update dragonfly and bactopia-py versions

bactopia · Jun 2, 2023 · f7611ad · f7611ad
1 parent 208a8c2
commit f7611ad
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Showing 6 changed files with 30 additions and 4 deletions.
diff --git a/data/conda/meta.yaml b/data/conda/meta.yaml
@@ -16,7 +16,7 @@ requirements:
     - pip
     - python >3.8
   run:
-    - bactopia-py >=1.0.2
+    - bactopia-py >=1.0.3
     - conda >=22.11.0
     - coreutils
     - mamba >=1.1.0

diff --git a/modules/local/bactopia/assembler/main.nf b/modules/local/bactopia/assembler/main.nf
@@ -4,7 +4,7 @@ RESOURCES      = get_resources(workflow.profile, params.max_memory, params.max_c
 options        = initOptions(params.options ? params.options : [:], 'assembler')
 options.ignore = [".fastq.gz"]
 options.btype  = options.btype ?: "main"
-conda_tools    = "bioconda::bactopia-assembler=1.0.1"
+conda_tools    = "bioconda::bactopia-assembler=1.0.2"
 conda_name     = conda_tools.replace("=", "-").replace(":", "-").replace(" ", "-")
 conda_env      = file("${params.condadir}/${conda_name}").exists() ? "${params.condadir}/${conda_name}" : conda_tools
 
@@ -15,8 +15,8 @@ process ASSEMBLER {
 
     conda (params.enable_conda ? conda_env : null)
     container "${ workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/bactopia-assembler:1.0.1--hdfd78af_0' :
-        'quay.io/biocontainers/bactopia-assembler:1.0.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/bactopia-assembler:1.0.2--hdfd78af_0' :
+        'quay.io/biocontainers/bactopia-assembler:1.0.2--hdfd78af_0' }"
 
     input:
     tuple val(meta), path(fq), path(extra)

diff --git a/modules/nf-core/snippy/core/params.config b/modules/nf-core/snippy/core/params.config
@@ -5,4 +5,7 @@ This file includes default values for shared parameters.
 params {
     // Snippy Parameters
     maxhap = 100
+    mask = null
+    mask_char = "X"
+    snippy_core_opts = null
 }
diff --git a/modules/nf-core/snippy/core/params.json b/modules/nf-core/snippy/core/params.json
@@ -16,6 +16,22 @@
                     "description": "Largest haplotype to decompose",
                     "default": 100,
                     "fa_icon": "fas fa-angle-double-down"
+                },
+                "mask": {
+                    "type": "string",
+                    "description": "BED file of sites to mask",
+                    "fa_icon": "fas fa-angle-double-down"
+                },
+                "mask_char": {
+                    "type": "string",
+                    "description": "Masking character",
+                    "default": "X",
+                    "fa_icon": "fas fa-angle-double-down"
+                },
+                "snippy_core_opts": {
+                    "type": "string",
+                    "description": "Extra options in quotes for snippy-core",
+                    "fa_icon": "fas fa-italic"
                 }
             }
         }

diff --git a/modules/nf-core/snippy/run/params.config b/modules/nf-core/snippy/run/params.config
@@ -13,4 +13,5 @@ params {
     maxsoft = 10
     bwaopt = null
     fbopt = null
+    snippy_opts = null
 }
diff --git a/modules/nf-core/snippy/run/params.json b/modules/nf-core/snippy/run/params.json
@@ -66,6 +66,12 @@
                     "type": "string",
                     "description": "Extra Freebayes options, eg. --theta 1E-6 --read-snp-limit 2",
                     "fa_icon": "fas fa-italic"
+                },
+                "snippy_opts": {
+                    "type": "string",
+                    "description": "Extra options in quotes for Snippy",
+                    "fa_icon": "fas fa-italic",
+                    "hidden": false
                 }
             }
         }