Commit aef7ba2b authored by Acivico's avatar Acivico
Browse files

gridss updated

parent 29cdf23e
process GRIDSS {
tag "gridss"
tag { "gridss" }
container 'quay.io/biocontainers/gridss:2.9.3--0'
input:
tuple path(input), path(bai)
tuple path(reference_genome), path(index_files), path(fai)
path reference_genome
path indexs
path blacklist
output:
......@@ -13,12 +14,17 @@ process GRIDSS {
script:
def threadsArgument = params.threads_gridss ? "--threads $params.threads_gridss" : ""
"""
gridss --reference $reference_genome \\
--output ${input.simpleName}.gridss.raw.vcf.gz \\
--assembly "$params.assemblyFilename" \\
$threadsArgument \\
--jar "/usr/local/share/gridss-2.9.3-0/gridss.jar" \\
--blacklist $blacklist \\
$input
for i in $input
do
srr=\$(echo \$i | cut -f 1 -d '.')
gridss --reference $reference_genome \\
--output \$(echo \${i%%.*}).gridss.raw.vcf.gz \\
--assembly "\$(echo \$srr).$params.assemblyFilename" \\
$threadsArgument \\
--jar "/usr/local/share/gridss-2.9.3-0/gridss.jar" \\
--blacklist $blacklist \\
\$i
done
"""
}
process GRIDSS_FILTER {
tag "gridss filter"
tag { "gridss filter" }
input:
path script
......@@ -14,6 +14,9 @@ process GRIDSS_FILTER {
script:
"""
sh $script $input $sample $min_len $max_len $min_q
for i in $input
do
sh $script \$i $sample $min_len $max_len $min_q
done
"""
}
process STRUCTURAL_VARIANTS {
tag "structural variants"
tag { "structural variants" }
container 'quay.io/biocontainers/bioconductor-structuralvariantannotation:1.6.0--r40_0'
input:
......@@ -11,6 +11,9 @@ process STRUCTURAL_VARIANTS {
script:
"""
Rscript $script $input
for i in $input
do
Rscript $script \$i
done
"""
}
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