From b064eafe016bfa0869385c5d27e81f0614825565 Mon Sep 17 00:00:00 2001
From: Erin Young <erin.olde@gmail.com>
Date: Fri, 1 Mar 2024 16:34:41 -0700
Subject: [PATCH] removed errorStragy comments

---
 donut_falls.nf | 694 +++++++++++++++++++++++++++++++------------------
 1 file changed, 437 insertions(+), 257 deletions(-)

diff --git a/donut_falls.nf b/donut_falls.nf
index 7c1a3e4..b395173 100755
--- a/donut_falls.nf
+++ b/donut_falls.nf
@@ -43,8 +43,7 @@ params.sequencing_summary = ''
 params.sample_sheet       = ''
 params.assembler          = 'flye'
 params.outdir             = 'donut_falls'
-params.test               = false
-params.ontime             = false
+params.test               = ''
 
 // ##### ##### ##### ##### ##### ##### ##### ##### ##### #####
 
@@ -79,10 +78,15 @@ paramCheck(params.keySet())
 
 // ##### ##### ##### ##### ##### ##### ##### ##### ##### #####
 
-// Channel
-//   .fromPath(params.sequencing_summary, type:'file')
-//   .view { "Summary File : $it" }
-//   .set { ch_sequencing_summary }
+if (params.sequencing_summary){
+  Channel
+    .fromPath("${params.sequencing_summary}", type:'file')
+    .view { "Summary File : $it" }
+    .set { ch_sequencing_summary }
+} else {
+  ch_sequencing_summary = Channel.empty()
+}
+
 
 // using a sample sheet with the column header of 'sample,fastq,fastq_1,fastq_2'
 // sample  = meta.id
@@ -90,19 +94,25 @@ paramCheck(params.keySet())
 // fastq_1 = illumina fastq file
 // fastq_2 = illumina fastq file
 
-Channel
-  .fromPath("${params.sample_sheet}", type: "file")
-  .splitCsv( header: true, sep: ',' )
-  .map { it ->
-    meta = [id:it.sample] 
-    tuple( meta,
-      "${it.fastq}",
-      "${it.fastq_1}",
-      "${it.fastq_2}" )
-  }
-  .set{ ch_input_files }
 
-// channel for illumina files
+if (params.sample_sheet) {
+  Channel
+    .fromPath("${params.sample_sheet}", type: "file")
+    .splitCsv( header: true, sep: ',' )
+    .map { it ->
+      meta = [id:it.sample] 
+      tuple( meta,
+        "${it.fastq}",
+        "${it.fastq_1}",
+        "${it.fastq_2}" )
+    }
+    .set{ ch_input_files }
+} else {
+  ch_input_files = Channel.empty()
+}
+
+
+// channel for illumina files (paired-end only)
 ch_input_files
   .filter { it[2] != it[3] }
   .map { it -> tuple (it[0], [file(it[2], checkIfExists: true), file(it[3], checkIfExists: true)])}
@@ -115,6 +125,275 @@ ch_input_files
 
 // ##### ##### ##### ##### ##### ##### ##### ##### ##### #####
 
+// TODO
+
+// ##### ##### ##### ##### ##### ##### ##### ##### ##### #####
+
+// process ontime {
+//   tag           "${meta.id}"
+//   label         "process_medium"
+//   publishDir    "${params.outdir}/${meta.id}", mode: 'copy'
+//   container     'staphb/ontime:0.2.3'
+//   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+//   time          '45m'
+//
+//   input:
+//   tuple val(meta), file(reads)
+//
+//   output:
+//   tuple val(meta), file("bbduk/*_rmphix_R{1,2}.fastq.gz"),  emit: fastq
+//   path "bbduk/*",                                           emit: files
+//   path "bbduk/*.phix.stats.txt",                            emit: stats
+//   path "logs/${task.process}/*.log",  emit: log
+//   path "versions.yml", emit: versions
+//
+//   when:
+//   task.ext.when == null || task.ext.when
+//
+//   shell:
+//   def args   = task.ext.args   ?: ''
+//   def prefix = task.ext.prefix ?: "${meta.id}"
+//   """
+//   ontime --version
+//
+//   ontime --help
+//
+//   cat <<-END_VERSIONS > versions.yml
+//   "${task.process}":
+//     ontime: "\$(ontime --version | awk '{print \$NF}')"
+//   END_VERSIONS
+//
+//   exit 1
+//   """
+// }
+
+
+// someday...
+// process dragonflye {
+//   tag           "${meta.id}"
+//   label         "process_high"
+//   publishDir    "${params.outdir}/${meta.id}", mode: 'copy'
+//   container     'staphb/dragonflye:1.1.2'
+//   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+//   time          '10h'
+//
+//   input:
+//   tuple val(meta), file(fastq)
+//
+//   output:
+//   tuple val(meta), file("dragonflye/*_dragonflye.fasta"), optional: true, emit: fasta
+//   tuple val(meta), file("dragonflye/*_dragonflye.gfa"),   optional: true, emit: gfa
+//   path "dragonflye/*_assembly_info.tsv", emit: summary
+//   path "dragonflye/*", emit: everything
+//   path "versions.yml", emit: versions
+//
+//   when:
+//   task.ext.when == null || task.ext.when
+//
+//   shell:
+//   def args   = task.ext.args   ?: ''
+//   def prefix = task.ext.prefix ?: "${meta.id}"
+//   """
+//   dragonflye ${args} \
+//     --reads ${fastq} \
+//     --cpus ${task.cpus} \
+//     --outdir dragonflye \
+//     --prefix ${prefix}
+//
+//   # renaming final files
+//   if [ -f "dragonflye/flye-unpolished.gfa" ] ; then cp dragonflye/flye-unpolished.gfa dragonflye/${prefix}_dragonflye.gfa   ; fi
+//   if [ -f "dragonflye/flye.fasta" ]          ; then cp dragonflye/flye.fasta          dragonflye/${prefix}_dragonflye.fasta ; fi
+//
+//   # getting a summary file
+//   head -n 1 dragonflye/flye-info.txt | awk '{print "sample\\t" \$0}' > dragonflye/${prefix}_assembly_info.tsv
+//   tail -n+2 dragonflye/flye-info.txt | awk -v sample=${prefix} '{print sample "\\t" \$0}' >> dragonflye/${prefix}_assembly_info.tsv
+//   
+//   cat <<-END_VERSIONS > versions.yml
+//   "${task.process}":
+//     dragonflye: \$(dragonflye --version | awk '{print \$NF}' )
+//   END_VERSIONS
+//   """
+// }
+
+// someday...
+// process hybracter {
+//   tag           "${meta.id}"
+//   label         "process_high"
+//   publishDir    "${params.outdir}/${meta.id}", mode: 'copy'
+//   container     'quay.io/biocontainers/hybracter:0.6.0--pyhdfd78af_0'
+//   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+//   time          '10h'
+//
+//   input:
+//   tuple val(meta), file(reads), file(illumina)
+//
+//   output:
+//   tuple val(meta), file("bbduk/*_rmphix_R{1,2}.fastq.gz"), emit: fasta
+//   tuple val(meta), file("bbduk/*_rmphix_R{1,2}.fastq.gz"), emit: gfa
+//   path "versions.yml", emit: versions
+//
+//   when:
+//   task.ext.when == null || task.ext.when
+//
+//   shell:
+//   def args   = task.ext.args   ?: ''
+//   def prefix = task.ext.prefix ?: "${meta.id}"
+//   """
+//   hybracter -h
+//
+//   hybracter version
+// 
+//   exit 1
+//
+//   cat <<-END_VERSIONS > versions.yml
+//   "${task.process}":
+//     hybracter: "\$(hybracter --version | awk '{print \$NF}')"
+//   END_VERSIONS
+//   exit 1
+//   """
+// }
+
+// process test_nfcore {
+//   tag           "Downloading subset15000"
+//   label         "process_single"
+//   publishDir    "${params.outdir}/test_files/nfcore", mode: 'copy'
+//   container     'staphb/multiqc:1.19'
+//   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+//   time          '1h'
+
+//   output:
+//   tuple val("nfcore-subset15000"), file("nfcore_subset15000.fa.gz"), emit: fastq
+
+//   when:
+//   task.ext.when == null || task.ext.when
+
+//   shell:
+//   """
+//   wget -q https://github.com/nf-core/test-datasets/blob/23f5b889e4736798c8692e9b92810d9a3e37ee97/nanopore/subset15000.fq.gz?raw=true -O nfcore_subset15000.fa.gz
+//   """
+// }
+
+// process test_great_dataset {
+//   tag           "Downloading the great dataset"
+//   label         "process_single"
+//   publishDir    "${params.outdir}/test_files/great", mode: 'copy'
+//   container     'staphb/multiqc:1.19'
+//   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+//   time          '1h'
+
+//   output:
+//   tuple val("great_dataset"), file("reads.fastq.gz"), emit: fastq
+
+//   when:
+//   task.ext.when == null || task.ext.when
+
+//   shell:
+//   """
+//   wget -q https://bridges.monash.edu/ndownloader/files/23754659 -O dataset.tar.gz
+//   tar -xvf dataset.tar.gz
+
+//   exit 1
+//   """
+// }
+
+
+// process test_good_dataset {
+//   tag           "Downloading the good dataset"
+//   label         "process_single"
+//   publishDir    "${params.outdir}/test_files/good", mode: 'copy'
+//   container     'staphb/multiqc:1.19'
+//   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+//   time          '1h'
+
+//   output:
+//   tuple val("good_dataset"), file("reads.fastq.gz"), emit: fastq
+
+//   when:
+//   task.ext.when == null || task.ext.when
+
+//   shell:
+//   """
+//   wget -q https://bridges.monash.edu/ndownloader/files/23754647 -O dataset.tar.gz
+//   tar -xvf dataset.tar.gz
+//   """
+// }
+
+// process test_mediocre_dataset {
+//   tag           "Downloading the mediocre dataset"
+//   label         "process_single"
+//   publishDir    "${params.outdir}/test_files/mediocre", mode: 'copy'
+//   container     'staphb/multiqc:1.19'
+//   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+//   time          '1h'
+
+//   output:
+//   tuple val("mediocre_dataset"), file("reads.fastq.gz"), emit: fastq
+
+//   when:
+//   task.ext.when == null || task.ext.when
+
+//   shell:
+//   """
+//   wget -q https://bridges.monash.edu/ndownloader/files/23754629 -O dataset.tar.gz
+//   tar -xvf dataset.tar.gz
+
+//   exit 1
+//   """
+// }
+
+// process test_bad_dataset {
+//   tag           "Downloading the bad dataset"
+//   label         "process_single"
+//   publishDir    "${params.outdir}/test_files/bad", mode: 'copy'
+//   container     'staphb/multiqc:1.19'
+//   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+//   time          '1h'
+
+//   output:
+//   tuple val("bad_dataset"), file("reads.fastq.gz"), emit: fastq
+
+//   when:
+//   task.ext.when == null || task.ext.when
+
+//   shell:
+//   """
+//   wget -q https://bridges.monash.edu/ndownloader/files/23754623 -O dataset.tar.gz
+//   tar -xvf dataset.tar.gz
+
+//   exit 1
+//   """
+// }
+
+    // in DONUT FALLS WORKFLOW
+    // hybracter and plassembler are on the to-do list
+    // if (params.assembler =~ /hybracter/ ) {
+    //   hybracter(ch_nanopore_input.join(ch_illumina_input, by: 0 , remainder: true))
+    //      
+    //   ch_gfa       = ch_gfa.mix(hybracter.out.gfa)
+    //   // no ch_summary
+    //   ch_consensus = ch_consensus.mix(hybracter.out.fasta)
+    //   ch_versions  = ch_versions.mix(hybracter.out.versions.first())
+    // } 
+
+    // if (params.assembler =~ /dragonflye/ ) {
+    //   dragonflye(ch_nanopore_input)
+    //
+    //   dragonflye.out.summary
+    //     .collectFile(
+    //       storeDir: "${params.outdir}/summary/",
+    //       keepHeader: true,
+    //       sort: { file -> file.text },
+    //       name: "dragonflye_summary.tsv")
+    //     .set { dragonflye_summary }
+    //
+    //   ch_gfa       = dragonflye.out.gfa
+    //   ch_summary   = ch_summary.mix(dragonflye_summary)
+    //   // no ch_consensus
+    //   ch_versions  = ch_versions.mix(dragonflye.out.versions.first())
+    // }
+
+// ##### ##### ##### ##### ##### ##### ##### ##### ##### #####
+
 // Processes
 
 // ##### ##### ##### ##### ##### ##### ##### ##### ##### #####
@@ -124,7 +403,7 @@ process bandage {
   label         "process_low"
   publishDir    "${params.outdir}/${meta.id}", mode: 'copy'
   container     'quay.io/biocontainers/bandage:0.8.1--hc9558a2_2'
-  ////errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '10m'
 
   input:
@@ -159,7 +438,7 @@ process busco {
   label         "process_medium"
   publishDir    "${params.outdir}/${meta.id}", mode: 'copy'
   container     'staphb/busco:5.6.1-prok-bacteria_odb10_2024-01-08'
-  ////errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '45m'
 
   input:
@@ -195,7 +474,7 @@ process bwa {
   label         'process_high'
   // no publishDir because the sam files are too big
   container     'staphb/bwa:0.7.17'
-  ////errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '2h'
 
   input:
@@ -230,7 +509,7 @@ process circulocov {
   label         "process_medium"
   publishDir    "${params.outdir}/${meta.id}", mode: 'copy'
   container     'quay.io/uphl/circulocov:0.1.20240104-2024-02-21'
-  ////errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '1h'
 
   input:
@@ -275,7 +554,7 @@ process copy {
   label         "process_single"
   publishDir    "${params.outdir}/${meta.id}", mode: 'copy'
   container     'staphb/multiqc:1.19'
-  ////errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '10m'
 
   input:
@@ -378,7 +657,7 @@ process dnaapler {
   label         "process_medium"
   publishDir    "${params.outdir}/${meta.id}", mode: 'copy'
   container     'staphb/dnaapler:0.7.0'
-  ////errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '1h'
 
   input:
@@ -410,107 +689,12 @@ process dnaapler {
   """
 }
 
-process download {
-  tag           "Downloading subset15000"
-  label         "process_single"
-  publishDir    "${params.outdir}/${meta.id}", mode: 'copy'
-  container     'staphb/multiqc:1.19'
-  ////errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
-  time          '1h'
-
-  output:
-  tuple val("subset15000"), file("nfcore_subset15000.fa.gz"), emit: fastq
-
-  when:
-  task.ext.when == null || task.ext.when
-
-  shell:
-  def args   = task.ext.args   ?: ''
-  def prefix = task.ext.prefix ?: "${meta.id}"
-  """
-  wget -q https://github.com/nf-core/test-datasets/blob/23f5b889e4736798c8692e9b92810d9a3e37ee97/nanopore/subset15000.fq.gz?raw=true -O nfcore_subset15000.fa.gz
-
-  exit 1
-  """
-}
-
-process great_dataset {
-  tag           "Downloading the great dataset"
-  label         "process_single"
-  publishDir    "${params.outdir}/${meta.id}", mode: 'copy'
-  container     'staphb/multiqc:1.19'
-  ////errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
-  time          '1h'
-
-  output:
-  tuple val("great_dataset"), file("reads.fastq.gz"), emit: fastq
-
-  when:
-  task.ext.when == null || task.ext.when
-
-  shell:
-  def args   = task.ext.args   ?: ''
-  def prefix = task.ext.prefix ?: "${meta.id}"
-  """
-  wget -q https://bridges.monash.edu/ndownloader/files/23754659 -O great_dataset.tar.gz
-  tar -xvf great_dataset.tar.gz
-
-  exit 1
-  """
-}
-
-process dragonflye {
-  tag           "${meta.id}"
-  label         "process_high"
-  publishDir    "${params.outdir}/${meta.id}", mode: 'copy'
-  container     'staphb/dragonflye:1.1.2'
-  ////errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
-  time          '10h'
-
-  input:
-  tuple val(meta), file(fastq)
-
-  output:
-  tuple val(meta), file("dragonflye/*_dragonflye.fasta"), optional: true, emit: fasta
-  tuple val(meta), file("dragonflye/*_dragonflye.gfa"),   optional: true, emit: gfa
-  path "dragonflye/*_assembly_info.tsv", emit: summary
-  path "dragonflye/*", emit: everything
-  path "versions.yml", emit: versions
-
-  when:
-  task.ext.when == null || task.ext.when
-
-  shell:
-  def args   = task.ext.args   ?: ''
-  def prefix = task.ext.prefix ?: "${meta.id}"
-  """
-  dragonflye ${args} \
-    --reads ${fastq} \
-    --cpus ${task.cpus} \
-    --outdir dragonflye \
-    --prefix ${prefix}
-
-  # renaming final files
-  if [ -f "dragonflye/flye-unpolished.gfa" ] ; then cp dragonflye/flye-unpolished.gfa dragonflye/${prefix}_dragonflye.gfa   ; fi
-  if [ -f "dragonflye/flye.fasta" ]          ; then cp dragonflye/flye.fasta          dragonflye/${prefix}_dragonflye.fasta ; fi
-
-  # getting a summary file
-  head -n 1 dragonflye/flye-info.txt | awk '{print "sample\\t" \$0}' > dragonflye/${prefix}_assembly_info.tsv
-  tail -n+2 dragonflye/flye-info.txt | awk -v sample=${prefix} '{print sample "\\t" \$0}' >> dragonflye/${prefix}_assembly_info.tsv
-    
-  cat <<-END_VERSIONS > versions.yml
-  "${task.process}":
-    dragonflye: \$(dragonflye --version | awk '{print \$NF}' )
-  END_VERSIONS
-  """
-}
-
 process fastp {
   tag           "${meta.id}"
   label         "process_low"
   publishDir    "${params.outdir}/${meta.id}", mode: 'copy'
   container     'staphb/fastp:0.23.4'
-  ////errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '10m'
 
   input:
@@ -573,7 +757,7 @@ process flye {
   label         "process_high"
   publishDir    "${params.outdir}/${meta.id}", mode: 'copy'
   container     'staphb/flye:2.9.3'
-  ////errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '10h'
 
   input:
@@ -620,7 +804,7 @@ process gfastats {
   label         "process_medium"
   publishDir    "${params.outdir}/${meta.id}", mode: 'copy', pattern: 'gfastats/*'
   container     'staphb/gfastats:1.3.6'
-  ////errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '10m'
 
   input:
@@ -664,7 +848,7 @@ process gfa_to_fasta {
   label         "process_low"
   // no publishDir
   container     'staphb/multiqc:1.19'
-  ////errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '10m'
 
   input:
@@ -716,44 +900,6 @@ process gfa_to_fasta {
   """
 }
 
-// someday...
-// process hybracter {
-//   tag           "${meta.id}"
-//   label         "process_high"
-//   publishDir    "${params.outdir}/${meta.id}", mode: 'copy'
-//   container     'quay.io/biocontainers/hybracter:0.6.0--pyhdfd78af_0'
-//   //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
-//   time          '10h'
-
-//   input:
-//   tuple val(meta), file(reads), file(illumina)
-
-//   output:
-//   tuple val(meta), file("bbduk/*_rmphix_R{1,2}.fastq.gz"), emit: fasta
-//   tuple val(meta), file("bbduk/*_rmphix_R{1,2}.fastq.gz"), emit: gfa
-//   path "versions.yml", emit: versions
-
-//   when:
-//   task.ext.when == null || task.ext.when
-
-//   shell:
-//   def args   = task.ext.args   ?: ''
-//   def prefix = task.ext.prefix ?: "${meta.id}"
-//   """
-//   hybracter -h
-
-//   hybracter version
-  
-//   exit 1
-
-//   cat <<-END_VERSIONS > versions.yml
-//   "${task.process}":
-//     hybracter: "\$(hybracter --version | awk '{print \$NF}')"
-//   END_VERSIONS
-//   exit 1
-//   """
-// }
-
 // From https://github.com/nanoporetech/medaka
 // > It is not recommended to specify a value of --threads greater than 2 for medaka consensus since the compute scaling efficiency is poor beyond this.
 // > Note also that medaka consensus may been seen to use resources equivalent to <threads> + 4 as an additional 4 threads are used for reading and preparing input data.
@@ -762,7 +908,7 @@ process medaka {
   label         "process_medium"
   publishDir    "${params.outdir}/${meta.id}", mode: 'copy'
   container     'ontresearch/medaka:v1.11.3'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '30m'
 
   input:
@@ -805,7 +951,7 @@ process multiqc {
   label         "process_low"
   publishDir    "${params.outdir}", mode: 'copy'
   container     'staphb/multiqc:1.19'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '10m'
 
   input:
@@ -988,10 +1134,10 @@ process multiqc {
 
 process nanoplot_summary {
   tag           "${summary}"
-  label         "process_medium"
-  publishDir    "${params.outdir}/${meta.id}", mode: 'copy'
+  label         "process_low"
+  publishDir    "${params.outdir}/summary", mode: 'copy'
   container     'staphb/nanoplot:1.42.0'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '10m'
 
   input:
@@ -1007,12 +1153,12 @@ process nanoplot_summary {
   shell:
   def args   = task.ext.args   ?: ''
   """
-  mkdir -p nanoplot/summary
+  mkdir -p nanoplot
   
   NanoPlot ${args} \
     --summary ${summary} \
     --threads ${task.cpus} \
-    --outdir nanoplot/summary \
+    --outdir nanoplot \
     --tsv_stats
 
   cat <<-END_VERSIONS > versions.yml
@@ -1029,7 +1175,7 @@ process nanoplot {
   label         "process_low"
   publishDir    "${params.outdir}/${meta.id}", mode: 'copy'
   container     'staphb/nanoplot:1.42.0'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '10m'
 
   input:
@@ -1068,51 +1214,12 @@ process nanoplot {
   """
 }
 
-// someday...
-// process ontime {
-//   tag           "${meta.id}"
-//   label         "process_medium"
-//   publishDir    "${params.outdir}/${meta.id}", mode: 'copy'
-//   container     'staphb/ontime:0.2.3'
-//   //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
-//   time          '45m'
-  
-//   input:
-//   tuple val(meta), file(reads)
-
-//   output:
-//   tuple val(meta), file("bbduk/*_rmphix_R{1,2}.fastq.gz"),  emit: fastq
-//   path "bbduk/*",                                           emit: files
-//   path "bbduk/*.phix.stats.txt",                            emit: stats
-//   path "logs/${task.process}/*.log",  emit: log
-//   path "versions.yml", emit: versions
-
-//   when:
-//   task.ext.when == null || task.ext.when
-
-//   shell:
-//   def args   = task.ext.args   ?: ''
-//   def prefix = task.ext.prefix ?: "${meta.id}"
-//   """
-//   ontime --version
-
-//   ontime --help
-
-//   cat <<-END_VERSIONS > versions.yml
-//   "${task.process}":
-//     ontime: "\$(ontime --version | awk '{print \$NF}')"
-//   END_VERSIONS
-
-//   exit 1
-//   """
-// }
-
 process polypolish {
   tag           "${meta.id}"
   label         "process_medium"
   publishDir    "${params.outdir}/${meta.id}", mode: 'copy'
   container     'staphb/polypolish:0.6.0'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '45m'
 
   input:
@@ -1158,7 +1265,7 @@ process pypolca {
   label         "process_medium"
   publishDir    "${params.outdir}/${meta.id}", mode: 'copy'
   container     'staphb/pypolca:0.3.1'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '30m'
   
   input:
@@ -1214,7 +1321,7 @@ process rasusa {
   label         "process_medium"
   publishDir    "${params.outdir}/${meta.id}", mode: 'copy'
   container     'staphb/rasusa:0.8.0'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '10m'
 
   input:
@@ -1249,7 +1356,7 @@ process raven {
   label         "process_high"
   publishDir    "${params.outdir}/${meta.id}", mode: 'copy'
   container     'staphb/raven:1.8.3'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '10h'
 
   input:
@@ -1265,7 +1372,7 @@ process raven {
   task.ext.when == null || task.ext.when
 
   shell:
-  def args   = task.ext.args   ?: ''
+  def args   = task.ext.args   ?: '--polishing-rounds 2'
   def prefix = task.ext.prefix ?: "${meta.id}"
   """
   mkdir -p raven
@@ -1288,7 +1395,7 @@ process summary {
   label         "process_single"
   publishDir    "${params.outdir}/summary", mode: 'copy'
   container     'staphb/multiqc:1.19'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '10m'
   
   input:
@@ -1445,7 +1552,7 @@ process unicycler {
   label         "process_high"
   publishDir    "${params.outdir}/${meta.id}", mode: 'copy'
   container     'staphb/unicycler:0.5.0'
-  ////errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '10h'
 
   input:
@@ -1489,7 +1596,7 @@ process versions {
   publishDir    "${params.outdir}/summary", mode: 'copy'
   container     'staphb/multiqc:1.19'
   time          '10m'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
   file(input)
@@ -1586,11 +1693,66 @@ process versions {
   """
 }
 
+// ##### ##### ##### ##### ##### ##### ##### ##### ##### #####
+
+// Downloading files for testing
+
+// ##### ##### ##### ##### ##### ##### ##### ##### ##### #####
+
+process test_unicycler {
+  tag           "Downloading Unicycler test files"
+  label         "process_single"
+  publishDir    "${params.outdir}/test_files/unicycler", mode: 'copy'
+  container     'staphb/multiqc:1.19'
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  time          '1h'
+
+  output:
+  tuple val("unicycler"), file("long_reads_low_depth.fastq.gz"), file("short_reads*.fastq.gz"), emit: fastq
+
+  when:
+  task.ext.when == null || task.ext.when
+
+  shell:
+  """
+  wget --quiet https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/short_reads_1.fastq.gz
+  wget --quiet https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/short_reads_2.fastq.gz
+  wget --quiet https://github.com/rrwick/Unicycler/raw/69e712eb95c4b9f8a46aade467260260a9ce7a91/sample_data/long_reads_low_depth.fastq.gz
+  """
+}
+
+process test_donut_falls {
+  tag           "Downloading R10.4 reads"
+  label         "process_single"
+  publishDir    "${params.outdir}/test_files/df", mode: 'copy'
+  container     'staphb/multiqc:1.19'
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  time          '1h'
+
+  output:
+  tuple val("df"), file("test_files/test.fastq.gz"), file("test_files/test_{1,2}.fastq.gz"), emit: fastq
+  tuple val("dflr"), file("test_files/test.fastq.gz"), emit: lrfastq
+
+  when:
+  task.ext.when == null || task.ext.when
+
+  shell:
+  """
+  wget --quiet https://zenodo.org/records/10733190/files/df_test_files.tar.gz?download=1 -O dataset.tar.gz
+  tar -xvf dataset.tar.gz
+  """
+}
+
+// ##### ##### ##### ##### ##### ##### ##### ##### ##### #####
+
+// Donut Falls
+
+// ##### ##### ##### ##### ##### ##### ##### ##### ##### #####
+
 workflow DONUT_FALLS {
   take:
     ch_nanopore_input
     ch_illumina_input
-    //ch_gridion_summary
 
   main:
     // channel for gfa files for gfa stats
@@ -1603,46 +1765,21 @@ workflow DONUT_FALLS {
     ch_versions  = Channel.empty()
 
     if (params.assembler =~ /unicycler/ ) {
-      unicycler(ch_illumina_input.join(ch_nanopore_input, by: 0 , remainder: false))
+      unicycler(ch_illumina_input.join(ch_nanopore_input, by: 0, remainder: false))
       
       ch_gfa       = ch_gfa.mix(unicycler.out.gfa)
       // no ch_summary
       ch_consensus = ch_consensus.mix(unicycler.out.fasta)
       ch_versions  = ch_versions.mix(unicycler.out.versions.first())
     }
-    
-    // hybracter and plassembler are on the to-do list
-    // if (params.assembler =~ /hybracter/ ) {
-    //   hybracter(ch_nanopore_input.join(ch_illumina_input, by: 0 , remainder: true))
-      
-    //   ch_gfa       = ch_gfa.mix(hybracter.out.gfa)
-    //   // no ch_summary
-    //   ch_consensus = ch_consensus.mix(hybracter.out.fasta)
-    //   ch_versions  = ch_versions.mix(hybracter.out.versions.first())
-    // } 
-
-    if (params.assembler =~ /dragonflye/ ) {
-      dragonflye(ch_nanopore_input)
-
-      dragonflye.out.summary
-        .collectFile(
-          storeDir: "${params.outdir}/summary/",
-          keepHeader: true,
-          sort: { file -> file.text },
-          name: "dragonflye_summary.tsv")
-        .set { dragonflye_summary }
 
-      ch_gfa       = dragonflye.out.gfa
-      ch_summary   = ch_summary.mix(dragonflye_summary)
-      // no ch_consensus
-      ch_versions  = ch_versions.mix(dragonflye.out.versions.first())
-    }
 
     if (params.assembler.replaceAll('dragonflye','dragon') =~ /flye/ || params.assembler =~ /raven/ ) {
-
       // quality filter
-      ch_illumina_input.map { it -> [it[0], it[1], "illumina"]}
+      ch_illumina_input
+        .map { it -> [it[0], it[1], "illumina"]}
         .mix(ch_nanopore_input.map { it -> [it[0], it[1], "nanopore"]})
+        .filter{it[0]}
         .set { ch_input }
 
       fastp(ch_input)
@@ -1850,21 +1987,64 @@ workflow DONUT_FALLS {
 
 // ##### ##### ##### ##### ##### ##### ##### ##### ##### #####
 
-
 workflow {
 
-//  if (params.ontime) {
-//    ontime(ch_nanopore_input)
-//  }
+  if (params.test) {
+
+    test_unicycler()
 
-//  nanoplot_summary(ch_nanoplot_summary)
+    test_unicycler.out.fastq
+      .map { it ->
+        meta = [id:it[0]] 
+        tuple( meta,
+          file("${it[1]}", checkIfExists: true),
+          [file("${it[2][0]}", checkIfExists: true), file("${it[2][1]}", checkIfExists: true)])
+      }
+      .set{ ch_unicycler_out }
+
+    test_donut_falls()
+
+    test_donut_falls.out.fastq
+      .map { it ->
+        meta = [id:it[0]] 
+        tuple( meta,
+          file("${it[1]}", checkIfExists: true),
+          [file("${it[2][0]}", checkIfExists: true), file("${it[2][1]}", checkIfExists: true)])
+      }
+      .set{ ch_test_df_out }
+
+    test_donut_falls.out.lrfastq
+      .map { it ->
+        meta = [id:it[0]] 
+        tuple( meta,
+          file("${it[1]}", checkIfExists: true),
+          null )
+      }
+      .set{ ch_test_dflr_out }
+
+    ch_unicycler_out
+      .mix(ch_test_df_out)
+      .mix(ch_test_dflr_out)
+      .set { ch_test }
+
+    ch_test
+      .map{it -> tuple(it[0], it[1])}
+      .set { ch_test_nanopore }
+
+    ch_test
+      .filter{ it[2] }
+      .map{it -> tuple(it[0], it[2])}
+      .set { ch_test_illumina }
+
+    ch_nanopore_input = ch_nanopore_input.mix(ch_test_nanopore)
+    ch_illumina_input = ch_illumina_input.mix(ch_test_illumina)
+  }
+
+  if (params.sequencing_summary) {
+    nanoplot_summary(ch_nanoplot_summary)
+  }
 
-  DONUT_FALLS(
-    ch_nanopore_input,
-    ch_illumina_input.ifEmpty([])
-    //,
-    //ch_nanoplot_summary.ifEmpty([])
-    )
+  DONUT_FALLS(ch_nanopore_input, ch_illumina_input.ifEmpty([]))
 }
 
 workflow.onComplete {