Save command-line options to a params file

.github/workflows/docker-build.yml

@@ -21,7 +21,7 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v3
 
-      - name: Build and push R container
+      - name: Build and push R container to docker hub
         uses: mr-smithers-excellent/[email protected]
         with:
           image: fishbotherer/r-tools
@@ -31,5 +31,4 @@ jobs:
           dockerfile: containers/r/Dockerfile
           directory: containers/r
           username: ${{ secrets.DOCKER_LOGIN }}
-          password: ${{ secrets.DOCKER_TOKEN }}
-
+          password: ${{ secrets.DOCKER_TOKEN }}

conf/base.config

@@ -1,31 +1,23 @@
-int cores = (int)get_p(params,'maxCpus')
-nextflow.util.MemoryUnit mem = get_p(params,'maxMemory') as nextflow.util.MemoryUnit
-nextflow.util.Duration d = get_p(params,'maxTime') as nextflow.util.Duration
-insect = get_p(params,"insect")
-blast = get_p(params,"blast")
-demux = get_p(params,"demultiplexedBy") == "index"
-split = get_p(params,"split")
-
-
 /*
  * general process options (mainly which labels go with which docker/singulariy images)
  * but also the base resource usage settings
 */
 process {
-  withLabel: 'fastqc'         { container = 'biocontainers/fastqc:v0.11.9_cv7' }
-  withLabel: 'adapterRemoval' { container = 'biocontainers/adapterremoval:v2.2.0-1-deb_cv1' }
-  withLabel: 'obitools'       { container = 'biocontainers/obitools:v1.2.12dfsg-2-deb_cv1' }
-  withLabel: 'r'              { container = 'fishbotherer/r-tools:latest' }
-  withLabel: 'shell'          { container = 'nextflow/bash:latest' }
-  withLabel: 'multiqc'        { container = 'multiqc/multiqc:latest'}
+  withName: 'fastqc'       { container = 'quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0 ' }
+  withName: 'filter_merge' { container = 'quay.io/biocontainers/adapterremoval:2.3.4--pl5321haf24da9_1' }
+  withName: 'multiqc'      { container = 'quay.io/biocontainers/multiqc:1.27.1--pyhdfd78af_0'}
+  withLabel: 'shell'       { container = 'quay.io/nextflow/bash:latest' }
+  withLabel: 'obitools'    { container = 'quay.io/biocontainers/obitools:1.2.13--py27heb79e2c_3' }
+  withLabel: 'blast'       { container = 'quay.io/biocontainers/blast:2.17.0--h66d330f_0' }
+  withLabel: 'r'           { container = 'fishbotherer/r-tools:latest' }
 
   withLabel: 'denoiser' {
     if (params.execDenoiser)
       container = ''
     else if (params.denoiser == "vsearch") {
-      container = 'biocontainers/vsearch:v2.10.4-1-deb_cv1'
+      container = 'quay.io/biocontainers/vsearch:2.30.0--hd6d6fdc_0'
     } else if (params.denoiser in ['usearch','usearch32']) {
-      container = 'sunqiangkun/usearch:v1' 
+      container = 'quay.io/biocontainers/usearch:12.0_beta--h9ee0642_1'
     }
   }
 
@@ -68,34 +60,10 @@ process {
     errorStrategy = 'retry'
     maxRetries  = 2
   } 
-
-//  // allocate cpus to AdapterRemoval
-// 	withLabel: 'demux_cpus' {
-//     if (get_p(params,'demultiplexedBy') == 'barcode' ) {
-//       cpus = cores > 1 ? cores-1 : cores
-//     } else {
-//       cpus = 4 * task.attempt
-//     }
-//   }
-
   // allow all cpus
-	withLabel: 'all_cpus' { cpus = { cores } }
-
-  // allocate blast cpus
-  withLabel: 'blast' {
-    // cpus = { params.insect ? cores / 2 : cores }
-    // memory = { params.insect ? mem / 2 : mem }
-    container = 'ncbi/blast:latest'
-  }
-
-  // alloacte insect cpus
-  withLabel: 'insect' {
-    // cpus = { params.blast ? cores / 2 : cores }
-    // memory = { params.blast ? mem / 2 : mem }
-    container = 'fishbotherer/r-tools:latest'
-  }
+	withLabel: 'all_cpus' { cpus = { (int)params.maxCpus } }
 
-  cache = 'lenient' 
+  cache = 'lenient'
 
   // set default cpus and memory
   cpus = { check_max( 1 * task.attempt, 'cpus' ) }

containers/r/Dockerfile

@@ -6,6 +6,6 @@ MAINTAINER "Mykle Hoban" [email protected]
 RUN /rocker_scripts/install_tidyverse.sh
 
 # install packages
-RUN Rscript -e 'install.packages(c("insect","optparse","phangorn","furrr","worrms","rentrez"))' 
+RUN Rscript -e 'install.packages(c("insect","optparse","phangorn"))' 
 RUN Rscript -e 'devtools::install_github(c("tobiasgf/lulu","GuillemSalazar/EcolUtils"))'
 RUN Rscript -e 'BiocManager::install(c("phyloseq","dada2","DECIPHER","decontam"))'

nextflow.config

@@ -6,7 +6,7 @@ manifest {
     mainScript = 'rainbow_bridge.nf'
     defaultBranch = 'main'
     version = '1.33.8'
-    nextflowVersion = '!>=22.03'
+    nextflowVersion = '!>=25.04.7'
 }
 
 
@@ -73,6 +73,7 @@ try {
 }
 
 /* general script options */
+params.saveConfig = false
 params.preDir = 'preprocess'
 params.outDir = 'output'
 params.publishMode = "symlink" 
@@ -164,53 +165,33 @@ params.maxTime = 240.h
 // ourselves if we want consisistency. what we'll do is give the
 // kebab-case version priority
 
-// convert string to camelCase
-def to_camel(s) {
-  return s.replaceAll(/(?<small>[a-z])-(?<big>[a-z])/) {
-    m,a,b -> a+b.toUpperCase()
-  }
-}
-
-// convert string to kebab-case
-def to_kebab(s) {
-  return s.replaceAll(/([a-z])([A-Z])/,'$1-$2').toLowerCase()
-}
-
-def get_p(p,k) {
-  if (p.containsKey(to_kebab(k))) {
-    return p.get(to_kebab(k))
-  } else {
-    return p.get(k)
-  }
-}
-
 // Function to ensure that resource requirements don't go beyond a maximum limit
 def check_max(obj, type) {
   if (type == 'memory') {
     try {
-      if (obj.compareTo(get_p(params,'maxMemory') as nextflow.util.MemoryUnit) == 1)
-        return get_p(params,'maxMemory') as nextflow.util.MemoryUnit
+      if (obj.compareTo(params.maxMemory as nextflow.util.MemoryUnit) == 1)
+        return params.maxMemory as nextflow.util.MemoryUnit
       else
         return obj
     } catch (all) {
-      println "   ### ERROR ###   Max memory '${get_p(params,'maxMemory')}' is not valid! Using default value: $obj"
+      println "   ### ERROR ###   Max memory '${params.maxMemory}' is not valid! Using default value: $obj"
       return obj
     }
   } else if (type == 'time') {
     try {
-      if (obj.compareTo(get_p(params,'maxTime') as nextflow.util.Duration) == 1)
-        return get_p(params,'maxTime') as nextflow.util.Duration
+      if (obj.compareTo(params.maxTime as nextflow.util.Duration) == 1)
+        return params.maxTime as nextflow.util.Duration
       else
         return obj
     } catch (all) {
-      println "   ### ERROR ###   Max time '${get_p(params,'maxTime')}' is not valid! Using default value: $obj"
+      println "   ### ERROR ###   Max time '${params.maxTime}' is not valid! Using default value: $obj"
       return obj
     }
   } else if (type == 'cpus') {
     try {
-      return Math.min( obj, get_p(params,'maxCpus') as int )
+      return Math.min( obj, params.maxCpus as int )
     } catch (all) {
-      println "   ### ERROR ###   Max cpus '${get_p(params,'maxCpus')}' is not valid! Using default value: $obj"
+      println "   ### ERROR ###   Max cpus '${params.maxCpus}' is not valid! Using default value: $obj"
       return obj
     }
   }
@@ -229,25 +210,22 @@ profiles {
     // make default executor local
     // and limit max cpus to param value
     executor.name = 'local'
-    executor.cpus = (int)get_p(params,'maxCpus')
-    executor.memory = get_p(params,'maxMemory')
+    executor.cpus = (int)params.maxCpus
+    executor.memory = params.maxMemory
 
     singularity {
       /* enable singularity and have it do automounts */
       enabled = true
       autoMounts = true
 
-      String bd = get_p(params,'bindDir')
-      String sc = get_p(params,'singularityCache')
-
       // construct options for singularity bind directories
-      if (bd && bd != '') {
-        runOptions = "-B " + bd.split().join(" -B ")
+      if (params.bindDir && params.bindDir != '') {
+        runOptions = "-B " + params.bindDir.split().join(" -B ")
       }
 
       // set singularity cache directory if specified
-      if (sc && sc != "") {
-        cacheDir = sc
+      if (params.singularityCache && params.singularityCache != "") {
+        cacheDir = params.singularityCache
       }
     }
   }