From a81eed0e4be2abb038e14dd8632f403d1262fc8d Mon Sep 17 00:00:00 2001 From: LilyAnderssonLee Date: Thu, 19 Dec 2024 14:21:23 +0100 Subject: [PATCH] correct the format --- assets/multiqc_config.yml | 208 +++++++++++++++++++------------------- ro-crate-metadata.json | 25 ++--- 2 files changed, 110 insertions(+), 123 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 7e1e10b6..a854ac98 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -61,23 +61,23 @@ custom_logo_url: https://nf-co.re/taxprofiler custom_logo_title: "nf-core/taxprofiler" run_modules: -- fastqc -- adapterremoval -- fastp -- nonpareil -- bbduk -- prinseqplusplus -- porechop -- filtlong -- nanoq -- bowtie2 -- samtools -- kraken -- kaiju -- diamond -- malt -- motus -- custom_content + - fastqc + - adapterremoval + - fastp + - nonpareil + - bbduk + - prinseqplusplus + - porechop + - filtlong + - nanoq + - bowtie2 + - samtools + - kraken + - kaiju + - diamond + - malt + - motus + - custom_content sp: diamond: @@ -93,81 +93,81 @@ sp: contents_re: " " top_modules: -- "fastqc": - name: "FastQC / Falco (pre-Trimming)" - path_filters: - - "*raw*" - path_filters_exclude: - - "*processed*" - extra: "If used in this run, Falco is a drop-in replacement for FastQC producing - the same output, written by Guilherme de Sena Brandine and Andrew D. Smith." -- "fastqc": - name: "FastQC / Falco (post-Trimming)" - path_filters: - - "*processed*" - path_filters_exclude: - - "*raw*" - extra: "If used in this run, Falco is a drop-in replacement for FastQC producing - the same output, written by Guilherme de Sena Brandine and Andrew D. Smith." -- nonpareil -- "porechop": - name: "Porechop" - anchor: "porechop" - target: "Porechop" - path_filters: - - "*porechop.log" - extra: "ℹ️: if you get the error message 'Error - was not able to plot data.' - this means that porechop did not detect any adapters and therefore no statistics - generated." -- "porechop": - name: "Porechop_ABI" - anchor: "porechop_abi" - target: "Porechop_ABI" - doi: "10.1093/bioadv/vbac085" - info: "find and remove adapters from Oxford Nanopore reads." - path_filters: - - "*porechop_abi.log" - extra: "ℹ️: if you get the error message 'Error - was not able to plot data.' - this means that porechop_abi did not detect any adapters and therefore no statistics - generated." -- "bowtie2": - name: "bowtie2" -- "samtools": - name: "Samtools Stats" -- "kraken": - name: "Kraken" - path_filters: - - "*.kraken2.kraken2.report.txt" -- "kraken": - name: "Bracken" - anchor: "bracken" - target: "Bracken" - doi: "10.7717/peerj-cs.104" - info: "Estimates species abundances in metagenomics samples by probabilistically - re-distributing reads in the taxonomic tree." - extra: "ℹ️: plot title will say Kraken2 due to the first step of bracken producing - the same output format as Kraken. Abundance information is currently not supported - in MultiQC." - path_filters: - - "*.bracken.kraken2.report.txt" -- "kraken": - name: "Centrifuge" - anchor: "centrifuge" - target: "Centrifuge" - doi: "10.1101/gr.210641.116" - info: "is a very rapid and memory-efficient system for the classification of DNA - sequences from microbial samples. The system uses a novel indexing scheme based - on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index. - Note: Figure title" - extra: "ℹ️: plot title will say Kraken2 due to Centrifuge producing the same output - format as Kraken. If activated, see the actual Kraken2 results in the section - above." - path_filters: - - "*.centrifuge.txt" -- "malt": - name: "MALT" -- "kaiju": - name: "Kaiju" + - "fastqc": + name: "FastQC / Falco (pre-Trimming)" + path_filters: + - "*raw*" + path_filters_exclude: + - "*processed*" + extra: "If used in this run, Falco is a drop-in replacement for FastQC producing + the same output, written by Guilherme de Sena Brandine and Andrew D. Smith." + - "fastqc": + name: "FastQC / Falco (post-Trimming)" + path_filters: + - "*processed*" + path_filters_exclude: + - "*raw*" + extra: "If used in this run, Falco is a drop-in replacement for FastQC producing + the same output, written by Guilherme de Sena Brandine and Andrew D. Smith." + - nonpareil + - "porechop": + name: "Porechop" + anchor: "porechop" + target: "Porechop" + path_filters: + - "*porechop.log" + extra: "ℹ️: if you get the error message 'Error - was not able to plot data.' + this means that porechop did not detect any adapters and therefore no statistics + generated." + - "porechop": + name: "Porechop_ABI" + anchor: "porechop_abi" + target: "Porechop_ABI" + doi: "10.1093/bioadv/vbac085" + info: "find and remove adapters from Oxford Nanopore reads." + path_filters: + - "*porechop_abi.log" + extra: "ℹ️: if you get the error message 'Error - was not able to plot data.' + this means that porechop_abi did not detect any adapters and therefore no statistics + generated." + - "bowtie2": + name: "bowtie2" + - "samtools": + name: "Samtools Stats" + - "kraken": + name: "Kraken" + path_filters: + - "*.kraken2.kraken2.report.txt" + - "kraken": + name: "Bracken" + anchor: "bracken" + target: "Bracken" + doi: "10.7717/peerj-cs.104" + info: "Estimates species abundances in metagenomics samples by probabilistically + re-distributing reads in the taxonomic tree." + extra: "ℹ️: plot title will say Kraken2 due to the first step of bracken producing + the same output format as Kraken. Abundance information is currently not supported + in MultiQC." + path_filters: + - "*.bracken.kraken2.report.txt" + - "kraken": + name: "Centrifuge" + anchor: "centrifuge" + target: "Centrifuge" + doi: "10.1101/gr.210641.116" + info: "is a very rapid and memory-efficient system for the classification of DNA + sequences from microbial samples. The system uses a novel indexing scheme based + on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index. + Note: Figure title" + extra: "ℹ️: plot title will say Kraken2 due to Centrifuge producing the same output + format as Kraken. If activated, see the actual Kraken2 results in the section + above." + path_filters: + - "*.centrifuge.txt" + - "malt": + name: "MALT" + - "kaiju": + name: "Kaiju" # It is not possible to set placement for custom kraken # and centrifuge columns. @@ -374,18 +374,18 @@ table_columns_name: reads_mapped_percent: "% Mapped Reads" extra_fn_clean_exts: -- "kraken2.report.txt" -- ".txt" -- ".settings" -- ".bbduk" -- ".unmapped" -- "_filtered" -- "porechop" -- "porechop_abi" -- "_processed" -- ".diamond" -- type: remove - pattern: "_falco" + - "kraken2.report.txt" + - ".txt" + - ".settings" + - ".bbduk" + - ".unmapped" + - "_filtered" + - "porechop" + - "porechop_abi" + - "_processed" + - ".diamond" + - type: remove + pattern: "_falco" section_comments: general_stats: "By default, all read count columns are displayed as millions (M) diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index d5053bf0..0770702c 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -124,11 +124,7 @@ }, { "@id": "main.nf", - "@type": [ - "File", - "SoftwareSourceCode", - "ComputationalWorkflow" - ], + "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], "creator": [ { "@id": "#jfy133@gmail.com" @@ -161,9 +157,7 @@ "taxonomic-classification", "taxonomic-profiling" ], - "license": [ - "MIT" - ], + "license": ["MIT"], "maintainer": [ { "@id": "#jfy133@gmail.com" @@ -175,22 +169,15 @@ "@id": "https://orcid.org/0009-0006-0893-3771" } ], - "name": [ - "nf-core/taxprofiler" - ], + "name": ["nf-core/taxprofiler"], "programmingLanguage": { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow" }, "sdPublisher": { "@id": "https://nf-co.re/" }, - "url": [ - "https://github.com/nf-core/taxprofiler", - "https://nf-co.re/taxprofiler/1.2.2/" - ], - "version": [ - "1.2.2" - ] + "url": ["https://github.com/nf-core/taxprofiler", "https://nf-co.re/taxprofiler/1.2.2/"], + "version": ["1.2.2"] }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow", @@ -370,4 +357,4 @@ "name": "Sofia Stamouli" } ] -} \ No newline at end of file +}