Merge pull request #210 from UPHL-BioNGS/update20240626

Update20240626

modules/local/bbduk.nf

@@ -3,7 +3,7 @@ process bbduk {
   label         "process_medium"
   publishDir    params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
   container     'staphb/bbtools:39.01'
-  //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
+  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '10m'
 
   input:

modules/local/datasets.nf

@@ -52,7 +52,7 @@ process datasets_download {
   // because there's no way to specify threads
   label         "process_medium"
   publishDir    path: "${params.outdir}", mode: 'copy', pattern: "logs/*/*log"
-  container     'staphb/ncbi-datasets:16.10.3'
+  container     'staphb/ncbi-datasets:16.15.0'
   time          '5h'
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 

modules/local/drprg.nf

@@ -8,7 +8,7 @@ process drprg {
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
-  tuple val(meta), file(contigs), val(flag)
+  tuple val(meta), file(contigs)
 
   output:
   tuple val(meta), val("drprg"), file("drprg/*/*.drprg.json"), emit: json
@@ -17,7 +17,7 @@ process drprg {
   path "versions.yml", emit: versions
 
   when:
-  (task.ext.when == null || task.ext.when) && flag =~ 'found'
+  (task.ext.when == null || task.ext.when)
 
   shell:
   def args   = task.ext.args   ?: ''
@@ -35,7 +35,7 @@ process drprg {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        drprg: \$( drprg --version )
+        drprg: \$( drprg --version | awk '{print \$NF}')
     END_VERSIONS
   """
 }

modules/local/elgato.nf

@@ -7,15 +7,15 @@ process elgato {
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
-  tuple val(meta), file(contigs), val(flag)
+  tuple val(meta), file(contigs)
 
   output:
   path "elgato/*/possible_mlsts.txt", emit: collect
   path "logs/${task.process}/*.log" , emit: log
   path "versions.yml"               , emit: versions
 
   when:
-  (task.ext.when == null || task.ext.when) && flag =~ 'found'
+  (task.ext.when == null || task.ext.when)
 
   shell:
   def args   = task.ext.args   ?: ''

modules/local/emmtyper.nf

@@ -8,10 +8,10 @@ process emmtyper {
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   when:
-  (task.ext.when == null || task.ext.when) && flag =~ 'found'
+  (task.ext.when == null || task.ext.when)
 
   input:
-  tuple val(meta), file(contigs), val(flag), file(script)
+  tuple val(meta), file(contigs), file(script)
 
   output:
   path "emmtyper/*_emmtyper.txt"   , emit: collect

modules/local/iqtree2.nf

@@ -2,7 +2,7 @@ process iqtree2 {
   tag           "Phylogenetic analysis"
   label         "process_high"
   publishDir    params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-  container     'staphb/iqtree2:2.3.1'
+  container     'staphb/iqtree2:2.3.4'
   time          '24h'
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 

modules/local/kaptive.nf

@@ -8,7 +8,7 @@ process kaptive {
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
-  tuple val(meta), file(contigs), val(flag)
+  tuple val(meta), file(contigs)
 
   output:
   path "kaptive/${meta.id}_table.txt", emit: collect
@@ -17,7 +17,7 @@ process kaptive {
   path "versions.yml", emit: versions
 
   when:
-  (task.ext.when == null || task.ext.when) && flag =~ 'found'
+  (task.ext.when == null || task.ext.when)
 
   shell:
   def args   = task.ext.args   ?: ''

modules/local/kleborate.nf

@@ -7,7 +7,7 @@ process kleborate {
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
-  tuple val(meta), file(contig), val(flag), file(script)
+  tuple val(meta), file(contig), file(script)
 
   output:
   path "kleborate/*_results.tsv"   , emit: collect, optional: true
@@ -16,7 +16,7 @@ process kleborate {
   path "versions.yml"              , emit: versions
 
   when:
-  (task.ext.when == null || task.ext.when) && flag =~ 'found'
+  (task.ext.when == null || task.ext.when)
 
   shell:
   def args   = task.ext.args   ?: '--all'

modules/local/local.nf

@@ -65,110 +65,6 @@ process download_sra {
   """
 }
 
-process flag {
-  tag           "${meta.id}"
-  label         "process_single"
-  //no publishDir    params.outdir, mode: 'copy'
-  container     'quay.io/biocontainers/pandas:1.5.2'
-  time          '10m'
-  errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
-
-  input:
-  tuple val(meta), file(files)
-
-  output:
-  tuple val(meta), file("${files[0]}"), env(salmonella_flag)    , emit: salmonella_flag
-  tuple val(meta), file("${files[0]}"), env(klebsiella_flag)    , emit: klebsiella_flag
-  tuple val(meta), file("${files[0]}"), env(ecoli_flag)         , emit: ecoli_flag
-  tuple val(meta), file("${files[0]}"), env(streppneu_flag)     , emit: streppneu_flag
-  tuple val(meta), file("${files[0]}"), env(legionella_flag)    , emit: legionella_flag
-  tuple val(meta), file("${files[0]}"), env(klebacin_flag)      , emit: klebacin_flag
-  tuple val(meta), file("${files[0]}"), env(strepa_flag)        , emit: strepa_flag
-  tuple val(meta), file("${files[0]}"), env(vibrio_flag)        , emit: vibrio_flag
-  tuple val(meta), file("${files[0]}"), env(myco_flag)          , emit: myco_flag
-  tuple val(meta), file("${files[0]}"), env(genus), env(species), emit: organism
-  path "flag/*_flag.csv", emit: collect
-  path "logs/${task.process}/*.log", emit: log_files
-
-  shell:
-  def prefix = task.ext.prefix ?: "${meta.id}"
-  """
-    mkdir -p flag logs/${task.process}
-    log_file=logs/${task.process}/${prefix}.${workflow.sessionId}.log
-
-    if [ -f "${prefix}_fastani.csv" ]
-    then 
-      awk -F "," '{if (\$4 > 90) print \$0}' ${prefix}_fastani.csv > smaller_fastani.csv
-      genus=\$(head   -n 2 ${prefix}_fastani.csv | tail -n 1 | cut -f 3 -d , | cut -f 1 -d "_")
-      species=\$(head -n 2 ${prefix}_fastani.csv | tail -n 1 | cut -f 3 -d , | cut -f 2 -d "_")
-    else
-      touch smaller_fastani.csv
-      genus="unknown"
-      species="unknown"
-    fi
-
-    touch ${prefix}_reads_summary_kraken2.csv  ${prefix}.summary.mash.csv ${prefix}_blobtools.txt
-
-    files="smaller_fastani.csv ${prefix}_reads_summary_kraken2.csv ${prefix}.summary.mash.csv ${prefix}_blobtools.txt"
-
-    echo "Looking for Salmonella:" >> \$log_file
-    salmonella_flag=''
-    find_salmonella=\$(head -n 10 \$files | grep "Salmonella" | tee -a \$log_file | head -n 1 )
-    if [ -n "\$find_salmonella" ] ; then salmonella_flag="found" ; else salmonella_flag="not" ; fi
-    
-    echo "Looking for E. coli and Shigella:" >> \$log_file
-    ecoli_flag=''
-    find_ecoli=\$(head -n 10 \$files | grep -e "Escherichia" -e "Shigella" | tee -a \$log_file | head -n 1 )
-    if [ -n "\$find_ecoli" ] ; then ecoli_flag="found" ; else ecoli_flag="not" ; fi
-
-    echo "Looking for Klebsiella:" >> \$log_file
-    klebsiella_flag=''
-    find_klebsiella=\$(head -n 10 \$files | grep -e "Klebsiella" -e "Enterobacter" -e "Serratia" | tee -a \$log_file | head -n 1 )
-    if [ -n "\$find_klebsiella" ] ; then klebsiella_flag="found" ; else klebsiella_flag="not" ; fi
-    
-    echo "Looking for Strep A organisms:" >> \$log_file
-    strepa_flag=''
-    find_strepa=\$(head -n 10 \$files | grep "Streptococcus" | grep -e "pyogenes" -e "dysgalactiae" -e "anginosus" | tee -a \$log_file | head -n 1 )
-    if [ -n "\$find_strepa" ] ; then strepa_flag='found' ; else strepa_flag='not' ; fi
-
-    echo "Looking for Streptococcus pneumoniae organisms:" >> \$log_file
-    streppneu_flag_flag=''
-    find_streppneu=\$(head -n 10 \$files | grep "Streptococcus" | grep "pneumoniae" | tee -a \$log_file | head -n 1 )
-    if [ -n "\$find_streppneu" ] ; then streppneu_flag='found' ; else streppneu_flag='not' ; fi
-  
-    echo "Looking for Legionella organisms:" >> \$log_file
-    legionella_flag=''
-    find_legionella=\$(head -n 10 \$files | grep "Legionella" | tee -a \$log_file | head -n 1 )
-    if [ -n "\$find_legionella" ] ; then legionella_flag='found' ; else legionella_flag='not' ; fi
-
-    echo "Looking for Vibrio organisms:" >> \$log_file
-    vibrio_flag=''
-    find_vibrio=\$(head -n 10 \$files | grep "Vibrio" | tee -a \$log_file | head -n 1 )
-    if [ -n "\$find_vibrio" ] ; then vibrio_flag='found' ; else vibrio_flag='not' ; fi
-
-    echo "Looking for Klebsiella or Acinetobacter:" >> \$log_file
-    klebacin_flag=''
-    if [ -n "\$find_klebsiella" ]
-    then
-      klebacin_flag='found'
-    else
-      find_acin=\$(head -n 10 \$files | grep "Acinetobacter" | tee -a \$log_file | head -n 1 )
-      if [ -n "\$find_acin" ] ; then klebacin_flag='found' ; else klebacin_flag='not' ; fi
-    fi
-
-    echo "Looking for Mycobacterium/Mycobacteria"
-    myco_flag=''
-    find_myco=\$(head -n 10 \$files | grep "Mycobacteri" | tee -a \$log_file | head -n 1 )
-    if [ -n "\$find_myco" ] ; then myco_flag='found' ; else myco_flag='not' ; fi
-
-    if [ -z "\$genus" ]   ; then genus=unknown   ; fi
-    if [ -z "\$species" ] ; then species=unknown ; fi
-
-    echo "sample,genus,species,salmonella_flag,ecoli_flag,klebsiella_flag,klebacin_flag,myco_flag,strepa_flag,streppneu_flag,legionella_flag,vibrio_flag" > flag/${prefix}_flag.csv
-    echo "${prefix},\$genus,\$species,\$salmonella_flag,\$ecoli_flag,\$klebsiella_flag,\$klebacin_flag,\$myco_flag,\$strepa_flag,\$streppneu_flag,\$legionella_flag,\$vibrio_flag" >> flag/${prefix}_flag.csv
-  """
-}
-
 process json_convert {
   tag       "${meta.id}"
   label     "process_single"
@@ -278,7 +174,7 @@ process references {
   tag       "Preparing references"
   // no publishDir
   label     "process_single"
-  container 'quay.io/uphl/grandeur_ref:2024-03-07'
+  container 'quay.io/uphl/grandeur_ref:2024-06-26'
   time      '10m'
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 

modules/local/mlst.nf

@@ -2,7 +2,7 @@ process mlst {
   tag           "${meta.id}"
   label         "process_medium"
   publishDir    params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-  container     'staphb/mlst:2.23.0-2024-05-01'
+  container     'staphb/mlst:2.23.0-2024-06-01'
   maxForks      10
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
   time          '10m'

modules/local/mykrobe.nf

@@ -8,7 +8,7 @@ process mykrobe {
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
-  tuple val(meta), file(contigs), val(flag)
+  tuple val(meta), file(contigs)
 
   output:
   path "mykrobe/*.csv", emit: collect
@@ -17,7 +17,7 @@ process mykrobe {
   path "versions.yml", emit: versions
 
   when:
-  (task.ext.when == null || task.ext.when) && flag =~ 'found'
+  (task.ext.when == null || task.ext.when)
 
   shell:
   def args   = task.ext.args   ?: ''

modules/local/pbptyper.nf

@@ -8,7 +8,7 @@ process pbptyper {
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
-  tuple val(meta), file(contigs), val(flag)
+  tuple val(meta), file(contigs)
 
   output:
   path "pbptyper/${meta.id}.tsv"   , emit: collect
@@ -17,7 +17,7 @@ process pbptyper {
   path "versions.yml"              , emit: versions
 
   when:
-  (task.ext.when == null || task.ext.when) && flag =~ 'found'
+  (task.ext.when == null || task.ext.when)
 
   shell:
   def args   = task.ext.args   ?: ''

modules/local/seqsero2.nf

@@ -7,7 +7,7 @@ process seqsero2 {
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
 
   input:
-  tuple val(meta), file(file), val(flag)
+  tuple val(meta), file(file)
 
   output:
   path "seqsero2/*/*"                                    , emit: files
@@ -16,7 +16,7 @@ process seqsero2 {
   path  "versions.yml"                          , emit: versions
 
   when:
-  (task.ext.when == null || task.ext.when) && flag =~ 'found'
+  (task.ext.when == null || task.ext.when)
 
   shell:
   def args = task.ext.args     ?: '-m a -b mem'

modules/local/serotypefinder.nf

@@ -8,7 +8,7 @@ process serotypefinder {
   errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}  
 
   input:
-  tuple val(meta), file(file), val(flag), file(script)
+  tuple val(meta), file(file), file(script)
 
   output:
   path "serotypefinder/*/*"                 , emit: files
@@ -17,7 +17,7 @@ process serotypefinder {
   path "versions.yml"                       , emit: versions
 
   when:
-  (task.ext.when == null || task.ext.when) && flag =~ 'found'
+  (task.ext.when == null || task.ext.when)
 
   shell:
   def args   = task.ext.args   ?: ''

modules/local/shigatyper.nf

@@ -8,7 +8,7 @@ process shigatyper {
   time          '10m'
 
   input:
-  tuple val(meta), file(input), val(flag), file(script)
+  tuple val(meta), file(input), file(script)
 
   output:
   path "shigatyper/*_shigatyper.tsv", optional: true, emit: files
@@ -17,7 +17,7 @@ process shigatyper {
   path "versions.yml", emit: versions
 
   when:
-  (task.ext.when == null || task.ext.when) && flag =~ 'found'
+  (task.ext.when == null || task.ext.when)
 
   shell:
   def args = task.ext.args ?: ''

nextflow.config

@@ -3,7 +3,7 @@ manifest {
   author                          = 'Erin Young'
   homePage                        = 'https://github.com/UPHL-BioNGS/Grandeur'
   mainScript                      = 'main.nf'
-  version                         = '4.4.240521'
+  version                         = '4.5.240626'
   defaultBranch                   = 'main'
   description                     = 'Grandeur is short-read de novo assembly pipeline with serotyping.'
   nextflowVersion                 = '!>=22.10.1'