diff --git a/CHANGELOG.md b/CHANGELOG.md index e6e05ffe..b4858fb9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,14 +3,22 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v1.0.0 - [date] - -Initial release of nf-core/metatdenovo, created with the [nf-core](https://nf-co.re/) template. +## v1.0.1 - [date] ### `Added` +### `Changed` + +- [#268]([https://github.com/nf-core/ampliseq/pull/681](https://github.com/nf-core/metatdenovo/pull/268)) - Don't save so many intermediate Megahit files by default + ### `Fixed` +- [#269]([https://github.com/nf-core/ampliseq/pull/681](https://github.com/nf-core/metatdenovo/pull/269)) - Make Transdecoder work better with `-resume` + ### `Dependencies` ### `Deprecated` + +## v1.0.0 - [2024-02-15] + +Initial release of nf-core/metatdenovo, created with the [nf-core](https://nf-co.re/) template. diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index fc79128c..e0817b8b 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/metatdenovo + This report has been generated by the nf-core/metatdenovo analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-metatdenovo-methods-description": order: -1000 diff --git a/conf/modules.config b/conf/modules.config index b83f9605..9441842f 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -170,7 +170,7 @@ process { ] } - withName: PREDICT { + withName: TRANSDECODER { publishDir = [ path: { "${params.outdir}/transdecoder" }, mode: params.publish_dir_mode, diff --git a/modules.json b/modules.json index 7ad9351c..5da9c3aa 100644 --- a/modules.json +++ b/modules.json @@ -110,16 +110,6 @@ "git_sha": "f6bba1a67cdbb605f24d7a4e8dd383b0eec45b52", "installed_by": ["modules"] }, - "transdecoder/longorf": { - "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] - }, - "transdecoder/predict": { - "branch": "master", - "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] - }, "trimgalore": { "branch": "master", "git_sha": "2e6c468e0ad43b23df71d7a7f130d5c0e0aa89e3", diff --git a/modules/nf-core/transdecoder/longorf/main.nf b/modules/local/transdecoder.nf similarity index 68% rename from modules/nf-core/transdecoder/longorf/main.nf rename to modules/local/transdecoder.nf index 19466443..a5b59509 100644 --- a/modules/nf-core/transdecoder/longorf/main.nf +++ b/modules/local/transdecoder.nf @@ -1,4 +1,4 @@ -process TRANSDECODER_LONGORF { +process TRANSDECODER { tag "$meta.id" label 'process_medium' @@ -11,12 +11,11 @@ process TRANSDECODER_LONGORF { tuple val(meta), path(fasta) output: - tuple val(meta), path("${meta.id}/*.pep") , emit: pep - tuple val(meta), path("${meta.id}/*.gff3"), emit: gff3 - tuple val(meta), path("${meta.id}/*.cds") , emit: cds - tuple val(meta), path("${meta.id}/*.dat") , emit: dat - path("${meta.id}/") , emit: folder - path "versions.yml" , emit: versions + tuple val(meta), path("*.pep") , emit: pep + tuple val(meta), path("*.gff3"), emit: gff + tuple val(meta), path("*.cds") , emit: cds + tuple val(meta), path("*.bed") , emit: bed + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -32,6 +31,12 @@ process TRANSDECODER_LONGORF { -t \\ $fasta + TransDecoder.Predict \\ + $args \\ + -O $prefix \\ + -t \\ + $fasta + cat <<-END_VERSIONS > versions.yml "${task.process}": transdecoder: \$(echo \$(TransDecoder.LongOrfs --version) | sed -e "s/TransDecoder.LongOrfs //g") diff --git a/modules/nf-core/transdecoder/longorf/environment.yml b/modules/nf-core/transdecoder/longorf/environment.yml deleted file mode 100644 index 29a06d31..00000000 --- a/modules/nf-core/transdecoder/longorf/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ -name: transdecoder_longorf -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - bioconda::transdecoder=5.5.0 diff --git a/modules/nf-core/transdecoder/longorf/meta.yml b/modules/nf-core/transdecoder/longorf/meta.yml deleted file mode 100644 index e6c6bea3..00000000 --- a/modules/nf-core/transdecoder/longorf/meta.yml +++ /dev/null @@ -1,55 +0,0 @@ -name: transdecoder_longorf -description: TransDecoder itentifies candidate coding regions within transcript sequences. it is used to build gff file. -keywords: - - eucaryotes - - gff -tools: - - transdecoder: - description: TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. - homepage: https://github.com/TransDecoder - documentation: https://github.com/TransDecoder/TransDecoder/wiki - tool_dev_url: https://github.com/TransDecoder/TransDecoder - licence: ["Broad Institute"] -input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: fasta file - pattern: "*.{fasta}" -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" - - pep: - type: Amino acids fasta file - description: all ORFs meeting the minimum length criteria, regardless of coding potential. file - pattern: "*.{pep}" - - gff3: - type: gff file - description: positions of all ORFs as found in the target transcripts. file - pattern: "*.{gff3}" - - cds: - type: fasta file - description: the nucleotide coding sequence for all detected ORFs. file - pattern: "*{cds}" - - dat: - type: tsv file - description: nucleotide frequencies - pattern: "*{dat}" - - folder: - type: directory - description: contains all the files from the run -authors: - - "@Danilo2771" -maintainers: - - "@Danilo2771" diff --git a/modules/nf-core/transdecoder/predict/environment.yml b/modules/nf-core/transdecoder/predict/environment.yml deleted file mode 100644 index 07efaa4f..00000000 --- a/modules/nf-core/transdecoder/predict/environment.yml +++ /dev/null @@ -1,7 +0,0 @@ -name: transdecoder_predict -channels: - - conda-forge - - bioconda - - defaults -dependencies: - - bioconda::transdecoder=5.5.0 diff --git a/modules/nf-core/transdecoder/predict/main.nf b/modules/nf-core/transdecoder/predict/main.nf deleted file mode 100644 index 7d56a79d..00000000 --- a/modules/nf-core/transdecoder/predict/main.nf +++ /dev/null @@ -1,40 +0,0 @@ -process TRANSDECODER_PREDICT { - tag "$meta.id" - label 'process_medium' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/transdecoder:5.5.0--pl5262hdfd78af_4': - 'quay.io/comp-bio-aging/transdecoder' }" - - input: - tuple val(meta), path(fasta) - path(fold) - - output: - tuple val(meta), path("*.transdecoder.pep") , emit: pep - tuple val(meta), path("*.transdecoder.gff3") , emit: gff3 - tuple val(meta), path("*.transdecoder.cds") , emit: cds - tuple val(meta), path("*.transdecoder.bed") , emit: bed - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - - """ - TransDecoder.Predict \\ - $args \\ - -O ${prefix} \\ - -t \\ - $fasta - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - transdecoder: \$(echo \$(TransDecoder.Predict --version) | sed -e "s/TransDecoder.Predict //g") - END_VERSIONS - """ -} diff --git a/modules/nf-core/transdecoder/predict/meta.yml b/modules/nf-core/transdecoder/predict/meta.yml deleted file mode 100644 index ea2c9b8e..00000000 --- a/modules/nf-core/transdecoder/predict/meta.yml +++ /dev/null @@ -1,56 +0,0 @@ -name: transdecoder_predict -description: TransDecoder identifies candidate coding regions within transcript sequences. It is used to build gff file. You can use this module after transdecoder_longorf -keywords: - - eukaryotes - - gff -tools: - - transdecoder: - description: TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. - homepage: https://github.com/TransDecoder - documentation: https://github.com/TransDecoder/TransDecoder/wiki - tool_dev_url: https://github.com/TransDecoder/TransDecoder - licence: ["Broad Institute"] -input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: fasta file - pattern: "*.{fasta}" - - fold: - type: directory - description: Output from the module transdecoder_longorf - pattern: "*" -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" - - pep: - type: amino acids fasta file - description: All ORFs meeting the minimum length criteria, regardless of coding potential - pattern: "*.{pep}" - - gff3: - type: gff3 file - description: Positions of all ORFs as found in the target transcripts - pattern: "*.{gff3}" - - cds: - type: nucleotide fasta file - description: the nucleotide coding sequence for all detected ORFs - pattern: "*{cds}" - - bed: - type: bed file - description: bed file - pattern: "*{bed}" -authors: - - "@Danilo2771" -maintainers: - - "@Danilo2771" diff --git a/nextflow.config b/nextflow.config index 54a62a8a..8af2eac3 100644 --- a/nextflow.config +++ b/nextflow.config @@ -288,7 +288,7 @@ manifest { description = """Assembly and annotation of metatranscriptomic data, both prokaryotic and eukaryotic""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.1.0dev' + version = '1.0.1' doi = '' } diff --git a/subworkflows/local/transdecoder.nf b/subworkflows/local/transdecoder.nf deleted file mode 100644 index d5aab6ea..00000000 --- a/subworkflows/local/transdecoder.nf +++ /dev/null @@ -1,28 +0,0 @@ -// -// TRANSDECODER SUBWORKFLOW -// - -include { TRANSDECODER_LONGORF as LONGORF } from '../../modules/nf-core/transdecoder/longorf/main' -include { TRANSDECODER_PREDICT as PREDICT } from '../../modules/nf-core/transdecoder/predict/main' - -workflow TRANSDECODER { - take: - contigs // channel: [ val(meta), [ contigs ] ] - - main: - ch_versions = Channel.empty() - - LONGORF (contigs) - ch_versions = ch_versions.mix(LONGORF.out.versions) - PREDICT (contigs, LONGORF.out.folder) - ch_versions = ch_versions.mix(PREDICT.out.versions) - - emit: - gff = PREDICT.out.gff3 - cds = PREDICT.out.cds - pep = PREDICT.out.pep - bed = PREDICT.out.bed - - versions = ch_versions - -} diff --git a/workflows/metatdenovo.nf b/workflows/metatdenovo.nf index ea51fb76..3d969827 100644 --- a/workflows/metatdenovo.nf +++ b/workflows/metatdenovo.nf @@ -82,6 +82,7 @@ include { UNPIGZ as UNPIGZ_CONTIGS } from '../modules/local/unpigz' include { UNPIGZ as UNPIGZ_GFF } from '../modules/local/unpigz' include { MERGE_TABLES } from '../modules/local/merge_summary_tables' include { TRANSRATE } from '../modules/local/transrate' +include { TRANSDECODER } from '../modules/local/transdecoder' // // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules @@ -95,7 +96,6 @@ include { EGGNOG } from '../subworkflows/local/eggnog' include { SUB_EUKULELE } from '../subworkflows/local/eukulele' include { HMMCLASSIFY } from '../subworkflows/local/hmmclassify' include { PROKKA_SUBSETS } from '../subworkflows/local/prokka_subsets' -include { TRANSDECODER } from '../subworkflows/local/transdecoder' include { FASTQC_TRIMGALORE } from '../subworkflows/local/fastqc_trimgalore' include { PRODIGAL } from '../subworkflows/local/prodigal' include { KOFAMSCAN } from '../subworkflows/local/kofamscan'