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Description of the bug

Hello, I am a co-worker of olgabot and this issue is following issue 196. Running the nf-core/differentialabundance pipeline with the current dev version has resolved the PLOT_EXPLORATORY step issue but a potentially similar issue arises later on in the pipeline at the MAKE_REPORT_BUNDLE step. In addition, although the SHINYNGS_APP step succeeds and publishes a shiny app to shinyapp.io, it has errors and crashes.

- Running the nf-core/differentialabundance pipeline. The `RE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE`, fails with the error message:

    Error in \`cor()\`:
	  ! supply both 'x' and 'y' or a matrix-like 'x'
	  Backtrace:
	   1. BiocGenerics::lapply(...)
	   2. base::lapply(...)
	   3. FUN(X[[i]], ...)
	   4. shinyngs::madScore(...)
	   6. base::lapply(...)
	   7. shinyngs (local) FUN(X[[i]], ...)
	   9. stats::cor(matrices[[g]])
	  Execution halted

- Below are the 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,
    "gprofiler2_max_qval": 0.05,
    "gprofiler2_significant": true,
    "exploratory_clustering_method": "ward.D2",
    "exploratory_palette_name": "Set1",
    "report_scree": true,
    "version": false,
    "publish_dir_mode": "copy",
    "input": "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": "REDACTED-matrix.tsv",
    "observations_name_col": "sample",
    "limma_trend": false,
    "shinyngs_build_app": true,
    "shinyngs_shinyapps_account": "REDACTED-account-name",
    "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",
    "gprofiler2_measure_underrepresentation": false,
    "differential_feature_name_column": "gene_name",
    "limma_proportion": 0.01,
    "gsea_nperm": 1000,
    "gprofiler2_background_file": "auto",
    "email": "[email protected]",
    "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",
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    "report_author": "None",
    "gprofiler2_min_diff": 1,
    "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,
    "email_on_fail": "[email protected]",
    "gprofiler2_domain_scope": "annotated",
    "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": "REDACTED-app-name",
    "deseq2_use_t": false,
    "gsea_metric": "Signal2Noise",
    "max_memory": "128.GB",
    "monochromeLogs": false,
    "deseq2_cores": 1,
    "contrasts": "REDACTED--contrasts.csv",
    "gprofiler2_run": false,
    "differential_max_qval": 0.05,
    "gprofiler2_palette_name": "Blues",
    "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,
    "report_round_digits": 4,
    "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
}

Command used and terminal output

nextflow run 'https://github.com/nf-core/differentialabundance'
		 -name REDACTED-run_name
		 -params-file 'https://api.tower.nf/ephemeral/XWd0e6Qm6HginhEUIhu8gQ.json'
		 -with-tower
		 -r dev



### Relevant files

	- Here is the full redacted error:

The exit status of the task that caused the workflow execution to fail was: 1

Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK (REDACTED-study_name)'

Caused by: Essential container in task exited

Command executed:

Dump .params.yml heredoc (section will be empty if parametrization is disabled)

cat <<"END_PARAMS_SECTION" > ./.params.yml cpus: 2 artifact_dir: artifacts input_dir: ./ meta: id: REDACTED-study_name study_name: REDACTED-study_name study_type: rnaseq study_abundance_type: counts report_file: /.nextflow/assets/nf-core/differentialabundance/assets/differentialabundance_report.Rmd report_title: None report_author: None report_description: None report_scree: true report_round_digits: 4 observations_type: sample observations_id_col: sample observations_name_col: sample features: matrix_as_anno.feature_metadata.tsv features_type: gene features_id_col: gene_id features_name_col: gene_name features_metadata_cols: gene_id,gene_name,gene_biotype features_log2_assays: null features_gtf_feature_type: transcript features_gtf_table_first_field: gene_id filtering_min_samples: 1 filtering_min_abundance: 1 filtering_min_proportion: null filtering_grouping_var: null exploratory_main_variable: auto_pca exploratory_clustering_method: ward.D2 exploratory_cor_method: spearman exploratory_n_features: 500 exploratory_whisker_distance: 1.5 exploratory_mad_threshold: -5 exploratory_assay_names: raw,normalised,variance_stabilised exploratory_final_assay: variance_stabilised exploratory_palette_name: Set1 differential_file_suffix: .deseq2.results.tsv differential_feature_id_column: gene_id differential_feature_name_column: gene_name differential_fc_column: log2FoldChange differential_pval_column: pvalue differential_qval_column: padj differential_min_fold_change: 2 differential_max_pval: 1 differential_max_qval: 0.05 differential_foldchanges_logged: true differential_palette_name: Set1 differential_subset_to_contrast_samples: false deseq2_test: Wald deseq2_fit_type: parametric deseq2_sf_type: ratio deseq2_min_replicates_for_replace: 7 deseq2_use_t: false deseq2_lfc_threshold: 0 deseq2_alt_hypothesis: greaterAbs deseq2_independent_filtering: true deseq2_p_adjust_method: BH deseq2_alpha: 0.1 deseq2_minmu: 0.5 deseq2_vs_method: vst deseq2_shrink_lfc: true deseq2_cores: 1 deseq2_vs_blind: true deseq2_vst_nsub: 1000 gene_sets_files: null observations: REDACTED-file.tsv raw_matrix: rsem.merged.gene_counts.assay.tsv normalised_matrix: all.normalised_counts.tsv variance_stabilised_matrix: all.vst.tsv contrasts_file: REDACTED-file.tsv versions_file: software_versions.yml logo: nf-core-differentialabundance_logo_light.png css: nf-core_style.css citations: CITATIONS.md END_PARAMS_SECTION

Create output directory

mkdir artifacts

Set parallelism for BLAS/MKL etc. to avoid over-booking of resources

export MKL_NUM_THREADS="2" export OPENBLAS_NUM_THREADS="2" export OMP_NUM_THREADS="2"

Work around https://github.com/rstudio/rmarkdown/issues/1508

If the symbolic link is not replaced by a physical file

output- and temporary files will be written to the original directory.

mv "differentialabundance_report.Rmd" "differentialabundance_report.Rmd.orig" cp -L "differentialabundance_report.Rmd.orig" "REDACTED-study_name.Rmd"

Render notebook

Rscript - <<EOF params = yaml::read_yaml('.params.yml')

  # Instead of rendering with params, produce a version of the R
  # markdown with param definitions set, so the notebook itself can
  # be reused
  rmd_content <- readLines('REDACTED-study_name.Rmd')

  # Extract YAML content between the first two '---'
  start_idx <- which(rmd_content == "---")[1]
  end_idx <- which(rmd_content == "---")[2]
  rmd_yaml_content <- paste(rmd_content[(start_idx+1):(end_idx-1)], collapse = "\n")
  rmd_params <- yaml::yaml.load(rmd_yaml_content)

  # Override the params
  rmd_params[['params']] <- modifyList(rmd_params[['params']], params)

  # Recursive function to add 'value' to list elements, except for top-level
  add_value_recursively <- function(lst, is_top_level = FALSE) {
      if (!is.list(lst)) {
          return(lst)
      }

      lst <- lapply(lst, add_value_recursively)
      if (!is_top_level) {
          lst <- list(value = lst)
      }
      return(lst)
  }

  # Reformat nested lists under 'params' to have a 'value' key recursively
  rmd_params[['params']] <- add_value_recursively(rmd_params[['params']], is_top_level = TRUE)

  # Convert back to YAML string
  updated_yaml_content <- as.character(yaml::as.yaml(rmd_params))

  # Remove the old YAML content
  rmd_content <- rmd_content[-((start_idx+1):(end_idx-1))]

  # Insert the updated YAML content at the right position
  rmd_content <- append(rmd_content, values = unlist(strsplit(updated_yaml_content, split = "\n")), after = start_idx)

  writeLines(rmd_content, 'REDACTED-study_name.parameterised.Rmd')

  # Render based on the updated file
  rmarkdown::render('REDACTED-study_name.parameterised.Rmd', output_file='REDACTED-study_name.html', envir = new.env())
  writeLines(capture.output(sessionInfo()), "session_info.log")

EOF

cat <<-END_VERSIONS > versions.yml "NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK": rmarkdown: $(Rscript -e "cat(paste(packageVersion('rmarkdown'), collapse='.'))") END_VERSIONS

Command exit status: 1

Command output: 1/72
2/72 [unnamed-chunk-1] 3/72
4/72 [unnamed-chunk-2] 5/72
6/72 [unnamed-chunk-3] 7/72
8/72 [unnamed-chunk-4] 9/72
10/72 [setup]
11/72
12/72 [unnamed-chunk-5] 13/72
14/72 [unnamed-chunk-6] 15/72
16/72 [unnamed-chunk-7] 17/72
18/72 [unnamed-chunk-8] 19/72
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38/72 [unnamed-chunk-18] 39/72
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42/72 [unnamed-chunk-20] 43/72
44/72 [unnamed-chunk-21]

Command error: (more omitted..) 7/72
8/72 [unnamed-chunk-4] 9/72
10/72 [setup]
11/72
12/72 [unnamed-chunk-5] 13/72
14/72 [unnamed-chunk-6] 15/72
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24/72 [unnamed-chunk-11] 25/72
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42/72 [unnamed-chunk-20] 43/72
44/72 [unnamed-chunk-21] Quitting from lines 706-752 [unnamed-chunk-21] (REDACTED-study_name.Rmd) Error in cor(): ! supply both 'x' and 'y' or a matrix-like 'x' Backtrace:

BiocGenerics::lapply(...)
base::lapply(...)
FUN(X[[i]], ...)
shinyngs::madScore(...)
base::lapply(...)
shinyngs (local) FUN(X[[i]], ...)
stats::cor(matrices[[g]]) Execution halted

Work dir: REDACTED-s3://path

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh


	-  The resulting shinyapp.io launches to the dashboard but has errors and crashes during exploration (ex. Trying to view PCA). The only thing viewable before crashing is the sample data table. Below are some screen shots for context:
![dashboard-issue](https://github.com/nf-core/differentialabundance/assets/128841322/a092fc78-65ba-4450-b7bf-2026ff234ac9)
![pca-crash](https://github.com/nf-core/differentialabundance/assets/128841322/b35d1e73-145f-42ab-a67a-0cb5315d4038)


### System information

This is running on AWS Batch via Sequera Tower.

Feb 02 '24 13:02 tracelail

Hey there, thanks for the bug report! Without the dataset, I won't be able to look into this. Maybe someone else stumbles across this error as well and can share their data for reproducing :)

Feb 15 '24 07:02 WackerO

Archive.zip Hello,

Hope you are doing well! I have created some reproducible data to elicit the error: "Error in cor(): supply both 'x' and 'y' or a matrix-like 'x'". Attached you will find the *example-params.json*, *example-samplesheet.csv*, *example-contrasts.csv*, and *example-matrix.tsv*.

The attached data will produce the error below when running the nf-core/differentialabundance pipeline:


<details><summary>"nextflow run" output </summary>

   ~/local-diffabundance ▓▒░ make nextflow-differentialabundance-example ░▒▓ ✔  base   09:20:43  nextflow run nf-core/differentialabundance -r 1.5.0 -profile podman -params-file example-params.json

N E X T F L O W ~ version 24.04.3

Launching https://github.com/nf-core/differentialabundance [redacted_run] DSL2 - revision: 3dd360fed0 [1.5.0]

                                    ,--./,-.
    ___     __   __   __   ___     /,-._.--~'

|\ | | / `/ \ |) | } { | \| | \, \/ | \ |___ \`-.,-`-,` .,._,' nf-core/differentialabundance v1.5.0-g3dd360f

Core Nextflow options revision : 1.5.0 runName : redacted_run containerEngine : podman container : [RMARKDOWNNOTEBOOK:biocontainers/r-shinyngs:1.8.8--r43hdfd78af_0] launchDir : /Users/user/local-diffabundance workDir : /Users/user/local-diffabundance/work projectDir : /Users/user/.nextflow/assets/nf-core/differentialabundance userName : user profile : podman configFiles :

Input/output options study_name : redacted_study_name input : s3://company-workflow-results/analyses/CG-2024-775/2024-07-18--CG-2024-775_example-samplesheet.csv contrasts : s3://company-workflow-results/analyses/CG-2024-775/2024-07-18--CG-2024-775__example-contrasts.csv outdir : /Users/user/local-diffabundance/outdir-example

Abundance values matrix : s3://company-workflow-results/analyses/CG-2024-775/2024-07-18--CG-2024-775_rsem.merged.example-gene_counts.tsv

Filtering filtering_min_abundance : 1 filtering_min_samples : 1

Exploratory analysis exploratory_log2_assays : raw,normalised

Differential analysis differential_min_fold_change: 2 differential_max_pval : 1

Limma specific options (microarray only) limma_p_value : 1

gprofiler2 gprofiler2_correction_method: gSCS gprofiler2_background_file : auto

Shiny app settings shinyngs_shinyapps_account : company-rnaseq shinyngs_shinyapps_app_name : redacted_study_name

Reporting options email : [email protected]

Max job request options max_cpus : 7 max_memory : 16.GB

!! Only displaying parameters that differ from the pipeline defaults !!

If you use nf-core/differentialabundance for your analysis please cite:

The pipeline https://doi.org/10.5281/zenodo.7568000
The nf-core framework https://doi.org/10.1038/s41587-020-0439-x
Software dependencies https://github.com/nf-core/differentialabundance/blob/master/CITATIONS.md

WARN: Access to undefined parameter gtf -- Initialise it to a default value eg. params.gtf = some_value executor > local (44) [3a/4ab044] NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR (2024-07-18--CG-2024-775_example-samplesheet.csv) [100%] 1 of 1 ✔ [cc/ed5dee] NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER ([id:redacted_study_name]) [100%] 1 of 1 ✔ [d9/8e4162] NFC…-timepoint1h, blocking:, exclude_samples_col:group_treatment2_vs_treatment1_timepoint1h_exclude, exclude_samples_values:True]) [100%] 1 of 1 ✔ [ed/9b34c0] NFC…replicate;bio_replicate, exclude_samples_col:group_treatment2_vs_treatment1_timepoint3h_exclude, exclude_samples_values:True]) [100%] 12 of 12 ✔ [b5/f07c30] NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:FILTER_DIFFTABLE (12) [100%] 12 of 12 ✔ [3e/4e7f12] NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY (group_treatment2_vs_treatment1_timepoint1h) [100%] 3 of 3 ✔ [97/a86960] NFC…ALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL (group_treatment2_vs_treatment1_timepoint3h_block_biorep_block_techbiorep) [100%] 12 of 12 ✔ [55/fdb625] NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP (redacted_study_name) [100%] 1 of 1 ✔ [24/2e6497] NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK (redacted_study_name) [ 0%] 0 of 1 [- ] NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE - ERROR ~ Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK (redacted_study_name)'

Caused by: Process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK (redacted_study_name) terminated with an error exit status (1)

Command executed:

Dump .params.yml heredoc (section will be empty if parametrization is disabled)

cat <<"END_PARAMS_SECTION" > ./.params.yml cpus: 2 artifact_dir: artifacts input_dir: ./ meta: id: redacted_study_name study_name: redacted_study_name study_type: rnaseq study_abundance_type: counts report_file: !!org.codehaus.groovy.runtime.GStringImpl {} report_title: 'null' report_author: 'null' report_contributors: null report_description: 'null' report_scree: true report_round_digits: 4 observations_type: sample observations_id_col: sample observations_name_col: null features: matrix_as_anno.feature_metadata.tsv features_type: gene features_id_col: gene_id features_name_col: gene_name features_metadata_cols: gene_id,gene_name,gene_biotype features_gtf_feature_type: transcript features_gtf_table_first_field: gene_id filtering_min_samples: 1 filtering_min_abundance: 1 filtering_min_proportion: null filtering_grouping_var: null filtering_min_proportion_not_na: 0.5 filtering_min_samples_not_na: null exploratory_main_variable: auto_pca exploratory_clustering_method: ward.D2 exploratory_cor_method: spearman exploratory_n_features: 500 exploratory_whisker_distance: 1.5 exploratory_mad_threshold: -5 exploratory_assay_names: raw,normalised,variance_stabilised exploratory_final_assay: variance_stabilised exploratory_log2_assays: raw,normalised exploratory_palette_name: Set1 differential_file_suffix: null differential_feature_id_column: gene_id differential_feature_name_column: gene_name differential_fc_column: log2FoldChange differential_pval_column: pvalue differential_qval_column: padj differential_min_fold_change: 2 differential_max_pval: 1 differential_max_qval: 0.05 differential_foldchanges_logged: true differential_palette_name: Set1 differential_subset_to_contrast_samples: false deseq2_test: Wald deseq2_fit_type: parametric deseq2_sf_type: ratio deseq2_min_replicates_for_replace: 7 deseq2_use_t: false deseq2_lfc_threshold: 0 deseq2_alt_hypothesis: greaterAbs deseq2_independent_filtering: true deseq2_p_adjust_method: BH deseq2_alpha: 0.1 deseq2_minmu: 0.5 deseq2_vs_method: vst deseq2_shrink_lfc: true deseq2_cores: 1 deseq2_vs_blind: true deseq2_vst_nsub: 1000 gene_sets_files: 'null' observations: 2024-07-18--CG-2024-775_example-samplesheet.sample_metadata.tsv raw_matrix: 2024-07-18--CG-2024-775_rsem.merged.example-gene_counts.assay.tsv normalised_matrix: all.normalised_counts.tsv variance_stabilised_matrix: all.vst.tsv contrasts_file: 2024-07-18--CG-2024-775__example-contrasts.contrasts_file.tsv versions_file: collated_versions.yml logo: nf-core-differentialabundance_logo_light.png css: nf-core_style.css citations: CITATIONS.md END_PARAMS_SECTION

Create output directory

mkdir artifacts

Set parallelism for BLAS/MKL etc. to avoid over-booking of resources

export MKL_NUM_THREADS="2" export OPENBLAS_NUM_THREADS="2" export OMP_NUM_THREADS="2"

Work around https://github.com/rstudio/rmarkdown/issues/1508

If the symbolic link is not replaced by a physical file

output- and temporary files will be written to the original directory.

mv "differentialabundance_report.Rmd" "differentialabundance_report.Rmd.orig" cp -L "differentialabundance_report.Rmd.orig" "redacted_study_name.Rmd"

Render notebook

Rscript - <<EOF params = yaml::read_yaml('.params.yml')

  # Instead of rendering with params, produce a version of the R
  # markdown with param definitions set, so the notebook itself can
  # be reused
  rmd_content <- readLines('redacted_study_name.Rmd')

  # Extract YAML content between the first two '---'
  start_idx <- which(rmd_content == "---")[1]
  end_idx <- which(rmd_content == "---")[2]
  rmd_yaml_content <- paste(rmd_content[(start_idx+1):(end_idx-1)], collapse = "\n")
  rmd_params <- yaml::yaml.load(rmd_yaml_content)

  # Override the params
  rmd_params[['params']] <- modifyList(rmd_params[['params']], params)

  # Recursive function to add 'value' to list elements, except for top-level
  add_value_recursively <- function(lst, is_top_level = FALSE) {
      if (!is.list(lst)) {
          return(lst)
      }

      lst <- lapply(lst, add_value_recursively)
      if (!is_top_level) {
          lst <- list(value = lst)
      }
      return(lst)
  }

  # Reformat nested lists under 'params' to have a 'value' key recursively
  rmd_params[['params']] <- add_value_recursively(rmd_params[['params']], is_top_level = TRUE)

  # Convert back to YAML string
  updated_yaml_content <- as.character(yaml::as.yaml(rmd_params))

  # Remove the old YAML content
  rmd_content <- rmd_content[-((start_idx+1):(end_idx-1))]

  # Insert the updated YAML content at the right position
  rmd_content <- append(rmd_content, values = unlist(strsplit(updated_yaml_content, split = "\n")), after = start_idx)

  writeLines(rmd_content, 'redacted_study_name.parameterised.Rmd')

  # Render based on the updated file
  rmarkdown::render('redacted_study_name.parameterised.Rmd', output_file='redacted_study_name.html', envir = new.env())
  writeLines(capture.output(sessionInfo()), "session_info.log")

EOF

cat <<-END_VERSIONS > versions.yml "NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK": rmarkdown: $(Rscript -e "cat(paste(packageVersion('rmarkdown'), collapse='.'))") END_VERSIONS

Command exit status: 1

Command output: 1/72 2/72 [unnamed-chunk-1] 3/72 4/72 [unnamed-chunk-2] 5/72 6/72 [unnamed-chunk-3] 7/72 8/72 [unnamed-chunk-4] 9/72 10/72 [setup] 11/72 12/72 [unnamed-chunk-5] 13/72 14/72 [unnamed-chunk-6] 15/72 16/72 [unnamed-chunk-7] 17/72 18/72 [unnamed-chunk-8] 19/72 20/72 [unnamed-chunk-9] 21/72 22/72 [unnamed-chunk-10] 23/72 24/72 [unnamed-chunk-11] 25/72 26/72 [unnamed-chunk-12] 27/72 28/72 [unnamed-chunk-13] 29/72 30/72 [unnamed-chunk-14] 31/72 32/72 [unnamed-chunk-15] 33/72 34/72 [unnamed-chunk-16] 35/72 36/72 [unnamed-chunk-17] 37/72 38/72 [unnamed-chunk-18] 39/72 40/72 [unnamed-chunk-19] 41/72 42/72 [unnamed-chunk-20] 43/72 44/72 [unnamed-chunk-21]

Command error: 8/72 [unnamed-chunk-4] 9/72 10/72 [setup] 11/72 12/72 [unnamed-chunk-5] 13/72 14/72 [unnamed-chunk-6] 15/72 16/72 [unnamed-chunk-7] executor > local (44) [3a/4ab044] NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR (2024-07-18--CG-2024-775_example-samplesheet.csv) [100%] 1 of 1 ✔ [cc/ed5dee] NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER ([id:redacted_study_name]) [100%] 1 of 1 ✔ [d9/8e4162] NFC…-timepoint1h, blocking:, exclude_samples_col:group_treatment2_vs_treatment1_timepoint1h_exclude, exclude_samples_values:True]) [100%] 1 of 1 ✔ [ed/9b34c0] NFC…replicate;bio_replicate, exclude_samples_col:group_treatment2_vs_treatment1_timepoint3h_exclude, exclude_samples_values:True]) [100%] 12 of 12 ✔ [b5/f07c30] NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:FILTER_DIFFTABLE (12) [100%] 12 of 12 ✔ [3e/4e7f12] NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY (group_treatment2_vs_treatment1_timepoint1h) [100%] 3 of 3 ✔ [97/a86960] NFC…ALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL (group_treatment2_vs_treatment1_timepoint3h_block_biorep_block_techbiorep) [100%] 12 of 12 ✔ [55/fdb625] NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP (redacted_study_name) [100%] 1 of 1 ✔ [24/2e6497] NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK (redacted_study_name) [100%] 1 of 1, failed: 1 ✘ [- ] NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE - Execution cancelled -- Finishing pending tasks before exit ERROR ~ Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK (redacted_study_name)'

Caused by: Process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK (redacted_study_name) terminated with an error exit status (1)

Command executed:

Dump .params.yml heredoc (section will be empty if parametrization is disabled)

cat <<"END_PARAMS_SECTION" > ./.params.yml cpus: 2 artifact_dir: artifacts input_dir: ./ meta: id: redacted_study_name study_name: redacted_study_name study_type: rnaseq study_abundance_type: counts report_file: !!org.codehaus.groovy.runtime.GStringImpl {} report_title: 'null' report_author: 'null' report_contributors: null report_description: 'null' report_scree: true report_round_digits: 4 observations_type: sample observations_id_col: sample observations_name_col: null features: matrix_as_anno.feature_metadata.tsv features_type: gene features_id_col: gene_id features_name_col: gene_name features_metadata_cols: gene_id,gene_name,gene_biotype features_gtf_feature_type: transcript features_gtf_table_first_field: gene_id filtering_min_samples: 1 filtering_min_abundance: 1 filtering_min_proportion: null filtering_grouping_var: null filtering_min_proportion_not_na: 0.5 filtering_min_samples_not_na: null exploratory_main_variable: auto_pca exploratory_clustering_method: ward.D2 exploratory_cor_method: spearman exploratory_n_features: 500 exploratory_whisker_distance: 1.5 exploratory_mad_threshold: -5 exploratory_assay_names: raw,normalised,variance_stabilised exploratory_final_assay: variance_stabilised exploratory_log2_assays: raw,normalised exploratory_palette_name: Set1 differential_file_suffix: null differential_feature_id_column: gene_id differential_feature_name_column: gene_name differential_fc_column: log2FoldChange differential_pval_column: pvalue differential_qval_column: padj differential_min_fold_change: 2 differential_max_pval: 1 differential_max_qval: 0.05 differential_foldchanges_logged: true differential_palette_name: Set1 differential_subset_to_contrast_samples: false deseq2_test: Wald deseq2_fit_type: parametric deseq2_sf_type: ratio deseq2_min_replicates_for_replace: 7 deseq2_use_t: false deseq2_lfc_threshold: 0 deseq2_alt_hypothesis: greaterAbs deseq2_independent_filtering: true deseq2_p_adjust_method: BH deseq2_alpha: 0.1 deseq2_minmu: 0.5 deseq2_vs_method: vst deseq2_shrink_lfc: true deseq2_cores: 1 deseq2_vs_blind: true deseq2_vst_nsub: 1000 gene_sets_files: 'null' observations: 2024-07-18--CG-2024-775_example-samplesheet.sample_metadata.tsv raw_matrix: 2024-07-18--CG-2024-775_rsem.merged.example-gene_counts.assay.tsv normalised_matrix: all.normalised_counts.tsv variance_stabilised_matrix: all.vst.tsv contrasts_file: 2024-07-18--CG-2024-775__example-contrasts.contrasts_file.tsv versions_file: collated_versions.yml logo: nf-core-differentialabundance_logo_light.png css: nf-core_style.css citations: CITATIONS.md END_PARAMS_SECTION

Create output directory

mkdir artifacts

Set parallelism for BLAS/MKL etc. to avoid over-booking of resources

export MKL_NUM_THREADS="2" export OPENBLAS_NUM_THREADS="2" export OMP_NUM_THREADS="2"

Work around https://github.com/rstudio/rmarkdown/issues/1508

If the symbolic link is not replaced by a physical file

output- and temporary files will be written to the original directory.

mv "differentialabundance_report.Rmd" "differentialabundance_report.Rmd.orig" cp -L "differentialabundance_report.Rmd.orig" "redacted_study_name.Rmd"

Render notebook

Rscript - <<EOF params = yaml::read_yaml('.params.yml')

  # Instead of rendering with params, produce a version of the R
  # markdown with param definitions set, so the notebook itself can
  # be reused
  rmd_content <- readLines('redacted_study_name.Rmd')

  # Extract YAML content between the first two '---'
  start_idx <- which(rmd_content == "---")[1]
  end_idx <- which(rmd_content == "---")[2]
  rmd_yaml_content <- paste(rmd_content[(start_idx+1):(end_idx-1)], collapse = "\n")
  rmd_params <- yaml::yaml.load(rmd_yaml_content)

  # Override the params
  rmd_params[['params']] <- modifyList(rmd_params[['params']], params)

  # Recursive function to add 'value' to list elements, except for top-level
  add_value_recursively <- function(lst, is_top_level = FALSE) {
      if (!is.list(lst)) {
          return(lst)
      }

      lst <- lapply(lst, add_value_recursively)
      if (!is_top_level) {
          lst <- list(value = lst)
      }
      return(lst)
  }

  # Reformat nested lists under 'params' to have a 'value' key recursively
  rmd_params[['params']] <- add_value_recursively(rmd_params[['params']], is_top_level = TRUE)

  # Convert back to YAML string
  updated_yaml_content <- as.character(yaml::as.yaml(rmd_params))

  # Remove the old YAML content
  rmd_content <- rmd_content[-((start_idx+1):(end_idx-1))]

  # Insert the updated YAML content at the right position
  rmd_content <- append(rmd_content, values = unlist(strsplit(updated_yaml_content, split = "\n")), after = start_idx)

  writeLines(rmd_content, 'redacted_study_name.parameterised.Rmd')

  # Render based on the updated file
  rmarkdown::render('redacted_study_name.parameterised.Rmd', output_file='redacted_study_name.html', envir = new.env())
  writeLines(capture.output(sessionInfo()), "session_info.log")

EOF

cat <<-END_VERSIONS > versions.yml "NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK": rmarkdown: $(Rscript -e "cat(paste(packageVersion('rmarkdown'), collapse='.'))") END_VERSIONS

Command exit status: 1

Command output: 1/72 2/72 [unnamed-chunk-1] 3/72 4/72 [unnamed-chunk-2] 5/72 6/72 [unnamed-chunk-3] 7/72 8/72 [unnamed-chunk-4] 9/72 10/72 [setup] 11/72 12/72 [unnamed-chunk-5] 13/72 14/72 [unnamed-chunk-6] 15/72 16/72 [unnamed-chunk-7] 17/72 18/72 [unnamed-chunk-8] 19/72 20/72 [unnamed-chunk-9] 21/72 22/72 [unnamed-chunk-10] 23/72 24/72 [unnamed-chunk-11] 25/72 26/72 [unnamed-chunk-12] 27/72 28/72 [unnamed-chunk-13] 29/72 30/72 [unnamed-chunk-14] 31/72 32/72 [unnamed-chunk-15] 33/72 34/72 [unnamed-chunk-16] 35/72 36/72 [unnamed-chunk-17] 37/72 38/72 [unnamed-chunk-18] 39/72 40/72 [unnamed-chunk-19] 41/72 42/72 [unnamed-chunk-20] 43/72 44/72 [unnamed-chunk-21]

Command error: 8/72 [unnamed-chunk-4] 9/72 10/72 [setup] 11/72 12/72 [unnamed-chunk-5] 13/72 14/72 [unnamed-chunk-6] 15/72 16/72 [unnamed-chunk-7] executor > local (44) [3a/4ab044] NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:VALIDATOR (2024-07-18--CG-2024-775_example-samplesheet.csv) [100%] 1 of 1 ✔ [cc/ed5dee] NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:CUSTOM_MATRIXFILTER ([id:redacted_study_name]) [100%] 1 of 1 ✔ [d9/8e4162] NFC…-timepoint1h, blocking:, exclude_samples_col:group_treatment2_vs_treatment1_timepoint1h_exclude, exclude_samples_values:True]) [100%] 1 of 1 ✔ [ed/9b34c0] NFC…replicate;bio_replicate, exclude_samples_col:group_treatment2_vs_treatment1_timepoint3h_exclude, exclude_samples_values:True]) [100%] 12 of 12 ✔ [b5/f07c30] NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:FILTER_DIFFTABLE (12) [100%] 12 of 12 ✔ [3e/4e7f12] NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_EXPLORATORY (group_treatment2_vs_treatment1_timepoint1h) [100%] 3 of 3 ✔ [97/a86960] NFC…ALABUNDANCE:DIFFERENTIALABUNDANCE:PLOT_DIFFERENTIAL (group_treatment2_vs_treatment1_timepoint3h_block_biorep_block_techbiorep) [100%] 12 of 12 ✔ [55/fdb625] NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:SHINYNGS_APP (redacted_study_name) [100%] 1 of 1 ✔ [24/2e6497] NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK (redacted_study_name) [100%] 1 of 1, failed: 1 ✘ [- ] NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:MAKE_REPORT_BUNDLE - Execution cancelled -- Finishing pending tasks before exit ERROR ~ Error executing process > 'NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK (redacted_study_name)'

Caused by: Process NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK (redacted_study_name) terminated with an error exit status (1)

Command executed:

Dump .params.yml heredoc (section will be empty if parametrization is disabled)

cat <<"END_PARAMS_SECTION" > ./.params.yml cpus: 2 artifact_dir: artifacts input_dir: ./ meta: id: redacted_study_name study_name: redacted_study_name study_type: rnaseq study_abundance_type: counts report_file: !!org.codehaus.groovy.runtime.GStringImpl {} report_title: 'null' report_author: 'null' report_contributors: null report_description: 'null' report_scree: true report_round_digits: 4 observations_type: sample observations_id_col: sample observations_name_col: null features: matrix_as_anno.feature_metadata.tsv features_type: gene features_id_col: gene_id features_name_col: gene_name features_metadata_cols: gene_id,gene_name,gene_biotype features_gtf_feature_type: transcript features_gtf_table_first_field: gene_id filtering_min_samples: 1 filtering_min_abundance: 1 filtering_min_proportion: null filtering_grouping_var: null filtering_min_proportion_not_na: 0.5 filtering_min_samples_not_na: null exploratory_main_variable: auto_pca exploratory_clustering_method: ward.D2 exploratory_cor_method: spearman exploratory_n_features: 500 exploratory_whisker_distance: 1.5 exploratory_mad_threshold: -5 exploratory_assay_names: raw,normalised,variance_stabilised exploratory_final_assay: variance_stabilised exploratory_log2_assays: raw,normalised exploratory_palette_name: Set1 differential_file_suffix: null differential_feature_id_column: gene_id differential_feature_name_column: gene_name differential_fc_column: log2FoldChange differential_pval_column: pvalue differential_qval_column: padj differential_min_fold_change: 2 differential_max_pval: 1 differential_max_qval: 0.05 differential_foldchanges_logged: true differential_palette_name: Set1 differential_subset_to_contrast_samples: false deseq2_test: Wald deseq2_fit_type: parametric deseq2_sf_type: ratio deseq2_min_replicates_for_replace: 7 deseq2_use_t: false deseq2_lfc_threshold: 0 deseq2_alt_hypothesis: greaterAbs deseq2_independent_filtering: true deseq2_p_adjust_method: BH deseq2_alpha: 0.1 deseq2_minmu: 0.5 deseq2_vs_method: vst deseq2_shrink_lfc: true deseq2_cores: 1 deseq2_vs_blind: true deseq2_vst_nsub: 1000 gene_sets_files: 'null' observations: 2024-07-18--CG-2024-775_example-samplesheet.sample_metadata.tsv raw_matrix: 2024-07-18--CG-2024-775_rsem.merged.example-gene_counts.assay.tsv normalised_matrix: all.normalised_counts.tsv variance_stabilised_matrix: all.vst.tsv contrasts_file: 2024-07-18--CG-2024-775__example-contrasts.contrasts_file.tsv versions_file: collated_versions.yml logo: nf-core-differentialabundance_logo_light.png css: nf-core_style.css citations: CITATIONS.md END_PARAMS_SECTION

Create output directory

mkdir artifacts

Set parallelism for BLAS/MKL etc. to avoid over-booking of resources

export MKL_NUM_THREADS="2" export OPENBLAS_NUM_THREADS="2" export OMP_NUM_THREADS="2"

Work around https://github.com/rstudio/rmarkdown/issues/1508

If the symbolic link is not replaced by a physical file

output- and temporary files will be written to the original directory.

mv "differentialabundance_report.Rmd" "differentialabundance_report.Rmd.orig" cp -L "differentialabundance_report.Rmd.orig" "redacted_study_name.Rmd"

Render notebook

Rscript - <<EOF params = yaml::read_yaml('.params.yml')

  # Instead of rendering with params, produce a version of the R
  # markdown with param definitions set, so the notebook itself can
  # be reused
  rmd_content <- readLines('redacted_study_name.Rmd')

  # Extract YAML content between the first two '---'
  start_idx <- which(rmd_content == "---")[1]
  end_idx <- which(rmd_content == "---")[2]
  rmd_yaml_content <- paste(rmd_content[(start_idx+1):(end_idx-1)], collapse = "\n")
  rmd_params <- yaml::yaml.load(rmd_yaml_content)

  # Override the params
  rmd_params[['params']] <- modifyList(rmd_params[['params']], params)

  # Recursive function to add 'value' to list elements, except for top-level
  add_value_recursively <- function(lst, is_top_level = FALSE) {
      if (!is.list(lst)) {
          return(lst)
      }

      lst <- lapply(lst, add_value_recursively)
      if (!is_top_level) {
          lst <- list(value = lst)
      }
      return(lst)
  }

  # Reformat nested lists under 'params' to have a 'value' key recursively
  rmd_params[['params']] <- add_value_recursively(rmd_params[['params']], is_top_level = TRUE)

  # Convert back to YAML string
  updated_yaml_content <- as.character(yaml::as.yaml(rmd_params))

  # Remove the old YAML content
  rmd_content <- rmd_content[-((start_idx+1):(end_idx-1))]

  # Insert the updated YAML content at the right position
  rmd_content <- append(rmd_content, values = unlist(strsplit(updated_yaml_content, split = "\n")), after = start_idx)

  writeLines(rmd_content, 'redacted_study_name.parameterised.Rmd')

  # Render based on the updated file
  rmarkdown::render('redacted_study_name.parameterised.Rmd', output_file='redacted_study_name.html', envir = new.env())
  writeLines(capture.output(sessionInfo()), "session_info.log")

EOF

cat <<-END_VERSIONS > versions.yml "NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:RMARKDOWNNOTEBOOK": rmarkdown: $(Rscript -e "cat(paste(packageVersion('rmarkdown'), collapse='.'))") END_VERSIONS

Command exit status: 1

Command output: 1/72 2/72 [unnamed-chunk-1] 3/72 4/72 [unnamed-chunk-2] 5/72 6/72 [unnamed-chunk-3] 7/72 8/72 [unnamed-chunk-4] 9/72 10/72 [setup] 11/72 12/72 [unnamed-chunk-5] 13/72 14/72 [unnamed-chunk-6] 15/72 16/72 [unnamed-chunk-7] 17/72 18/72 [unnamed-chunk-8] 19/72 20/72 [unnamed-chunk-9] 21/72 22/72 [unnamed-chunk-10] 23/72 24/72 [unnamed-chunk-11] 25/72 26/72 [unnamed-chunk-12] 27/72 28/72 [unnamed-chunk-13] 29/72 30/72 [unnamed-chunk-14] 31/72 32/72 [unnamed-chunk-15] 33/72 34/72 [unnamed-chunk-16] 35/72 36/72 [unnamed-chunk-17] 37/72 38/72 [unnamed-chunk-18] 39/72 40/72 [unnamed-chunk-19] 41/72 42/72 [unnamed-chunk-20] 43/72 44/72 [unnamed-chunk-21]

Command error: 8/72 [unnamed-chunk-4] 9/72 10/72 [setup] 11/72 12/72 [unnamed-chunk-5] 13/72 14/72 [unnamed-chunk-6] 15/72 16/72 [unnamed-chunk-7] 17/72 18/72 [unnamed-chunk-8] 19/72 20/72 [unnamed-chunk-9] 21/72 22/72 [unnamed-chunk-10] 23/72 24/72 [unnamed-chunk-11] 25/72 26/72 [unnamed-chunk-12] 27/72 28/72 [unnamed-chunk-13] 29/72 30/72 [unnamed-chunk-14] 31/72 32/72 [unnamed-chunk-15] 33/72 34/72 [unnamed-chunk-16] 35/72 36/72 [unnamed-chunk-17] 37/72 38/72 [unnamed-chunk-18] 39/72 40/72 [unnamed-chunk-19] 41/72 42/72 [unnamed-chunk-20] 43/72 44/72 [unnamed-chunk-21]

Quitting from lines at lines 721-767 [unnamed-chunk-21] (redacted_study_name.parameterised.Rmd) Error in cor(): ! supply both 'x' and 'y' or a matrix-like 'x' Backtrace:

BiocGenerics::lapply(...)
base::lapply(...)
FUN(X[[i]], ...)
shinyngs::madScore(...)
base::lapply(...)
shinyngs (local) FUN(X[[i]], ...)
stats::cor(matrices[[g]]) Execution halted

Work dir: /Users/user/local-diffabundance/work/24/2e6497d6608e3e571c93b8752e50d3

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

-- Check '.nextflow.log' file for details


</details>

I performed some local troubleshooting by removing all blocking and exclusions from the contrast file (i.e. maintaining the four required fields id, variable , reference, target) but the error still persists.

Jul 23 '24 17:07 tracelail

Hello @tracelail, thanks for the dataset! The error is caused by the NA values in your samplesheet 🙂 I tried running the pipeline again after filling those in with a copy of some other value in the same column, and then the pipeline finished without issues.

Jul 29 '24 09:07 WackerO

differentialabundance
differentialabundance copied to clipboard

RMARKDOWNNOTEBOOK - Error in \`cor()\`: ! supply both 'x' and 'y' or a matrix-like 'x'

Description of the bug

Command used and terminal output

Dump .params.yml heredoc (section will be empty if parametrization is disabled)

Create output directory

Set parallelism for BLAS/MKL etc. to avoid over-booking of resources

Work around https://github.com/rstudio/rmarkdown/issues/1508

If the symbolic link is not replaced by a physical file

output- and temporary files will be written to the original directory.

Render notebook

|\ | | / `/ \ |) | } { | \| | \, \/ | \ |___ \`-.,-`-,` .,._,' nf-core/differentialabundance v1.5.0-g3dd360f

!! Only displaying parameters that differ from the pipeline defaults !!

Dump .params.yml heredoc (section will be empty if parametrization is disabled)

Create output directory

Set parallelism for BLAS/MKL etc. to avoid over-booking of resources

Work around https://github.com/rstudio/rmarkdown/issues/1508

If the symbolic link is not replaced by a physical file

output- and temporary files will be written to the original directory.

Render notebook

Dump .params.yml heredoc (section will be empty if parametrization is disabled)

Create output directory

Set parallelism for BLAS/MKL etc. to avoid over-booking of resources

Work around https://github.com/rstudio/rmarkdown/issues/1508

If the symbolic link is not replaced by a physical file

output- and temporary files will be written to the original directory.

Render notebook

Dump .params.yml heredoc (section will be empty if parametrization is disabled)

Create output directory

Set parallelism for BLAS/MKL etc. to avoid over-booking of resources

Work around https://github.com/rstudio/rmarkdown/issues/1508

If the symbolic link is not replaced by a physical file

output- and temporary files will be written to the original directory.

Render notebook

differentialabundance differentialabundance copied to clipboard

RMARKDOWNNOTEBOOK - Error in \`cor()\`: ! supply both 'x' and 'y' or a matrix-like 'x'

Description of the bug

Command used and terminal output

Dump .params.yml heredoc (section will be empty if parametrization is disabled)

Create output directory

Set parallelism for BLAS/MKL etc. to avoid over-booking of resources

Work around https://github.com/rstudio/rmarkdown/issues/1508

If the symbolic link is not replaced by a physical file

output- and temporary files will be written to the original directory.

Render notebook

|\ | |__ __ / / \ |__) |__ } { | \| | \__, \__/ | \ |___ \-.,--, .,._,' nf-core/differentialabundance v1.5.0-g3dd360f

!! Only displaying parameters that differ from the pipeline defaults !!

Dump .params.yml heredoc (section will be empty if parametrization is disabled)

Create output directory

Set parallelism for BLAS/MKL etc. to avoid over-booking of resources

Work around https://github.com/rstudio/rmarkdown/issues/1508

If the symbolic link is not replaced by a physical file

output- and temporary files will be written to the original directory.

Render notebook

Dump .params.yml heredoc (section will be empty if parametrization is disabled)

Create output directory

Set parallelism for BLAS/MKL etc. to avoid over-booking of resources

Work around https://github.com/rstudio/rmarkdown/issues/1508

If the symbolic link is not replaced by a physical file

output- and temporary files will be written to the original directory.

Render notebook

Dump .params.yml heredoc (section will be empty if parametrization is disabled)

Create output directory

Set parallelism for BLAS/MKL etc. to avoid over-booking of resources

Work around https://github.com/rstudio/rmarkdown/issues/1508

If the symbolic link is not replaced by a physical file

output- and temporary files will be written to the original directory.

Render notebook

differentialabundance
differentialabundance copied to clipboard

|\ | | / `/ \ |) | } { | \| | \, \/ | \ |___ \`-.,-`-,` .,._,' nf-core/differentialabundance v1.5.0-g3dd360f