Minor inconcistencies

.nf-core.yml

@@ -9,4 +9,4 @@ template:
   name: metatdenovo
   org: nf-core
   outdir: .
-  version: "1.1"
+  version: "1.1dev"

CHANGELOG.md

@@ -18,7 +18,9 @@ Initial release of nf-core/metatdenovo, created with the [nf-core](https://nf-co
 
 ### `Changed`
 
-- [#311](<[https://github.com/nf-core/metatdenovo/pull/311](https://github.com/nf-core/metatdenovo/pull/311)>) - update modules and subworkflows
+- [#323](<[https://github.com/nf-core/metatdenovo/pull/323](https://github.com/nf-core/metatdenovo/pull/323)>) - Modified param names for input of assembly and ORFs; added name params for output file naming
+- [#323](<[https://github.com/nf-core/metatdenovo/pull/323](https://github.com/nf-core/metatdenovo/pull/323)>) - Removed default for `assembler` and `orf_caller` parameters
+- [#311](<[https://github.com/nf-core/metatdenovo/pull/311](https://github.com/nf-core/metatdenovo/pull/311)>) - Update modules and subworkflows
 - [#295](<[https://github.com/nf-core/metatdenovo/pull/295](https://github.com/nf-core/metatdenovo/pull/295)>) - Update documentation
 - [#292](<[https://github.com/nf-core/metatdenovo/pull/292](https://github.com/nf-core/metatdenovo/pull/292)>) - Specify memory to Megahit process
 - [#290](<[https://github.com/nf-core/metatdenovo/pull/290](https://github.com/nf-core/metatdenovo/pull/290)>) - Template update to v2.14.1

assets/multiqc_config.yml

@@ -1,7 +1,8 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/metatdenovo/releases/tag/1.1" 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/1.1/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/metatdenovo/tree/dev"
+  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>.
 report_section_order:
   "nf-core-metatdenovo-methods-description":
     order: -1000

conf/test.config

@@ -26,6 +26,9 @@ params {
     input    = params.pipelines_testdata_base_path + 'metatdenovo/samplesheet/samplesheet.csv'
     hmmfiles = 'https://raw.githubusercontent.com/nf-core/test-datasets/metatdenovo/test_data/PF00317.hmm,https://raw.githubusercontent.com/nf-core/test-datasets/metatdenovo/test_data/PF00848.hmm,https://raw.githubusercontent.com/nf-core/test-datasets/metatdenovo/test_data/PF03477.hmm,https://raw.githubusercontent.com/nf-core/test-datasets/metatdenovo/test_data/PF13597.hmm'
 
+    assembler      = 'megahit'
+    orf_caller     = 'prodigal'
+
     // Other options
     skip_eukulele  = true
     skip_eggnog    = true

conf/test_eggnog.config

@@ -17,6 +17,9 @@ params {
     // Input data
     input    = 'https://raw.githubusercontent.com/nf-core/test-datasets/metatdenovo/samplesheet/samplesheet.csv'
 
+    assembler      = 'megahit'
+    orf_caller     = 'prodigal'
+
     // parameters
     skip_eukulele  = true
     skip_eggnog    = false

conf/test_eukulele.config

@@ -17,6 +17,9 @@ params {
     // Input data
     input    = 'https://raw.githubusercontent.com/nf-core/test-datasets/metatdenovo/samplesheet/samplesheet.csv'
 
+    assembler      = 'megahit'
+    orf_caller     = 'prodigal'
+
     skip_eggnog    = true
     skip_kofamscan = true
     eukulele_db    = 'phylodb'

conf/test_filter.config

@@ -19,6 +19,9 @@ params {
 
     sequence_filter = 'https://github.com/nf-core/test-datasets/raw/metatdenovo/test_data/rrna.fna.gz'
 
+    assembler      = 'megahit'
+    orf_caller     = 'prodigal'
+
     skip_eukulele  = true
     skip_eggnog    = true
     skip_kofamscan = true

conf/test_full.config

@@ -17,6 +17,9 @@ params {
     // Input data for full size test
     input = params.pipelines_testdata_base_path + 'metatdenovo/samplesheet/samplesheet_full_test.csv'
 
+    assembler      = 'megahit'
+    orf_caller     = 'prodigal'
+
     // parameters
     skip_eukulele   = false
     skip_eggnog     = false

conf/test_kofamscan.config

@@ -17,6 +17,9 @@ params {
     // Input data
     input    = 'https://raw.githubusercontent.com/nf-core/test-datasets/metatdenovo/samplesheet/samplesheet.csv'
 
+    assembler      = 'megahit'
+    orf_caller     = 'prodigal'
+
     // parameters
     skip_eukulele  = true
     skip_eggnog    = true

conf/test_prokka.config

@@ -17,6 +17,9 @@ params {
     // Input data
     input    = 'https://raw.githubusercontent.com/nf-core/test-datasets/metatdenovo/samplesheet/samplesheet.csv'
 
+    assembler      = 'megahit'
+    orf_caller     = 'prodigal'
+
     // skip taxonomy
     orf_caller     = 'prokka'
     skip_eukulele  = true

conf/test_spades.config

@@ -19,11 +19,9 @@ params {
 
     // Assembler option
     assembler     = 'spades'
+    orf_caller     = 'prodigal'
 
     skip_eukulele  = true
     skip_eggnog    = true
     skip_kofamscan = true
-
-    // genomes parameter
-    genomes = ''
 }

conf/test_transdecoder.config

@@ -17,6 +17,9 @@ params {
     // Input data
     input    = 'https://raw.githubusercontent.com/nf-core/test-datasets/metatdenovo/samplesheet/samplesheet.csv'
 
+    assembler     = 'megahit'
+    orf_caller     = 'prodigal'
+
     // params
     orf_caller     = 'transdecoder'
     skip_eukulele  = true

docs/usage.md

@@ -181,7 +181,7 @@ Here's the whole procedure for the NCBI NR example (worked for us in January 202
 wget ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nr.gz
 
 # Download and untar the taxonomy dump
-ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
+wget ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
 tar xfz taxdump.tar.gz
 
 # Download all the individual mapping files and concatenate them (also takes long)

main.nf

@@ -18,12 +18,6 @@ include { METATDENOVO             } from './workflows/metatdenovo'
 include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_metatdenovo_pipeline'
 include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_metatdenovo_pipeline'
 
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     NAMED WORKFLOWS FOR PIPELINE

nextflow.config

@@ -11,51 +11,53 @@ params {
 
     // Input options
     input                        = null
-    assembly                     = null
     genomes                      = null
-    protein_fasta                = null
-    gff                          = null
     se_reads                     = false
     validationSkipDuplicateCheck = false
     validationS3PathCheck        = false
 
     // QC options
-    skip_qc                     = false
-    skip_fastqc                 = false
+    skip_qc                      = false
+    skip_fastqc                  = false
 
     // Trimming options
-    clip_r1                     = null
-    clip_r2                     = null
-    three_prime_clip_r1         = null
-    three_prime_clip_r2         = null
-    trim_nextseq                = null
-    save_trimmed                = false
-    skip_trimming               = false
+    clip_r1                      = null
+    clip_r2                      = null
+    three_prime_clip_r1          = null
+    three_prime_clip_r2          = null
+    trim_nextseq                 = null
+    save_trimmed                 = false
+    skip_trimming                = false
 
     // BBDuk options
-    sequence_filter             = null
+    sequence_filter              = null
 
     // Digital normalization options
-    bbnorm                      = false
-    bbnorm_target               = 100
-    bbnorm_min                  = 5
-    save_bbnorm_fastq           = false
+    bbnorm                       = false
+    bbnorm_target                = 100
+    bbnorm_min                   = 5
+    save_bbnorm_fastq            = false
 
     // assembler option
-    assembler                   = 'megahit'
-    min_contig_length           = 0
-    spades_flavor               = 'rna'
-    save_formatspades           = false
+    assembler                    = null
+    user_assembly                = null
+    user_assembly_name           = 'user_assembly'
+    min_contig_length            = 0
+    spades_flavor                = 'rna'
+    save_formatspades            = false
 
     // Mapping options
-    save_samtools               = false
-    save_bam                    = false
-    bbmap_minid                 = 0.9
+    save_samtools                = false
+    save_bam                     = false
+    bbmap_minid                  = 0.9
 
     // orf caller options
-    orf_caller                  = 'prodigal'
-    prodigal_trainingfile       = null
-    prokka_batchsize            = 10.MB
+    orf_caller                   = null
+    user_orfs_faa                = null
+    user_orfs_gff                = null
+    user_orfs_name               = 'user_orfs'
+    prodigal_trainingfile        = null
+    prokka_batchsize             = 10.MB
 
     // HMMSEARCH options
     hmmdir                      = null
@@ -303,15 +305,14 @@ dag {
 
 manifest {
     name            = 'nf-core/metatdenovo'
-    author          = """Danilo Di Leo, Emelie Nilsson & Daniel Lundin""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead
     contributors    = [
         [
             name: 'Danilo Di Leo',
             affiliation: 'Linnaeus University, Kalmar, Sweden',
             email: '[email protected]',
             github: '@danilodileo',
             contribution:  [ 'author', 'maintainer' ],
-            orcid: ''
+            orcid: 'https://orcid.org/0009-0009-6639-7876'
         ],
         [
             name: ' Emelie Nilsson',
@@ -335,7 +336,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'master'
     nextflowVersion = '!>=24.04.2'
-    version         = '1.1'
+    version         = '1.1dev'
     doi             = ''
 }
 
@@ -349,7 +350,7 @@ validation {
     monochromeLogs = params.monochrome_logs
     help {
         enabled = true
-        command = "nextflow run nf-core/metatdenovo -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
+        command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
         fullParameter = "help_full"
         showHiddenParameter = "show_hidden"
         beforeText = """
@@ -362,12 +363,12 @@ validation {
 \033[0;35m  nf-core/metatdenovo ${manifest.version}\033[0m
 -\033[2m----------------------------------------------------\033[0m-
 """
-        afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
+        afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "  https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
 * The nf-core framework
     https://doi.org/10.1038/s41587-020-0439-x
 
 * Software dependencies
-    https://github.com/nf-core/metatdenovo/blob/master/CITATIONS.md
+    https://github.com/${manifest.name}/blob/master/CITATIONS.md
 """
     }
     summary {

nextflow_schema.json

@@ -169,19 +169,24 @@
             "properties": {
                 "assembler": {
                     "type": "string",
-                    "default": "megahit",
                     "enum": ["megahit", "spades"],
                     "description": "Specify which assembler you would like to run, possible alternatives: megahit, spades. default: megahit",
                     "fa_icon": "fas fa-bezier-curve"
                 },
-                "assembly": {
+                "user_assembly": {
                     "type": "string",
                     "format": "file-path",
                     "exists": true,
                     "mimetype": "text/plain",
                     "description": "Path to a fasta file with a finished assembly. Assembly will be skipped by the pipeline.",
                     "fa_icon": "far fa-file-code"
                 },
+                "user_assembly_name": {
+                    "type": "string",
+                    "default": "user_assembly",
+                    "description": "Name to give to the user-provided assembly.",
+                    "fa_icon": "fas fa-bezier-curve"
+                },
                 "min_contig_length": {
                     "type": "integer",
                     "default": 0,
@@ -235,23 +240,34 @@
             "description": "",
             "default": "",
             "properties": {
-                "protein_fasta": {
-                    "type": "string",
-                    "fa_icon": "fas fa-file-code",
-                    "description": "Path to a protein fasta file"
-                },
-                "gff": {
-                    "type": "string",
-                    "fa_icon": "fas fa-file-code",
-                    "description": "Path to a gff file"
-                },
                 "orf_caller": {
                     "type": "string",
-                    "default": "prodigal",
                     "enum": ["prodigal", "prokka", "transdecoder"],
                     "description": "Specify which ORF caller you would like to run, possible alternatives: prodigal, prokka, transdecoder, default: prodigal.",
                     "fa_icon": "fas fa-phone-volume"
                 },
+                "user_orfs_faa": {
+                    "type": "string",
+                    "format": "file-path",
+                    "exists": true,
+                    "mimetype": "text/plain",
+                    "description": "Path to a protein fasta file for user-provided ORFs",
+                    "fa_icon": "far fa-file-code"
+                },
+                "user_orfs_gff": {
+                    "type": "string",
+                    "format": "file-path",
+                    "exists": true,
+                    "mimetype": "text/plain",
+                    "description": "Path to a gff file for user-provided ORFs",
+                    "fa_icon": "far fa-file-code"
+                },
+                "user_orfs_name": {
+                    "type": "string",
+                    "default": "user_orfs",
+                    "description": "Name to give to user-provided ORFs.",
+                    "fa_icon": "fas fa-bezier-curve"
+                },
                 "prodigal_trainingfile": {
                     "type": "string",
                     "description": "Specify a training file for prodigal. By default prodigal will learn from the input sequences",
@@ -337,7 +353,7 @@
                     "mimetype": "text/csv",
                     "pattern": "^\\S+\\.csv$",
                     "description": "Path to comma-separated file containing information about Diamond database files you want to use for taxonomy assignment.",
-                    "help_text": "This has to be a comma-separated file with four columns, and a header row: db, dmnd_path, taxid2lineage_path, taxdump_dir",
+                    "help_text": "This has to be a comma-separated file with a header row and four mandatory columns: db, dmnd_path, taxdump_names, taxdump_nodes, plus two optional: ranks and parse_with_taxdump",
                     "fa_icon": "fas fa-file-csv"
                 },
                 "diamond_top": {