Merge branch 'release/3.2.0'

.dockerignore

@@ -5,3 +5,5 @@
 /*.*
 /LICENSE
 /scripts/timeCleaner.pl
+/venv
+/local

.travis.yml

@@ -22,11 +22,12 @@ script:
  - echo 'Build and check docker image'
  - docker build -t dockstore-cgpmap .
  - docker images | grep -c dockstore-cgpmap
- - echo 'Verify program from each inherited package is found (dockstore-cgpbigwig)'
+ - echo 'Verify program(s) from each inherited package (cgpbigwig)'
  - docker run -t --rm dockstore-cgpmap bwjoin --version
- - echo 'Verify a program from each new package is found (dockstore-cgpmap)'
- - docker run -t --rm dockstore-cgpmap ds-cgpmap.pl -h
+ - echo 'Verify program(s) from each inherited package (pcap-core)'
  - docker run -t --rm dockstore-cgpmap bwa_mem.pl -version
  - docker run -t --rm dockstore-cgpmap bammarkduplicates2 --version
  - docker run -t --rm dockstore-cgpmap samtools --version
  - docker run -t --rm dockstore-cgpmap bash -c 'bwa 2>&1 | grep Version'
+ - echo 'Verify program(s) this layer are found (dockstore-cgpmap)'
+ - docker run -t --rm dockstore-cgpmap ds-cgpmap.pl -h

CHANGES.md

@@ -1,9 +1,15 @@
 # CHANGES
 
+## 3.2.0
+
+* Update PCAP-core to 5.4.0, new ubuntu htslib/samtools 1.11.
+* `-scramble` deprecated, see `seqslice`
+* New options to control duplicate marking
+
 ## 3.1.4
 
 * Update PCAP-core to 4.3.5
-  * Sppedup bamsort by adding sort helpers
+  * Speedup bamsort by adding sort helpers
 
 ## 3.1.3
 

Dockerfile

@@ -1,94 +1,17 @@
-FROM  quay.io/wtsicgp/dockstore-cgpbigwig:2.1.1 as builder
-
-USER  root
-
-RUN apt-get -yq update
-RUN apt-get install -yq --no-install-recommends\
-  apt-transport-https\
-  locales\
-  curl\
-  ca-certificates\
-  libperlio-gzip-perl\
-  make\
-  bzip2\
-  gcc\
-  psmisc\
-  time\
-  zlib1g-dev\
-  libbz2-dev\
-  liblzma-dev\
-  libcurl4-gnutls-dev\
-  libncurses5-dev\
-  nettle-dev\
-  libp11-kit-dev\
-  libtasn1-dev\
-  libgnutls-dev\
-  libgd-dev\
-  libdb-dev
-
-RUN locale-gen en_US.UTF-8
-RUN update-locale LANG=en_US.UTF-8
-
-ENV OPT /opt/wtsi-cgp
-ENV PATH $OPT/bin:$OPT/biobambam2/bin:$PATH
-ENV PERL5LIB $OPT/lib/perl5
-ENV LD_LIBRARY_PATH $OPT/lib
-ENV LC_ALL en_US.UTF-8
-ENV LANG en_US.UTF-8
-
-RUN mkdir -p $OPT/bin
-
-ADD build/opt-build.sh build/
-RUN bash build/opt-build.sh $OPT
-
-FROM  ubuntu:16.04
-
-MAINTAINER  [email protected]
+FROM  quay.io/wtsicgp/pcap-core:5.4.0
 
 LABEL vendor="Cancer, Ageing and Somatic Mutation, Wellcome Trust Sanger Institute"
+LABEL maintainer="[email protected]"
 LABEL uk.ac.sanger.cgp.description="PCAP-core for dockstore.org"
-LABEL uk.ac.sanger.cgp.version="3.1.4"
-
-RUN apt-get -yq update
-RUN apt-get install -yq --no-install-recommends \
-apt-transport-https \
-locales \
-curl \
-ca-certificates \
-libperlio-gzip-perl \
-bzip2 \
-psmisc \
-time \
-zlib1g \
-liblzma5 \
-libncurses5 \
-p11-kit \
-unattended-upgrades && \
-unattended-upgrade -d -v && \
-apt-get remove -yq unattended-upgrades && \
-apt-get autoremove -yq
+LABEL uk.ac.sanger.cgp.version="3.2.0"
 
-RUN locale-gen en_US.UTF-8
-RUN update-locale LANG=en_US.UTF-8
-
-ENV OPT /opt/wtsi-cgp
-ENV PATH $OPT/bin:$OPT/biobambam2/bin:$PATH
-ENV PERL5LIB $OPT/lib/perl5
-ENV LD_LIBRARY_PATH $OPT/lib
-ENV LC_ALL en_US.UTF-8
-ENV LANG en_US.UTF-8
-
-RUN mkdir -p $OPT
-COPY --from=builder $OPT $OPT
+USER root
 
 ADD scripts/mapping.sh $OPT/bin/mapping.sh
 ADD scripts/ds-cgpmap.pl $OPT/bin/ds-cgpmap.pl
-RUN chmod a+x $OPT/bin/mapping.sh $OPT/bin/ds-cgpmap.pl
-
-## USER CONFIGURATION
-RUN adduser --disabled-password --gecos '' ubuntu && chsh -s /bin/bash && mkdir -p /home/ubuntu
+RUN chmod +rx $OPT/bin/mapping.sh $OPT/bin/ds-cgpmap.pl
 
-USER    ubuntu
+USER ubuntu
 WORKDIR /home/ubuntu
 
 CMD ["/bin/bash"]

cwls/cgpmap-bamBaiOut.cwl

@@ -76,14 +76,52 @@ inputs:
       position: 7
       separate: true
 
+  threads:
+    type: int?
+    doc: "Number of CPUs to use where possible - 0/null/not defined to query host for max"
+    inputBinding:
+      prefix: -threads
+      position: 8
+      separate: true
+
+  bwamem2:
+    type: boolean
+    doc: "Use bwa-mem2 binary"
+    inputBinding:
+      prefix: -bwamem2
+      position: 9
+
+  nomarkdup:
+    type: boolean
+    doc: "Do not mark duplicates"
+    inputBinding:
+      prefix: -nomarkdup
+      position: 10
+
+  dupmode:
+    type: string?
+    doc: "Duplicate mode as defined by 'samtools markdup' (t)emplate or (s)equence"
+    default: 't'
+    inputBinding:
+      prefix: -dupmode
+      position: 11
+      separate: true
+
+  legacy:
+    type: boolean
+    doc: "Use legacy merge/dupmark from biobambam2 tools, slower, more memory"
+    inputBinding:
+      prefix: -legacy
+      position: 12
+
   seq_in:
     type:
     - 'null'
     - type: array
       items: File
     doc: "Can be BAM, CRAM, fastq (paired or interleaved), BAM/CRAM can be mixed together but not FASTQ."
     inputBinding:
-      position: 8
+      position: 13
 
 outputs:
   out_bam:
@@ -99,8 +137,7 @@ outputs:
 
 baseCommand: ["/opt/wtsi-cgp/bin/ds-cgpmap.pl"]
 
-$schemas:
-  - http://schema.org/docs/schema_org_rdfa.html
+$schemas: [ http://schema.org/version/9.0/schemaorg-current-http.rdf ]
 
 $namespaces:
   s: http://schema.org/