add ADMIE and ACCESS_CNV tools / dockerfiles

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

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/

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

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')

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

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/