From 65a17a1925e990971ff0cff3bae7929d9d4e22f2 Mon Sep 17 00:00:00 2001 From: Danilo Di Leo Date: Mon, 4 Mar 2024 13:35:21 +0100 Subject: [PATCH 01/11] make a local module for transdecoder and remove the nf-core modules --- modules.json | 108 ++++++++++++------ .../longorf/main.nf => local/transdecoder.nf} | 19 +-- .../transdecoder/longorf/environment.yml | 7 -- modules/nf-core/transdecoder/longorf/meta.yml | 55 --------- .../transdecoder/predict/environment.yml | 7 -- modules/nf-core/transdecoder/predict/main.nf | 40 ------- modules/nf-core/transdecoder/predict/meta.yml | 56 --------- subworkflows/local/transdecoder.nf | 28 ----- workflows/metatdenovo.nf | 2 +- 9 files changed, 86 insertions(+), 236 deletions(-) rename modules/{nf-core/transdecoder/longorf/main.nf => local/transdecoder.nf} (68%) delete mode 100644 modules/nf-core/transdecoder/longorf/environment.yml delete mode 100644 modules/nf-core/transdecoder/longorf/meta.yml delete mode 100644 modules/nf-core/transdecoder/predict/environment.yml delete mode 100644 modules/nf-core/transdecoder/predict/main.nf delete mode 100644 modules/nf-core/transdecoder/predict/meta.yml delete mode 100644 subworkflows/local/transdecoder.nf diff --git a/modules.json b/modules.json index 7ad9351c..2ba56b55 100644 --- a/modules.json +++ b/modules.json @@ -8,122 +8,156 @@ "bbmap/align": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bbmap/bbduk": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bbmap/bbnorm": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bbmap/index": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cat/cat": { "branch": "master", "git_sha": "81f27e75847087865299cc46605deb3b09b4e0a2", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "cat/fastq": { "branch": "master", "git_sha": "02fd5bd7275abad27aad32d5c852e0a9b1b98882", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "custom/dumpsoftwareversions": { "branch": "master", "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "fastqc": { "branch": "master", "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "hmmer/hmmsearch": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "multiqc": { "branch": "master", "git_sha": "9e71d8519dfbfc328c078bba14d4bd4c99e39a94", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "prodigal": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "prokka": { "branch": "master", "git_sha": "49ebda931c36c2b282f7958d00e1236b751f1031", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/flagstat": { "branch": "master", "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": ["bam_stats_samtools"] + "installed_by": [ + "bam_stats_samtools" + ] }, "samtools/idxstats": { "branch": "master", "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": ["bam_stats_samtools"] + "installed_by": [ + "bam_stats_samtools" + ] }, "samtools/index": { "branch": "master", "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": ["bam_sort_stats_samtools"] + "installed_by": [ + "bam_sort_stats_samtools" + ] }, "samtools/sort": { "branch": "master", "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": ["bam_sort_stats_samtools"] + "installed_by": [ + "bam_sort_stats_samtools" + ] }, "samtools/stats": { "branch": "master", "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": ["bam_stats_samtools"] + "installed_by": [ + "bam_stats_samtools" + ] }, "seqtk/mergepe": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "seqtk/seq": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "spades": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "subread/featurecounts": { "branch": "master", "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"] + "installed_by": [ + "modules" + ] }, "trimgalore": { "branch": "master", "git_sha": "2e6c468e0ad43b23df71d7a7f130d5c0e0aa89e3", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] } } }, @@ -132,15 +166,19 @@ "bam_sort_stats_samtools": { "branch": "master", "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "bam_stats_samtools": { "branch": "master", "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": ["bam_sort_stats_samtools"] + "installed_by": [ + "bam_sort_stats_samtools" + ] } } } } } -} +} \ No newline at end of file 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..9e595711 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("*/*.dat") , emit: dat + 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/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' From 186ed47d8c22f4d3e1b9e1babe283f1775aa44a4 Mon Sep 17 00:00:00 2001 From: Danilo Di Leo Date: Mon, 4 Mar 2024 13:39:31 +0100 Subject: [PATCH 02/11] linting --- modules.json | 98 ++++++++++++++-------------------------------------- 1 file changed, 25 insertions(+), 73 deletions(-) diff --git a/modules.json b/modules.json index 2ba56b55..5da9c3aa 100644 --- a/modules.json +++ b/modules.json @@ -8,156 +8,112 @@ "bbmap/align": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bbmap/bbduk": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bbmap/bbnorm": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bbmap/index": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cat/cat": { "branch": "master", "git_sha": "81f27e75847087865299cc46605deb3b09b4e0a2", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "cat/fastq": { "branch": "master", "git_sha": "02fd5bd7275abad27aad32d5c852e0a9b1b98882", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "custom/dumpsoftwareversions": { "branch": "master", "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "fastqc": { "branch": "master", "git_sha": "f4ae1d942bd50c5c0b9bd2de1393ce38315ba57c", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "hmmer/hmmsearch": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "multiqc": { "branch": "master", "git_sha": "9e71d8519dfbfc328c078bba14d4bd4c99e39a94", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "prodigal": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "prokka": { "branch": "master", "git_sha": "49ebda931c36c2b282f7958d00e1236b751f1031", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/flagstat": { "branch": "master", "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": [ - "bam_stats_samtools" - ] + "installed_by": ["bam_stats_samtools"] }, "samtools/idxstats": { "branch": "master", "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": [ - "bam_stats_samtools" - ] + "installed_by": ["bam_stats_samtools"] }, "samtools/index": { "branch": "master", "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": [ - "bam_sort_stats_samtools" - ] + "installed_by": ["bam_sort_stats_samtools"] }, "samtools/sort": { "branch": "master", "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": [ - "bam_sort_stats_samtools" - ] + "installed_by": ["bam_sort_stats_samtools"] }, "samtools/stats": { "branch": "master", "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": [ - "bam_stats_samtools" - ] + "installed_by": ["bam_stats_samtools"] }, "seqtk/mergepe": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "seqtk/seq": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "spades": { "branch": "master", "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "subread/featurecounts": { "branch": "master", "git_sha": "f6bba1a67cdbb605f24d7a4e8dd383b0eec45b52", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "trimgalore": { "branch": "master", "git_sha": "2e6c468e0ad43b23df71d7a7f130d5c0e0aa89e3", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -166,19 +122,15 @@ "bam_sort_stats_samtools": { "branch": "master", "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "bam_stats_samtools": { "branch": "master", "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62", - "installed_by": [ - "bam_sort_stats_samtools" - ] + "installed_by": ["bam_sort_stats_samtools"] } } } } } -} \ No newline at end of file +} From 8f6390b4ef734c18abe4d6d107a6103e5b08faa2 Mon Sep 17 00:00:00 2001 From: Danilo Di Leo Date: Mon, 4 Mar 2024 13:48:16 +0100 Subject: [PATCH 03/11] changed the emit files --- conf/modules.config | 2 +- modules/local/transdecoder.nf | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index b1d5db6c..669a0897 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/local/transdecoder.nf b/modules/local/transdecoder.nf index 9e595711..a5b59509 100644 --- a/modules/local/transdecoder.nf +++ b/modules/local/transdecoder.nf @@ -11,10 +11,10 @@ process TRANSDECODER { tuple val(meta), path(fasta) output: - 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("*/*.dat") , emit: dat + 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: From 50919850e6e1645695079fec76b23eab2504270a Mon Sep 17 00:00:00 2001 From: Danilo Di Leo Date: Mon, 4 Mar 2024 13:50:16 +0100 Subject: [PATCH 04/11] fix transdecoder --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e6e05ffe..da40b9f8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,14 +3,14 @@ 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] +## v1.0.1 - [4-03-2024] Initial release of nf-core/metatdenovo, created with the [nf-core](https://nf-co.re/) template. ### `Added` ### `Fixed` - +Trandecoder subworkflow didn't cache properly. We made a local module that fixed the issue. ### `Dependencies` ### `Deprecated` From 6b1a5130b1903aeddea2acb5f0d10f6d6dd6a54e Mon Sep 17 00:00:00 2001 From: Danilo Di Leo Date: Mon, 4 Mar 2024 13:51:39 +0100 Subject: [PATCH 05/11] bump version --- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 4c8e1f76..3c93488b 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/nextflow.config b/nextflow.config index 266de3d6..a30dd825 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 = '1.0.0' + version = '1.0.2' doi = '' } From aadfcd01eac12716ed8468bfcc51fc358248c781 Mon Sep 17 00:00:00 2001 From: Daniel Lundin Date: Mon, 4 Mar 2024 14:05:12 +0100 Subject: [PATCH 06/11] Update CHANGELOG.md --- CHANGELOG.md | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index da40b9f8..3ae0f3bb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,17 @@ 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). -## v1.0.1 - [4-03-2024] +## v1.0.1 - [2024-03-04] + +### `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` + +## v1.0.0 - [2024-02-15] Initial release of nf-core/metatdenovo, created with the [nf-core](https://nf-co.re/) template. From 3f397d56e1373eea21cf6686e9db0e2c109c6247 Mon Sep 17 00:00:00 2001 From: Daniel Lundin Date: Mon, 4 Mar 2024 14:06:38 +0100 Subject: [PATCH 07/11] Update CHANGELOG.md --- CHANGELOG.md | 14 ++++++-------- 1 file changed, 6 insertions(+), 8 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3ae0f3bb..526b6040 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## v1.0.1 - [2024-03-04] +### `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 @@ -13,14 +15,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#269]([https://github.com/nf-core/ampliseq/pull/681](https://github.com/nf-core/metatdenovo/pull/269)) - Make Transdecoder work better with `-resume` -## v1.0.0 - [2024-02-15] - -Initial release of nf-core/metatdenovo, created with the [nf-core](https://nf-co.re/) template. - -### `Added` - -### `Fixed` -Trandecoder subworkflow didn't cache properly. We made a local module that fixed the issue. ### `Dependencies` ### `Deprecated` + +## v1.0.0 - [2024-02-15] + +Initial release of nf-core/metatdenovo, created with the [nf-core](https://nf-co.re/) template. From 3c53b92b2d1e291099a692b48b5831aeaef6ceb0 Mon Sep 17 00:00:00 2001 From: Danilo Di Leo <78909156+danilodileo@users.noreply.github.com> Date: Mon, 4 Mar 2024 14:52:10 +0100 Subject: [PATCH 08/11] Update assets/multiqc_config.yml Co-authored-by: Daniel Lundin --- assets/multiqc_config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 3c93488b..80243831 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,5 +1,5 @@ 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. report_section_order: From 0f12b8740820d0538a06f751a4b58eca8f471e12 Mon Sep 17 00:00:00 2001 From: Danilo Di Leo <78909156+danilodileo@users.noreply.github.com> Date: Mon, 4 Mar 2024 14:52:17 +0100 Subject: [PATCH 09/11] Update assets/multiqc_config.yml Co-authored-by: Daniel Lundin --- assets/multiqc_config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 80243831..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 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 From e393769f21fcdc8bec25c45fd6ac3b39c9c36c92 Mon Sep 17 00:00:00 2001 From: Danilo Di Leo <78909156+danilodileo@users.noreply.github.com> Date: Mon, 4 Mar 2024 14:52:29 +0100 Subject: [PATCH 10/11] Update nextflow.config Co-authored-by: Daniel Lundin --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index d6ab62a9..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 = '1.0.2dev' + version = '1.0.1' doi = '' } From 071a1d6bd7a8f6c4c00adf8602077533718b681c Mon Sep 17 00:00:00 2001 From: Danilo Di Leo <78909156+danilodileo@users.noreply.github.com> Date: Mon, 4 Mar 2024 14:53:41 +0100 Subject: [PATCH 11/11] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 526b6040..b4858fb9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ 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). -## v1.0.1 - [2024-03-04] +## v1.0.1 - [date] ### `Added`