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Adding intervals to sentieon driver cmd #4160

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merged 4 commits into from
Oct 19, 2023
Merged

Adding intervals to sentieon driver cmd #4160

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29a4ab7
Adding intervals to sentieon driver cmd
asp8200 Oct 18, 2023
e885f29
Merge branch 'master' into fix_sentieon_tnhaplotyper2
asp8200 Oct 18, 2023
6298861
Merge branch 'master' into fix_sentieon_tnhaplotyper2
asp8200 Oct 18, 2023
9eecd99
Merge branch 'master' into fix_sentieon_tnhaplotyper2
asp8200 Oct 19, 2023
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Adding intervals to sentieon driver cmd
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@asp8200
asp8200 committed Oct 18, 2023
commit 29a4ab7a1571a889431f3af7e96ffeaffbf5dc28
4 changes: 3 additions & 1 deletion modules/nf-core/sentieon/tnhaplotyper2/main.nf
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Expand Up @@ -43,8 +43,9 @@ process SENTIEON_TNHAPLOTYPER2 {
def args3 = task.ext.args3 ?: '' // options for the OrientationBias algorithm. It could be something like "--tumor_sample <tumour_id>"
def args4 = task.ext.args4 ?: '' // options for the ContaminationModel algorithm. It could be something like "--tumor_sample <tumour_id> --normal_sample <normal_id>"
def prefix = task.ext.prefix ?: "${meta.id}"
def pon_command = panel_of_normals ? "--pon $panel_of_normals" : ""
def gr_command = germline_resource ? "--germline_vcf $germline_resource" : ""
def interval_command = intervals ? "--interval $intervals" : ""
def pon_command = panel_of_normals ? "--pon $panel_of_normals" : ""
def inputs = input.collect{ "-i $it"}.join(" ")
def orientation_bias_cmd = ""
def contamination_cmd = ""
Expand Down Expand Up @@ -79,6 +80,7 @@ process SENTIEON_TNHAPLOTYPER2 {
-r $fasta \\
$args \\
$inputs \\
$interval_command \\
--algo TNhaplotyper2 \\
$args2 \\
$gr_command \\
Expand Down