From e623dca3b739ada28d1ccfac1bb63e3ae34947b5 Mon Sep 17 00:00:00 2001
From: annacprice <PriceA35@cardiff.ac.uk>
Date: Thu, 5 Mar 2020 09:29:23 +0000
Subject: [PATCH] initial commit of shovill

---
 tools/shovill/main.nf              | 20 ++++++++++++++++++++
 tools/shovill/meta.yml             | 30 ++++++++++++++++++++++++++++++
 tools/shovill/test/main.nf         | 17 +++++++++++++++++
 tools/shovill/test/nextflow.config |  5 +++++
 4 files changed, 72 insertions(+)
 create mode 100644 tools/shovill/main.nf
 create mode 100644 tools/shovill/meta.yml
 create mode 100644 tools/shovill/test/main.nf
 create mode 100644 tools/shovill/test/nextflow.config

diff --git a/tools/shovill/main.nf b/tools/shovill/main.nf
new file mode 100644
index 00000000..cf52ba10
--- /dev/null
+++ b/tools/shovill/main.nf
@@ -0,0 +1,20 @@
+process shovill {
+
+    tag { shovill }
+
+    publishDir "${params.outdir}", pattern: '*.fasta', mode: 'copy'
+  
+    container "quay.io/biocontainers/shovill:1.0.9--0"
+
+    input:
+    tuple(sample_id, path(forward), path(reverse))
+
+    output:
+    path("${sample_id}.fasta")
+   
+    script:
+    """
+    shovill --R1 ${forward} --R2 ${reverse} --outdir shovill_out
+    mv shovill_out/contigs.fa ${sample_id}.fasta
+    """
+}
diff --git a/tools/shovill/meta.yml b/tools/shovill/meta.yml
new file mode 100644
index 00000000..7c204c24
--- /dev/null
+++ b/tools/shovill/meta.yml
@@ -0,0 +1,30 @@
+name: Shovill
+description: Create a bacterial assembly from paired fastq using shovill
+keywords:
+    - Genome Assembly
+    - Bacterial Isolates
+tools:
+    - fastqc:
+        description: |
+            Shovill assembles bacterial isolate genomes from Illumina
+            paired-end reads. Shovill uses the SPAdes genome assembler,
+            providing pre and post-processing to the SPAdes assembly.
+            It also supports SKESA, Velvet and Megahit.
+        homepage: https://github.com/tseemann/shovill
+        documentation: https://github.com/tseemann/shovill/blob/master/README.md
+input:
+    -
+        - sample_id:
+            type: string
+            description: Sample identifier
+        - reads:
+            type: file
+            description: pair of fastq files
+output:
+    -
+        - assembly:
+            type: file
+            description: fasta file
+            pattern: ${sample_id}.fasta
+authors:
+    - @annacprice
diff --git a/tools/shovill/test/main.nf b/tools/shovill/test/main.nf
new file mode 100644
index 00000000..85ba6627
--- /dev/null
+++ b/tools/shovill/test/main.nf
@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.preview.dsl = 2
+
+// import shovill
+include {shovill} from '../main.nf' params(params)
+
+// define input channel
+readsPath = '../../../test-datasets/tools/shovill/input/SRR3609257_{1,2}.fastq.gz'
+Channel
+  .fromFilePairs( "${readsPath}", flat: true )
+  .set{ ch_reads  }
+ 
+// main workflow
+workflow {
+    shovill(ch_reads)
+}
diff --git a/tools/shovill/test/nextflow.config b/tools/shovill/test/nextflow.config
new file mode 100644
index 00000000..44cfb78d
--- /dev/null
+++ b/tools/shovill/test/nextflow.config
@@ -0,0 +1,5 @@
+// docker
+docker.enabled = true
+
+// output directory
+params.outdir = './results'