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fix: manifest update for docker
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@dnousome
dnousome committed Oct 25, 2023
1 parent efecf3e commit 5899742
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Showing 2 changed files with 32 additions and 29 deletions.
7 changes: 5 additions & 2 deletions docker/logan_base/Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
FROM --platform=linux/amd64 nciccbr/ccbr_ubuntu_base_20.04:v5
FROM nciccbr/ccbr_ubuntu_base_20.04:v5

# build time variables
ARG BUILD_DATE="000000"
Expand Down Expand Up @@ -103,7 +103,6 @@ RUN wget https://github.com/BoevaLab/FREEC/archive/refs/tags/v11.6.zip \
ENV PATH="/opt2/FREEC-11.6/src:$PATH"
WORKDIR /opt2


# Install Somalier/v0.2.16
# download static binary
RUN mkdir somalier \
Expand Down Expand Up @@ -139,6 +138,10 @@ RUN git clone https://github.com/GregoryFaust/samblaster.git \
ENV PATH="/opt2/samblaster:$PATH"
WORKDIR /opt2

#Install Mosdeph
RUN wget https://github.com/brentp/mosdepth/releases/download/v0.3.5/mosdepth \
&& chmod a+x mosdepth

# Install strelka/2.9.10, requires python2.7 (already satisfied)
# and set python2.7 as the default interpreter
RUN wget https://github.com/Illumina/strelka/releases/download/v2.9.10/strelka-2.9.10.centos6_x86_64.tar.bz2 \
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54 changes: 27 additions & 27 deletions nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@ profiles {
process {
executor = 'local'
withName:fc_lane {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
}
withName:fastq_screen {
container= 'docker://nciccbr/ccbr_fastq_screen_0.13.0:v2.0'
Expand All @@ -69,7 +69,7 @@ profiles {
container= 'docker://nciccbr/ccbr_qualimap:v0.0.1'
}
withName: 'samtools_flagstats|vcftools|bcftools_stats|gatk_varianteval|snpeff|somalier_extract|somalier_analysis' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
}
withName: 'multiqc' {
container= 'docker://nciccbr/ccbr_multiqc_1.9:v0.0.1'
Expand All @@ -78,22 +78,22 @@ profiles {
container= 'docker://nciccbr/ccbr_picard:v0.0.1'
}
withName: 'fastp|bwamem2|indelrealign|bqsr|gatherbqsr|samtoolsindex|applybqsr' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
}
withName:'mutect2|mutect2_t|mutect2_t_tonly|mutect2filter|mutect2filter_tonly|learnreadorientationmodel|learnreadorientationmodel_tonly|contamination_paired|contamination_tumoronly|pileup_paired_t|pileup_paired_n|pileup_paired_tonly' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
}
withName: 'strelka_tn|vardict_tn|vardict_tonly|varscan_tn|varscan_tonly|combineVariants|combineVariants_strelka' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
}
withName: 'annotvep_tn|annotvep_tonly' {
container= 'docker://dnousome/ccbr_vcf2maf:v102.0.0'
}
withName: 'svaba_somatic|manta_somatic' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
}
withName: 'sequenza' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
}


Expand Down Expand Up @@ -152,88 +152,88 @@ profiles {
cpus=8
}
withName:fastp {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory=24.GB
time=24.h
cpus=4
}
withName:fc_lane {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
}
withName:bwamem2 {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory=200.GB
time=48.h
cpus=17
}
withName:indelrealign{
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory=48.GB
time=72.h
cpus=16
}
withName:bqsr{
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 32.GB
time= 48.h
}
withName:gatherbqsr{
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 16.GB
time= 2.h
}
withName:applybqsr{
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 48.GB
time= 48.h
}
withName:samtoolsindex{
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 16.GB
time= 12.h
cpus= 4
}
withName: 'mutect2|mutect2_t|mutect2_t_tonly' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 48.GB
cpus= 4
time= 72.h
}
withName: 'vardict_tn|vardict_tonly|varscan_tn|varscan_tonly|combineVariants|combineVariants_strelka' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 32.GB
cpus= 2
time= 72.h
}
withName: 'strelka_tn' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 48.GB
cpus= 16
time= 72.h
}
withName:'mutect2filter|mutect2filter_tonly' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 24.GB
time= 24.h
cpus= 4
}
withName:'contamination_paired|contamination_tumoronly'{
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 24.GB
time= 24.h
}
withName:'learnreadorientationmodel|learnreadorientationmodel_tonly' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 48.GB
time= 24.h
}
withName:'mergemut2stats|mergemut2stats_tonly' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 16.GB
time= 24.h
}
withName:'pileup_paired_t|pileup_paired_n|pileup_paired_tonly' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 16.GB
time= 12.h
}
Expand Down Expand Up @@ -273,12 +273,12 @@ profiles {
scratch='/lscratch/$SLURM_JOB_ID/dv'
}
withName:'somalier_extract|somalier_analysis' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 16.GB
time= 12.h
}
withName:'gatk_varianteval' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 16.GB
time= 12.h
}
Expand All @@ -295,13 +295,13 @@ profiles {
cpus=16
}
withName:'svaba_somatic|manta_somatic' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 64.GB
time= 24.h
cpus=16
}
withName: 'sequenza' {
container= 'docker://dnousome/ccbr_logan_base:v0.3.0'
container= 'docker://dnousome/ccbr_logan_base:v0.3.1'
memory= 64.GB
time= 24.h
cpus=12
Expand Down

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