add example for running in nextflow, close #142

nextflow/main.nf

@@ -171,4 +171,24 @@ process COGAPS_ADATA2DGC {
         R: \$(Rscript -e 'print(packageVersion("base"))' | awk '{print \$2}')
   END_VERSIONS
   """
-}
+}
+
+//example channel with data folders, for example
+ch_data = Channel.fromPath('./test/**gist.rds')
+  .map { tuple([id:it.getParent().getName()], it)}
+
+//example channel with cparams
+ch_cparams = Channel.of([npatterns: 7, niterations: 100, sparse: 1, distributed: 'null', nsets:1, nthreads:1],
+                        [npatterns: 7, niterations: 100, sparse: 0, distributed: 'null', nsets:1, nthreads:1])
+
+// combine the two channels as input to CoGAPS
+ch_input = ch_data.combine(ch_cparams)
+
+//run the workflow
+workflow {
+  COGAPS(ch_input)
+}
+
+//example:
+//nextflow run main.nf -profile docker -resume
+//nextflow run main.nf -profile slurm -resume

nextflow/nextflow.config

@@ -0,0 +1,165 @@
+// default params
+params {
+    outdir = 'out'
+    input = ''
+
+    //cogaps params
+    npatterns = 7
+    nsets = 1
+    niterations = 100
+    sparse = 1
+    seed = 42
+    distributed = 'null'
+    nthreads = 1
+
+    max_memory = '8.GB'
+    max_cpus = 4
+    max_time = '48.h'
+}
+
+//reporting
+def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
+timeline {
+    enabled = true
+    file    = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
+}
+report {
+    enabled = true
+    file    = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
+}
+trace {
+    enabled = true
+    file    = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
+}
+dag {
+    enabled = true
+    file    = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
+}
+
+//output
+process {
+    publishDir = { "${params.outdir}" }
+}
+
+//resources
+def check_max(obj, type) {
+    if (type == 'memory') {
+        try {
+            if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
+                return params.max_memory as nextflow.util.MemoryUnit
+            else
+                return obj
+        } catch (all) {
+            println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
+            return obj
+        }
+    } else if (type == 'time') {
+        try {
+            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
+                return params.max_time as nextflow.util.Duration
+            else
+                return obj
+        } catch (all) {
+            println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
+            return obj
+        }
+    } else if (type == 'cpus') {
+        try {
+            return Math.min( obj, params.max_cpus as int )
+        } catch (all) {
+            println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
+            return obj
+        }
+    }
+}
+
+process {
+    /*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    btc/spatial Nextflow base config file
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    A 'blank slate' config file, appropriate for general use on most high performance
+    compute environments. Assumes that all software is installed and available on
+    the PATH. Runs in `local` mode - all jobs will be run on the logged in environment.
+----------------------------------------------------------------------------------------
+    */
+
+    // TODO nf-core: Check the defaults for all processes
+    cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
+    memory = { check_max( 6.GB * task.attempt, 'memory' ) }
+    time   = { check_max( 4.h  * task.attempt, 'time'   ) }
+
+    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
+    maxRetries    = 1
+    maxErrors     = '-1'
+
+    // Process-specific resource requirements
+    // NOTE - Please try and re-use the labels below as much as possible.
+    //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
+    //        If possible, it would be nice to keep the same label naming convention when
+    //        adding in your local modules too.
+    // TODO nf-core: Customise requirements for specific processes.
+    // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
+    withLabel:process_single {
+        cpus   = { check_max( 1                  , 'cpus'    ) }
+        memory = { check_max( 6.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
+    }
+    withLabel:process_low {
+        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
+        memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
+    }
+    withLabel:process_medium {
+        cpus   = { check_max( 6     * task.attempt, 'cpus'    ) }
+        memory = { check_max( 24.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 8.h   * task.attempt, 'time'    ) }
+    }
+    withLabel:process_high {
+        cpus   = { check_max( 12    * task.attempt, 'cpus'    ) }
+        memory = { check_max( 72.GB * task.attempt, 'memory'  ) }
+        time   = { check_max( 16.h  * task.attempt, 'time'    ) }
+    }
+    withLabel:process_long {
+        time   = { check_max( 48.h  * task.attempt, 'time'    ) }
+    }
+    withLabel:process_high_memory {
+        memory = { check_max( 200.GB * task.attempt, 'memory' ) }
+    }
+    withLabel:error_ignore {
+        errorStrategy = 'ignore'
+    }
+    withLabel:error_retry {
+        errorStrategy = 'retry'
+        maxRetries    = 2
+    }
+}
+
+// profiles to run the pipeline
+profiles {
+    docker {
+        docker.enabled         = true
+    }
+
+    singularity {
+        singularity.enabled    = true
+        singularity.autoMounts = true
+    }
+
+    slurm {
+        singularity.enabled =    true
+        singularity.autoMounts = true
+        process {
+            executor = 'slurm'
+            cpus = 10
+            memory = '10 GB'
+        }
+    }
+    test {
+        process {
+            withName: COGAPS {
+                cpus = 1
+            }
+        }
+    }
+}