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68 changes: 68 additions & 0 deletions access_CNV_0.1.0/access_cnv_0.1.0.cwl
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class: CommandLineTool
cwlVersion: v1.0
$namespaces:
sbg: 'https://www.sevenbridges.com/'
baseCommand:
- copynumber_tm.batchdiff_cfdna.R
inputs:
- id: do_full
type: string
inputBinding:
position: 5
doc: either 'FULL' or 'MIN'
- id: loess_normals
type: File
inputBinding:
position: 2
doc: normal_ALL_intervalnomapqcoverage_loess.txt
- id: loess_tumors
type: File
inputBinding:
position: 4
doc: tumor_ALL_intervalnomapqcoverage_loess.txt
- id: project_name_cnv
type: string
inputBinding:
position: 1
doc: e.g. ACCESSv1-VAL-20180001
- id: targets_coverage_annotation
type: File
inputBinding:
position: 3
doc: >-
ACCESS_targets_coverage.txt Full Path to text file of target annotations.
Columns = (Chrom, Start, End, Target, GC_150bp, GeneExon, Cyt, Interval)
outputs:
- id: copy_pdf
type: File
outputBinding:
glob: $('*copynumber_segclusp.pdf')
- id: copy_standard_err
type: stderr
- id: copy_standard_out
type: stdout
- id: genes_file
type: File
outputBinding:
glob: $('*copynumber_segclusp.genes.txt')
- id: intragenic_file
type: File
outputBinding:
glob: $('*copynumber_segclusp.intragenic.txt')
- id: probes_file
type: File
outputBinding:
glob: $('*copynumber_segclusp.probes.txt')
- id: seg_files
type: 'File[]'
outputBinding:
glob: $('*.seg')
requirements:
- class: ResourceRequirement
ramMin: 10000
coresMin: 1
- class: DockerRequirement
dockerPull: 'mskaccess/access_CNV_0.1.0:0.1.0'
- class: InlineJavascriptRequirement
stdout: copy_number.stdout
stderr: copy_number.stderr
31 changes: 31 additions & 0 deletions access_CNV_0.1.0/container/Dockerfile
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################## BASE IMAGE ######################

FROM python:3

################## ARGUMENTS/Environments ##########

ARG BUILD_DATE
ARG BUILD_VERSION
ARG LICENSE="Apache-2.0"
ARG ACCESS_CNV_VERSION=0.1.0
ARG PYTHON_VERSION=3
ARG R_VERSION=3.5.1

################## METADATA ########################
LABEL org.opencontainers.image.vendor="MSKCC"
LABEL org.opencontainers.image.authors="Ian Johnson ([email protected])"

LABEL org.opencontainers.image.created=${BUILD_DATE} \
org.opencontainers.image.version=${BUILD_VERSION} \
org.opencontainers.image.licenses=${LICENSE} \
org.opencontainers.image.version.R=${R_VERSION} \
org.opencontainers.image.source.admie="https://github.com/rptashkin/ACCESS_CNV"

LABEL org.opencontainers.image.description="This container uses python ${PYTHON_VERSION} as the base image to build \
ACCESS_CNV version ${ACCESS_CNV_VERSION}"

WORKDIR /usr/src

RUN wget "https://github.com/rptashkin/ACCESS_CNV/archive/master.zip" && \
unzip master.zip && \
cp -s /usr/src/ACCESS_CNV/* /usr/local/bin/
73 changes: 73 additions & 0 deletions access_CNV_0.1.0/coverage.cwl
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class: CommandLineTool
cwlVersion: v1.0
$namespaces:
sbg: 'https://www.sevenbridges.com/'
baseCommand:
- cfdna_scna
inputs:
- id: normal_sample_list
type: File
inputBinding:
position: 0
prefix: '--normalManifest'
doc: >-
normal_manifest.txt Full path to the normal sample manifest, tab
serparated BAM path, patient sex
- id: project_name_cnv
type: string
inputBinding:
position: 0
prefix: '--runID'
doc: e.g. ACCESSv1-VAL-20180001
- id: reference_fasta
type: File
inputBinding:
position: 0
prefix: '--genomeReference'
doc: Homo_Sapeins_hg19.fasta Full Path to the reference fasta file
- id: targets_coverage_bed
type: File
inputBinding:
position: 0
prefix: '--bedTargets'
doc: ACCESS_targets_coverage.bed Full Path to BED file of panel targets
- id: threads
type: int
inputBinding:
position: 0
prefix: '--threads'
doc: Number of Threads to be used to generate coverage metrics
- id: tumor_sample_list
type: File
inputBinding:
position: 0
prefix: '--tumorManifest'
doc: >-
tumor_manifest.txt Full path to the tumor sample manifest, tab serparated
BAM path, patient sex
outputs:
- id: bam_list
type: 'File[]'
outputBinding:
glob: $('*_bams.list')
- id: normals_covg
type: File
outputBinding:
glob: $('*normals_targets_nomapq.covg_interval_summary')
- id: standard_err
type: stderr
- id: standard_out
type: stdout
- id: tumors_covg
type: File
outputBinding:
glob: $('*tumors_targets_nomapq.covg_interval_summary')
requirements:
- class: ResourceRequirement
ramMin: 10000
coresMin: 8
- class: DockerRequirement
dockerPull: 'mskaccess/access_CNV_0.1.0:0.1.0'
- class: InlineJavascriptRequirement
stdout: coverage.stdout
stderr: coverage.stderr
53 changes: 53 additions & 0 deletions access_CNV_0.1.0/loess.cwl
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class: CommandLineTool
cwlVersion: v1.0
$namespaces:
sbg: 'https://www.sevenbridges.com/'
baseCommand:
- loessnormalize_nomapq_cfdna.R
inputs:
- id: coverage_file
type: File
inputBinding:
position: 3
doc: 'coverage files, targets_nomapq.covg_interval_summary'
- id: project_name_cnv
type: string
inputBinding:
position: 1
doc: e.g. ACCESSv1-VAL-20180001
- id: run_type
type: string
inputBinding:
position: 4
doc: tumor or normal
- id: targets_coverage_annotation
type: File
inputBinding:
position: 2
doc: >-
ACCESS_targets_coverage.txt Full Path to text file of target annotations.
Columns = (Chrom, Start, End, Target, GC_150bp, GeneExon, Cyt, Interval)
outputs:
- id: loess_pdf
type: File
outputBinding:
glob: $('*_loessnorm.pdf')
- id: loess_text
type: File
outputBinding:
glob: $('*_ALL_intervalnomapqcoverage_loess.txt')
- id: standard_err
type: stderr
- id: standard_out
type: stdout
arguments:
- $(runtime.outdir)
requirements:
- class: ResourceRequirement
ramMin: 10000
coresMin: 1
- class: DockerRequirement
dockerPull: 'mskaccess/access_CNV_0.1.0:0.1.0'
- class: InlineJavascriptRequirement
stdout: $(inputs.run_type + '_loess.stdout')
stderr: $(inputs.run_type + '_loess.stderr')
64 changes: 64 additions & 0 deletions admie_0.1.0/admie_0.1.0.cwl
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cwlVersion: v1.0

class: CommandLineTool

requirements:
- class: InlineJavascriptRequirement
- class: DockerRequirement
dockerPull: 'mskaccess/admie_0.1.0:0.1.0'
- class: ResourceRequirement
ramMin: 16000 # todo: how to get 4GB when dividing by 6!!!!!!!!!!....
coresMin: 6

baseCommand: admie_analyze

stdout: admie.stdout
stderr: admie.stderr

inputs:

project_name_msi: string?

msisensor_allele_counts:
type: Directory?
inputBinding:
prefix: --allele-counts

allele_counts_list:
type: File[]?
inputBinding:
prefix: --allele-list

model:
type: File
inputBinding:
prefix: --model

coverage_data:
type: Directory?
inputBinding:
prefix: --qc-directory

outputs:

distance_vectors:
type: File
outputBinding:
glob: $('distance_vectors.tsv')

admie_results:
type: File
outputBinding:
glob: $('msi_results.txt')

# TODO: Fix the plots output on admie module
plots:
type: File[]?
outputBinding:
glob: '*_MSI_QC.pdf'

standard_out:
type: stdout

standard_err:
type: stderr
29 changes: 29 additions & 0 deletions admie_0.1.0/container/Dockerfile
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################## BASE IMAGE ######################

FROM python:3

################## ARGUMENTS/Environments ##########

ARG BUILD_DATE
ARG BUILD_VERSION
ARG LICENSE="Apache-2.0"
ARG ADMIE_VERSION=0.0.0
ARG PYTHON_VERSION=3

################## METADATA ########################
LABEL org.opencontainers.image.vendor="MSKCC"
LABEL org.opencontainers.image.authors="Ian Johnson ([email protected])"

LABEL org.opencontainers.image.created=${BUILD_DATE} \
org.opencontainers.image.version=${BUILD_VERSION} \
org.opencontainers.image.licenses=${LICENSE} \
org.opencontainers.image.source.admie="https://github.com/mskcc/ADMIE"

LABEL org.opencontainers.image.description="This container uses python ${PYTHON_VERSION} as the base image to build \
ADMIE version ${ADMIE_VERSION}"

WORKDIR /usr/src

RUN wget "https://github.com/mskcc/ADMIE/archive/master.zip" && \
unzip master.zip && \
cp -s /usr/src/ADMIE/* /usr/local/bin/