Add singularity profile

README.md

@@ -10,7 +10,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 
 i. Install [`nextflow`](https://nf-co.re/usage/installation)
 
-ii. Install [`docker`](https://docs.docker.com/engine/installation/) or [`conda`](https://conda.io/miniconda.html)
+ii. Install [`docker`](https://docs.docker.com/engine/installation/), [`singularity`/`apptainer`](https://apptainer.org/docs/user/latest/quick_start.html#quick-installation), or [`conda`](https://conda.io/miniconda.html)
 
 iii. Clone the NanoCLUST repository and test the pipeline on a minimal dataset with a single command and docker/conda profiles.
 

conf/test.config

@@ -20,8 +20,8 @@ params {
   // TODO nf-core: Give any required params for the test so that command line flags are not needed
   singleEnd = false
   reads = "$baseDir/test_datasets/mock4_run3bc08_5000.fastq"
-  db ="db/16S_ribosomal_RNA"
-  tax = "db/taxdb/"
+  db ="$baseDir/db/16S_ribosomal_RNA"
+  tax = "$baseDir/db/taxdb/"
   polishing_reads = 20
   min_cluster_size = 50
 }

docs/2usage.md

@@ -15,9 +15,9 @@ NXF_OPTS='-Xms1g -Xmx4g'
 The typical command for running the pipeline is as follows:
 
 ```bash
-nextflow run main.nf --reads 'data/mock_sample.fastq' --db 'db/blastdb' --tax 'db/taxdb' -profile <conda,docker>
+nextflow run main.nf --reads 'data/mock_sample.fastq' --db 'db/blastdb' --tax 'db/taxdb' -profile <conda,docker,singularity>
 ```
-This will launch the pipeline with the `conda` or `docker` configuration profiles. See below for more information about profiles.
+This will launch the pipeline with the `conda`, `docker`, or `singularity` configuration profiles. See below for more information about profiles.
 
 *Database and taxdb should be downloaded in the NanoCLUST dir.
 

docs/index.md

@@ -10,7 +10,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 
 i. Install [`nextflow`](https://nf-co.re/usage/installation)
 
-ii. Install [`docker`](https://docs.docker.com/engine/installation/) or [`conda`](https://conda.io/miniconda.html)
+ii. Install [`docker`](https://docs.docker.com/engine/installation/), [`singularity`/`apptainer`](https://apptainer.org/docs/user/latest/quick_start.html#quick-installation), or [`conda`](https://conda.io/miniconda.html)
 
 iii. Clone the NanoCLUST repository and test the pipeline on a minimal dataset with a single command
 

main.nf

@@ -22,7 +22,7 @@ def helpMessage() {
     Mandatory arguments:
       --reads                       Path to input data (must be surrounded with quotes)
       -profile                      Configuration profile to use. Can use multiple (comma separated)
-                                    Available: conda, docker, singularity, awsbatch, test and more.
+                                    Available: conda, docker, singularity, test, and more.
 
     UMAP and HDBSCAN clustering parameters:
       --umap_set_size               Number of reads used to perform the UMAP+HDBSCAN clustering (100000)

nextflow.config

@@ -66,6 +66,7 @@ process {
 profiles {
   test { includeConfig 'conf/test.config' }
   conda { 
+    conda.enabled = true
     process {
       withName: demultiplex { conda = "$baseDir/conda_envs/demultiplex/environment.yml" }
       withName: demultiplex_porechop { conda = "$baseDir/conda_envs/demultiplex_porechop/environment.yml" }
@@ -86,7 +87,7 @@ profiles {
     }
   }
   docker { 
-    docker.enabled = true 
+    docker.enabled = true
     //process.container = 'nf-core/nanoclust:latest'
     process {
       withName: demultiplex { container = 'hecrp/nanoclust-demultiplex' }
@@ -101,12 +102,34 @@ profiles {
       withName: draft_selection { container = 'hecrp/nanoclust-draft_selection' }
       withName: racon_pass { container = 'hecrp/nanoclust-racon_pass' }
       withName: medaka_pass { container = 'hecrp/nanoclust-medaka_pass' }
-      withName: consensus_classification { container = 'hecrp/nanoclust-consensus_classification'
+      withName: consensus_classification { container = 'ncbi/blast:latest'
                                            docker.temp = "$baseDir/" }
       withName: get_abundances { container = 'hecrp/nanoclust-plot_abundances' }
       withName: plot_abundances { container = 'hecrp/nanoclust-plot_abundances' }
       withName: output_documentation { container = 'hecrp/nanoclust-output_documentation' }
     }
+  }
+  singularity {
+    singularity.enabled = true
+    singularity.autoMounts = true
+    process {
+      withName: demultiplex { container = 'docker://hecrp/nanoclust-demultiplex' }
+      withName: demultiplex_porechop { container = 'docker://hecrp/nanoclust-demultiplex_porechop' }
+      withName: QC { container = 'docker://hecrp/nanoclust-qc' }
+      withName: fastqc { container = 'docker://hecrp/nanoclust-fastqc' }
+      withName: multiqc { container = 'docker://hecrp/nanoclust-fastqc' }
+      withName: kmer_freqs { container = 'docker://hecrp/nanoclust-kmer_freqs' }
+      withName: read_clustering { container = 'docker://hecrp/nanoclust-read_clustering' }
+      withName: split_by_cluster { container = 'docker://hecrp/nanoclust-split_by_cluster' }
+      withName: read_correction { container = 'docker://hecrp/nanoclust-read_correction' }
+      withName: draft_selection { container = 'docker://hecrp/nanoclust-draft_selection' }
+      withName: racon_pass { container = 'docker://hecrp/nanoclust-racon_pass' }
+      withName: medaka_pass { container = 'docker://hecrp/nanoclust-medaka_pass' }
+      withName: consensus_classification { container = 'docker://ncbi/blast:latest' }
+      withName: get_abundances { container = 'docker://hecrp/nanoclust-plot_abundances' }
+      withName: plot_abundances { container = 'docker://hecrp/nanoclust-plot_abundances' }
+      withName: output_documentation { container = 'docker://hecrp/nanoclust-output_documentation' }
+        }
     }
 }