Singularity images

docs/Dockerfile

@@ -0,0 +1,10 @@
+#Dockerfile for documentation
+#
+#
+#
+#
+
+FROM sphinxdoc/sphinx
+WORKDIR /docs
+ADD requirements.txt /docs
+RUN pip3 install -r requirements.txt

modules/local/align_reads.nf

@@ -15,7 +15,7 @@ process ALIGN_READS {
 
     conda (params.enable_conda ? "bioconda::autometa" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
+        container "https://depot.galaxyproject.org/singularity/autometa:2.2.0--pyh7cba7a3_0"
     } else {
         container "jasonkwan/autometa:${params.autometa_image_tag}"
     }

modules/local/binning.nf

@@ -11,7 +11,7 @@ process BINNING {
 
     conda (params.enable_conda ? "bioconda::autometa" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
+        container "https://depot.galaxyproject.org/singularity/autometa:2.2.0--pyh7cba7a3_0"
     } else {
         container "jasonkwan/autometa:${params.autometa_image_tag}"
     }

modules/local/binning_summary.nf

@@ -12,7 +12,7 @@ process BINNING_SUMMARY {
 
     conda (params.enable_conda ? "bioconda::autometa" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
+        container "https://depot.galaxyproject.org/singularity/autometa:2.2.0--pyh7cba7a3_0"
     } else {
         container "jasonkwan/autometa:${params.autometa_image_tag}"
     }

modules/local/hmmer_hmmsearch_filter.nf

@@ -24,7 +24,7 @@ process HMMER_HMMSEARCH_FILTER {
 
     conda (params.enable_conda ? "autometa" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
+        container "https://depot.galaxyproject.org/singularity/autometa:2.2.0--pyh7cba7a3_0"
     } else {
         container "jasonkwan/autometa:${params.autometa_image_tag}"
     }

modules/local/length_table.nf

@@ -12,7 +12,7 @@ process LENGTH_TABLE {
 
     conda (params.enable_conda ? "bioconda::autometa" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
+        container "https://depot.galaxyproject.org/singularity/autometa:2.2.0--pyh7cba7a3_0"
     } else {
         container "jasonkwan/autometa:${params.autometa_image_tag}"
     }

modules/local/majority_vote.nf

@@ -12,7 +12,7 @@ process MAJORITY_VOTE {
 
     conda (params.enable_conda ? "bioconda::autometa" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
+        container "https://depot.galaxyproject.org/singularity/autometa:2.2.0--pyh7cba7a3_0"
     } else {
         container "jasonkwan/autometa:${params.autometa_image_tag}"
     }

modules/local/markers.nf

@@ -13,7 +13,7 @@ process MARKERS {
 
     conda (params.enable_conda ? "autometa" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
+        container "https://depot.galaxyproject.org/singularity/autometa:2.2.0--pyh7cba7a3_0"
     } else {
         container "jasonkwan/autometa:${params.autometa_image_tag}"
     }

modules/local/prepare_lca.nf

@@ -10,7 +10,7 @@ process PREPARE_LCA {
 
     conda (params.enable_conda ? "bioconda::autometa" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
+        container "https://depot.galaxyproject.org/singularity/autometa:2.2.0--pyh7cba7a3_0"
     } else {
         container "jasonkwan/autometa:${params.autometa_image_tag}"
     }

modules/local/reduce_lca.nf

@@ -12,7 +12,7 @@ process REDUCE_LCA {
 
     conda (params.enable_conda ? "bioconda::autometa" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
+        container "https://depot.galaxyproject.org/singularity/autometa:2.2.0--pyh7cba7a3_0"
     } else {
         container "jasonkwan/autometa:${params.autometa_image_tag}"
     }

modules/local/spades_kmer_coverage.nf

@@ -12,7 +12,7 @@ process SPADES_KMER_COVERAGE {
 
     conda (params.enable_conda ? "autometa" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
+        container "https://depot.galaxyproject.org/singularity/autometa:2.2.0--pyh7cba7a3_0"
     } else {
         container "jasonkwan/autometa:${params.autometa_image_tag}"
     }

modules/local/split_kingdoms.nf

@@ -12,7 +12,7 @@ process SPLIT_KINGDOMS {
 
     conda (params.enable_conda ? "bioconda::autometa" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
+        container "https://depot.galaxyproject.org/singularity/autometa:2.2.0--pyh7cba7a3_0"
     } else {
         container "jasonkwan/autometa:${params.autometa_image_tag}"
     }

modules/local/unclustered_recruitment.nf

@@ -12,7 +12,7 @@ process RECRUIT {
 
     conda (params.enable_conda ? "autometa" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
+        container "https://depot.galaxyproject.org/singularity/autometa:2.2.0--pyh7cba7a3_0"
     } else {
         container "jasonkwan/autometa:${params.autometa_image_tag}"
     }

subworkflows/local/prepare_ncbi_taxinfo.nf

@@ -71,7 +71,7 @@ process DOWNLOAD_TAXDUMP {
 
     conda (params.enable_conda ? "conda-forge::rsync=3.2.3" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
+        container "https://depot.galaxyproject.org/singularity/autometa:2.2.0--pyh7cba7a3_0"
     } else {
         container "jasonkwan/autometa:${params.autometa_image_tag}"
     }

subworkflows/local/prepare_nr.nf

@@ -16,7 +16,7 @@ process DOWNLOAD_NR {
 
     conda (params.enable_conda ? "conda-forge::rsync=3.2.3" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
+        container "https://depot.galaxyproject.org/singularity/autometa:2.2.0--pyh7cba7a3_0"
     } else {
         container "jasonkwan/autometa:${params.autometa_image_tag}"
     }
@@ -46,7 +46,7 @@ process TEST_DOWNLOAD {
 
     conda (params.enable_conda ? "conda-forge::rsync=3.2.3" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
+        container "https://depot.galaxyproject.org/singularity/autometa:2.2.0--pyh7cba7a3_0"
     } else {
         container "jasonkwan/autometa:${params.autometa_image_tag}"
     }