Merge pull request #270 from danilodileo/transdecoder-bug

Transdecoder bug

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.

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/metatdenovo/tree/dev" target="_blank">nf-core/metatdenovo</a>
+  This report has been generated by the <a href="https://github.com/nf-core/metatdenovo/releases/tag/1.0.1" target="_blank">nf-core/metatdenovo</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/metatdenovo/dev/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/metatdenovo/1.0.1/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-metatdenovo-methods-description":
     order: -1000

conf/modules.config

@@ -170,7 +170,7 @@ process {
         ]
     }
 
-    withName: PREDICT {
+    withName: TRANSDECODER {
         publishDir = [
             path: { "${params.outdir}/transdecoder" },
             mode: params.publish_dir_mode,

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",

modules/nf-core/transdecoder/longorf/main.nf → 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")

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             = ''
 }
 

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'