From 15c89588ac10f8f76e907f6600527f6304229c17 Mon Sep 17 00:00:00 2001 From: mashehu Date: Wed, 22 Feb 2023 15:59:14 +0100 Subject: [PATCH 1/9] add schema to validate meta.ymls --- .pre-commit-config.yaml | 6 ++ yaml-schema.json | 137 ++++++++++++++++++++++++++++++++++++++++ 2 files changed, 143 insertions(+) create mode 100644 yaml-schema.json diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 0c31cdb99ff..147e0073d9e 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -3,3 +3,9 @@ repos: rev: "v2.7.1" hooks: - id: prettier + - repo: https://github.com/python-jsonschema/check-jsonschema + rev: 0.21.0 + hooks: + - id: check-jsonschema + files: ^modules/nf-core/**/meta.yml$ + args: ["--schemafile", "yaml-schema.json"] diff --git a/yaml-schema.json b/yaml-schema.json new file mode 100644 index 00000000000..3c569694064 --- /dev/null +++ b/yaml-schema.json @@ -0,0 +1,137 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema", + "title": "Meta yaml", + "description": "Validate the meta yaml file for an nf-core module", + "type": "object", + "properties": { + "name": { + "type": "string", + "description": "Name of the module" + }, + "description": { + "type": "string", + "description": "Description of the module" + }, + "keywords": { + "type": "array", + "description": "Keywords for the module", + "items": { + "type": "string" + } + }, + "authors": { + "type": "array", + "description": "Authors of the module", + "items": { + "type": "string" + } + }, + "input": { + "type": "array", + "description": "Input channels for the module", + "items": { + "type": "object", + "patternProperties": { + ".*": { + "type": "object", + "properties": { + "type": { + "type": "string", + "description": "Type of the input channel" + }, + "description": { + "type": "string", + "description": "Description of the input channel" + }, + "pattern": { + "type": "string", + "description": "Pattern of the input channel" + }, + "default": { + "type": "string", + "description": "Default value for the input channel" + } + }, + "required": ["type", "description"] + } + } + } + }, + "output": { + "type": "array", + "description": "Output channels for the module", + "items": { + "type": "object", + "patternProperties": { + ".*": { + "type": "object", + "properties": { + "type": { + "type": "string", + "description": "Type of the input channel" + }, + "description": { + "type": "string", + "description": "Description of the input channel" + }, + "pattern": { + "type": "string", + "description": "Pattern of the input channel" + } + }, + "required": ["type", "description"] + } + } + } + }, + "tools": { + "type": "array", + "description": "Tools used by the module", + "items": { + "type": "object", + "patternProperties": { + ".*": { + "type": "object", + "properties": { + "description": { + "type": "string", + "description": "Description of the output channel" + }, + "homepage": { + "type": "string", + "description": "Homepage of the tool" + }, + "documentation": { + "type": "string", + "description": "Documentation of the tool" + }, + "tool_dev_url": { + "type": "string", + "description": "URL of the development version of the tool's documentation" + }, + "doi": { + "type": "string", + "description": "DOI of the tool" + }, + "licence": { + "type": ["array", "string"], + "description": "Licence of the tool", + "items": { + "type": "string" + } + } + }, + "required": ["description"], + "anyOf": [ + { "required": ["homepage"] }, + { "required": ["documentation"] }, + { "required": ["tool_dev_url"] }, + { "required": ["doi"] } + ] + } + } + } + } + }, + "required": ["name", "description", "keywords", "authors", "output", "tools"] +} From e7f3386638eb21d0b39e593258f7c6bd468e75c9 Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 23 Feb 2023 09:46:28 +0100 Subject: [PATCH 2/9] apply suggestion --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 147e0073d9e..ff22e6bc326 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -7,5 +7,5 @@ repos: rev: 0.21.0 hooks: - id: check-jsonschema - files: ^modules/nf-core/**/meta.yml$ + files: ^modules/nf-core/*/meta.yml$ args: ["--schemafile", "yaml-schema.json"] From 2184c653ee4ddb353e2bb00be00bd87a57c61d70 Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 23 Feb 2023 09:47:01 +0100 Subject: [PATCH 3/9] add check for unique license entries --- yaml-schema.json | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/yaml-schema.json b/yaml-schema.json index 3c569694064..43c75c36243 100644 --- a/yaml-schema.json +++ b/yaml-schema.json @@ -48,7 +48,7 @@ "description": "Pattern of the input channel" }, "default": { - "type": "string", + "type": ["string", "number", "boolean", "array", "object"], "description": "Default value for the input channel" } }, @@ -68,15 +68,15 @@ "properties": { "type": { "type": "string", - "description": "Type of the input channel" + "description": "Type of the output channel" }, "description": { "type": "string", - "description": "Description of the input channel" + "description": "Description of the output channel" }, "pattern": { "type": "string", - "description": "Pattern of the input channel" + "description": "Pattern of the output channel" } }, "required": ["type", "description"] @@ -118,7 +118,8 @@ "description": "Licence of the tool", "items": { "type": "string" - } + }, + "uniqueItems": true } }, "required": ["description"], From 0abc645a8f5271d861f7f7bb75b81665d2ce8cbc Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 23 Feb 2023 09:59:21 +0100 Subject: [PATCH 4/9] fix pre-commit config --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index ff22e6bc326..6c46610a9b3 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -7,5 +7,5 @@ repos: rev: 0.21.0 hooks: - id: check-jsonschema - files: ^modules/nf-core/*/meta.yml$ + files: ^modules/nf-core/[^/]+/[^/]+/meta.yml$ args: ["--schemafile", "yaml-schema.json"] From 268a8e9e427cf26ee6bb64279568597089113525 Mon Sep 17 00:00:00 2001 From: mashehu Date: Thu, 23 Feb 2023 10:09:44 +0100 Subject: [PATCH 5/9] fix regex in pre-commit config --- .pre-commit-config.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 6c46610a9b3..bf9d67755da 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -7,5 +7,6 @@ repos: rev: 0.21.0 hooks: - id: check-jsonschema - files: ^modules/nf-core/[^/]+/[^/]+/meta.yml$ + # match meta.ymls in one of the subdirectories of modules/nf-core + files: ^modules/nf-core/.*/meta\.yml$ args: ["--schemafile", "yaml-schema.json"] From 70ced589f202152a3c4e6a6db68c59d477969f6e Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 28 Feb 2023 16:21:25 +0100 Subject: [PATCH 6/9] Add enums and patterns based on code review --- modules/nf-core/ampcombi/meta.yml | 6 +- modules/nf-core/cellranger/count/meta.yml | 2 +- modules/nf-core/cellranger/mkgtf/meta.yml | 2 +- modules/nf-core/cellranger/mkref/meta.yml | 2 +- .../determinegermlinecontigploidy/meta.yml | 6 +- modules/nf-core/mapdamage2/meta.yml | 118 +++++++++--------- modules/nf-core/phyloflash/meta.yml | 6 +- modules/nf-core/segemehl/align/meta.yml | 2 +- modules/nf-core/transdecoder/longorf/meta.yml | 2 +- modules/nf-core/transdecoder/predict/meta.yml | 2 +- yaml-schema.json | 26 ++-- 11 files changed, 91 insertions(+), 83 deletions(-) diff --git a/modules/nf-core/ampcombi/meta.yml b/modules/nf-core/ampcombi/meta.yml index aa6eaa3282f..979785fb681 100644 --- a/modules/nf-core/ampcombi/meta.yml +++ b/modules/nf-core/ampcombi/meta.yml @@ -35,7 +35,7 @@ input: description: The path to the folder or file corresponding to the respective protein fasta files with '.faa' extension. Filenames have to contain the corresponding sample-name, i.e. sample_1.faa pattern: "*/" - amp_database: - type: folder + type: directory description: The path to the folder containing the fasta and tsv database files. pattern: "*/" @@ -66,11 +66,11 @@ output: description: A log file that captures the standard output ina log file. Can be activated by `--log`. pattern: "*.log" - sample_dir: - type: folder + type: directory description: The output directory that contains the summary output and related alignment files for one sample. pattern: "/*" - results_db: - type: folder + type: directory description: If the AMP reference database is not provided by the user using the flag `--amp_database', by default the DRAMP database will be downloaded, filtered and stored in this folder. pattern: "/amp_ref_database" - results_db_fasta: diff --git a/modules/nf-core/cellranger/count/meta.yml b/modules/nf-core/cellranger/count/meta.yml index c7c657515f9..8a5bcd8852f 100644 --- a/modules/nf-core/cellranger/count/meta.yml +++ b/modules/nf-core/cellranger/count/meta.yml @@ -24,7 +24,7 @@ input: List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. - reference: - type: folder + type: directory description: Folder containing all the reference indices needed by Cell Ranger output: - outs: diff --git a/modules/nf-core/cellranger/mkgtf/meta.yml b/modules/nf-core/cellranger/mkgtf/meta.yml index 2136ef4e574..45a2c4c8b1d 100644 --- a/modules/nf-core/cellranger/mkgtf/meta.yml +++ b/modules/nf-core/cellranger/mkgtf/meta.yml @@ -19,7 +19,7 @@ input: pattern: "*.gtf" output: - gtf: - type: folder + type: directory description: gtf transcriptome file pattern: "*.filtered.gtf" - versions: diff --git a/modules/nf-core/cellranger/mkref/meta.yml b/modules/nf-core/cellranger/mkref/meta.yml index 171f6d08367..ac79f50a29f 100644 --- a/modules/nf-core/cellranger/mkref/meta.yml +++ b/modules/nf-core/cellranger/mkref/meta.yml @@ -27,7 +27,7 @@ input: pattern: str output: - reference: - type: folder + type: directory description: Folder containing all the reference indices needed by Cell Ranger - versions: type: file diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml b/modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml index f79caa1f832..1a624a5d0ff 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml @@ -39,7 +39,7 @@ input: description: The contig ploidy priors table pattern: "*.tsv" - ploidy_model: - type: folder + type: directory description: | Optional - A folder containing the ploidy model. When a model is supplied to tool will run in CASE mode. @@ -57,11 +57,11 @@ output: description: File containing software versions pattern: "versions.yml" - calls: - type: folder + type: directory description: A folder containing the calls from the input files pattern: "*.tar.gz" - model: - type: folder + type: directory description: | A folder containing the model from the input files. This will only be created in COHORT mode (when no model is supplied to the process). diff --git a/modules/nf-core/mapdamage2/meta.yml b/modules/nf-core/mapdamage2/meta.yml index 561a396010e..8cca9f6a4ba 100644 --- a/modules/nf-core/mapdamage2/meta.yml +++ b/modules/nf-core/mapdamage2/meta.yml @@ -31,84 +31,84 @@ input: output: - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + type: file + description: File containing software versions + pattern: "versions.yml" - runtime_log: - type: file - description: Log file with a summary of command lines used and timestamps. - pattern: "Runtime_log.txt" + type: file + description: Log file with a summary of command lines used and timestamps. + pattern: "Runtime_log.txt" - fragmisincorporation_plot: - type: file - description: A pdf file that displays both fragmentation and misincorporation patterns. - pattern: "Fragmisincorporation_plot.pdf" + type: file + description: A pdf file that displays both fragmentation and misincorporation patterns. + pattern: "Fragmisincorporation_plot.pdf" - length_plot: - type: file - description: A pdf file that displays length distribution of singleton reads per strand and cumulative frequencies of C->T at 5'-end and G->A at 3'-end are also displayed per strand. - pattern: "Length_plot.pdf" + type: file + description: A pdf file that displays length distribution of singleton reads per strand and cumulative frequencies of C->T at 5'-end and G->A at 3'-end are also displayed per strand. + pattern: "Length_plot.pdf" - misincorporation: - type: file - description: Contains a table with occurrences for each type of mutations and relative positions from the reads ends. - pattern: "misincorporation.txt" + type: file + description: Contains a table with occurrences for each type of mutations and relative positions from the reads ends. + pattern: "misincorporation.txt" - pctot_freq: - type: file - description: Contains frequencies of Cytosine to Thymine mutations per position from the 5'-ends. - pattern: "5pCtoT_freq.txt" + type: file + description: Contains frequencies of Cytosine to Thymine mutations per position from the 5'-ends. + pattern: "5pCtoT_freq.txt" - pgtoa_freq: - type: file - description: Contains frequencies of Guanine to Adenine mutations per position from the 3'-ends. - pattern: "3pGtoA_freq.txt" + type: file + description: Contains frequencies of Guanine to Adenine mutations per position from the 3'-ends. + pattern: "3pGtoA_freq.txt" - dnacomp: - type: file - description: Contains a table of the reference genome base composition per position, inside reads and adjacent regions. - pattern: "dnacomp.txt" + type: file + description: Contains a table of the reference genome base composition per position, inside reads and adjacent regions. + pattern: "dnacomp.txt" - lgdistribution: - type: file - description: Contains a table with read length distributions per strand. - pattern: "lgdistribution.txt" + type: file + description: Contains a table with read length distributions per strand. + pattern: "lgdistribution.txt" - stats_out_mcmc_hist: - type: file - description: A MCMC histogram for the damage parameters and log likelihood. - pattern: "Stats_out_MCMC_hist.pdf" + type: file + description: A MCMC histogram for the damage parameters and log likelihood. + pattern: "Stats_out_MCMC_hist.pdf" - stats_out_mcmc_iter: - type: file - description: Values for the damage parameters and log likelihood in each MCMC iteration. - pattern: "Stats_out_MCMC_iter.csv" + type: file + description: Values for the damage parameters and log likelihood in each MCMC iteration. + pattern: "Stats_out_MCMC_iter.csv" - stats_out_mcmc_trace: - type: file - description: A MCMC trace plot for the damage parameters and log likelihood. - pattern: "Stats_out_MCMC_trace.pdf" + type: file + description: A MCMC trace plot for the damage parameters and log likelihood. + pattern: "Stats_out_MCMC_trace.pdf" - stats_out_mcmc_iter_summ_stat: - type: file - description: Summary statistics for the damage parameters estimated posterior distributions. - pattern: "Stats_out_MCMC_iter_summ_stat.csv" + type: file + description: Summary statistics for the damage parameters estimated posterior distributions. + pattern: "Stats_out_MCMC_iter_summ_stat.csv" - stats_out_mcmc_post_pred: - type: file - description: Empirical misincorporation frequency and posterior predictive intervals from the fitted model. - pattern: "Stats_out_MCMC_post_pred.pdf" + type: file + description: Empirical misincorporation frequency and posterior predictive intervals from the fitted model. + pattern: "Stats_out_MCMC_post_pred.pdf" - stats_out_mcmc_correct_prob: - type: file - description: Position specific probability of a C->T and G->A misincorporation is due to damage. - pattern: "Stats_out_MCMC_correct_prob.csv" + type: file + description: Position specific probability of a C->T and G->A misincorporation is due to damage. + pattern: "Stats_out_MCMC_correct_prob.csv" - dnacomp_genome: - type: file - description: Contains the global reference genome base composition (computed by seqtk). - pattern: "dnacomp_genome.csv" + type: file + description: Contains the global reference genome base composition (computed by seqtk). + pattern: "dnacomp_genome.csv" - rescaled: - type: file - description: Rescaled BAM file, where likely post-mortem damaged bases have downscaled quality scores. - pattern: "*.{bam}" + type: file + description: Rescaled BAM file, where likely post-mortem damaged bases have downscaled quality scores. + pattern: "*.{bam}" - fasta: - type: file - description: Allignments in a FASTA file, only if flagged by -d. - pattern: "*.{fasta}" + type: file + description: Allignments in a FASTA file, only if flagged by -d. + pattern: "*.{fasta}" - folder: - type: folder - description: Folder created when --plot-only, --rescale and --stats-only flags are passed. - pattern: "*/" + type: directory + description: Folder created when --plot-only, --rescale and --stats-only flags are passed. + pattern: "*/" authors: - "@darcy220606" diff --git a/modules/nf-core/phyloflash/meta.yml b/modules/nf-core/phyloflash/meta.yml index d44001da854..07e6ea4fd8e 100644 --- a/modules/nf-core/phyloflash/meta.yml +++ b/modules/nf-core/phyloflash/meta.yml @@ -25,11 +25,11 @@ input: description: Channel containing single or paired-end reads pattern: "*.{fastq.gz,fq.gz}" - sliva_db: - type: folder + type: directory description: Folder containing the SILVA database pattern: "ref" - univec_db: - type: folder + type: directory description: Folder containing UniVec database pattern: "UniVec" @@ -40,7 +40,7 @@ output: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - results: - type: folder + type: directory description: Folder containing the results of phyloFlash analysis pattern: "${prefix}*" - versions: diff --git a/modules/nf-core/segemehl/align/meta.yml b/modules/nf-core/segemehl/align/meta.yml index bb5ac49ff6a..7059cee8008 100644 --- a/modules/nf-core/segemehl/align/meta.yml +++ b/modules/nf-core/segemehl/align/meta.yml @@ -39,7 +39,7 @@ output: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - results: - type: folder + type: directory description: | Directory containing genomic alignments in SAM format (please add "-b" flag to task.ext.args for BAM) diff --git a/modules/nf-core/transdecoder/longorf/meta.yml b/modules/nf-core/transdecoder/longorf/meta.yml index b039a261d29..55d5e86a38a 100644 --- a/modules/nf-core/transdecoder/longorf/meta.yml +++ b/modules/nf-core/transdecoder/longorf/meta.yml @@ -50,7 +50,7 @@ output: description: nucleotide frequencies pattern: "*{dat}" - folder: - type: folder + type: directory description: contains all the files from the run authors: diff --git a/modules/nf-core/transdecoder/predict/meta.yml b/modules/nf-core/transdecoder/predict/meta.yml index cb972112e4d..2d3999ce136 100644 --- a/modules/nf-core/transdecoder/predict/meta.yml +++ b/modules/nf-core/transdecoder/predict/meta.yml @@ -24,7 +24,7 @@ input: description: fasta file pattern: "*.{fasta}" - fold: - type: folder + type: directory description: Output from the module transdecoder_longorf pattern: "*" diff --git a/yaml-schema.json b/yaml-schema.json index 43c75c36243..350ad1bcb4f 100644 --- a/yaml-schema.json +++ b/yaml-schema.json @@ -17,7 +17,8 @@ "description": "Keywords for the module", "items": { "type": "string" - } + }, + "minItems": 3 }, "authors": { "type": "array", @@ -29,6 +30,7 @@ "input": { "type": "array", "description": "Input channels for the module", + "items": { "type": "object", "patternProperties": { @@ -37,7 +39,8 @@ "properties": { "type": { "type": "string", - "description": "Type of the input channel" + "description": "Type of the input channel", + "enum": ["map", "file", "directory", "string", "integer", "float"] }, "description": { "type": "string", @@ -45,7 +48,7 @@ }, "pattern": { "type": "string", - "description": "Pattern of the input channel" + "description": "Pattern of the input channel, given in Java glob syntax" }, "default": { "type": ["string", "number", "boolean", "array", "object"], @@ -68,7 +71,8 @@ "properties": { "type": { "type": "string", - "description": "Type of the output channel" + "description": "Type of the output channel", + "enum": ["map", "file", "directory", "string", "integer", "float"] }, "description": { "type": "string", @@ -76,7 +80,7 @@ }, "pattern": { "type": "string", - "description": "Pattern of the output channel" + "description": "Pattern of the input channel, given in Java glob syntax" } }, "required": ["type", "description"] @@ -99,19 +103,23 @@ }, "homepage": { "type": "string", - "description": "Homepage of the tool" + "description": "Homepage of the tool", + "pattern": "^(http|https)://.*$" }, "documentation": { "type": "string", - "description": "Documentation of the tool" + "description": "Documentation of the tool", + "pattern": "^(http|https)://.*$" }, "tool_dev_url": { "type": "string", - "description": "URL of the development version of the tool's documentation" + "description": "URL of the development version of the tool's documentation", + "pattern": "^(http|https)://.*$" }, "doi": { "type": "string", - "description": "DOI of the tool" + "description": "DOI of the tool", + "pattern": "^10.\\d{4,9}\\/[^,]+$" }, "licence": { "type": ["array", "string"], From f60adc27e175c094b0cee15530d63e1e9cc2e18f Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 7 Mar 2023 09:58:39 +0100 Subject: [PATCH 7/9] revert changes in phyloflash to pass tests --- modules/nf-core/phyloflash/meta.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/phyloflash/meta.yml b/modules/nf-core/phyloflash/meta.yml index 07e6ea4fd8e..87da34f2f78 100644 --- a/modules/nf-core/phyloflash/meta.yml +++ b/modules/nf-core/phyloflash/meta.yml @@ -25,11 +25,11 @@ input: description: Channel containing single or paired-end reads pattern: "*.{fastq.gz,fq.gz}" - sliva_db: - type: directory + type: folder description: Folder containing the SILVA database pattern: "ref" - univec_db: - type: directory + type: folder description: Folder containing UniVec database pattern: "UniVec" From f12fe5d2450e2b616b5207ae3847c0ea2da5af6d Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 7 Mar 2023 10:20:41 +0100 Subject: [PATCH 8/9] revert changes on meta.ymls to keep this PR clean --- modules/nf-core/ampcombi/meta.yml | 6 +- modules/nf-core/cellranger/count/meta.yml | 2 +- modules/nf-core/cellranger/mkgtf/meta.yml | 3 +- modules/nf-core/cellranger/mkref/meta.yml | 5 +- .../determinegermlinecontigploidy/meta.yml | 6 +- modules/nf-core/mapdamage2/meta.yml | 118 +++++++++--------- modules/nf-core/phyloflash/meta.yml | 2 +- modules/nf-core/segemehl/align/meta.yml | 2 +- modules/nf-core/transdecoder/longorf/meta.yml | 2 +- modules/nf-core/transdecoder/predict/meta.yml | 2 +- 10 files changed, 75 insertions(+), 73 deletions(-) diff --git a/modules/nf-core/ampcombi/meta.yml b/modules/nf-core/ampcombi/meta.yml index 979785fb681..aa6eaa3282f 100644 --- a/modules/nf-core/ampcombi/meta.yml +++ b/modules/nf-core/ampcombi/meta.yml @@ -35,7 +35,7 @@ input: description: The path to the folder or file corresponding to the respective protein fasta files with '.faa' extension. Filenames have to contain the corresponding sample-name, i.e. sample_1.faa pattern: "*/" - amp_database: - type: directory + type: folder description: The path to the folder containing the fasta and tsv database files. pattern: "*/" @@ -66,11 +66,11 @@ output: description: A log file that captures the standard output ina log file. Can be activated by `--log`. pattern: "*.log" - sample_dir: - type: directory + type: folder description: The output directory that contains the summary output and related alignment files for one sample. pattern: "/*" - results_db: - type: directory + type: folder description: If the AMP reference database is not provided by the user using the flag `--amp_database', by default the DRAMP database will be downloaded, filtered and stored in this folder. pattern: "/amp_ref_database" - results_db_fasta: diff --git a/modules/nf-core/cellranger/count/meta.yml b/modules/nf-core/cellranger/count/meta.yml index 8a5bcd8852f..c7c657515f9 100644 --- a/modules/nf-core/cellranger/count/meta.yml +++ b/modules/nf-core/cellranger/count/meta.yml @@ -24,7 +24,7 @@ input: List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. - reference: - type: directory + type: folder description: Folder containing all the reference indices needed by Cell Ranger output: - outs: diff --git a/modules/nf-core/cellranger/mkgtf/meta.yml b/modules/nf-core/cellranger/mkgtf/meta.yml index f1c1ed43185..3fe40375832 100644 --- a/modules/nf-core/cellranger/mkgtf/meta.yml +++ b/modules/nf-core/cellranger/mkgtf/meta.yml @@ -10,6 +10,7 @@ tools: homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov + doi: "" licence: 10x Genomics EULA input: - gtf: @@ -18,7 +19,7 @@ input: pattern: "*.gtf" output: - gtf: - type: directory + type: folder description: The filtered GTF transcriptome file pattern: "*.filtered.gtf" - versions: diff --git a/modules/nf-core/cellranger/mkref/meta.yml b/modules/nf-core/cellranger/mkref/meta.yml index 429bada4248..5419931d3a1 100644 --- a/modules/nf-core/cellranger/mkref/meta.yml +++ b/modules/nf-core/cellranger/mkref/meta.yml @@ -21,11 +21,12 @@ input: description: Reference transcriptome GTF file pattern: "*.gtf" - reference_name: - type: directory + type: val description: The name to give the new reference folder + pattern: str output: - reference: - type: directory + type: folder description: Folder containing all the reference indices needed by Cell Ranger - versions: type: file diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml b/modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml index 1a624a5d0ff..f79caa1f832 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml @@ -39,7 +39,7 @@ input: description: The contig ploidy priors table pattern: "*.tsv" - ploidy_model: - type: directory + type: folder description: | Optional - A folder containing the ploidy model. When a model is supplied to tool will run in CASE mode. @@ -57,11 +57,11 @@ output: description: File containing software versions pattern: "versions.yml" - calls: - type: directory + type: folder description: A folder containing the calls from the input files pattern: "*.tar.gz" - model: - type: directory + type: folder description: | A folder containing the model from the input files. This will only be created in COHORT mode (when no model is supplied to the process). diff --git a/modules/nf-core/mapdamage2/meta.yml b/modules/nf-core/mapdamage2/meta.yml index 8cca9f6a4ba..79332d77cec 100644 --- a/modules/nf-core/mapdamage2/meta.yml +++ b/modules/nf-core/mapdamage2/meta.yml @@ -31,84 +31,84 @@ input: output: - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + type: file + description: File containing software versions + pattern: "versions.yml" - runtime_log: - type: file - description: Log file with a summary of command lines used and timestamps. - pattern: "Runtime_log.txt" + type: file + description: Log file with a summary of command lines used and timestamps. + pattern: "Runtime_log.txt" - fragmisincorporation_plot: - type: file - description: A pdf file that displays both fragmentation and misincorporation patterns. - pattern: "Fragmisincorporation_plot.pdf" + type: file + description: A pdf file that displays both fragmentation and misincorporation patterns. + pattern: "Fragmisincorporation_plot.pdf" - length_plot: - type: file - description: A pdf file that displays length distribution of singleton reads per strand and cumulative frequencies of C->T at 5'-end and G->A at 3'-end are also displayed per strand. - pattern: "Length_plot.pdf" + type: file + description: A pdf file that displays length distribution of singleton reads per strand and cumulative frequencies of C->T at 5'-end and G->A at 3'-end are also displayed per strand. + pattern: "Length_plot.pdf" - misincorporation: - type: file - description: Contains a table with occurrences for each type of mutations and relative positions from the reads ends. - pattern: "misincorporation.txt" + type: file + description: Contains a table with occurrences for each type of mutations and relative positions from the reads ends. + pattern: "misincorporation.txt" - pctot_freq: - type: file - description: Contains frequencies of Cytosine to Thymine mutations per position from the 5'-ends. - pattern: "5pCtoT_freq.txt" + type: file + description: Contains frequencies of Cytosine to Thymine mutations per position from the 5'-ends. + pattern: "5pCtoT_freq.txt" - pgtoa_freq: - type: file - description: Contains frequencies of Guanine to Adenine mutations per position from the 3'-ends. - pattern: "3pGtoA_freq.txt" + type: file + description: Contains frequencies of Guanine to Adenine mutations per position from the 3'-ends. + pattern: "3pGtoA_freq.txt" - dnacomp: - type: file - description: Contains a table of the reference genome base composition per position, inside reads and adjacent regions. - pattern: "dnacomp.txt" + type: file + description: Contains a table of the reference genome base composition per position, inside reads and adjacent regions. + pattern: "dnacomp.txt" - lgdistribution: - type: file - description: Contains a table with read length distributions per strand. - pattern: "lgdistribution.txt" + type: file + description: Contains a table with read length distributions per strand. + pattern: "lgdistribution.txt" - stats_out_mcmc_hist: - type: file - description: A MCMC histogram for the damage parameters and log likelihood. - pattern: "Stats_out_MCMC_hist.pdf" + type: file + description: A MCMC histogram for the damage parameters and log likelihood. + pattern: "Stats_out_MCMC_hist.pdf" - stats_out_mcmc_iter: - type: file - description: Values for the damage parameters and log likelihood in each MCMC iteration. - pattern: "Stats_out_MCMC_iter.csv" + type: file + description: Values for the damage parameters and log likelihood in each MCMC iteration. + pattern: "Stats_out_MCMC_iter.csv" - stats_out_mcmc_trace: - type: file - description: A MCMC trace plot for the damage parameters and log likelihood. - pattern: "Stats_out_MCMC_trace.pdf" + type: file + description: A MCMC trace plot for the damage parameters and log likelihood. + pattern: "Stats_out_MCMC_trace.pdf" - stats_out_mcmc_iter_summ_stat: - type: file - description: Summary statistics for the damage parameters estimated posterior distributions. - pattern: "Stats_out_MCMC_iter_summ_stat.csv" + type: file + description: Summary statistics for the damage parameters estimated posterior distributions. + pattern: "Stats_out_MCMC_iter_summ_stat.csv" - stats_out_mcmc_post_pred: - type: file - description: Empirical misincorporation frequency and posterior predictive intervals from the fitted model. - pattern: "Stats_out_MCMC_post_pred.pdf" + type: file + description: Empirical misincorporation frequency and posterior predictive intervals from the fitted model. + pattern: "Stats_out_MCMC_post_pred.pdf" - stats_out_mcmc_correct_prob: - type: file - description: Position specific probability of a C->T and G->A misincorporation is due to damage. - pattern: "Stats_out_MCMC_correct_prob.csv" + type: file + description: Position specific probability of a C->T and G->A misincorporation is due to damage. + pattern: "Stats_out_MCMC_correct_prob.csv" - dnacomp_genome: - type: file - description: Contains the global reference genome base composition (computed by seqtk). - pattern: "dnacomp_genome.csv" + type: file + description: Contains the global reference genome base composition (computed by seqtk). + pattern: "dnacomp_genome.csv" - rescaled: - type: file - description: Rescaled BAM file, where likely post-mortem damaged bases have downscaled quality scores. - pattern: "*.{bam}" + type: file + description: Rescaled BAM file, where likely post-mortem damaged bases have downscaled quality scores. + pattern: "*.{bam}" - fasta: - type: file - description: Allignments in a FASTA file, only if flagged by -d. - pattern: "*.{fasta}" + type: file + description: Allignments in a FASTA file, only if flagged by -d. + pattern: "*.{fasta}" - folder: - type: directory - description: Folder created when --plot-only, --rescale and --stats-only flags are passed. - pattern: "*/" + type: directory + description: Folder created when --plot-only, --rescale and --stats-only flags are passed. + pattern: "*/" authors: - "@darcy220606" diff --git a/modules/nf-core/phyloflash/meta.yml b/modules/nf-core/phyloflash/meta.yml index 87da34f2f78..d44001da854 100644 --- a/modules/nf-core/phyloflash/meta.yml +++ b/modules/nf-core/phyloflash/meta.yml @@ -40,7 +40,7 @@ output: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - results: - type: directory + type: folder description: Folder containing the results of phyloFlash analysis pattern: "${prefix}*" - versions: diff --git a/modules/nf-core/segemehl/align/meta.yml b/modules/nf-core/segemehl/align/meta.yml index 7059cee8008..bb5ac49ff6a 100644 --- a/modules/nf-core/segemehl/align/meta.yml +++ b/modules/nf-core/segemehl/align/meta.yml @@ -39,7 +39,7 @@ output: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - results: - type: directory + type: folder description: | Directory containing genomic alignments in SAM format (please add "-b" flag to task.ext.args for BAM) diff --git a/modules/nf-core/transdecoder/longorf/meta.yml b/modules/nf-core/transdecoder/longorf/meta.yml index 55d5e86a38a..b039a261d29 100644 --- a/modules/nf-core/transdecoder/longorf/meta.yml +++ b/modules/nf-core/transdecoder/longorf/meta.yml @@ -50,7 +50,7 @@ output: description: nucleotide frequencies pattern: "*{dat}" - folder: - type: directory + type: folder description: contains all the files from the run authors: diff --git a/modules/nf-core/transdecoder/predict/meta.yml b/modules/nf-core/transdecoder/predict/meta.yml index 2d3999ce136..cb972112e4d 100644 --- a/modules/nf-core/transdecoder/predict/meta.yml +++ b/modules/nf-core/transdecoder/predict/meta.yml @@ -24,7 +24,7 @@ input: description: fasta file pattern: "*.{fasta}" - fold: - type: directory + type: folder description: Output from the module transdecoder_longorf pattern: "*" From 867327bbb923642f500b5db79631c8e3c03936e2 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 7 Mar 2023 10:26:11 +0100 Subject: [PATCH 9/9] more reverts --- modules/nf-core/cellranger/mkref/meta.yml | 1 + modules/nf-core/mapdamage2/meta.yml | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/modules/nf-core/cellranger/mkref/meta.yml b/modules/nf-core/cellranger/mkref/meta.yml index 5419931d3a1..b95f5f09d92 100644 --- a/modules/nf-core/cellranger/mkref/meta.yml +++ b/modules/nf-core/cellranger/mkref/meta.yml @@ -10,6 +10,7 @@ tools: homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov + doi: "" licence: 10x Genomics EULA input: - fasta: diff --git a/modules/nf-core/mapdamage2/meta.yml b/modules/nf-core/mapdamage2/meta.yml index 79332d77cec..561a396010e 100644 --- a/modules/nf-core/mapdamage2/meta.yml +++ b/modules/nf-core/mapdamage2/meta.yml @@ -106,7 +106,7 @@ output: description: Allignments in a FASTA file, only if flagged by -d. pattern: "*.{fasta}" - folder: - type: directory + type: folder description: Folder created when --plot-only, --rescale and --stats-only flags are passed. pattern: "*/"