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* updated nextflow.config with pipeline rename to omicsgenetraitassociation * Template update for nf-core/tools version 2.11.1 * added modules CMA, MMAP, and PASCAL * fixed versions emit values for cma/main.nf and pascal/main.nf * added when directives to cma/main.nf * added MEA modules * pipeline works from CMA to MEA * added config for CMA and MEA configs in modules.config * updated .gitignore to exclude downloaded singularity images and added new config file for testing cma + mea modules * added temporary subworkflow CMA_SUBWORKFLOW which will later be modified to run CMA and MEA * commented out workflow initialization and validation steps for testing * pascal/main.nf edited to extract tarball as nextflow does not support s3 glob support * fixed versions emit name * added test_local.config, modules.config, and updated subworkflows
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| Original file line number | Diff line number | Diff line change |
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| params { | ||
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| // pipeline parameters | ||
| trait = 'fhshdl' | ||
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| // PASCAL | ||
| pascal_gwas_file = 's3://brentlab-nextflow-testdata/omicsgenetraitassociation/pascal/gwasA.csv.gz' | ||
| pascal_gene_annotation = 's3://brentlab-nextflow-testdata/omicsgenetraitassociation/pascal/gene_annotation.tsv' | ||
| // nextflow does not support s3 glob operations (tarballed) | ||
| pascal_ref_panel = 's3://brentlab-nextflow-testdata/omicsgenetraitassociation/pascal/EUR_simulated.tar.gz' | ||
| pascal_header = 0 | ||
| pascal_pval_col = 1 | ||
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| // MMAP | ||
| mmap_gene_list = 's3://brentlab-nextflow-testdata/omicsgenetraitassociation/mmap/gene_list_gwasA_twas.txt' | ||
| mmap_pheno_file = 's3://brentlab-nextflow-testdata/omicsgenetraitassociation/mmap/mmap_pheno_adjusted_fhshdl_HGNC_gwasA_genes.csv' | ||
| mmap_pedigree_file = 's3://brentlab-nextflow-testdata/omicsgenetraitassociation/mmap/mmap.ped.v5.csv' | ||
| mmap_cov_matrix_file = 's3://brentlab-nextflow-testdata/omicsgenetraitassociation/mmap/llfs.kinship.bin' | ||
| mmap_header = 1 | ||
| mmap_pval_col = 'p_vals' | ||
| mmap_beta_col = 'betas_genes' | ||
| mmap_se_genes = 'se_genes' | ||
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| // CMA module test files from S3 | ||
| cma_two_traits = 's3://brentlab-nextflow-testdata/omicsgenetraitassociation/cma/two_traits/fhshdl/' | ||
| cma_three_complete_corr = 's3://brentlab-nextflow-testdata/omicsgenetraitassociation/cma/three-traits/test_category_complete_correlation/' | ||
| cma_three_missing_obs = 's3://brentlab-nextflow-testdata/omicsgenetraitassociation/cma/three-traits/test_category_missing_observations/' | ||
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| // MEA preprocess | ||
| pipeline = 'cma' | ||
| module_file_dir = 's3://brentlab-nextflow-testdata/omicsgenetraitassociation/mea/preprocess/cherryPickModules/' | ||
| gene_col_name = 'markname' | ||
| pval_col_name = 'meta_p' | ||
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| // MEA postprocess | ||
| numtests = 17551 | ||
| alpha = 0.05 | ||
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| // Boilerplate options | ||
| publish_dir_mode = 'copy' | ||
| email = '[email protected]' | ||
| //email_on_fail = null | ||
| outdir = 'results' | ||
| //monochrome_logs = null | ||
| //hook_url = null | ||
| } | ||
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| includeConfig 'modules.config' | ||
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| process { | ||
| executor = 'local' | ||
| publishDir = [ | ||
| mode: "copy", | ||
| path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, | ||
| ] | ||
| } | ||
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| singularity { | ||
| enabled = true | ||
| autoMounts = true | ||
| cacheDir = "singularity_images" | ||
| } | ||
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| conda.enabled = true | ||
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| NXF_SINGULARITY_CACHEDIR="/scratch/mblab/jungw/singularity_cache/" | ||
| NXF_CONDA_CACHEDIR="/scratch/mblab/jungw/conda_cache/" |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,62 @@ | ||
| // | ||
| // workflow for running MMAP, parsing the output, and formatting it for CMA | ||
| // | ||
| include { MMAP } from '../../modules/local/mmap/mmap' | ||
| include { MMAP_PARSE } from '../../modules/local/mmap/mmap_parse' | ||
| include { FORMAT_CMA_INPUT } from '../../modules/local/cma/format_cma_input' | ||
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| workflow MMAP_SUBWORKFLOW { | ||
| take: | ||
| gene_list_file | ||
| trait | ||
| phenotype_file | ||
| pedigree_file | ||
| covariance_matrix_file | ||
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| main: | ||
| ch_versions = Channel.empty() | ||
| ch_concatenated_mmap = Channel.empty() | ||
| ch_mmap_genes = Channel.fromPath(gene_list_file) | ||
| .splitText() | ||
| .map ( gene -> gene.trim() ) | ||
| ch_mmap_cma_format = Channel.empty() | ||
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| // | ||
| // MODULE: MMAP | ||
| // | ||
| MMAP ( | ||
| ch_mmap_genes, trait, phenotype_file, pedigree_file, covariance_matrix_file | ||
| ) | ||
| ch_concatenated_mmap = MMAP.out.csv | ||
| .collectFile(name: 'mmap_results.csv', cache:false) | ||
| ch_versions = ch_versions.mix(MMAP.out.versions) | ||
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| // | ||
| // MODULE: MMAP PARSE | ||
| // | ||
| MMAP_PARSE ( | ||
| ch_concatenated_mmap | ||
| ) | ||
| ch_mmap_parsed = MMAP_PARSE.out.mmap_parsed_output | ||
| ch_versions = ch_versions.mix(MMAP_PARSE.out.versions) | ||
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| // | ||
| // MODULE: FORMAT_CMA_INPUT | ||
| // | ||
| FORMAT_CMA_INPUT ( | ||
| ch_mmap_parsed, | ||
| "MMAP", | ||
| params.mmap_header, | ||
| params.mmap_pval_col, | ||
| params.mmap_beta_col, | ||
| params.mmap_se_genes | ||
| ) | ||
| ch_mmap_cma_format = FORMAT_CMA_INPUT.out.csv | ||
| ch_versions = ch_versions.mix(FORMAT_CMA_INPUT.out.versions) | ||
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| emit: | ||
| parsed_mmap_output = ch_mmap_parsed | ||
| cma_format_output = ch_mmap_cma_format | ||
| versions = ch_versions | ||
| } |
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| Original file line number | Diff line number | Diff line change |
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| // | ||
| // workflow for running PASCAL and formatting the output for CMA | ||
| // | ||
| include { PASCAL } from '../../modules/local/pascal' | ||
| include { FORMAT_CMA_INPUT } from '../../modules/local/cma/format_cma_input' | ||
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| workflow PASCAL_SUBWORKFLOW { | ||
| take: | ||
| gwas_file | ||
| gene_annotation | ||
| ref_panel | ||
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| main: | ||
| ch_versions = Channel.empty() | ||
| ch_pascal_out = Channel.empty() | ||
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| PASCAL ( | ||
| gwas_file, gene_annotation, ref_panel | ||
| ) | ||
| ch_pascal_out = PASCAL.out.tsv | ||
| ch_versions = ch_versions.mix(PASCAL.out.versions) | ||
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| FORMAT_CMA_INPUT ( | ||
| ch_pascal_out, | ||
| "PASCAL", | ||
| params.pascal_header, | ||
| params.pascal_pval_col, | ||
| [], | ||
| [] | ||
| ) | ||
| ch_pascal_cma_format = FORMAT_CMA_INPUT.out.csv | ||
| ch_versions = ch_versions.mix(FORMAT_CMA_INPUT.out.versions) | ||
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| emit: | ||
| pascal_output = ch_pascal_out | ||
| cma_format_output = ch_pascal_cma_format | ||
| versions = ch_versions | ||
| } |