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removed flag
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@erinyoung
erinyoung committed Jun 26, 2024
1 parent f731820 commit 3c3ecdb
Showing 1 changed file with 1 addition and 105 deletions.
106 changes: 1 addition & 105 deletions modules/local/local.nf
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Original file line number Diff line number Diff line change
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'}

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