From 5e4bdf5de5ea47f6ee209a80fa3774849235a317 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Thu, 10 Oct 2024 13:22:19 +1300 Subject: [PATCH] Updated samtools faidx to 1.21 --- CHANGELOG.md | 1 + modules.json | 90 +++---- modules/gallvp/busco/busco/main.nf | 2 +- modules/gallvp/busco/busco/meta.yml | 172 ++++++++----- .../busco/busco/tests/main.nf.test.snap | 38 +-- modules/gallvp/busco/generateplot/meta.yml | 27 +- modules/gallvp/bwa/index/meta.yml | 41 +-- modules/gallvp/bwa/mem/meta.yml | 111 +++++---- modules/gallvp/cat/cat/meta.yml | 39 +-- modules/gallvp/custom/relabelfasta/meta.yml | 57 ++--- modules/gallvp/custom/restoregffids/meta.yml | 56 +++-- .../gallvp/custom/shortenfastaids/meta.yml | 60 +++-- modules/gallvp/gffread/meta.yml | 84 ++++--- modules/gallvp/gt/gff3/meta.yml | 59 +++-- modules/gallvp/gt/gff3validator/meta.yml | 56 +++-- modules/gallvp/gt/stat/meta.yml | 47 ++-- modules/gallvp/ltrfinder/meta.yml | 60 +++-- modules/gallvp/ltrfinder/tests/main.nf.test | 4 +- modules/gallvp/ltrharvest/meta.yml | 59 +++-- modules/gallvp/ltrretriever/lai/meta.yml | 88 ++++--- .../gallvp/ltrretriever/ltrretriever/meta.yml | 142 +++++++---- .../ltrretriever/tests/main.nf.test | 16 +- modules/gallvp/plotsr/meta.yml | 117 ++++----- modules/gallvp/samblaster/meta.yml | 45 ++-- modules/gallvp/samtools/faidx/environment.yml | 4 +- modules/gallvp/samtools/faidx/main.nf | 4 +- modules/gallvp/samtools/faidx/meta.yml | 85 ++++--- .../samtools/faidx/tests/main.nf.test.snap | 50 ++-- modules/gallvp/seqkit/seq/meta.yml | 47 ++-- modules/gallvp/syri/meta.yml | 90 ++++--- .../custom/sratoolsncbisettings/meta.yml | 20 +- modules/nf-core/fastavalidator/meta.yml | 56 +++-- modules/nf-core/fastp/meta.yml | 138 ++++++---- modules/nf-core/fastqc/meta.yml | 57 +++-- modules/nf-core/fcs/fcsadaptor/meta.yml | 91 ++++--- modules/nf-core/gunzip/meta.yml | 37 +-- modules/nf-core/merqury/hapmers/meta.yml | 115 +++++---- modules/nf-core/merqury/merqury/meta.yml | 235 ++++++++++++------ modules/nf-core/meryl/count/meta.yml | 53 ++-- modules/nf-core/meryl/unionsum/meta.yml | 49 ++-- modules/nf-core/minimap2/align/meta.yml | 115 +++++---- modules/nf-core/seqkit/rmdup/meta.yml | 59 +++-- modules/nf-core/seqkit/seq/meta.yml | 47 ++-- modules/nf-core/seqkit/sort/meta.yml | 44 ++-- modules/nf-core/sratools/fasterqdump/meta.yml | 71 +++--- modules/nf-core/sratools/prefetch/meta.yml | 72 +++--- modules/nf-core/tidk/explore/meta.yml | 63 +++-- modules/nf-core/tidk/plot/meta.yml | 47 ++-- modules/nf-core/tidk/search/meta.yml | 65 ++--- modules/nf-core/umitools/extract/meta.yml | 64 +++-- modules/nf-core/untar/meta.yml | 43 ++-- .../tests/main.nf.test.snap | 42 ++-- .../nf-core/utils_nextflow_pipeline/main.nf | 8 +- .../nf-core/utils_nfcore_pipeline/main.nf | 8 +- 54 files changed, 1940 insertions(+), 1410 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 386e75e1..99704fe9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 1. Added Gfastats [#126](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/126) 2. Updated nf-core/template to 3.0.1 [#149](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/149) +3. Updated `samtools faidx` to 1.21 ### `Fixed` diff --git a/modules.json b/modules.json index 2aaa9306..e5e4e979 100644 --- a/modules.json +++ b/modules.json @@ -7,107 +7,107 @@ "gallvp": { "busco/busco": { "branch": "main", - "git_sha": "cc6ea1f3e96e8264d2cc99afed31bcf3b0bb03ca", + "git_sha": "92d59e5f578a2929b75f7588985b9bf451f4c370", "installed_by": ["fasta_gxf_busco_plot"] }, "busco/generateplot": { "branch": "main", - "git_sha": "cc6ea1f3e96e8264d2cc99afed31bcf3b0bb03ca", + "git_sha": "ae9714c21ede9199a3118e3c20b65484aa73e232", "installed_by": ["fasta_gxf_busco_plot"] }, "bwa/index": { "branch": "main", - "git_sha": "cc6ea1f3e96e8264d2cc99afed31bcf3b0bb03ca", + "git_sha": "ae9714c21ede9199a3118e3c20b65484aa73e232", "installed_by": ["fastq_bwa_mem_samblaster"] }, "bwa/mem": { "branch": "main", - "git_sha": "a203a6035aed3f9b345ee380f5d497ca98504d98", + "git_sha": "ae9714c21ede9199a3118e3c20b65484aa73e232", "installed_by": ["fastq_bwa_mem_samblaster"] }, "cat/cat": { "branch": "main", - "git_sha": "cc6ea1f3e96e8264d2cc99afed31bcf3b0bb03ca", + "git_sha": "ae9714c21ede9199a3118e3c20b65484aa73e232", "installed_by": ["fasta_ltrretriever_lai"] }, "custom/relabelfasta": { "branch": "main", - "git_sha": "a203a6035aed3f9b345ee380f5d497ca98504d98", + "git_sha": "a8939d36280e7d9037c7cf164eeede19e46546a4", "installed_by": ["modules"] }, "custom/restoregffids": { "branch": "main", - "git_sha": "a203a6035aed3f9b345ee380f5d497ca98504d98", + "git_sha": "a8939d36280e7d9037c7cf164eeede19e46546a4", "installed_by": ["fasta_ltrretriever_lai"] }, "custom/shortenfastaids": { "branch": "main", - "git_sha": "a203a6035aed3f9b345ee380f5d497ca98504d98", + "git_sha": "a8939d36280e7d9037c7cf164eeede19e46546a4", "installed_by": ["fasta_ltrretriever_lai"] }, "gffread": { "branch": "main", - "git_sha": "cc6ea1f3e96e8264d2cc99afed31bcf3b0bb03ca", + "git_sha": "ae9714c21ede9199a3118e3c20b65484aa73e232", "installed_by": ["fasta_gxf_busco_plot"] }, "gt/gff3": { "branch": "main", - "git_sha": "cc6ea1f3e96e8264d2cc99afed31bcf3b0bb03ca", + "git_sha": "ae9714c21ede9199a3118e3c20b65484aa73e232", "installed_by": ["gff3_gt_gff3_gff3validator_stat"] }, "gt/gff3validator": { "branch": "main", - "git_sha": "cc6ea1f3e96e8264d2cc99afed31bcf3b0bb03ca", + "git_sha": "ae9714c21ede9199a3118e3c20b65484aa73e232", "installed_by": ["gff3_gt_gff3_gff3validator_stat"] }, "gt/stat": { "branch": "main", - "git_sha": "cc6ea1f3e96e8264d2cc99afed31bcf3b0bb03ca", + "git_sha": "ae9714c21ede9199a3118e3c20b65484aa73e232", "installed_by": ["gff3_gt_gff3_gff3validator_stat"] }, "ltrfinder": { "branch": "main", - "git_sha": "cc6ea1f3e96e8264d2cc99afed31bcf3b0bb03ca", + "git_sha": "ae9714c21ede9199a3118e3c20b65484aa73e232", "installed_by": ["fasta_ltrretriever_lai"] }, "ltrharvest": { "branch": "main", - "git_sha": "cc6ea1f3e96e8264d2cc99afed31bcf3b0bb03ca", + "git_sha": "ae9714c21ede9199a3118e3c20b65484aa73e232", "installed_by": ["fasta_ltrretriever_lai"] }, "ltrretriever/lai": { "branch": "main", - "git_sha": "cc6ea1f3e96e8264d2cc99afed31bcf3b0bb03ca", + "git_sha": "ae9714c21ede9199a3118e3c20b65484aa73e232", "installed_by": ["fasta_ltrretriever_lai"] }, "ltrretriever/ltrretriever": { "branch": "main", - "git_sha": "cc6ea1f3e96e8264d2cc99afed31bcf3b0bb03ca", + "git_sha": "ae9714c21ede9199a3118e3c20b65484aa73e232", "installed_by": ["fasta_ltrretriever_lai"] }, "plotsr": { "branch": "main", - "git_sha": "a203a6035aed3f9b345ee380f5d497ca98504d98", + "git_sha": "a8939d36280e7d9037c7cf164eeede19e46546a4", "installed_by": ["modules"] }, "samblaster": { "branch": "main", - "git_sha": "cc6ea1f3e96e8264d2cc99afed31bcf3b0bb03ca", + "git_sha": "ae9714c21ede9199a3118e3c20b65484aa73e232", "installed_by": ["fastq_bwa_mem_samblaster"] }, "samtools/faidx": { "branch": "main", - "git_sha": "cc6ea1f3e96e8264d2cc99afed31bcf3b0bb03ca", + "git_sha": "ae9714c21ede9199a3118e3c20b65484aa73e232", "installed_by": ["gff3_gt_gff3_gff3validator_stat"] }, "seqkit/seq": { "branch": "main", - "git_sha": "cc6ea1f3e96e8264d2cc99afed31bcf3b0bb03ca", + "git_sha": "ae9714c21ede9199a3118e3c20b65484aa73e232", "installed_by": ["fasta_ltrretriever_lai"] }, "syri": { "branch": "main", - "git_sha": "a203a6035aed3f9b345ee380f5d497ca98504d98", + "git_sha": "a8939d36280e7d9037c7cf164eeede19e46546a4", "installed_by": ["modules"] } } @@ -131,7 +131,7 @@ }, "gff3_gt_gff3_gff3validator_stat": { "branch": "main", - "git_sha": "58c5f9e695b9e03d43e4c59d9339af7c93f0acbe", + "git_sha": "92d59e5f578a2929b75f7588985b9bf451f4c370", "installed_by": ["subworkflows"] } } @@ -142,27 +142,27 @@ "nf-core": { "custom/sratoolsncbisettings": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"] }, "fastavalidator": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "fastp": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["fastq_fastqc_umitools_fastp"] }, "fastqc": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["fastq_fastqc_umitools_fastp"] }, "fcs/fcsadaptor": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "gfastats": { @@ -172,82 +172,82 @@ }, "gunzip": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "merqury/hapmers": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "merqury/merqury": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "meryl/count": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "meryl/unionsum": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "minimap2/align": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "seqkit/rmdup": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "seqkit/seq": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["fasta_explore_search_plot_tidk", "fasta_ltrretriever_lai"] }, "seqkit/sort": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["fasta_explore_search_plot_tidk"] }, "sratools/fasterqdump": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["fastq_download_prefetch_fasterqdump_sratools", "modules"] }, "sratools/prefetch": { "branch": "master", - "git_sha": "368e6c90b91adbd171e7c0a1c85a700b86a915af", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["fastq_download_prefetch_fasterqdump_sratools", "modules"] }, "tidk/explore": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["fasta_explore_search_plot_tidk"] }, "tidk/plot": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["fasta_explore_search_plot_tidk"] }, "tidk/search": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["fasta_explore_search_plot_tidk"] }, "umitools/extract": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["fastq_fastqc_umitools_fastp"] }, "untar": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] } } @@ -271,12 +271,12 @@ }, "utils_nextflow_pipeline": { "branch": "master", - "git_sha": "9d05360da397692321d377b6102d2fb22507c6ef", + "git_sha": "f533459a222ac53eb4c6bb7a5f574e4069197cdb", "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", - "git_sha": "772684d9d66f37b650c8ba5146ac1ee3ecba2acb", + "git_sha": "f533459a222ac53eb4c6bb7a5f574e4069197cdb", "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { diff --git a/modules/gallvp/busco/busco/main.nf b/modules/gallvp/busco/busco/main.nf index f7c1a662..98cf5b04 100644 --- a/modules/gallvp/busco/busco/main.nf +++ b/modules/gallvp/busco/busco/main.nf @@ -11,7 +11,7 @@ process BUSCO_BUSCO { tuple val(meta), path(fasta, stageAs:'tmp_input/*') val mode // Required: One of genome, proteins, or transcriptome val lineage // Required: lineage to check against, "auto" enables --auto-lineage instead - path busco_lineages_path // Recommended: path to busco lineages - downloads if not set + path busco_lineages_path // Recommended: p_ath to busco lineages - downloads if not set path config_file // Optional: busco configuration file output: diff --git a/modules/gallvp/busco/busco/meta.yml b/modules/gallvp/busco/busco/meta.yml index 29745d2c..7cb6d69c 100644 --- a/modules/gallvp/busco/busco/meta.yml +++ b/modules/gallvp/busco/busco/meta.yml @@ -7,81 +7,135 @@ keywords: - proteome tools: - busco: - description: BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB. + description: BUSCO provides measures for quantitative assessment of genome assembly, + gene set, and transcriptome completeness based on evolutionarily informed expectations + of gene content from near-universal single-copy orthologs selected from OrthoDB. homepage: https://busco.ezlab.org/ documentation: https://busco.ezlab.org/busco_userguide.html tool_dev_url: https://gitlab.com/ezlab/busco doi: "10.1007/978-1-4939-9173-0_14" licence: ["MIT"] + identifier: biotools:busco input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Nucleic or amino acid sequence file in FASTA format. - pattern: "*.{fasta,fna,fa,fasta.gz,fna.gz,fa.gz}" - - mode: - type: string - description: The mode to run Busco in. One of genome, proteins, or transcriptome - pattern: "{genome,proteins,transcriptome}" - - lineage: - type: string - description: The BUSCO lineage to use, or "auto" to automatically select lineage - - busco_lineages_path: - type: directory - description: Path to local BUSCO lineages directory. - - config_file: - type: file - description: Path to BUSCO config file. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Nucleic or amino acid sequence file in FASTA format. + pattern: "*.{fasta,fna,fa,fasta.gz,fna.gz,fa.gz}" + - - mode: + type: string + description: The mode to run Busco in. One of genome, proteins, or transcriptome + pattern: "{genome,proteins,transcriptome}" + - - lineage: + type: string + description: The BUSCO lineage to use, or "auto" to automatically select lineage + - - busco_lineages_path: + type: directory + description: Path to local BUSCO lineages directory. + - - config_file: + type: file + description: Path to BUSCO config file. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - batch_summary: - type: file - description: Summary of all sequence files analyzed - pattern: "*-busco.batch_summary.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-busco.batch_summary.txt": + type: file + description: Summary of all sequence files analyzed + pattern: "*-busco.batch_summary.txt" - short_summaries_txt: - type: file - description: Short Busco summary in plain text format - pattern: "short_summary.*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - short_summary.*.txt: + type: file + description: Short Busco summary in plain text format + pattern: "short_summary.*.txt" - short_summaries_json: - type: file - description: Short Busco summary in JSON format - pattern: "short_summary.*.json" - - busco_dir: - type: directory - description: BUSCO lineage specific output - pattern: "*-busco" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - short_summary.*.json: + type: file + description: Short Busco summary in JSON format + pattern: "short_summary.*.json" - full_table: - type: file - description: Full BUSCO results table - pattern: "full_table.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-busco/*/run_*/full_table.tsv": + type: file + description: Full BUSCO results table + pattern: "full_table.tsv" - missing_busco_list: - type: file - description: List of missing BUSCOs - pattern: "missing_busco_list.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-busco/*/run_*/missing_busco_list.tsv": + type: file + description: List of missing BUSCOs + pattern: "missing_busco_list.tsv" - single_copy_proteins: - type: file - description: Fasta file of single copy proteins (transcriptome mode) - pattern: "single_copy_proteins.faa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-busco/*/run_*/single_copy_proteins.faa": + type: file + description: Fasta file of single copy proteins (transcriptome mode) + pattern: "single_copy_proteins.faa" - seq_dir: - type: directory - description: BUSCO sequence directory - pattern: "busco_sequences" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-busco/*/run_*/busco_sequences": + type: directory + description: BUSCO sequence directory + pattern: "busco_sequences" - translated_dir: - type: directory - description: Six frame translations of each transcript made by the transcriptome mode - pattern: "translated_dir" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-busco/*/translated_proteins": + type: directory + description: Six frame translations of each transcript made by the transcriptome + mode + pattern: "translated_dir" + - busco_dir: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-busco": + type: directory + description: BUSCO lineage specific output + pattern: "*-busco" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@priyanka-surana" - "@charles-plessy" diff --git a/modules/gallvp/busco/busco/tests/main.nf.test.snap b/modules/gallvp/busco/busco/tests/main.nf.test.snap index 1140d5de..825ddb98 100644 --- a/modules/gallvp/busco/busco/tests/main.nf.test.snap +++ b/modules/gallvp/busco/busco/tests/main.nf.test.snap @@ -11,19 +11,19 @@ ] ], "1": [ - + ], "2": [ - + ], "3": [ - + ], "4": [ - + ], "5": [ - + ], "6": [ [ @@ -31,12 +31,12 @@ "id": "test" }, [ - + ] ] ], "7": [ - + ], "8": [ [ @@ -47,7 +47,7 @@ [ [ [ - + ] ] ] @@ -74,7 +74,7 @@ [ [ [ - + ] ] ] @@ -82,10 +82,10 @@ ] ], "full_table": [ - + ], "missing_busco_list": [ - + ], "seq_dir": [ [ @@ -93,21 +93,21 @@ "id": "test" }, [ - + ] ] ], "short_summaries_json": [ - + ], "short_summaries_txt": [ - + ], "single_copy_proteins": [ - + ], "translated_dir": [ - + ], "versions": [ "versions.yml:md5,3fc94714b95c2dc15399a4229d9dd1d9" @@ -159,9 +159,9 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nextflow": "23.10.1" }, - "timestamp": "2024-08-22T11:24:24.828742" + "timestamp": "2024-05-03T13:23:50.255602" }, "test_busco_eukaryote_metaeuk": { "content": [ @@ -227,4 +227,4 @@ }, "timestamp": "2024-05-03T13:27:12.724862" } -} \ No newline at end of file +} diff --git a/modules/gallvp/busco/generateplot/meta.yml b/modules/gallvp/busco/generateplot/meta.yml index 796f32b4..72ad2c92 100644 --- a/modules/gallvp/busco/generateplot/meta.yml +++ b/modules/gallvp/busco/generateplot/meta.yml @@ -9,26 +9,31 @@ keywords: - quality control tools: - busco: - description: BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB. + description: BUSCO provides measures for quantitative assessment of genome assembly, + gene set, and transcriptome completeness based on evolutionarily informed expectations + of gene content from near-universal single-copy orthologs selected from OrthoDB. homepage: https://busco.ezlab.org/ documentation: https://busco.ezlab.org/busco_userguide.html tool_dev_url: https://gitlab.com/ezlab/busco doi: "10.1007/978-1-4939-9173-0_14" licence: ["MIT"] + identifier: biotools:busco input: - - short_summary_txt: - type: file - description: One or more short summary txt files from BUSCO - pattern: "short_summary.*.txt" + - - short_summary_txt: + type: file + description: One or more short summary txt files from BUSCO + pattern: "short_summary.*.txt" output: - png: - type: file - description: A summary plot in png format - pattern: "*.png" + - "*.png": + type: file + description: A summary plot in png format + pattern: "*.png" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/gallvp/bwa/index/meta.yml b/modules/gallvp/bwa/index/meta.yml index 6bbc87a6..4884bca2 100644 --- a/modules/gallvp/bwa/index/meta.yml +++ b/modules/gallvp/bwa/index/meta.yml @@ -14,29 +14,32 @@ tools: documentation: https://bio-bwa.sourceforge.net/bwa.shtml arxiv: arXiv:1303.3997 licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file + - - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input genome fasta file output: - - meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - index: - type: file - description: BWA genome index files - pattern: "*.{amb,ann,bwt,pac,sa}" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - bwa: + type: file + description: BWA genome index files + pattern: "*.{amb,ann,bwt,pac,sa}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@maxulysse" diff --git a/modules/gallvp/bwa/mem/meta.yml b/modules/gallvp/bwa/mem/meta.yml index b126dd86..37467d29 100644 --- a/modules/gallvp/bwa/mem/meta.yml +++ b/modules/gallvp/bwa/mem/meta.yml @@ -17,55 +17,82 @@ tools: documentation: https://bio-bwa.sourceforge.net/bwa.shtml arxiv: arXiv:1303.3997 licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - index: - type: file - description: BWA genome index files - pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" - - fasta: - type: file - description: Reference genome in FASTA format - pattern: "*.{fasta,fa}" - - sort_bam: - type: boolean - description: use samtools sort (true) or samtools view (false) - pattern: "true or false" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - index: + type: file + description: BWA genome index files + pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Reference genome in FASTA format + pattern: "*.{fasta,fa}" + - - sort_bam: + type: boolean + description: use samtools sort (true) or samtools view (false) + pattern: "true or false" output: - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" + - meta: + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" + - "*.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" - cram: - type: file - description: Output CRAM file containing read alignments - pattern: "*.{cram}" + - meta: + type: file + description: Output CRAM file containing read alignments + pattern: "*.{cram}" + - "*.cram": + type: file + description: Output CRAM file containing read alignments + pattern: "*.{cram}" - csi: - type: file - description: Optional index file for BAM file - pattern: "*.{csi}" + - meta: + type: file + description: Optional index file for BAM file + pattern: "*.{csi}" + - "*.csi": + type: file + description: Optional index file for BAM file + pattern: "*.{csi}" - crai: - type: file - description: Optional index file for CRAM file - pattern: "*.{crai}" + - meta: + type: file + description: Optional index file for CRAM file + pattern: "*.{crai}" + - "*.crai": + type: file + description: Optional index file for CRAM file + pattern: "*.{crai}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@jeremy1805" diff --git a/modules/gallvp/cat/cat/meta.yml b/modules/gallvp/cat/cat/meta.yml index 00a8db0b..81778a06 100644 --- a/modules/gallvp/cat/cat/meta.yml +++ b/modules/gallvp/cat/cat/meta.yml @@ -9,25 +9,32 @@ tools: description: Just concatenation documentation: https://man7.org/linux/man-pages/man1/cat.1.html licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - files_in: - type: file - description: List of compressed / uncompressed files - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - files_in: + type: file + description: List of compressed / uncompressed files + pattern: "*" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - file_out: - type: file - description: Concatenated file. Will be gzipped if file_out ends with ".gz" - pattern: "${file_out}" + - meta: + type: file + description: Concatenated file. Will be gzipped if file_out ends with ".gz" + pattern: "${file_out}" + - ${prefix}: + type: file + description: Concatenated file. Will be gzipped if file_out ends with ".gz" + pattern: "${file_out}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" - "@FriederikeHanssen" diff --git a/modules/gallvp/custom/relabelfasta/meta.yml b/modules/gallvp/custom/relabelfasta/meta.yml index 7935872a..bf563aad 100644 --- a/modules/gallvp/custom/relabelfasta/meta.yml +++ b/modules/gallvp/custom/relabelfasta/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "custom_relabelfasta" description: | @@ -20,36 +19,38 @@ tools: documentation: "https://docs.python.org/3/" tool_dev_url: "https://github.com/python/cpython" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fasta: - type: file - description: Input fasta file - pattern: "*.fasta" - - labels: - type: file - description: | - A TSV file with original (first column) and new ids (second column) - pattern: "*.tsv" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: Input fasta file + pattern: "*.fasta" + - - labels: + type: file + description: | + A TSV file with original (first column) and new ids (second column) + pattern: "*.tsv" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: Output fasta file - pattern: "*.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.fasta": + type: file + description: Output fasta file + pattern: "*.fasta" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/gallvp/custom/restoregffids/meta.yml b/modules/gallvp/custom/restoregffids/meta.yml index 4e42b829..dea75778 100644 --- a/modules/gallvp/custom/restoregffids/meta.yml +++ b/modules/gallvp/custom/restoregffids/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "custom_restoregffids" description: | @@ -22,36 +21,39 @@ tools: documentation: "https://docs.python.org/3/" tool_dev_url: "https://github.com/python/cpython" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - gff3: - type: file - description: Input gff3 file - pattern: "*.{gff,gff3}" - - ids_tsv: - type: file - description: | - A TSV file with original (first column) and new ids (second column) - if id change was required - pattern: "*.tsv" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - gff3: + type: file + description: Input gff3 file + pattern: "*.{gff,gff3}" + - - ids_tsv: + type: file + description: | + A TSV file with original (first column) and new ids (second column) + if id change was required + pattern: "*.tsv" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - restored_ids_gff3: - type: file - description: GFF3 file with restored ids - pattern: "*.restored.ids.gff3" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*.restored.ids.gff3": + type: file + description: GFF3 file with restored ids + pattern: "*.restored.ids.gff3" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/gallvp/custom/shortenfastaids/meta.yml b/modules/gallvp/custom/shortenfastaids/meta.yml index 2425810d..bb14b0ae 100644 --- a/modules/gallvp/custom/shortenfastaids/meta.yml +++ b/modules/gallvp/custom/shortenfastaids/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "custom_shortenfastaids" description: | @@ -22,36 +21,45 @@ tools: tool_dev_url: "https://github.com/biopython/biopython" doi: "10.1093/bioinformatics/btp163" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - fasta: - type: file - description: Input fasta file - pattern: "*.{fsa,fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - fasta: + type: file + description: Input fasta file + pattern: "*.{fsa,fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - short_ids_fasta: - type: file - description: Fasta file with shortened ids if id change is required - pattern: "*.{fsa,fa,fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*.short.ids.fasta": + type: file + description: Fasta file with shortened ids if id change is required + pattern: "*.{fsa,fa,fasta}" - short_ids_tsv: - type: file - description: | - A TSV file with original (first column) and new ids (second column) - if id change is required - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*.short.ids.tsv": + type: file + description: | + A TSV file with original (first column) and new ids (second column) + if id change is required + pattern: "*.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/gallvp/gffread/meta.yml b/modules/gallvp/gffread/meta.yml index c0602820..bebe7f57 100644 --- a/modules/gallvp/gffread/meta.yml +++ b/modules/gallvp/gffread/meta.yml @@ -1,53 +1,73 @@ name: gffread -description: Validate, filter, convert and perform various other operations on GFF files +description: Validate, filter, convert and perform various other operations on GFF + files keywords: - gff - conversion - validation tools: - gffread: - description: GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more. + description: GFF/GTF utility providing format conversions, region filtering, FASTA + sequence extraction and more. homepage: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread documentation: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread tool_dev_url: https://github.com/gpertea/gffread doi: 10.12688/f1000research.23297.1 licence: ["MIT"] + identifier: biotools:gffread input: - - meta: - type: map - description: | - Groovy Map containing meta data - e.g. [ id:'test' ] - - gff: - type: file - description: A reference file in either the GFF3, GFF2 or GTF format. - pattern: "*.{gff, gtf}" - - fasta: - type: file - description: A multi-fasta file with the genomic sequences - pattern: "*.{fasta,fa,faa,fas,fsa}" + - - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test' ] + - gff: + type: file + description: A reference file in either the GFF3, GFF2 or GTF format. + pattern: "*.{gff, gtf}" + - - fasta: + type: file + description: A multi-fasta file with the genomic sequences + pattern: "*.{fasta,fa,faa,fas,fsa}" output: - - meta: - type: map - description: | - Groovy Map containing meta data - e.g. [ id:'test' ] - gtf: - type: file - description: GTF file resulting from the conversion of the GFF input file if '-T' argument is present - pattern: "*.{gtf}" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test' ] + - "*.gtf": + type: file + description: GTF file resulting from the conversion of the GFF input file if + '-T' argument is present + pattern: "*.{gtf}" - gffread_gff: - type: file - description: GFF3 file resulting from the conversion of the GFF input file if '-T' argument is absent - pattern: "*.gff3" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test' ] + - "*.gff3": + type: file + description: GFF3 file resulting from the conversion of the GFF input file if + '-T' argument is absent + pattern: "*.gff3" - gffread_fasta: - type: file - description: Fasta file produced when either of '-w', '-x', '-y' parameters is present - pattern: "*.fasta" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test' ] + - "*.fasta": + type: file + description: Fasta file produced when either of '-w', '-x', '-y' parameters + is present + pattern: "*.fasta" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" maintainers: diff --git a/modules/gallvp/gt/gff3/meta.yml b/modules/gallvp/gt/gff3/meta.yml index 5cecd8d0..62c4cbc6 100644 --- a/modules/gallvp/gt/gff3/meta.yml +++ b/modules/gallvp/gt/gff3/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "gt_gff3" -description: "GenomeTools gt-gff3 utility to parse, possibly transform, and output GFF3 files" +description: "GenomeTools gt-gff3 utility to parse, possibly transform, and output + GFF3 files" keywords: - genome - gff3 @@ -14,34 +14,43 @@ tools: tool_dev_url: "https://github.com/genometools/genometools" doi: "10.1109/TCBB.2013.68" licence: ["ISC"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - gff3: - type: file - description: Input gff3 file - pattern: "*.{gff,gff3}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - gff3: + type: file + description: Input gff3 file + pattern: "*.{gff,gff3}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - gt_gff3: - type: file - description: Parsed gff3 file produced only if there is no parsing error - pattern: "*.gt.gff3" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*.gt.gff3": + type: file + description: Parsed gff3 file produced only if there is no parsing error + pattern: "*.gt.gff3" - error_log: - type: file - description: Error log if gt-gff3 failed to parse the input gff3 file - pattern: "*.error.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*.error.log": + type: file + description: Error log if gt-gff3 failed to parse the input gff3 file + pattern: "*.error.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@gallvp" maintainers: diff --git a/modules/gallvp/gt/gff3validator/meta.yml b/modules/gallvp/gt/gff3validator/meta.yml index 3322faf9..98ff256d 100644 --- a/modules/gallvp/gt/gff3validator/meta.yml +++ b/modules/gallvp/gt/gff3validator/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "gt_gff3validator" description: "GenomeTools gt-gff3validator utility to strictly validate a GFF3 file" @@ -15,34 +14,43 @@ tools: tool_dev_url: "https://github.com/genometools/genometools" doi: "10.1109/TCBB.2013.68" licence: ["ISC"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - gff3: - type: file - description: Input gff3 file - pattern: "*.{gff,gff3}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - gff3: + type: file + description: Input gff3 file + pattern: "*.{gff,gff3}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - success_log: - type: file - description: Log file for successful validation - pattern: "*.success.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*.success.log": + type: file + description: Log file for successful validation + pattern: "*.success.log" - error_log: - type: file - description: Log file for failed validation - pattern: "*.error.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*.error.log": + type: file + description: Log file for failed validation + pattern: "*.error.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/gallvp/gt/stat/meta.yml b/modules/gallvp/gt/stat/meta.yml index fa477f34..3f62f8eb 100644 --- a/modules/gallvp/gt/stat/meta.yml +++ b/modules/gallvp/gt/stat/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "gt_stat" -description: "GenomeTools gt-stat utility to show statistics about features contained in GFF3 files" +description: "GenomeTools gt-stat utility to show statistics about features contained + in GFF3 files" keywords: - genome - gff3 @@ -16,30 +16,33 @@ tools: tool_dev_url: "https://github.com/genometools/genometools" doi: "10.1109/TCBB.2013.68" licence: ["ISC"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - gff3: - type: file - description: Input gff3 file - pattern: "*.{gff,gff3}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - gff3: + type: file + description: Input gff3 file + pattern: "*.{gff,gff3}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - stats: - type: file - description: Stats file in yaml format - pattern: "*.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - ${prefix}.yml: + type: file + description: Stats file in yaml format + pattern: "*.yml" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/gallvp/ltrfinder/meta.yml b/modules/gallvp/ltrfinder/meta.yml index e3c672b9..547fb67d 100644 --- a/modules/gallvp/ltrfinder/meta.yml +++ b/modules/gallvp/ltrfinder/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "ltrfinder" description: | @@ -19,41 +18,52 @@ tools: tool_dev_url: "https://github.com/oushujun/LTR_FINDER_parallel" doi: "10.1186/s13100-019-0193-0" licence: ["MIT"] + identifier: "" - "LTR_Finder": - description: An efficient program for finding full-length LTR retrotranspsons in genome sequences + description: An efficient program for finding full-length LTR retrotranspsons + in genome sequences homepage: "https://github.com/xzhub/LTR_Finder" documentation: "https://github.com/xzhub/LTR_Finder" tool_dev_url: "https://github.com/xzhub/LTR_Finder" doi: "10.1093/nar/gkm286" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fasta: - type: file - description: Genome sequences in fasta format - pattern: "*.{fsa,fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: Genome sequences in fasta format + pattern: "*.{fsa,fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - scn: - type: file - description: Annotation in LTRharvest or LTR_FINDER format - pattern: "*.scn" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.scn": + type: file + description: Annotation in LTRharvest or LTR_FINDER format + pattern: "*.scn" - gff: - type: file - description: Annotation in gff3 format - pattern: "*.gff3" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.gff3": + type: file + description: Annotation in gff3 format + pattern: "*.gff3" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/gallvp/ltrfinder/tests/main.nf.test b/modules/gallvp/ltrfinder/tests/main.nf.test index c08af00a..4af6bba5 100644 --- a/modules/gallvp/ltrfinder/tests/main.nf.test +++ b/modules/gallvp/ltrfinder/tests/main.nf.test @@ -7,13 +7,13 @@ nextflow_process { tag "modules" tag "modules_gallvp" tag "ltrfinder" - tag "gunzip/main" + tag "gunzip" test("actinidia_chinensis-genome_21_fasta_gz-success") { setup { run('GUNZIP') { - script "../../gunzip/main" + script "../../gunzip/main.nf" process { """ diff --git a/modules/gallvp/ltrharvest/meta.yml b/modules/gallvp/ltrharvest/meta.yml index 256b3ce5..18064183 100644 --- a/modules/gallvp/ltrharvest/meta.yml +++ b/modules/gallvp/ltrharvest/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "ltrharvest" description: | @@ -18,6 +17,7 @@ tools: documentation: "https://github.com/oushujun/EDTA/tree/v2.2.0/bin/LTR_HARVEST_parallel" tool_dev_url: "https://github.com/oushujun/EDTA/tree/v2.2.0/bin/LTR_HARVEST_parallel" licence: ["MIT"] + identifier: "" - "gt": description: "The GenomeTools genome analysis system" homepage: "https://genometools.org/index.html" @@ -25,34 +25,43 @@ tools: tool_dev_url: "https://github.com/genometools/genometools" doi: "10.1109/TCBB.2013.68" licence: ["ISC"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fasta: - type: file - description: Input genome fasta - pattern: "*.{fsa,fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: Input genome fasta + pattern: "*.{fsa,fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gff3: - type: file - description: Predicted LTR candidates in gff3 format - pattern: "*.gff3" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.gff3": + type: file + description: Predicted LTR candidates in gff3 format + pattern: "*.gff3" - scn: - type: file - description: Predicted LTR candidates in scn format - pattern: "*.scn" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.scn": + type: file + description: Predicted LTR candidates in scn format + pattern: "*.scn" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/gallvp/ltrretriever/lai/meta.yml b/modules/gallvp/ltrretriever/lai/meta.yml index f84cf6ca..56efcccc 100644 --- a/modules/gallvp/ltrretriever/lai/meta.yml +++ b/modules/gallvp/ltrretriever/lai/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "ltrretriever_lai" description: | @@ -20,50 +19,59 @@ tools: tool_dev_url: "https://github.com/oushujun/LTR_retriever" doi: "10.1093/nar/gky730" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fasta: - type: file - description: The genome file that is used to generate everything - pattern: "*.{fsa,fa,fasta}" - - pass_list: - type: file - description: A list of intact LTR-RTs generated by LTR_retriever - pattern: "*.pass.list" - - annotation_out: - type: file - description: RepeatMasker annotation of all LTR sequences in the genome - pattern: "*.out" - - monoploid_seqs: - type: file - description: | - This parameter is mainly for ployploid genomes. User provides a list of - sequence names that represent a monoploid (1x). LAI will be calculated only - on these sequences if provided. - pattern: "*.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: The genome file that is used to generate everything + pattern: "*.{fsa,fa,fasta}" + - - pass_list: + type: file + description: A list of intact LTR-RTs generated by LTR_retriever + pattern: "*.pass.list" + - - annotation_out: + type: file + description: RepeatMasker annotation of all LTR sequences in the genome + pattern: "*.out" + - - monoploid_seqs: + type: file + description: | + This parameter is mainly for ployploid genomes. User provides a list of + sequence names that represent a monoploid (1x). LAI will be calculated only + on these sequences if provided. + pattern: "*.txt" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - log: - type: file - description: Log from LAI - pattern: "*.LAI.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.LAI.log": + type: file + description: Log from LAI + pattern: "*.LAI.log" - lai_out: - type: file - description: | - Output file from LAI if LAI is able to estimate the index from the inputs - pattern: "*.LAI.out" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.LAI.out": + type: file + description: | + Output file from LAI if LAI is able to estimate the index from the inputs + pattern: "*.LAI.out" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/gallvp/ltrretriever/ltrretriever/meta.yml b/modules/gallvp/ltrretriever/ltrretriever/meta.yml index a310b04a..9645de2d 100644 --- a/modules/gallvp/ltrretriever/ltrretriever/meta.yml +++ b/modules/gallvp/ltrretriever/ltrretriever/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "ltrretriever_ltrretriever" description: Identifies LTR retrotransposons using LTR_retriever @@ -16,67 +15,104 @@ tools: tool_dev_url: "https://github.com/oushujun/LTR_retriever" doi: "10.1104/pp.17.01310" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - genome: - type: file - description: Genomic sequences in fasta format - pattern: "*.{fsa,fa,fasta}" - - harvest: - type: file - description: LTR-RT candidates from GenomeTools ltrharvest in the old tabular format - pattern: "*.tabout" - - finder: - type: file - description: LTR-RT candidates from LTR_FINDER - pattern: "*.scn" - - mgescan: - type: file - description: LTR-RT candidates from MGEScan_LTR - pattern: "*.out" - - non_tgca: - type: file - description: Non-canonical LTR-RT candidates from GenomeTools ltrharvest in the old tabular format - pattern: "*.tabout" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - genome: + type: file + description: Genomic sequences in fasta format + pattern: "*.{fsa,fa,fasta}" + - - harvest: + type: file + description: LTR-RT candidates from GenomeTools ltrharvest in the old tabular + format + pattern: "*.tabout" + - - finder: + type: file + description: LTR-RT candidates from LTR_FINDER + pattern: "*.scn" + - - mgescan: + type: file + description: LTR-RT candidates from MGEScan_LTR + pattern: "*.out" + - - non_tgca: + type: file + description: Non-canonical LTR-RT candidates from GenomeTools ltrharvest in + the old tabular format + pattern: "*.tabout" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - log: - type: file - description: Output log from LTR_retriever - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.log": + type: file + description: Output log from LTR_retriever + pattern: "*.log" - pass_list: - type: file - description: Intact LTR-RTs with coordinate and structural information in summary table format - pattern: "*.pass.list" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}.pass.list: + type: file + description: Intact LTR-RTs with coordinate and structural information in summary + table format + pattern: "*.pass.list" - pass_list_gff: - type: file - description: Intact LTR-RTs with coordinate and structural information in gff3 format - pattern: "*.pass.list.gff3" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.pass.list.gff3": + type: file + description: Intact LTR-RTs with coordinate and structural information in gff3 + format + pattern: "*.pass.list.gff3" - ltrlib: - type: file - description: All non-redundant LTR-RTs - pattern: "*.LTRlib.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.LTRlib.fa": + type: file + description: All non-redundant LTR-RTs + pattern: "*.LTRlib.fa" - annotation_out: - type: file - description: Whole-genome LTR-RT annotation by the non-redundant library - pattern: "*.out" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}.out: + type: file + description: Whole-genome LTR-RT annotation by the non-redundant library + pattern: "*.out" - annotation_gff: - type: file - description: Whole-genome LTR-RT annotation by the non-redundant library in gff3 format - pattern: "*.out.gff3" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.out.gff3": + type: file + description: Whole-genome LTR-RT annotation by the non-redundant library in + gff3 format + pattern: "*.out.gff3" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/gallvp/ltrretriever/ltrretriever/tests/main.nf.test b/modules/gallvp/ltrretriever/ltrretriever/tests/main.nf.test index 91b1a104..52dd7ac0 100644 --- a/modules/gallvp/ltrretriever/ltrretriever/tests/main.nf.test +++ b/modules/gallvp/ltrretriever/ltrretriever/tests/main.nf.test @@ -9,7 +9,7 @@ nextflow_process { tag "modules_gallvp" tag "ltrretriever" tag "ltrretriever/ltrretriever" - tag "gunzip/main" + tag "gunzip" tag "ltrharvest" tag "ltrfinder" tag "cat/cat" @@ -19,7 +19,7 @@ nextflow_process { setup { run("LTRHARVEST") { - script "../../../ltrharvest" + script "../../../ltrharvest/main.nf" process { """ @@ -32,7 +32,7 @@ nextflow_process { } run("LTRFINDER") { - script "../../../ltrfinder" + script "../../../ltrfinder/main.nf" process { """ @@ -45,7 +45,7 @@ nextflow_process { } run("CAT_CAT") { - script "../../../cat/cat" + script "../../../cat/cat/main.nf" process { """ @@ -85,7 +85,7 @@ nextflow_process { setup { run('GUNZIP') { - script "../../../gunzip/main" + script "../../../gunzip/main.nf" process { """ @@ -98,7 +98,7 @@ nextflow_process { } run("LTRHARVEST") { - script "../../../ltrharvest" + script "../../../ltrharvest/main.nf" process { """ @@ -108,7 +108,7 @@ nextflow_process { } run("LTRFINDER") { - script "../../../ltrfinder" + script "../../../ltrfinder/main.nf" process { """ @@ -118,7 +118,7 @@ nextflow_process { } run("CAT_CAT") { - script "../../../cat/cat" + script "../../../cat/cat/main.nf" process { """ diff --git a/modules/gallvp/plotsr/meta.yml b/modules/gallvp/plotsr/meta.yml index c728b683..c2bc2993 100644 --- a/modules/gallvp/plotsr/meta.yml +++ b/modules/gallvp/plotsr/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "plotsr" -description: Plotsr generates high-quality visualisation of synteny and structural rearrangements between multiple genomes. +description: Plotsr generates high-quality visualisation of synteny and structural + rearrangements between multiple genomes. keywords: - genomics - synteny @@ -15,64 +15,67 @@ tools: tool_dev_url: "https://github.com/schneebergerlab/plotsr" doi: "10.1093/bioinformatics/btac196" licence: ["MIT"] + identifier: biotools:plotsr input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - syri: - type: file - description: Structural annotation mappings (syri.out) identified by SyRI - pattern: "*syri.out" - - fastas: - type: list - description: Fasta files in the sequence specified by the `genomes` file - pattern: "*.{fasta,fa,fsa,faa}" - - genomes: - type: string - description: | - String containing the genomes.txt file contents including the header, but excluding the path to genome fasta files. - The path to staged genome files is automatically added by the process script. For example, see the included nf-test. - pattern: "*.txt" - - bedpe: - type: file - description: Structural annotation mappings in BEDPE format - pattern: "*.bedpe" - - markers: - type: file - description: File containing path to markers - pattern: "*.bed" - - tracks: - type: file - description: File listing paths and details for all tracks to be plotted - pattern: "*.txt" - - chrord: - type: file - description: | - File containing reference (first genome) chromosome IDs in the order in which they are to be plotted. - File requires one chromosome ID per line. Not compatible with --chr - pattern: "*.txt" - - chrname: - type: file - description: | - File containing reference (first genome) chromosome names to be used in the plot. - File needs to be a TSV with the chromosome ID in first column and chromosome name in the second. - pattern: "*.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - syri: + type: file + description: Structural annotation mappings (syri.out) identified by SyRI + pattern: "*syri.out" + - - fastas: + type: list + description: Fasta files in the sequence specified by the `genomes` file + pattern: "*.{fasta,fa,fsa,faa}" + - - genomes: + type: string + description: | + String containing the genomes.txt file contents including the header, but excluding the path to genome fasta files. + The path to staged genome files is automatically added by the process script. For example, see the included nf-test. + pattern: "*.txt" + - - bedpe: + type: file + description: Structural annotation mappings in BEDPE format + pattern: "*.bedpe" + - - markers: + type: file + description: File containing path to markers + pattern: "*.bed" + - - tracks: + type: file + description: File listing paths and details for all tracks to be plotted + pattern: "*.txt" + - - chrord: + type: file + description: | + File containing reference (first genome) chromosome IDs in the order in which they are to be plotted. + File requires one chromosome ID per line. Not compatible with --chr + pattern: "*.txt" + - - chrname: + type: file + description: | + File containing reference (first genome) chromosome names to be used in the plot. + File needs to be a TSV with the chromosome ID in first column and chromosome name in the second. + pattern: "*.txt" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - png: - type: file - description: Synteny plot - pattern: "*.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.png": + type: file + description: Synteny plot + pattern: "*.png" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/gallvp/samblaster/meta.yml b/modules/gallvp/samblaster/meta.yml index 5c1e5a97..5faf3a6c 100644 --- a/modules/gallvp/samblaster/meta.yml +++ b/modules/gallvp/samblaster/meta.yml @@ -23,30 +23,33 @@ tools: tool_dev_url: https://github.com/GregoryFaust/samblaster doi: "10.1093/bioinformatics/btu314" licence: ["MIT"] + identifier: biotools:samblaster input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.bam" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.bam" output: - - meta: - 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" - bam: - type: file - description: Tagged or filtered BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Tagged or filtered BAM file + pattern: "*.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lescai" maintainers: diff --git a/modules/gallvp/samtools/faidx/environment.yml b/modules/gallvp/samtools/faidx/environment.yml index b98cbb99..2bcd47ee 100644 --- a/modules/gallvp/samtools/faidx/environment.yml +++ b/modules/gallvp/samtools/faidx/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/gallvp/samtools/faidx/main.nf b/modules/gallvp/samtools/faidx/main.nf index bdcdbc95..28c0a81c 100644 --- a/modules/gallvp/samtools/faidx/main.nf +++ b/modules/gallvp/samtools/faidx/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FAIDX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/gallvp/samtools/faidx/meta.yml b/modules/gallvp/samtools/faidx/meta.yml index f3c25de2..6721b2cb 100644 --- a/modules/gallvp/samtools/faidx/meta.yml +++ b/modules/gallvp/samtools/faidx/meta.yml @@ -14,47 +14,62 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: FASTA file - pattern: "*.{fa,fasta}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fai: - type: file - description: FASTA index file - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fa,fasta}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fai: + type: file + description: FASTA index file + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fa: - type: file - description: FASTA file - pattern: "*.{fa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{fa,fasta}": + type: file + description: FASTA file + pattern: "*.{fa}" - fai: - type: file - description: FASTA index file - pattern: "*.{fai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fai": + type: file + description: FASTA index file + pattern: "*.{fai}" - gzi: - type: file - description: Optional gzip index file for compressed inputs - pattern: "*.gzi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gzi": + type: file + description: Optional gzip index file for compressed inputs + pattern: "*.gzi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" diff --git a/modules/gallvp/samtools/faidx/tests/main.nf.test.snap b/modules/gallvp/samtools/faidx/tests/main.nf.test.snap index 3223b72b..1bbb3ec2 100644 --- a/modules/gallvp/samtools/faidx/tests/main.nf.test.snap +++ b/modules/gallvp/samtools/faidx/tests/main.nf.test.snap @@ -18,7 +18,7 @@ ], "3": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ], "fa": [ @@ -36,15 +36,15 @@ ], "versions": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:42:14.779784761" + "timestamp": "2024-09-16T07:57:47.450887871" }, "test_samtools_faidx_bgzip": { "content": [ @@ -71,7 +71,7 @@ ] ], "3": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ], "fa": [ @@ -95,15 +95,15 @@ ] ], "versions": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:42:20.256633877" + "timestamp": "2024-09-16T07:58:04.804905659" }, "test_samtools_faidx_fasta": { "content": [ @@ -124,7 +124,7 @@ ], "3": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ], "fa": [ [ @@ -142,15 +142,15 @@ ], "versions": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:42:25.632577273" + "timestamp": "2024-09-16T07:58:23.831268154" }, "test_samtools_faidx_stub_fasta": { "content": [ @@ -171,7 +171,7 @@ ], "3": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ], "fa": [ [ @@ -189,15 +189,15 @@ ], "versions": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:42:31.058424849" + "timestamp": "2024-09-16T07:58:35.600243706" }, "test_samtools_faidx_stub_fai": { "content": [ @@ -218,7 +218,7 @@ ], "3": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ], "fa": [ @@ -236,14 +236,14 @@ ], "versions": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:42:36.479929617" + "timestamp": "2024-09-16T07:58:54.705460167" } } \ No newline at end of file diff --git a/modules/gallvp/seqkit/seq/meta.yml b/modules/gallvp/seqkit/seq/meta.yml index 8d4e2b16..7d32aba5 100644 --- a/modules/gallvp/seqkit/seq/meta.yml +++ b/modules/gallvp/seqkit/seq/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "seqkit_seq" -description: Transforms sequences (extract ID, filter by length, remove gaps, reverse complement...) +description: Transforms sequences (extract ID, filter by length, remove gaps, reverse + complement...) keywords: - genomics - fasta @@ -18,30 +18,33 @@ tools: tool_dev_url: "https://github.com/shenwei356/seqkit" doi: "10.1371/journal.pone.0163962" licence: ["MIT"] + identifier: biotools:seqkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fastx: - type: file - description: Input fasta/fastq file - pattern: "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fastx: + type: file + description: Input fasta/fastq file + pattern: "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - fastx: - type: file - description: Output fasta/fastq file - pattern: "*.{fasta,fasta.gz,fastq,fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}.*: + type: file + description: Output fasta/fastq file + pattern: "*.{fasta,fasta.gz,fastq,fastq.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/gallvp/syri/meta.yml b/modules/gallvp/syri/meta.yml index d7801532..9699bacd 100644 --- a/modules/gallvp/syri/meta.yml +++ b/modules/gallvp/syri/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "syri" -description: Syri compares alignments between two chromosome-level assemblies and identifies synteny and structural rearrangements. +description: Syri compares alignments between two chromosome-level assemblies and + identifies synteny and structural rearrangements. keywords: - genomics - synteny @@ -15,49 +15,57 @@ tools: tool_dev_url: "https://github.com/schneebergerlab/syri" doi: "10.1186/s13059-019-1911-0" licence: ["MIT License"] + identifier: biotools:SyRI input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - infile: - type: file - description: File containing alignment coordinates - pattern: "*.{table, sam, bam, paf}" - - query_fasta: - type: file - description: Query genome for the alignments - pattern: "*.fasta" - - reference_fasta: - type: file - description: Reference genome for the alignments - pattern: "*.fasta" - - file_type: - type: string - description: | - Input file type which is one of T: Table, S: SAM, B: BAM, P: PAF - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - infile: + type: file + description: File containing alignment coordinates + pattern: "*.{table, sam, bam, paf}" + - - query_fasta: + type: file + description: Query genome for the alignments + pattern: "*.fasta" + - - reference_fasta: + type: file + description: Reference genome for the alignments + pattern: "*.fasta" + - - file_type: + type: string + description: | + Input file type which is one of T: Table, S: SAM, B: BAM, P: PAF output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - syri: - type: file - description: Syri output file - pattern: "*syri.out" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*syri.out": + type: file + description: Syri output file + pattern: "*syri.out" - error: - type: file - description: | - Error log if syri fails. This error log enables the pipeline to detect if syri has failed due to one of its - known limitations and pass the information to the user in a user-friendly manner such as a HTML report - pattern: "*.error.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.error.log": + type: file + description: | + Error log if syri fails. This error log enables the pipeline to detect if syri has failed due to one of its + known limitations and pass the information to the user in a user-friendly manner such as a HTML report + pattern: "*.error.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/custom/sratoolsncbisettings/meta.yml b/modules/nf-core/custom/sratoolsncbisettings/meta.yml index 46a6cd32..2938a35d 100644 --- a/modules/nf-core/custom/sratoolsncbisettings/meta.yml +++ b/modules/nf-core/custom/sratoolsncbisettings/meta.yml @@ -1,5 +1,6 @@ name: "custom_sratoolsncbisettings" -description: Test for the presence of suitable NCBI settings or create them on the fly. +description: Test for the presence of suitable NCBI settings or create them on the + fly. keywords: - NCBI - settings @@ -13,15 +14,18 @@ tools: documentation: https://github.com/ncbi/sra-tools/wiki tool_dev_url: https://github.com/ncbi/sra-tools licence: ["Public Domain"] + identifier: "" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - ncbi_settings: - type: file - description: An NCBI user settings file. - pattern: "*.mkfg" + - "*.mkfg": + type: file + description: An NCBI user settings file. + pattern: "*.mkfg" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Midnighter" maintainers: diff --git a/modules/nf-core/fastavalidator/meta.yml b/modules/nf-core/fastavalidator/meta.yml index c5c4371c..94198e62 100644 --- a/modules/nf-core/fastavalidator/meta.yml +++ b/modules/nf-core/fastavalidator/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "fastavalidator" description: | @@ -19,34 +18,43 @@ tools: tool_dev_url: "https://github.com/linsalrob/py_fasta_validator" doi: "10.5281/zenodo.5002710" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing file information - e.g. [ id:'test' ] - - fasta: - type: file - description: Input fasta file - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing file information + e.g. [ id:'test' ] + - fasta: + type: file + description: Input fasta file + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing file information - e.g. [ id:'test' ] - success_log: - type: file - description: Log file for successful validation - pattern: "*.success.log" + - meta: + type: map + description: | + Groovy Map containing file information + e.g. [ id:'test' ] + - "*.success.log": + type: file + description: Log file for successful validation + pattern: "*.success.log" - error_log: - type: file - description: Log file for failed validation - pattern: "*.error.log" + - meta: + type: map + description: | + Groovy Map containing file information + e.g. [ id:'test' ] + - "*.error.log": + type: file + description: Log file for failed validation + pattern: "*.error.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@gallvp" maintainers: diff --git a/modules/nf-core/fastp/meta.yml b/modules/nf-core/fastp/meta.yml index 8dfecc18..159404d0 100644 --- a/modules/nf-core/fastp/meta.yml +++ b/modules/nf-core/fastp/meta.yml @@ -11,66 +11,100 @@ tools: documentation: https://github.com/OpenGene/fastp doi: 10.1093/bioinformatics/bty560 licence: ["MIT"] + identifier: biotools:fastp input: - - meta: - type: map - description: | - Groovy Map containing sample information. Use 'single_end: true' to specify single ended or interleaved FASTQs. Use 'single_end: false' for paired-end reads. - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. If you wish to run interleaved paired-end data, supply as single-end data - but with `--interleaved_in` in your `modules.conf`'s `ext.args` for the module. - - adapter_fasta: - type: file - description: File in FASTA format containing possible adapters to remove. - pattern: "*.{fasta,fna,fas,fa}" - - discard_trimmed_pass: - type: boolean - description: Specify true to not write any reads that pass trimming thresholds. | - This can be used to use fastp for the output report only. - - save_trimmed_fail: - type: boolean - description: Specify true to save files that failed to pass trimming thresholds ending in `*.fail.fastq.gz` - - save_merged: - type: boolean - description: Specify true to save all merged reads to a file ending in `*.merged.fastq.gz` + - - meta: + type: map + description: | + Groovy Map containing sample information. Use 'single_end: true' to specify single ended or interleaved FASTQs. Use 'single_end: false' for paired-end reads. + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. If you wish to run interleaved paired-end data, supply as single-end data + but with `--interleaved_in` in your `modules.conf`'s `ext.args` for the module. + - - adapter_fasta: + type: file + description: File in FASTA format containing possible adapters to remove. + pattern: "*.{fasta,fna,fas,fa}" + - - discard_trimmed_pass: + type: boolean + description: Specify true to not write any reads that pass trimming thresholds. + | This can be used to use fastp for the output report only. + - - save_trimmed_fail: + type: boolean + description: Specify true to save files that failed to pass trimming thresholds + ending in `*.fail.fastq.gz` + - - save_merged: + type: boolean + description: Specify true to save all merged reads to a file ending in `*.merged.fastq.gz` output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - reads: - type: file - description: The trimmed/modified/unmerged fastq reads - pattern: "*fastp.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastp.fastq.gz": + type: file + description: The trimmed/modified/unmerged fastq reads + pattern: "*fastp.fastq.gz" - json: - type: file - description: Results in JSON format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: Results in JSON format + pattern: "*.json" - html: - type: file - description: Results in HTML format - pattern: "*.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: Results in HTML format + pattern: "*.html" - log: - type: file - description: fastq log file - pattern: "*.log" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: fastq log file + pattern: "*.log" - reads_fail: - type: file - description: Reads the failed the preprocessing - pattern: "*fail.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fail.fastq.gz": + type: file + description: Reads the failed the preprocessing + pattern: "*fail.fastq.gz" - reads_merged: - type: file - description: Reads that were successfully merged - pattern: "*.{merged.fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.merged.fastq.gz": + type: file + description: Reads that were successfully merged + pattern: "*.{merged.fastq.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index ee5507e0..4827da7a 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -16,35 +16,44 @@ tools: homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ licence: ["GPL-2.0-only"] + identifier: biotools:fastqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - html: - type: file - description: FastQC report - pattern: "*_{fastqc.html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: FastQC report + pattern: "*_{fastqc.html}" - zip: - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.zip": + type: file + description: FastQC report archive + pattern: "*_{fastqc.zip}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@grst" diff --git a/modules/nf-core/fcs/fcsadaptor/meta.yml b/modules/nf-core/fcs/fcsadaptor/meta.yml index 54fca1bb..83cae5b7 100644 --- a/modules/nf-core/fcs/fcsadaptor/meta.yml +++ b/modules/nf-core/fcs/fcsadaptor/meta.yml @@ -18,45 +18,72 @@ tools: documentation: "https://github.com/ncbi/fcs/wiki/FCS-adaptor" tool_dev_url: "https://github.com/ncbi/fcs" licence: ["United States Government Work"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - assembly: - type: file - description: assembly fasta file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - assembly: + type: file + description: assembly fasta file output: - - meta: - 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" - cleaned_assembly: - type: file - description: Cleaned assembly in fasta format - pattern: "*.{cleaned_sequences.fa.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cleaned_sequences.fa.gz": + type: file + description: Cleaned assembly in fasta format + pattern: "*.{cleaned_sequences.fa.gz}" - adaptor_report: - type: file - description: Report of identified adaptors - pattern: "*.{fcs_adaptor_report.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fcs_adaptor_report.txt": + type: file + description: Report of identified adaptors + pattern: "*.{fcs_adaptor_report.txt}" - log: - type: file - description: Log file - pattern: "*.{fcs_adaptor.log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fcs_adaptor.log": + type: file + description: Log file + pattern: "*.{fcs_adaptor.log}" - pipeline_args: - type: file - description: Run arguments - pattern: "*.{pipeline_args.yaml}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pipeline_args.yaml": + type: file + description: Run arguments + pattern: "*.{pipeline_args.yaml}" - skipped_trims: - type: file - description: Skipped trim information - pattern: "*.{skipped_trims.jsonl}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.skipped_trims.jsonl": + type: file + description: Skipped trim information + pattern: "*.{skipped_trims.jsonl}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@d4straub" maintainers: diff --git a/modules/nf-core/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml index f32973a0..9066c035 100644 --- a/modules/nf-core/gunzip/meta.yml +++ b/modules/nf-core/gunzip/meta.yml @@ -10,25 +10,32 @@ tools: gzip is a file format and a software application used for file compression and decompression. documentation: https://www.gnu.org/software/gzip/manual/gzip.html licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Optional groovy Map containing meta information - e.g. [ id:'test', single_end:false ] - - archive: - type: file - description: File to be compressed/uncompressed - pattern: "*.*" + - - meta: + type: map + description: | + Optional groovy Map containing meta information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: File to be compressed/uncompressed + pattern: "*.*" output: - gunzip: - type: file - description: Compressed/uncompressed file - pattern: "*.*" + - meta: + type: file + description: Compressed/uncompressed file + pattern: "*.*" + - $gunzip: + type: file + description: Compressed/uncompressed file + pattern: "*.*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/merqury/hapmers/meta.yml b/modules/nf-core/merqury/hapmers/meta.yml index 6693f540..2c37d3ac 100644 --- a/modules/nf-core/merqury/hapmers/meta.yml +++ b/modules/nf-core/merqury/hapmers/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "merqury_hapmers" description: A script to generate hap-mer dbs for trios @@ -13,57 +12,85 @@ tools: tool_dev_url: "https://github.com/marbl/merqury" doi: "10.1186/s13059-020-02134-9" licence: ["United States Government Work"] + identifier: biotools:merqury input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - child_meryl: - type: directory - description: Childs' k-mers (all, from WGS reads) - pattern: "*.meryl" - - maternal_meryl: - type: directory - description: Haplotype1 k-mers (all, ex. maternal) - pattern: "*.meryl" - - paternal_meryl: - type: directory - description: Haplotype2 k-mers (all, ex. paternal) - pattern: "*.meryl" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - child_meryl: + type: directory + description: Childs' k-mers (all, from WGS reads) + pattern: "*.meryl" + - - maternal_meryl: + type: directory + description: Haplotype1 k-mers (all, ex. maternal) + pattern: "*.meryl" + - - paternal_meryl: + type: directory + description: Haplotype2 k-mers (all, ex. paternal) + pattern: "*.meryl" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - mat_hapmer_meryl: - type: directory - description: Inherited maternal hap-mer dbs - pattern: "*_mat.hapmer.meryl" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*_mat.hapmer.meryl": + type: directory + description: Inherited maternal hap-mer dbs + pattern: "*_mat.hapmer.meryl" - pat_hapmer_meryl: - type: directory - description: Inherited paternal hap-mer dbs - pattern: "*_pat.hapmer.meryl" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*_pat.hapmer.meryl": + type: directory + description: Inherited paternal hap-mer dbs + pattern: "*_pat.hapmer.meryl" - inherited_hapmers_fl_png: - type: file - description: k-mer distribution of the inherited dbs and cutoffs used to generate hap-mer dbs - pattern: "*_inherited_hapmers.fl.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*_inherited_hapmers.fl.png": + type: file + description: k-mer distribution of the inherited dbs and cutoffs used to generate + hap-mer dbs + pattern: "*_inherited_hapmers.fl.png" - inherited_hapmers_ln_png: - type: file - description: k-mer distribution of the inherited dbs and cutoffs used to generate hap-mer dbs - pattern: "*_inherited_hapmers.ln.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*_inherited_hapmers.ln.png": + type: file + description: k-mer distribution of the inherited dbs and cutoffs used to generate + hap-mer dbs + pattern: "*_inherited_hapmers.ln.png" - inherited_hapmers_st_png: - type: file - description: k-mer distribution of the inherited dbs and cutoffs used to generate hap-mer dbs - pattern: "*_inherited_hapmers.st.png" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*_inherited_hapmers.st.png": + type: file + description: k-mer distribution of the inherited dbs and cutoffs used to generate + hap-mer dbs + pattern: "*_inherited_hapmers.st.png" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/merqury/merqury/meta.yml b/modules/nf-core/merqury/merqury/meta.yml index 19cb11b3..7e8d875a 100644 --- a/modules/nf-core/merqury/merqury/meta.yml +++ b/modules/nf-core/merqury/merqury/meta.yml @@ -10,92 +10,187 @@ tools: tool_dev_url: "https://github.com/marbl/merqury" doi: "10.1186/s13059-020-02134-9" licence: ["PUBLIC DOMAIN"] + identifier: biotools:merqury input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meryl_db: - type: file - description: "Meryl read database" - - assembly: - type: file - description: FASTA assembly file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - meryl_db: + type: file + description: "Meryl read database" + - assembly: + type: file + description: FASTA assembly file output: - - meta: - 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" - assembly_only_kmers_bed: - type: file - description: "The positions of the k-mers found only in an assembly for further investigation in .bed" - pattern: "*_only.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_only.bed": + type: file + description: "The positions of the k-mers found only in an assembly for further + investigation in .bed" + pattern: "*_only.bed" - assembly_only_kmers_wig: - type: file - description: "The positions of the k-mers found only in an assembly for further investigation in .wig" - pattern: "*_only.wig" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_only.wig": + type: file + description: "The positions of the k-mers found only in an assembly for further + investigation in .wig" + pattern: "*_only.wig" - stats: - type: file - description: Assembly statistics file - pattern: "*.completeness.stats" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.completeness.stats": + type: file + description: Assembly statistics file + pattern: "*.completeness.stats" - dist_hist: - type: file - description: Histogram - pattern: "*.dist_only.hist" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.dist_only.hist": + type: file + description: Histogram + pattern: "*.dist_only.hist" - spectra_cn_fl_png: - type: file - description: "Unstacked copy number spectra filled plot in PNG format" - pattern: "*.spectra-cn.fl.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.spectra-cn.fl.png": + type: file + description: "Unstacked copy number spectra filled plot in PNG format" + pattern: "*.spectra-cn.fl.png" + - spectra_cn_hist: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.spectra-cn.hist": + type: file + description: "Copy number spectra histogram" + pattern: "*.spectra-cn.hist" - spectra_cn_ln_png: - type: file - description: "Unstacked copy number spectra line plot in PNG format" - pattern: "*.spectra-cn.ln.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.spectra-cn.ln.png": + type: file + description: "Unstacked copy number spectra line plot in PNG format" + pattern: "*.spectra-cn.ln.png" - spectra_cn_st_png: - type: file - description: "Stacked copy number spectra line plot in PNG format" - pattern: "*.spectra-cn.st.png" - - spectra_cn_hist: - type: file - description: "Copy number spectra histogram" - pattern: "*.spectra-cn.hist" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.spectra-cn.st.png": + type: file + description: "Stacked copy number spectra line plot in PNG format" + pattern: "*.spectra-cn.st.png" - spectra_asm_fl_png: - type: file - description: "Unstacked assembly spectra filled plot in PNG format" - pattern: "*.spectra-asm.fl.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.spectra-asm.fl.png": + type: file + description: "Unstacked assembly spectra filled plot in PNG format" + pattern: "*.spectra-asm.fl.png" + - spectra_asm_hist: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.spectra-asm.hist": + type: file + description: "Assembly spectra histogram" + pattern: "*.spectra-asm.hist" - spectra_asm_ln_png: - type: file - description: "Unstacked assembly spectra line plot in PNG format" - pattern: "*.spectra-asm.ln.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.spectra-asm.ln.png": + type: file + description: "Unstacked assembly spectra line plot in PNG format" + pattern: "*.spectra-asm.ln.png" - spectra_asm_st_png: - type: file - description: "Stacked assembly spectra line plot in PNG format" - pattern: "*.spectra-asm.st.png" - - spectra_asm_hist: - type: file - description: "Assembly spectra histogram" - pattern: "*.spectra-asm.hist" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.spectra-asm.st.png": + type: file + description: "Stacked assembly spectra line plot in PNG format" + pattern: "*.spectra-asm.st.png" - assembly_qv: - type: file - description: "Assembly consensus quality estimation" - pattern: "*.qv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.qv: + type: file + description: "Assembly consensus quality estimation" + pattern: "*.qv" - scaffold_qv: - type: file - description: "Scaffold consensus quality estimation" - pattern: "*.qv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.*.qv: + type: file + description: "Scaffold consensus quality estimation" + pattern: "*.qv" - read_ploidy: - type: file - description: "Ploidy estimate from read k-mer database" - pattern: "*.hist.ploidy" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hist.ploidy": + type: file + description: "Ploidy estimate from read k-mer database" + pattern: "*.hist.ploidy" - hapmers_blob_png: - type: file - description: "Hap-mer blob plot" - pattern: "*.hapmers.blob.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hapmers.blob.png": + type: file + description: "Hap-mer blob plot" + pattern: "*.hapmers.blob.png" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/meryl/count/meta.yml b/modules/nf-core/meryl/count/meta.yml index 809a32fe..a110a610 100644 --- a/modules/nf-core/meryl/count/meta.yml +++ b/modules/nf-core/meryl/count/meta.yml @@ -11,34 +11,37 @@ tools: documentation: "https://meryl.readthedocs.io/en/latest/quick-start.html" tool_dev_url: "https://github.com/marbl/meryl" licence: ["GPL"] + identifier: biotools:meryl input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - kvalue: - type: integer - description: An integer value of k to use as the k-mer value. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - kvalue: + type: integer + description: An integer value of k to use as the k-mer value. output: - - meta: - 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" - meryl_db: - type: directory - description: A Meryl k-mer database - pattern: "*.meryl" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.meryl": + type: directory + description: A Meryl k-mer database + pattern: "*.meryl" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/meryl/unionsum/meta.yml b/modules/nf-core/meryl/unionsum/meta.yml index 77d0784c..e9e13051 100644 --- a/modules/nf-core/meryl/unionsum/meta.yml +++ b/modules/nf-core/meryl/unionsum/meta.yml @@ -11,32 +11,35 @@ tools: documentation: "https://meryl.readthedocs.io/en/latest/quick-start.html" tool_dev_url: "https://github.com/marbl/meryl" licence: ["GPL"] + identifier: biotools:meryl input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meryl_dbs: - type: directory - description: Meryl k-mer databases - - kvalue: - type: integer - description: An integer value of k to use as the k-mer value. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - meryl_dbs: + type: directory + description: Meryl k-mer databases + - - kvalue: + type: integer + description: An integer value of k to use as the k-mer value. output: - - meta: - 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" - meryl_db: - type: directory - description: A Meryl k-mer database that is the union sum of the input databases - pattern: "*.unionsum.meryl" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.unionsum.meryl": + type: directory + description: A Meryl k-mer database that is the union sum of the input databases + pattern: "*.unionsum.meryl" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/minimap2/align/meta.yml b/modules/nf-core/minimap2/align/meta.yml index 8996f881..a4cfc891 100644 --- a/modules/nf-core/minimap2/align/meta.yml +++ b/modules/nf-core/minimap2/align/meta.yml @@ -14,62 +14,77 @@ tools: homepage: https://github.com/lh3/minimap2 documentation: https://github.com/lh3/minimap2#uguide licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FASTA or FASTQ files of size 1 and 2 for single-end - and paired-end data, respectively. - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test_ref'] - - reference: - type: file - description: | - Reference database in FASTA format. - - bam_format: - type: boolean - description: Specify that output should be in BAM format - - bam_index_extension: - type: string - description: BAM alignment index extension (e.g. "bai") - - cigar_paf_format: - type: boolean - description: Specify that output CIGAR should be in PAF format - - cigar_bam: - type: boolean - description: | - Write CIGAR with >65535 ops at the CG tag. This is recommended when - doing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FASTA or FASTQ files of size 1 and 2 for single-end + and paired-end data, respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test_ref'] + - reference: + type: file + description: | + Reference database in FASTA format. + - - bam_format: + type: boolean + description: Specify that output should be in BAM format + - - bam_index_extension: + type: string + description: BAM alignment index extension (e.g. "bai") + - - cigar_paf_format: + type: boolean + description: Specify that output CIGAR should be in PAF format + - - cigar_bam: + type: boolean + description: | + Write CIGAR with >65535 ops at the CG tag. This is recommended when + doing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - paf: - type: file - description: Alignment in PAF format - pattern: "*.paf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.paf": + type: file + description: Alignment in PAF format + pattern: "*.paf" - bam: - type: file - description: Alignment in BAM format - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Alignment in BAM format + pattern: "*.bam" - index: - type: file - description: BAM alignment index - pattern: "*.bam.*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam.${bam_index_extension}": + type: file + description: BAM alignment index + pattern: "*.bam.*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heuermh" - "@sofstam" diff --git a/modules/nf-core/seqkit/rmdup/meta.yml b/modules/nf-core/seqkit/rmdup/meta.yml index d0addd45..22e29c11 100644 --- a/modules/nf-core/seqkit/rmdup/meta.yml +++ b/modules/nf-core/seqkit/rmdup/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "seqkit_rmdup" -description: Transforms sequences (extract ID, filter by length, remove gaps, reverse complement...) +description: Transforms sequences (extract ID, filter by length, remove gaps, reverse + complement...) keywords: - genomics - fasta @@ -16,34 +16,43 @@ tools: tool_dev_url: "https://github.com/shenwei356/seqkit" doi: "10.1371/journal.pone.0163962" licence: ["MIT"] + identifier: biotools:seqkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fastx: - type: file - description: Input fasta/fastq file - pattern: "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fastx: + type: file + description: Input fasta/fastq file + pattern: "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - fastx: - type: file - description: Output fasta/fastq file - pattern: "*.{fasta,fasta.gz,fastq,fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}.${extension}: + type: file + description: Output fasta/fastq file + pattern: "*.{fasta,fasta.gz,fastq,fastq.gz}" - log: - type: file - description: Log containing information regarding removed duplicates - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.log": + type: file + description: Log containing information regarding removed duplicates + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/seqkit/seq/meta.yml b/modules/nf-core/seqkit/seq/meta.yml index 8d4e2b16..7d32aba5 100644 --- a/modules/nf-core/seqkit/seq/meta.yml +++ b/modules/nf-core/seqkit/seq/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "seqkit_seq" -description: Transforms sequences (extract ID, filter by length, remove gaps, reverse complement...) +description: Transforms sequences (extract ID, filter by length, remove gaps, reverse + complement...) keywords: - genomics - fasta @@ -18,30 +18,33 @@ tools: tool_dev_url: "https://github.com/shenwei356/seqkit" doi: "10.1371/journal.pone.0163962" licence: ["MIT"] + identifier: biotools:seqkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fastx: - type: file - description: Input fasta/fastq file - pattern: "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fastx: + type: file + description: Input fasta/fastq file + pattern: "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - fastx: - type: file - description: Output fasta/fastq file - pattern: "*.{fasta,fasta.gz,fastq,fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}.*: + type: file + description: Output fasta/fastq file + pattern: "*.{fasta,fasta.gz,fastq,fastq.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/seqkit/sort/meta.yml b/modules/nf-core/seqkit/sort/meta.yml index 2e61ce15..157ff85c 100644 --- a/modules/nf-core/seqkit/sort/meta.yml +++ b/modules/nf-core/seqkit/sort/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "seqkit_sort" description: Sorts sequences by id/name/sequence/length @@ -15,30 +14,33 @@ tools: tool_dev_url: "https://github.com/shenwei356/seqkit" doi: "10.1371/journal.pone.0163962" licence: ["MIT"] + identifier: biotools:seqkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fastx: - type: file - description: Input fasta/fastq file - pattern: "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fastx: + type: file + description: Input fasta/fastq file + pattern: "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - fastx: - type: file - description: Output fasta/fastq file - pattern: "*.{fasta.gz,fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}.*: + type: file + description: Output fasta/fastq file + pattern: "*.{fasta.gz,fastq.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/sratools/fasterqdump/meta.yml b/modules/nf-core/sratools/fasterqdump/meta.yml index 6a2151a8..42e2c07c 100644 --- a/modules/nf-core/sratools/fasterqdump/meta.yml +++ b/modules/nf-core/sratools/fasterqdump/meta.yml @@ -1,5 +1,6 @@ name: sratools_fasterqdump -description: Extract sequencing reads in FASTQ format from a given NCBI Sequence Read Archive (SRA). +description: Extract sequencing reads in FASTQ format from a given NCBI Sequence Read + Archive (SRA). keywords: - sequencing - FASTQ @@ -11,42 +12,44 @@ tools: documentation: https://github.com/ncbi/sra-tools/wiki tool_dev_url: https://github.com/ncbi/sra-tools licence: ["Public Domain"] + identifier: "" input: - - meta: - type: map - description: > - Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - - sra: - type: directory - description: Directory containing ETL data for the given SRA. - pattern: "*/*.sra" - - ncbi_settings: - type: file - description: > - An NCBI user settings file. - - pattern: "*.mkfg" - - certificate: - type: file - description: > - Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit - - pattern: "*.cart" + - - meta: + type: map + description: > + Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - sra: + type: directory + description: Directory containing ETL data for the given SRA. + pattern: "*/*.sra" + - - ncbi_settings: + type: file + description: > + An NCBI user settings file. + pattern: "*.mkfg" + - - certificate: + type: file + description: > + Path to a JWT cart file used to access protected dbGAP data on SRA using the + sra-toolkit + pattern: "*.cart" output: - - meta: - 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" - reads: - type: file - description: Extracted FASTQ file or files if the sequencing reads are paired-end. - pattern: "*.fastq.gz" + - meta: + type: map + description: > + Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*.fastq.gz": + type: file + description: Extracted FASTQ file or files if the sequencing reads are paired-end. + pattern: "*.fastq.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Midnighter" maintainers: diff --git a/modules/nf-core/sratools/prefetch/meta.yml b/modules/nf-core/sratools/prefetch/meta.yml index 7ed42d49..3a537bfe 100644 --- a/modules/nf-core/sratools/prefetch/meta.yml +++ b/modules/nf-core/sratools/prefetch/meta.yml @@ -11,45 +11,47 @@ tools: documentation: https://github.com/ncbi/sra-tools/wiki tool_dev_url: https://github.com/ncbi/sra-tools licence: ["Public Domain"] + identifier: "" input: - - meta: - type: map - description: > - Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - - id: - type: string - description: > - A string denoting an SRA id. - - - ncbi_settings: - type: file - description: > - An NCBI user settings file. - - pattern: "*.mkfg" - - certificate: - type: file - description: > - Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit - - pattern: "*.cart" + - - meta: + type: map + description: > + Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - id: + type: string + description: > + A string denoting an SRA id. + - - ncbi_settings: + type: file + description: > + An NCBI user settings file. + pattern: "*.mkfg" + - - certificate: + type: file + description: > + Path to a JWT cart file used to access protected dbGAP data on SRA using the + sra-toolkit + pattern: "*.cart" output: - - meta: - type: map - description: > - Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - sra: - type: directory - description: > - Directory containing the ETL data for the given SRA id. - - pattern: "*/*.sra" + - meta: + type: map + description: > + Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + pattern: "*/*.sra" + - "id, type: 'dir": + type: map + description: > + Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + pattern: "*/*.sra" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Midnighter" maintainers: diff --git a/modules/nf-core/tidk/explore/meta.yml b/modules/nf-core/tidk/explore/meta.yml index 582aaf56..72d15954 100644 --- a/modules/nf-core/tidk/explore/meta.yml +++ b/modules/nf-core/tidk/explore/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "tidk_explore" description: | @@ -10,42 +9,52 @@ keywords: - search tools: - "tidk": - description: tidk is a toolkit to identify and visualise telomeric repeats in genomes + description: tidk is a toolkit to identify and visualise telomeric repeats in + genomes homepage: "https://github.com/tolkit/telomeric-identifier" documentation: "https://github.com/tolkit/telomeric-identifier" tool_dev_url: "https://github.com/tolkit/telomeric-identifier" doi: "10.5281/zenodo.10091385" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fasta: - type: file - description: The input fasta file - pattern: "*.{fsa,fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: The input fasta file + pattern: "*.{fsa,fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - explore_tsv: - type: file - description: Telomeres and their frequencies in TSV format - pattern: "*.tidk.explore.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.tidk.explore.tsv": + type: file + description: Telomeres and their frequencies in TSV format + pattern: "*.tidk.explore.tsv" - top_sequence: - type: file - description: | - The most frequent telomere sequence if one or more - sequences are identified by the toolkit - pattern: "*.top.sequence.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.top.sequence.txt": + type: file + description: | + The most frequent telomere sequence if one or more + sequences are identified by the toolkit + pattern: "*.top.sequence.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/tidk/plot/meta.yml b/modules/nf-core/tidk/plot/meta.yml index 451195c8..75289b28 100644 --- a/modules/nf-core/tidk/plot/meta.yml +++ b/modules/nf-core/tidk/plot/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "tidk_plot" description: | @@ -11,36 +10,40 @@ keywords: - plot tools: - "tidk": - description: tidk is a toolkit to identify and visualise telomeric repeats in genomes + description: tidk is a toolkit to identify and visualise telomeric repeats in + genomes homepage: "https://github.com/tolkit/telomeric-identifier" documentation: "https://github.com/tolkit/telomeric-identifier" tool_dev_url: "https://github.com/tolkit/telomeric-identifier" doi: "10.5281/zenodo.10091385" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - tsv: - type: file - description: Search results in TSV format from `tidk search` - pattern: "*.tsv" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - tsv: + type: file + description: Search results in TSV format from `tidk search` + pattern: "*.tsv" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - svg: - type: file - description: Telomere search plot - pattern: "*.svg" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.svg": + type: file + description: Telomere search plot + pattern: "*.svg" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/tidk/search/meta.yml b/modules/nf-core/tidk/search/meta.yml index 8ba07350..9a30ff15 100644 --- a/modules/nf-core/tidk/search/meta.yml +++ b/modules/nf-core/tidk/search/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "tidk_search" description: Searches a genome for a telomere string such as TTAGGG @@ -8,43 +7,53 @@ keywords: - search tools: - "tidk": - description: tidk is a toolkit to identify and visualise telomeric repeats in genomes + description: tidk is a toolkit to identify and visualise telomeric repeats in + genomes homepage: "https://github.com/tolkit/telomeric-identifier" documentation: "https://github.com/tolkit/telomeric-identifier" tool_dev_url: "https://github.com/tolkit/telomeric-identifier" doi: "10.5281/zenodo.10091385" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fasta: - type: file - description: The input fasta file - pattern: "*.{fsa,fa,fasta}" - - string: - type: string - description: Search string such as TTAGGG + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: The input fasta file + pattern: "*.{fsa,fa,fasta}" + - - string: + type: string + description: Search string such as TTAGGG output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - tsv: - type: file - description: Search results in TSV format - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.tsv": + type: file + description: Search results in TSV format + pattern: "*.tsv" - bedgraph: - type: file - description: Search results in BEDGRAPH format - pattern: "*.bedgraph" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.bedgraph": + type: file + description: Search results in BEDGRAPH format + pattern: "*.bedgraph" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/umitools/extract/meta.yml b/modules/nf-core/umitools/extract/meta.yml index 7695b271..648ffbd2 100644 --- a/modules/nf-core/umitools/extract/meta.yml +++ b/modules/nf-core/umitools/extract/meta.yml @@ -1,5 +1,6 @@ name: umitools_extract -description: Extracts UMI barcode from a read and add it to the read name, leaving any sample barcode in place +description: Extracts UMI barcode from a read and add it to the read name, leaving + any sample barcode in place keywords: - UMI - barcode @@ -8,38 +9,49 @@ keywords: tools: - umi_tools: description: > - UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes + UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random + Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes documentation: https://umi-tools.readthedocs.io/en/latest/ license: "MIT" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: list - description: | - List of input FASTQ files whose UMIs will be extracted. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: list + description: | + List of input FASTQ files whose UMIs will be extracted. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - reads: - type: file - description: > - Extracted FASTQ files. | For single-end reads, pattern is \${prefix}.umi_extract.fastq.gz. | For paired-end reads, pattern is \${prefix}.umi_extract_{1,2}.fastq.gz. - pattern: "*.{fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: > + Extracted FASTQ files. | For single-end reads, pattern is \${prefix}.umi_extract.fastq.gz. + | For paired-end reads, pattern is \${prefix}.umi_extract_{1,2}.fastq.gz. + pattern: "*.{fastq.gz}" - log: - type: file - description: Logfile for umi_tools - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Logfile for umi_tools + pattern: "*.{log}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@grst" diff --git a/modules/nf-core/untar/meta.yml b/modules/nf-core/untar/meta.yml index a9a2110f..290346b3 100644 --- a/modules/nf-core/untar/meta.yml +++ b/modules/nf-core/untar/meta.yml @@ -10,30 +10,33 @@ tools: Extract tar.gz files. documentation: https://www.gnu.org/software/tar/manual/ licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - archive: - type: file - description: File to be untar - pattern: "*.{tar}.{gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: File to be untar + pattern: "*.{tar}.{gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - untar: - type: directory - description: Directory containing contents of archive - pattern: "*/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - $prefix: + type: directory + description: Directory containing contents of archive + pattern: "*/" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/subworkflows/gallvp/gff3_gt_gff3_gff3validator_stat/tests/main.nf.test.snap b/subworkflows/gallvp/gff3_gt_gff3_gff3validator_stat/tests/main.nf.test.snap index 660f7e0b..1ec2fb46 100644 --- a/subworkflows/gallvp/gff3_gt_gff3_gff3validator_stat/tests/main.nf.test.snap +++ b/subworkflows/gallvp/gff3_gt_gff3_gff3validator_stat/tests/main.nf.test.snap @@ -18,7 +18,7 @@ ], "3": [ "versions.yml:md5,0cb9519e626e5128d8495cf29b7d59ff", - "versions.yml:md5,8a418ac34d045b0cdac812eb2dc9c106" + "versions.yml:md5,2f7fe3865b17dd2edde1881a95930174" ], "gff3_stats": [ @@ -36,15 +36,15 @@ ], "versions": [ "versions.yml:md5,0cb9519e626e5128d8495cf29b7d59ff", - "versions.yml:md5,8a418ac34d045b0cdac812eb2dc9c106" + "versions.yml:md5,2f7fe3865b17dd2edde1881a95930174" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-29T16:21:54.482267" + "timestamp": "2024-09-25T11:11:44.756433" }, "sarscov2-genome_gff3-test_fasta-correspondence_fail-out_of_bounds": { "content": [ @@ -53,15 +53,15 @@ ], [ "versions.yml:md5,0cb9519e626e5128d8495cf29b7d59ff", - "versions.yml:md5,8a418ac34d045b0cdac812eb2dc9c106", + "versions.yml:md5,2f7fe3865b17dd2edde1881a95930174", "versions.yml:md5,c89b081a13c68acc5326e43ca9104344" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-29T16:22:06.684959" + "timestamp": "2024-09-25T11:11:57.27286" }, "sarscov2 - fasta - circular_region - pass": { "content": [ @@ -87,8 +87,8 @@ ], "3": [ "versions.yml:md5,0cb9519e626e5128d8495cf29b7d59ff", + "versions.yml:md5,2f7fe3865b17dd2edde1881a95930174", "versions.yml:md5,80555fe6e28e9564cb534f5478842286", - "versions.yml:md5,8a418ac34d045b0cdac812eb2dc9c106", "versions.yml:md5,c89b081a13c68acc5326e43ca9104344" ], "gff3_stats": [ @@ -112,8 +112,8 @@ ], "versions": [ "versions.yml:md5,0cb9519e626e5128d8495cf29b7d59ff", + "versions.yml:md5,2f7fe3865b17dd2edde1881a95930174", "versions.yml:md5,80555fe6e28e9564cb534f5478842286", - "versions.yml:md5,8a418ac34d045b0cdac812eb2dc9c106", "versions.yml:md5,c89b081a13c68acc5326e43ca9104344" ] } @@ -122,7 +122,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-19T13:53:32.901064" + "timestamp": "2024-09-25T11:12:04.099852" }, "sarscov2-genome_gff3-homo_sapiens-genome_fasta-correspondence_fail": { "content": [ @@ -131,15 +131,15 @@ ], [ "versions.yml:md5,0cb9519e626e5128d8495cf29b7d59ff", - "versions.yml:md5,8a418ac34d045b0cdac812eb2dc9c106", + "versions.yml:md5,2f7fe3865b17dd2edde1881a95930174", "versions.yml:md5,c89b081a13c68acc5326e43ca9104344" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-29T16:22:00.684573" + "timestamp": "2024-09-25T11:11:50.869233" }, "sarscov2-genome_gff3-all_pass": { "content": [ @@ -165,8 +165,8 @@ ], "3": [ "versions.yml:md5,0cb9519e626e5128d8495cf29b7d59ff", + "versions.yml:md5,2f7fe3865b17dd2edde1881a95930174", "versions.yml:md5,80555fe6e28e9564cb534f5478842286", - "versions.yml:md5,8a418ac34d045b0cdac812eb2dc9c106", "versions.yml:md5,c89b081a13c68acc5326e43ca9104344" ], "gff3_stats": [ @@ -190,16 +190,16 @@ ], "versions": [ "versions.yml:md5,0cb9519e626e5128d8495cf29b7d59ff", + "versions.yml:md5,2f7fe3865b17dd2edde1881a95930174", "versions.yml:md5,80555fe6e28e9564cb534f5478842286", - "versions.yml:md5,8a418ac34d045b0cdac812eb2dc9c106", "versions.yml:md5,c89b081a13c68acc5326e43ca9104344" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-29T16:21:49.138904" + "timestamp": "2024-09-25T11:11:39.62609" } } \ No newline at end of file diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index 2b0dc67a..4d7f09c0 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -3,9 +3,9 @@ // /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NEXTFLOW_PIPELINE { @@ -44,9 +44,9 @@ workflow UTILS_NEXTFLOW_PIPELINE { } /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index b78273ca..805dcc42 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -3,9 +3,9 @@ // /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NFCORE_PIPELINE { @@ -21,9 +21,9 @@ workflow UTILS_NFCORE_PIPELINE { } /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ //