Merge pull request #38 from nf-core/iss-multifasta

Added option for using draft genomes with insilicoseq
nf-core · Mar 20, 2024 · 7c807dd · 7c807dd
2 parents cb84711 + ed43715
commit 7c807dd
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Showing 4 changed files with 16 additions and 7 deletions.
diff --git a/README.md b/README.md
@@ -6,7 +6,7 @@
 </h1>
 
 [![GitHub Actions CI Status](https://github.com/nf-core/readsimulator/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/readsimulator/actions/workflows/ci.yml)
-[![GitHub Actions Linting Status](https://github.com/nf-core/readsimulator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/readsimulator/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/readsimulator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
+[![GitHub Actions Linting Status](https://github.com/nf-core/readsimulator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/readsimulator/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/readsimulator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.10622410-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.10622410)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
@@ -113,8 +113,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 ## Citations
 
-<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
-<!-- If you use nf-core/readsimulator for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
+If you use nf-core/readsimulator for your analysis, please cite it using the following doi: [10.5281/zenodo.10622410](https://doi.org/10.5281/zenodo.10622410)
 
 <!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
 

diff --git a/modules/local/insilicoseq/generate/main.nf b/modules/local/insilicoseq/generate/main.nf
@@ -9,6 +9,7 @@ process INSILICOSEQ_GENERATE {
 
     input:
     tuple val(meta), path(fasta)
+    val(input_format)
 
     output:
     tuple val(meta), path("*.fastq.gz*"), emit: fastq
@@ -22,6 +23,7 @@ process INSILICOSEQ_GENERATE {
     def args2         = task.ext.args2 ?: ''
     def prefix        = task.ext.prefix ?: "${meta.id}"
     def seed          = task.ext.seed ?: "${meta.seed}"
+    def input_format  = input_format == "genomes" ? "--genomes": "--draft"
     if (fasta) {
         def is_compressed = fasta.name.endsWith(".gz")
         def fasta_name    = fasta.name.replace(".gz", "")
@@ -34,7 +36,7 @@ process INSILICOSEQ_GENERATE {
         fi
 
         iss generate \\
-            --genomes ${fasta_name} \\
+            ${input_format} ${fasta_name} \\
             --seed \$seed \\
             --output \$prefix \\
             --compress \\

diff --git a/nextflow.config b/nextflow.config
@@ -55,6 +55,7 @@ params {
     metagenome_abundance_file  = null
     metagenome_coverage        = null
     metagenome_coverage_file   = null
+    metagenome_input_format    = 'genomes'
     metagenome_n_reads         = '1M'
     metagenome_mode            = 'kde'
     metagenome_model           = 'MiSeq'
@@ -290,7 +291,7 @@ manifest {
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
     version         = '1.0.0'
-    doi             = ''
+    doi             = '10.5281/zenodo.10622410'
 }
 
 // Load modules.config for DSL2 module specific options

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -158,7 +158,7 @@
                 },
                 "target_capture_fshape": {
                     "type": "number",
-                    "default": 6.0,
+                    "default": 6,
                     "description": "Shape parameter of the fragment size distribution."
                 },
                 "target_capture_smedian": {
@@ -168,7 +168,7 @@
                 },
                 "target_capture_sshape": {
                     "type": "number",
-                    "default": 6.0,
+                    "default": 6,
                     "description": "Shape parameter of the fragment size distribution."
                 },
                 "target_capture_tmedian": {
@@ -240,6 +240,13 @@
                     "description": "Path to tab-separated file containing coverage information.",
                     "help_text": "The first column should contain the genome and the second column should contain the coverage (e.g., use the value 20 for a coverage of 20X)."
                 },
+                "metagenome_input_format": {
+                    "type": "string",
+                    "default": "genomes",
+                    "description": "Format of FASTA file used to generate reads",
+                    "help_text": "If complete genomes are used (i.e. 1 sequence per genome FASTA) choose 'genomes'; if draft genomes are used (i.e. multiple sequences per genome FASTA) choose 'draft'",
+                    "enum": ["genomes", "draft"]
+                },
                 "metagenome_n_reads": {
                     "type": "string",
                     "default": "1M",