Merge pull request #133 from biowdl/BIOWDL-302

Simplify cutadapt.

.travis.yml

-language: java
+# We use conda to install cromwell.
+
+language: python
+
+python:
+  - 3.6
+
+before_install:
+  # Install conda
+  - export MINICONDA=${HOME}/miniconda
+  - export PATH=${MINICONDA}/bin:${PATH}
+  - wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
+  - bash miniconda.sh -b -f -p ${MINICONDA}
+  - conda config --set always_yes yes
+  - conda config --add channels defaults
+  - conda config --add channels bioconda
+  - conda config --add channels conda-forge
+
+install:
+  - conda install cromwell
+
 script:
-- set -e
-- export CROMWELL_VERSION=35
-- wget https://github.com/broadinstitute/cromwell/releases/download/$CROMWELL_VERSION/womtool-$CROMWELL_VERSION.jar
-- for F in `find -name "*.wdl"`; do echo $F; java -jar womtool-*.jar validate $F; done
-- 'if [ "$TRAVIS_PULL_REQUEST" != "false" ]; then git submodule foreach --recursive git checkout $TRAVIS_BRANCH && git submodule foreach --recursive git pull; fi'
-- "git diff --exit-code || (echo ERROR: Git changes detected. Please update submodules && exit 1)"
+  - set -e
+  - for FILE in $(find -name "*.wdl"); do echo $FILE; womtool validate $FILE; done
+  - 'if [ "$TRAVIS_PULL_REQUEST" != "false" ]; then git submodule foreach git checkout develop && git submodule foreach git pull; fi'
+  - "git diff --exit-code || (echo ERROR: Git changes detected. Please update submodules && exit 1)"

CHANGELOG.md

@@ -11,6 +11,7 @@ that users understand how the changes affect the new version.
 
 version 1.0.0-dev
 ---------------------------
++ Cutadapt: simplify interface
 + Bigger memory multiplier in mutect to take in account bigger vmem usage
 + Cutadapt: Remove default adapter
 + Fastqsplitter: use version 1.1.

cutadapt.wdl

@@ -7,15 +7,12 @@ task Cutadapt {
         String read1output = "cut_r1.fq.gz"
         String? read2output
         String? format
-        Array[String]+? adapter
-        Array[String]+? front
-        Array[String]+? anywhere
-        Array[String]+? adapterRead2
-        Array[String]+? frontRead2
-        Array[String]+? anywhereRead2
-        Array[String]+? adapterBoth
-        # contaminations = anywhereBoth
-        Array[String]+? contaminations
+        Array[String] adapter = []
+        Array[String] front = []
+        Array[String] anywhere = []
+        Array[String] adapterRead2 = []
+        Array[String] frontRead2 = []
+        Array[String] anywhereRead2 = []
         Boolean? interleaved
         String? pairFilter
         Float? errorRate
@@ -73,25 +70,7 @@ task Cutadapt {
         then "mkdir -p $(dirname " + realRead2output + ")"
         else ""
 
-    # FIXME: This crappy overengineering can be removed once cromwell can handle subworkflow inputs correctly.
-    # Some WDL magic here to set both adapters with one setting.
-    # If then else's are needed to keep the variable optional and undefined
-    Array[String]+? adapterForward = if (defined(adapter) || defined(adapterBoth))
-                                     then select_first([adapter, adapterBoth])
-                                     else adapter
-    # Check if read2 is defined before applying adapters.
-    Array[String]+? adapterReverse = if (defined(read2) && (defined(adapterRead2) || defined(adapterBoth)))
-                                     then select_first([adapterRead2, adapterBoth])
-                                     else adapterRead2
-
-    # Same for contaminations
-    Array[String]+? anywhereForward = if (defined(anywhere) || defined(contaminations))
-                                      then select_first([anywhere, contaminations])
-                                      else anywhere
-    Array[String]+? anywhereReverse = if (defined(read2) && (defined(anywhereRead2) || defined(contaminations)))
-                                      then select_first([anywhereRead2, contaminations])
-                                      else anywhereRead2
-
+    # FIXME: Use prefix() function for adapter, adapterRead2, etc.
     command {
         set -e
         ~{"mkdir -p $(dirname " + read1output + ")"}
@@ -99,12 +78,12 @@ task Cutadapt {
         cutadapt \
         ~{"--cores=" + cores} \
         ~{true="-Z" false="" Z} \
-        ~{true="-a" false="" defined(adapterForward)} ~{sep=" -a " adapterForward} \
-        ~{true="-A" false="" defined(adapterReverse)} ~{sep=" -A " adapterReverse} \
-        ~{true="-g" false="" defined(front)} ~{sep=" -g " front} \
-        ~{true="-G" false="" defined(frontRead2)} ~{sep=" -G " frontRead2} \
-        ~{true="-b" false="" defined(anywhereForward)} ~{sep=" -b " anywhereForward} \
-        ~{true="-B" false="" defined(anywhereReverse)} ~{sep=" -B " anywhereReverse} \
+        ~{true="-a" false="" length(adapter) > 0} ~{sep=" -a " adapter} \
+        ~{true="-A" false="" length(adapterRead2) > 0} ~{sep=" -A " adapterRead2} \
+        ~{true="-g" false="" length(front) > 0} ~{sep=" -g " front} \
+        ~{true="-G" false="" length(frontRead2) > 0} ~{sep=" -G " frontRead2} \
+        ~{true="-b" false="" length(anywhere) > 0} ~{sep=" -b " anywhere} \
+        ~{true="-B" false="" length(anywhereRead2) > 0} ~{sep=" -B " anywhereRead2} \
         --output ~{read1output} ~{if defined(read2) then "-p " + realRead2output else ""} \
         ~{"--to-short-output " + tooShortOutputPath} \
         ~{"--to-short-paired-output " + tooShortPairedOutputPath} \