suffix = .deseq2.results.tsv
observations_type = sample
deseq2_sf_type = ratio
features_name_col = gene_name
deseq2_p_adjust_method = BH
deseq2_vs_blind = true
deseq2_vs_method = vst
gsea_scoring_scheme = weighted
gsea_permute = phenotype
limma_confint = false
shinyngs_shinyapps_app_name = None
deseq2_use_t = false
gsea_metric = Signal2Noise
max_memory = 128.GB
monochromeLogs = false
deseq2_cores = 1
contrasts = https://api.tower.nf/workspaces/REDACTED/contrasts.csv
differential_max_qval = 0.05
report_file = /.nextflow/assets/nf-core/differentialabundance/assets/differentialabundance_report.Rmd
report_title = None
affy_cel_files_archive = None
affy_rm_outliers = false
validationLenientMode = false
proteus_plotsd_method = violin
igenomes_ignore = false
validation-fail-unrecognised-params = false
observations_id_col = sample
limma_method = ls
shinyngs_guess_unlog_matrices = true
validation-schema-ignore-params = genomes,igenomes_base
differential_fc_column = log2FoldChange
deseq2_shrink_lfc = true

The final part of the error message is:

  [1] "Writing sample dendrogram..."
  null device
            1
  Error in cor(matrices[[g]]) :
    supply both 'x' and 'y' or a matrix-like 'x'
  Calls: madScore -> do.call -> lapply -> FUN -> cor -> cor
  Execution halted

Following this trace:

  1. This repo imports SHINYNGS_STATICEXPLORATORY as PLOT_EXPLORATORY:

    differentialabundance/workflows/differentialabundance.nf

    Line 110 in 44c449b

    include { SHINYNGS_STATICEXPLORATORY as PLOT_EXPLORATORY } from '../modules/nf-core/shinyngs/staticexploratory/main'
  2. Following the nf-core/modules repo, SHINYNGS_STATICEXPLORATORY (Shinyngs/staticexploratory modules#2364) calls exploratory_plots.R
  3. Stack trace references madScore in exploratory_plots.R from pinin4fjords/shinyngs: https://github.com/pinin4fjords/shinyngs/blob/develop/exec/exploratory_plots.R#L339

Command used and terminal output

I'm submitting this job via Seqera Platform which uses the following redacted command:


nextflow run 'https://github.com/nf-core/differentialabundance' \
		 -name REDACTED_2 \
		 -params-file 'https://api.tower.nf/ephemeral/REDACTED.json' \
		 -with-tower \
		 -r 44c449be0a703c64a7c323a2b431ec6627194f00 \
		 -resume REDACTED

Relevant files

Here's the redacted log of this error:

Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY (TREATMENT)'

Caused by:
  Essential container in task exited

Command executed:

  exploratory_plots.R \
      --sample_metadata "sample_metadata.tsv" \
      --feature_metadata "matrix_as_anno.feature_metadata.tsv" \
      --assay_files "salmon.merged.gene_counts.assay.tsv,all.normalised_counts.tsv,all.vst.tsv" \
      --contrast_variable "TREATMENT" \
      --outdir "TREATMENT" \
      --sample_id_col "sample" --feature_id_col "gene_id" --assay_names "raw,normalised,variance_stabilised" --final_assay "variance_stabilised" --outlier_mad_threshold -5 --palette_name "Set1"

  cat <<-END_VERSIONS > versions.yml
  "NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY":
      r-base: $(echo $(R --version 2>&1) | sed 's/^.*R version //; s/ .*$//')
      r-shinyngs: $(Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))")
  END_VERSIONS

Command exit status:
  1

Command output:
  [1] "Reading inputs..."
  [1] "Creating output paths..."
  [1] "Writing boxplots..."
  [1] "... static"
  null device
            1
  [1] "Writing density plots..."
  [1] "... static"
  null device
            1
  [1] "Writing PCA plots..."
  [1] "...static (2d)"
  [1] "...static (3d)"
  NULL
  [1] "Writing sample dendrogram..."
  null device
            1

Command error:
  (more omitted..)
      anyDuplicated, aperm, append, as.data.frame, basename, cbind,
      colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
      get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
      match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
      Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
      table, tapply, union, unique, unsplit, which.max, which.min
  Loading required package: S4Vectors
  Attaching package: ‘S4Vectors’
  The following object is masked from ‘package:utils’:
      findMatches
  The following objects are masked from ‘package:base’:
      expand.grid, I, unname
  Loading required package: IRanges
  Loading required package: GenomeInfoDb
  Loading required package: Biobase
  Welcome to Bioconductor
      Vignettes contain introductory material; view with
      'browseVignettes()'. To cite Bioconductor, see
      'citation("Biobase")', and for packages 'citation("pkgname")'.
  Attaching package: ‘Biobase’
  The following object is masked from ‘package:MatrixGenerics’:
      rowMedians
  The following objects are masked from ‘package:matrixStats’:
      anyMissing, rowMedians
  Attaching package: ‘shinyngs’
  The following object is masked from ‘package:MatrixGenerics’:
      colMedians
  The following object is masked from ‘package:matrixStats’:
      colMedians
  [1] "Reading inputs..."
  [1] "Creating output paths..."
  [1] "Writing boxplots..."
  [1] "... static"
  null device
            1
  [1] "Writing density plots..."
  [1] "... static"
  null device
            1
  [1] "Writing PCA plots..."
  [1] "...static (2d)"
  [1] "...static (3d)"
  NULL
  [1] "Writing sample dendrogram..."
  null device
            1
  Error in cor(matrices[[g]]) :
    supply both 'x' and 'y' or a matrix-like 'x'
  Calls: madScore -> do.call -> lapply -> FUN -> cor -> cor
  Execution halted

Work dir:
  s3://REDACTED/scratch/3jFH9XRwVZ3oVL/ff/54c1599dfd4830a927ff33f1caa023

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

System information

This is running on AWS Batch via Sequera Tower.
@olgabot olgabot added the bug Something isn't working label Nov 8, 2023
@olgabot olgabot mentioned this issue Nov 27, 2023
Open
@olgabot
Copy link
Author

olgabot commented Nov 29, 2023

Hello, I've done a bit of digging, and I think this error is happening because exclude samples in my --contrasts file aren't getting excluded in the ShinyNGS Exploratory Plot generation.

Digging into one of the runs, I saw that this plot has three categories: green, blue, and red. But it should only show blue and red, the green samples shouldn't be there in this comparison:

image

My contrasts file (redacted) is like this, as a nicely formatted table:

id variable reference target blocking exclude_samples_col exclude_samples_values
A_vs_B A_vs_B groupA groupB A_vs_B_exclude TRUE
B_vs_C B_vs_C groupB groupC B_vs_C_exclude TRUE

And then the samplesheet is like this:

sample fastq_1 fastq_2 A_vs_B A_vs_B_exclude B_vs_C B_vs_C_exclude
groupA_sample1 groupA_sample1_R1_001.fastq.gz groupA_sample1_R1_001.fastq.gz_R2_001.fastq.gz groupA FALSE   TRUE
groupA_sample2 groupA_sample2_R1_001.fastq.gz groupA_sample2_R1_001.fastq.gz_R2_001.fastq.gz groupA FALSE   TRUE
groupA_sample3 groupA_sample3_R1_001.fastq.gz groupA_sample3_R1_001.fastq.gz_R2_001.fastq.gz groupA FALSE   TRUE
groupB_sample1 groupB_sample1_R1_001.fastq.gz groupB_sample1_R1_001.fastq.gz_R2_001.fastq.gz groupB FALSE groupB FALSE
groupB_sample2 groupB_sample2_R1_001.fastq.gz groupB_sample2_R1_001.fastq.gz_R2_001.fastq.gz groupB FALSE groupB FALSE
groupB_sample3 groupB_sample3_R1_001.fastq.gz groupB_sample3_R1_001.fastq.gz_R2_001.fastq.gz groupB FALSE groupB FALSE
groupC_sample1 groupC_sample1_R1_001.fastq.gz groupC_sample1_R1_001.fastq.gz_R2_001.fastq.gz   TRUE groupC FALSE
groupC_sample2 groupC_sample2_R1_001.fastq.gz groupC_sample2_R1_001.fastq.gz_R2_001.fastq.gz   TRUE groupC FALSE
groupC_sample3 groupC_sample3_R1_001.fastq.gz groupC_sample3_R1_001.fastq.gz_R2_001.fastq.gz   TRUE groupC FALSE

So I think the issue is in providing matrices for EXPLORATORY_PLOTS from SHINYNGS, to remove the exclude samples. Or to provide a non-null value for the exclude samples -- I'll try this for now and let you know.

@olgabot olgabot changed the title Error in cor(matrices[[g]]) : supply both 'x' and 'y' or a matrix-like 'x' "exclude" samples aren't respected in SHINYNGS_STATICEXPLORATORY - Error in cor(matrices[[g]]) : supply both 'x' and 'y' or a matrix-like 'x' Nov 29, 2023
@olgabot
Copy link
Author

olgabot commented Nov 29, 2023

Update: Still getting the same error, even when the empty/null/None/NA values in A_vs_B are replaced with "Other":

sample fastq_1 fastq_2 A_vs_B A_vs_B_exclude B_vs_C B_vs_C_exclude
groupA_sample1 groupA_sample1_R1_001.fastq.gz groupA_sample1_R1_001.fastq.gz_R2_001.fastq.gz groupA FALSE Other TRUE
groupA_sample2 groupA_sample2_R1_001.fastq.gz groupA_sample2_R1_001.fastq.gz_R2_001.fastq.gz groupA FALSE Other TRUE
groupA_sample3 groupA_sample3_R1_001.fastq.gz groupA_sample3_R1_001.fastq.gz_R2_001.fastq.gz groupA FALSE Other TRUE
groupB_sample1 groupB_sample1_R1_001.fastq.gz groupB_sample1_R1_001.fastq.gz_R2_001.fastq.gz groupB FALSE groupB FALSE
groupB_sample2 groupB_sample2_R1_001.fastq.gz groupB_sample2_R1_001.fastq.gz_R2_001.fastq.gz groupB FALSE groupB FALSE
groupB_sample3 groupB_sample3_R1_001.fastq.gz groupB_sample3_R1_001.fastq.gz_R2_001.fastq.gz groupB FALSE groupB FALSE
groupC_sample1 groupC_sample1_R1_001.fastq.gz groupC_sample1_R1_001.fastq.gz_R2_001.fastq.gz Other TRUE groupC FALSE
groupC_sample2 groupC_sample2_R1_001.fastq.gz groupC_sample2_R1_001.fastq.gz_R2_001.fastq.gz Other TRUE groupC FALSE
groupC_sample3 groupC_sample3_R1_001.fastq.gz groupC_sample3_R1_001.fastq.gz_R2_001.fastq.gz Other TRUE groupC FALSE

@pinin4fjords
Copy link
Member

Thanks for the report and the detective work- I'll look into this soon!

@pinin4fjords pinin4fjords self-assigned this Dec 4, 2023
@pinin4fjords
Copy link
Member

So, I can't reproduce this error exactly. For example, I unset the sample grouping variable in the test profile for one sample, and whilst it plotted a group with an empty legend entry, I didn't get an error at the dendrogram stage.

I'm making a PR here to prevent unlabelled samples getting plotted, and I notice a fix is also needed for GSEA.

It's important to note that the exploratory script isn't designed to plot per contrast, just per unique contrast variable, and does not pay any attention to the exclude_samples column in the contrast.

I hope that the above PR may help your case (once we update the module, and update the module in the workflow), but if not you will need to provide me with something reproducible for me to do more.

@pinin4fjords pinin4fjords mentioned this issue Jan 8, 2024
Merged
10 tasks
@pinin4fjords pinin4fjords linked a pull request Jan 10, 2024 that will close this issue
Update shinyngs modules to address density plots issue #221
Merged
10 tasks
@pinin4fjords
Copy link
Member

@olgabot could you test with current dev to see if the issue persists after the above fixes?

@tracelail tracelail mentioned this issue Feb 2, 2024
Open
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@pinin4fjords pinin4fjords

Labels
bug Something isn't working
Projects
None yet
Milestone
No milestone
Development

Successfully merging a pull request may close this issue.

Update shinyngs modules to address density plots issue nf-core/differentialabundance
2 participants
@olgabot @pinin4fjords