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Tumor-only mode for Mutect2 and MSIsensor #354

Merged
merged 17 commits into from
Mar 10, 2021
Merged

Tumor-only mode for Mutect2 and MSIsensor #354

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a1f11f0
Merge pull request #2 from nf-core/master
jfnavarro Feb 22, 2021
ac90102
Add Mutect2 tumor-only mode
jfnavarro Feb 22, 2021
f402d60
Update for Mutect2 and MSIsensor in tumor only mode
jfnavarro Feb 23, 2021
8a57b7a
Update for Mutect2 and MSIsensor in tumor only mode
jfnavarro Feb 23, 2021
9335338
Update
jfnavarro Feb 23, 2021
5f6af94
Update
jfnavarro Feb 23, 2021
4571ade
Update container
jfnavarro Feb 23, 2021
68929bc
Updading container for MSIsensor process
jfnavarro Feb 23, 2021
a1b880b
Update main.nf
jfnavarro Feb 23, 2021
192e5df
Update in msisensor tumor only
jfnavarro Feb 24, 2021
527fcd5
Container should be dev
jfnavarro Feb 24, 2021
52154b0
Correct name for Mutect2 tumor-only process
jfnavarro Feb 24, 2021
25113f1
Fix an issue with Mutect2
jfnavarro Mar 2, 2021
e91a68a
Make sure Mutect2 works when both tumor-only and tumor-normal samples…
jfnavarro Mar 9, 2021
0b8889d
Make sure Mutect2 works when both tumor-only and tumor-normal samples…
jfnavarro Mar 9, 2021
0e7d5c4
More adjustments to make sure Mutect2 works in tumor-only and tumor-n…
jfnavarro Mar 9, 2021
d68befa
Update main.nf
jfnavarro Mar 9, 2021
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3 changes: 3 additions & 0 deletions conf/base.config
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Original file line number Diff line number Diff line change
Expand Up @@ -97,4 +97,7 @@ process {
container = {(params.annotation_cache && params.vep_cache) ? 'nfcore/sarek:2.7' : "nfcore/sarekvep:2.7.${params.genome}"}
errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
}
withLabel:msisensor {
container = "quay.io/biocontainers/msisensor-pro:1.1.a--hb3646a4_0"
}
}
2 changes: 1 addition & 1 deletion environment.yml
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Expand Up @@ -38,4 +38,4 @@ dependencies:
- bioconda::vcfanno=0.3.2=0
- bioconda::vcftools=0.1.16=he513fc3_4
- conda-forge::pigz=2.3.4=hed695b0_1
- conda-forge::r-ggplot2=3.3.0=r40h6115d3f_1
- conda-forge::r-ggplot2=3.3.0=r40h6115d3f_1
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