From 23cb2a7ce75682eaddc2fd59f2cb31491b22d13f Mon Sep 17 00:00:00 2001
From: xiaoli-dong <xiaolid@gmail.com>
Date: Fri, 19 Jan 2024 14:09:24 -0700
Subject: [PATCH] update

---
 modules/local/shovill/main.nf           |  2 +-
 modules/nf-core/shovill/environment.yml |  6 ---
 modules/nf-core/shovill/main.nf         | 42 -------------------
 modules/nf-core/shovill/meta.yml        | 55 -------------------------
 4 files changed, 1 insertion(+), 104 deletions(-)
 delete mode 100644 modules/nf-core/shovill/environment.yml
 delete mode 100644 modules/nf-core/shovill/main.nf
 delete mode 100644 modules/nf-core/shovill/meta.yml

diff --git a/modules/local/shovill/main.nf b/modules/local/shovill/main.nf
index 6bbf532..a89e09b 100644
--- a/modules/local/shovill/main.nf
+++ b/modules/local/shovill/main.nf
@@ -12,7 +12,7 @@ process SHOVILL {
 
     output:
     tuple val(meta), path("*contigs.fa.gz")                         , emit: contigs
-    tuple val(meta), path("shovill.corrections")                , emit: corrections
+    tuple val(meta), path("shovill.corrections")                , optional: true, emit: corrections
     tuple val(meta), path("shovill.log")                        , emit: log
     tuple val(meta), path("{skesa,spades,megahit,velvet}.fasta"), emit: raw_contigs
     tuple val(meta), path("*contigs.{fastg,gfa,LastGraph}.gz")      , optional:true, emit: gfa
diff --git a/modules/nf-core/shovill/environment.yml b/modules/nf-core/shovill/environment.yml
deleted file mode 100644
index f21b1ec..0000000
--- a/modules/nf-core/shovill/environment.yml
+++ /dev/null
@@ -1,6 +0,0 @@
-channels:
-  - conda-forge
-  - bioconda
-  - defaults
-dependencies:
-  - bioconda::shovill=1.1.0
diff --git a/modules/nf-core/shovill/main.nf b/modules/nf-core/shovill/main.nf
deleted file mode 100644
index f92ce94..0000000
--- a/modules/nf-core/shovill/main.nf
+++ /dev/null
@@ -1,42 +0,0 @@
-process SHOVILL {
-    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/shovill:1.1.0--0' :
-        'biocontainers/shovill:1.1.0--0' }"
-
-    input:
-    tuple val(meta), path(reads)
-
-    output:
-    tuple val(meta), path("contigs.fa")                         , emit: contigs
-    tuple val(meta), path("shovill.corrections")                , emit: corrections
-    tuple val(meta), path("shovill.log")                        , emit: log
-    tuple val(meta), path("{skesa,spades,megahit,velvet}.fasta"), emit: raw_contigs
-    tuple val(meta), path("contigs.{fastg,gfa,LastGraph}")      , optional:true, emit: gfa
-    path "versions.yml"                                         , emit: versions
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args = task.ext.args ?: ''
-    def memory = task.memory.toGiga()
-    """
-    shovill \\
-        --R1 ${reads[0]} \\
-        --R2 ${reads[1]} \\
-        $args \\
-        --cpus $task.cpus \\
-        --ram $memory \\
-        --outdir ./ \\
-        --force
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        shovill: \$(echo \$(shovill --version 2>&1) | sed 's/^.*shovill //')
-    END_VERSIONS
-    """
-}
diff --git a/modules/nf-core/shovill/meta.yml b/modules/nf-core/shovill/meta.yml
deleted file mode 100644
index cdeb015..0000000
--- a/modules/nf-core/shovill/meta.yml
+++ /dev/null
@@ -1,55 +0,0 @@
-name: shovill
-description: Assemble bacterial isolate genomes from Illumina paired-end reads
-keywords:
-  - bacterial
-  - assembly
-  - illumina
-tools:
-  - shovill:
-      description: Microbial assembly pipeline for Illumina paired-end reads
-      homepage: https://github.com/tseemann/shovill
-      documentation: https://github.com/tseemann/shovill/blob/master/README.md
-      licence: ["GPL v2"]
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'test', single_end:false ]
-  - reads:
-      type: file
-      description: List of input paired-end FastQ files
-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"
-  - contigs:
-      type: file
-      description: The final assembly produced by Shovill
-      pattern: "contigs.fa"
-  - corrections:
-      type: file
-      description: List of post-assembly corrections made by Shovill
-      pattern: "shovill.corrections"
-  - log:
-      type: file
-      description: Full log file for bug reporting
-      pattern: "shovill.log"
-  - raw_contigs:
-      type: file
-      description: Raw assembly produced by the assembler (SKESA, SPAdes, MEGAHIT, or Velvet)
-      pattern: "{skesa,spades,megahit,velvet}.fasta"
-  - gfa:
-      type: file
-      description: Assembly graph produced by MEGAHIT, SPAdes, or Velvet
-      pattern: "contigs.{fastg,gfa,LastGraph}"
-authors:
-  - "@rpetit3"
-maintainers:
-  - "@rpetit3"