diff --git a/modules/deepbgc/download/main.nf b/modules/deepbgc/download/main.nf index 1da817a6..bf0a4904 100644 --- a/modules/deepbgc/download/main.nf +++ b/modules/deepbgc/download/main.nf @@ -1,5 +1,4 @@ process DEEPBGC_DOWNLOAD { - tag "download" label 'process_low' conda (params.enable_conda ? "bioconda::deepbgc=0.1.30" : null) @@ -8,8 +7,8 @@ process DEEPBGC_DOWNLOAD { 'quay.io/biocontainers/deepbgc:0.1.30--pyhb7b1952_1' }" output: - path "deepbgc_db/" , emit: db - path "versions.yml" , emit: versions + path "deepbgc_db/" , emit: db + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when diff --git a/modules/deepbgc/download/meta.yml b/modules/deepbgc/download/meta.yml index 5089142d..c2d74aa6 100644 --- a/modules/deepbgc/download/meta.yml +++ b/modules/deepbgc/download/meta.yml @@ -1,13 +1,13 @@ name: "deepbgc_download" -description: database to detect BGCs in bacterial and fungal genomes using deep learning +description: Database download module for DeepBGC which detects BGCs in bacterial and fungal genomes using deep learning. keywords: - database - download - BGC - - Biosynthetic Gene Cluster + - biosynthetic gene cluster - deep learning - neural network - - random forrest + - random forest - genomes - bacteria - fungi @@ -27,8 +27,8 @@ output: pattern: "versions.yml" - deepbgc_db: type: directory - description: contains files of reference db from 'deepbgc download' - pattern: "*db" + description: Contains reference database files + pattern: "deepbgc_db" authors: - "@louperelo" diff --git a/modules/deepbgc/pipeline/meta.yml b/modules/deepbgc/pipeline/meta.yml index 6a9a2b6c..fb388661 100644 --- a/modules/deepbgc/pipeline/meta.yml +++ b/modules/deepbgc/pipeline/meta.yml @@ -1,7 +1,8 @@ name: "deepbgc_pipeline" -description: detect BGCs in bacterial and fungal genomes using deep learning +description: DeepBGC detects BGCs in bacterial and fungal genomes using deep learning. keywords: - - Biosynthetic Gene Cluster + - BGC + - biosynthetic gene cluster - deep learning - neural network - random forest @@ -48,15 +49,15 @@ output: pattern: "*.{txt}" - json: type: file - description: AntiSMASH JSON file for sideloading. + description: AntiSMASH JSON file for sideloading pattern: "*.{json}" - bgc_gbk: type: file - description: Sequences and features of all detected BGCs in GenBank format. + description: Sequences and features of all detected BGCs in GenBank format pattern: "*.{bgc.gbk}" - bgc_tsv: type: file - description: Table of detected BGCs and their properties. + description: Table of detected BGCs and their properties pattern: "*.{bgc.tsv}" - full_gbk: type: file @@ -64,23 +65,23 @@ output: pattern: "*.{full.gbk}" - pfam_tsv: type: file - description: Table of Pfam domains (pfam_id) from given sequence (sequence_id) in genomic order, with BGC detection scores. + description: Table of Pfam domains (pfam_id) from given sequence (sequence_id) in genomic order, with BGC detection scores pattern: "*.{pfam.tsv}" - bgc_png: type: file - description: Detected BGCs plotted by their nucleotide coordinates. + description: Detected BGCs plotted by their nucleotide coordinates pattern: "*.{bgc.png}" - pr_png: type: file - description: Precision-Recall curve based on predicted per-Pfam BGC scores. + description: Precision-Recall curve based on predicted per-Pfam BGC scores pattern: "*.{pr.png}" - roc_png: type: file - description: ROC curve based on predicted per-Pfam BGC scores. + description: ROC curve based on predicted per-Pfam BGC scores pattern: "*.{roc.png}" - score_png: type: file - description: BGC detection scores of each Pfam domain in genomic order. + description: BGC detection scores of each Pfam domain in genomic order pattern: "*.{score.png}" authors: