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Update20240626 #210

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merged 14 commits into from
Jun 27, 2024
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Merged

Update20240626 #210

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bbbe8ad
update to 16.15.0
erinyoung Jun 26, 2024
6ac636d
removed flag and fixed version
erinyoung Jun 26, 2024
a7e196d
removed flag
erinyoung Jun 26, 2024
5abf53a
removed flag
erinyoung Jun 26, 2024
400284d
update to 2.3.4
erinyoung Jun 26, 2024
68a8488
removed flag
erinyoung Jun 26, 2024
f731820
removed flag
erinyoung Jun 26, 2024
3c3ecdb
removed flag
erinyoung Jun 26, 2024
ed4635b
added errorStrategy
erinyoung Jun 26, 2024
b596fe0
update to 2.23.0-2024-06-01
erinyoung Jun 26, 2024
d46878d
added errorStrategy
erinyoung Jun 26, 2024
6f90843
removed flag
erinyoung Jun 26, 2024
f7c147e
version change to 4.5.240626
erinyoung Jun 26, 2024
1a34385
replaced flag process with functions
erinyoung Jun 26, 2024
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2 changes: 1 addition & 1 deletion modules/local/bbduk.nf
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Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion modules/local/datasets.nf
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Expand Up @@ -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'}

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6 changes: 3 additions & 3 deletions modules/local/drprg.nf
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Expand Up @@ -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
Expand All @@ -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 ?: ''
Expand All @@ -35,7 +35,7 @@ process drprg {
cat <<-END_VERSIONS > versions.yml
"${task.process}":
drprg: \$( drprg --version )
drprg: \$( drprg --version | awk '{print \$NF}')
END_VERSIONS
"""
}
4 changes: 2 additions & 2 deletions modules/local/elgato.nf
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Expand Up @@ -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 ?: ''
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4 changes: 2 additions & 2 deletions modules/local/emmtyper.nf
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion modules/local/iqtree2.nf
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Expand Up @@ -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'}

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4 changes: 2 additions & 2 deletions modules/local/kaptive.nf
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Expand Up @@ -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
Expand All @@ -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 ?: ''
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4 changes: 2 additions & 2 deletions modules/local/kleborate.nf
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Expand Up @@ -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
Expand All @@ -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'
Expand Down
106 changes: 1 addition & 105 deletions modules/local/local.nf
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Expand Up @@ -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"
Expand Down Expand Up @@ -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'}

Expand Down
2 changes: 1 addition & 1 deletion modules/local/mlst.nf
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Expand Up @@ -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'
Expand Down
4 changes: 2 additions & 2 deletions modules/local/mykrobe.nf
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Expand Up @@ -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
Expand All @@ -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 ?: ''
Expand Down
4 changes: 2 additions & 2 deletions modules/local/pbptyper.nf
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Expand Up @@ -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
Expand All @@ -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 ?: ''
Expand Down
4 changes: 2 additions & 2 deletions modules/local/seqsero2.nf
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Expand Up @@ -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
Expand All @@ -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'
Expand Down
4 changes: 2 additions & 2 deletions modules/local/serotypefinder.nf
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Expand Up @@ -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
Expand All @@ -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 ?: ''
Expand Down
4 changes: 2 additions & 2 deletions modules/local/shigatyper.nf
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Expand Up @@ -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
Expand All @@ -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 ?: ''
Expand Down
2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -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'
Expand Down
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