diff --git a/.github/workflows/docker-build.yml b/.github/workflows/docker-build.yml
index 0540c37..595eff1 100644
--- a/.github/workflows/docker-build.yml
+++ b/.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/docker-build-push@v6.4
         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 }}
\ No newline at end of file
diff --git a/conf/base.config b/conf/base.config
index 80854f0..ba04208 100644
--- a/conf/base.config
+++ b/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' ) }
diff --git a/containers/r/Dockerfile b/containers/r/Dockerfile
index 44d13ed..31f8cf7 100644
--- a/containers/r/Dockerfile
+++ b/containers/r/Dockerfile
@@ -6,6 +6,6 @@ MAINTAINER "Mykle Hoban" mykle.hoban@hawaii.edu
 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"))'
\ No newline at end of file
diff --git a/nextflow.config b/nextflow.config
index 2dfe8f3..18f8228 100644
--- a/nextflow.config
+++ b/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
       }
     }
   }
diff --git a/rainbow_bridge.nf b/rainbow_bridge.nf
index a2eb260..e6b739d 100755
--- a/rainbow_bridge.nf
+++ b/rainbow_bridge.nf
@@ -196,7 +196,6 @@ def check_params() {
 
 // trim and (where relevant) merge paired-end reads
 process filter_merge {
-  label 'adapterRemoval'
   label 'process_medium'
 
   publishDir "${params.preDir}/trim_merge", mode: params.publishMode
@@ -364,7 +363,6 @@ process relabel {
     tuple val(key), path(fastq, name: 'input-????.fastq')
   output:
     path('*_relabeled.fasta'), optional: true, emit: result
-    path 'settings.txt'
 
 
   script:
@@ -372,10 +370,9 @@ process relabel {
   if (params.denoiser == "vsearch") {
     def combined = "<(cat input-*.fastq)"
     """
-    echo "denoiser: vsearch" > settings.txt
     # this may or may not be necessary anymore, but it seems like a good sanity check
     # since this will fail on empty files
-    vsearch --threads ${task.cpus} --fastq_qmax ${params.maxQuality} --fastx_filter ${combined} --relabel "${key}." --fastaout - | \
+    vsearch --threads ${task.cpus} --fastq_qmax ${params.maxQuality} --fastx_filter ${combined} --relabel "${key}." --label_suffix ";sample=${key}" --fastaout - | \
       awk '/^>/ {print;} !/^>/ {print(toupper(\$0))}' > "${key}_relabeled.fasta"
     """
   } else {
@@ -383,7 +380,6 @@ process relabel {
     def combined = "combined.fastq"
     def denoiser = params.execDenoiser ? params.denoiser : 'usearch'
     """
-    echo "denoiser: ${params.denoiser}" > settings.txt
     cat input-*.fastq > ${combined}
     # we have to convert everything to uppercase because obisplit --uppercase is broken
     ${denoiser} -fastx_relabel ${combined} -prefix "${key}." -fastaout /dev/stdout | \
@@ -426,16 +422,11 @@ process dereplicate {
 
   output:
     tuple val(id), path("${id}_unique.fasta"), path("${id}_zotus.fasta"), path("zotu_table.tsv"), emit: result
-    path 'settings.txt'
     path 'zotu_map.tsv'
 
   script:
   if (params.denoiser == "vsearch") {
     """
-    echo "denoiser: vsearch" > settings.txt
-    echo "minimum sequence abundance: ${params.minAbundance}" >> settings.txt
-    echo "alpha: ${params.alpha}" >> settings.txt
-    echo "fractional identity: ${params.zotuIdentity}" >> settings.txt
     # steps:
     # 1. get unique sequence variants
     # 2. run denoising algorithm
@@ -443,19 +434,19 @@ process dereplicate {
     # 4. match original sequences to zotus by 97% identity
     if [ -s "${relabeled_merged}" ]; then
       vsearch \
-        --threads ${task.cpus} --fastq_qmax ${params.maxQuality} \
+        --threads ${task.cpus} \
         --derep_fulllength ${relabeled_merged} --sizeout \
         --output "${id}_unique.fasta"
       vsearch \
-        --threads ${task.cpus} --fastq_qmax ${params.maxQuality} \
+        --threads ${task.cpus} \
         --cluster_unoise "${id}_unique.fasta" --centroids "${id}_centroids.fasta" \
         --minsize ${params.minAbundance} --unoise_alpha ${params.alpha}
       vsearch \
-        --threads ${task.cpus} --fastq_qmax ${params.maxQuality} \
+        --threads ${task.cpus} \
         --uchime3_denovo "${id}_centroids.fasta" --nonchimeras "${id}_zotus.fasta" \
         --relabel Zotu
       vsearch \
-        --threads ${task.cpus} --fastq_qmax ${params.maxQuality} \
+        --threads ${task.cpus} \
         --usearch_global ${relabeled_merged} --db "${id}_zotus.fasta" \
         --id ${params.zotuIdentity} --otutabout zotu_table.tsv \
         --userout zotu_map.tsv --userfields "query+target" \
@@ -468,10 +459,6 @@ process dereplicate {
   } else {
     def denoiser = params.execDenoiser ? params.denoiser : 'usearch'
     """
-    echo "denoiser: ${denoiser}" > settings.txt
-    echo "minimum sequence abundance: ${params.minAbundance}" >> settings.txt
-    echo "alpha: ${params.alpha}" >> settings.txt
-    echo "fractional identity: ${params.zotuIdentity}" >> settings.txt
     # steps:
     # 1. get unique sequences
     # 2. run denoising & chimera removal
@@ -509,7 +496,7 @@ process blast {
 
   output:
     path("blast_result.tsv"), emit: result
-    path 'blast_settings.txt'
+    path 'settings.yml'
 
   script:
 
@@ -530,8 +517,8 @@ process blast {
 
   // get extra blast options passed on the command line as --blastn-*
   def extra_options = params
-    .findAll { it.key =~ /^blastn-/ }
-    .collectEntries { k, v -> [k.tokenize('-')[1],v] }
+    .findAll { it.key =~ /^blastn[A-Z].+/ }
+    .collectEntries { k, v -> [k.replaceAll(/^blastn/,'').toLowerCase(),v] }
 
   // merge blast options with any extra options
   blast_options = blast_options << extra_options
@@ -541,10 +528,10 @@ process blast {
     .join(" ")
   """
   # record blast settings
-  echo "Percent identity: ${pid}" > blast_settings.txt
-  echo "e-value: ${evalue}" >> blast_settings.txt
-  echo "Query qoverage: ${qcov}" >> blast_settings.txt
-  echo "Max. target sequences: ${params.maxQueryResults}" >> blast_settings.txt
+  echo "percent_identity: ${pid}" > settings.yml
+  echo "e_value: ${evalue}" >> settings.yml
+  echo "query_coverage: ${qcov}" >> settings.yml
+  echo "max_sequences: ${params.maxQueryResults}" >> settings.yml
 
   # set BLASTDB to local working directory
   export BLASTDB=.
@@ -595,14 +582,9 @@ process lulu {
 
   output:
     tuple path("lulu_zotu_table.tsv"), path("lulu_zotu_map.tsv"), path("lulu_result_object.rds"), emit: result
-    path 'settings.txt'
 
   script:
   """
-  echo "minimum ratio: ${params.luluMinRatio}" > settings.txt
-  echo "minimum ratio type: ${params.luluMinRatioType}" >> settings.txt
-  echo "minimum match: ${params.luluMinMatch}" >> settings.txt
-  echo "minimum RC: ${params.luluMinRc}" >> settings.txt
   lulu.R \
     -m ${params.luluMinRatio} \
     -t ${params.luluMinRatioType} \
@@ -629,7 +611,7 @@ process collapse_taxonomy {
   output:
     path("lca_taxonomy.tsv"), emit: taxonomy
     path("lca_intermediate.tsv")
-    path 'lca_settings.txt'
+    path 'settings.yml'
 
 
   script:
@@ -638,12 +620,12 @@ process collapse_taxonomy {
   params.lcaCaseInsensitive && pf << "--case-insensitive"
   """
   # save settings
-  echo "Minimum query coverage %: ${params.lcaQcov}" > lca_settings.txt
-  echo "Minimum percent identity: ${params.lcaPid}" >> lca_settings.txt
-  echo "Minium percent identity difference: ${params.lcaDiff}" >> lca_settings.txt
-  echo "Filter to maximum query coverage: ${params.lcaFilterMaxQcov ? 'yes' : 'no'}" >> lca_settings.txt
-  echo "Filter taxa by regex: ${params.lcaTaxonFilter}" >> lca_settings.txt
-  echo "Taxon filter case sensitive: ${!params.lcaCaseInsensitive ? 'yes' : 'no'}" >> lca_settings.txt
+  echo "min_query_coverage: ${params.lcaQcov}" > settings.yml
+  echo "min_percent_identity: ${params.lcaPid}" >> settings.yml
+  echo "pid_diff: ${params.lcaDiff}" >> settings.yml
+  echo "filter_max_query_coverage: ${params.lcaFilterMaxQcov ? 'yes' : 'no'}" >> settings.yml
+  echo "taxon_filter: ${params.lcaTaxonFilter}" >> settings.yml
+  echo "taxon_filter_case_sensitive: ${!params.lcaCaseInsensitive ? 'yes' : 'no'}" >> settings.yml
 
   collapse_taxonomy.R \
     --qcov ${params.lcaQcov} \
@@ -663,7 +645,7 @@ process collapse_taxonomy {
 
 // run insect classifier model
 process insect {
-  label 'insect'
+  label 'r'
   label 'all_cpus'
 
   publishDir {
@@ -680,7 +662,7 @@ process insect {
   output:
     path('insect_taxonomy.tsv'), emit: taxonomy
     path('insect_model.rds')
-    path('insect_settings.txt')
+    path('settings.yml')
 
   script:
   def offs = String.format("%d",(Integer)num(params.insectOffset))
@@ -690,10 +672,10 @@ process insect {
 
   """
   # record insect settings
-  echo "Offset: ${offs}" > insect_settings.txt
-  echo "Threshold: ${thresh}" >> insect_settings.txt
-  echo "Minimum count: ${minc}" >> insect_settings.txt
-  echo "Ping: ${ping}" >> insect_settings.txt
+  echo "offset: ${offs}" > settings.yml
+  echo "threshold: ${thresh}" >> settings.yml
+  echo "minimum_count: ${minc}" >> settings.yml
+  echo "ping: ${ping}" >> settings.yml
 
   if [ "${classifier}" != "insect_model.rds" ]; then
     mv ${classifier} insect_model.rds
@@ -1074,9 +1056,8 @@ workflow {
           // (notably vsearch) will cut on hyphens as a delimiter and potentially cause havok as a result.
 
           Channel.fromFilePairs(pattern, checkIfExists: true) |
-            // make sure we have a key value and replace dashes with underscores 
-            // (although this may be a problem sometimes! see #138)
-            map { key,reads -> [ (key ?: params.project).replaceAll(/-/,'_'), reads ] } |
+            // make sure we have a key value (project ID)
+            map { key,reads -> [ key ?: params.project, reads ] } |
             ifEmpty {
               // bail if we didn't find anything
               exit(1,"No paired reads matched by pattern '${pattern}'. Check command-line options.")
@@ -1596,4 +1577,27 @@ workflow {
       }
     }
   }
+
+  // save the config file in yaml format
+  // TODO: saving the config file to a new file seems to break caching for the blast process?
+  // but downstream things that rely on blast are still cached. it makes no sense
+  if (params.saveConfig) {
+    // default to 'options.yml' in the launch directory
+    def config_file = launchDir / "options.yml"
+    // if it's a string, use that as the location
+    if (params.saveConfig instanceof String) {
+      config_file = params.saveConfig
+    }
+
+    // make sure the yaml is dumped in block format
+    def opts = new org.yaml.snakeyaml.DumperOptions()
+    opts.setDefaultFlowStyle(org.yaml.snakeyaml.DumperOptions.FlowStyle.BLOCK)
+    opts.setPrettyFlow(true)
+    def y = new org.yaml.snakeyaml.Yaml(opts)
+
+    // dump the yaml file
+    new File(config_file.toString()).withWriter { w -> 
+      y.dump(new LinkedHashMap(params).collectEntries{ [it.key.toString(), it.value instanceof nextflow.util.Duration ? it.value.toString() : it.value ]}, w) 
+    }
+  }
 }