Merge remote-tracking branch 'origin/develop' into memory_strings

CHANGELOG.md

@@ -11,6 +11,8 @@ that users understand how the changes affect the new version.
 
 version 1.1.0-dev
 ---------------------------
++ Use the biowdl-input-converter container for JsonToYaml, to reduce the amount of containers needed.
++ Add biowdl-input-converter and remove SampleConfigToSampleReadgroupLists which it replaces.
 + GATK.GenotypeGVCFs: Increased memoryMultiplier from 2.0 to 3.0 
 + Minimap2: Add -k option to minimap2 mapping
 + Added bwakit task

biowdl.wdl

+version 1.0
+
+# Copyright (c) 2018 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+task InputConverter {
+    input {
+        File samplesheet
+        String outputFile = "samplesheet.json"
+        # File checking only works when:
+        # 1. Paths are absolute
+        # 2. When containers have the directory with the files mounted.
+        # Therefore this functionality does not work well with cromwell.
+        Boolean skipFileCheck=true
+        Boolean checkFileMd5sums=false
+        Boolean old=false
+        String dockerImage = "quay.io/biocontainers/biowdl-input-converter:0.1.0--py_0"
+    }
+
+    command <<<
+        biowdl-input-converter \
+        -o ~{outputFile} \
+        ~{true="--skip-file-check" false="" skipFileCheck} \
+        ~{true="--check-file-md5sums" false="" checkFileMd5sums} \
+        ~{true="--old" false="" old} \
+        ~{samplesheet}
+    >>>
+
+    output {
+        File json = outputFile
+    }
+
+    runtime {
+        docker: dockerImage
+    }
+}

common.wdl

@@ -134,47 +134,6 @@ task MapMd5 {
     }
 }
 
-task SampleConfigToSampleReadgroupLists {
-    input {
-        File yaml
-        String outputJson = "samples.json"
-
-        String dockerImage = "biowdl/pyyaml:3.13-py37-slim"
-    }
-
-    command <<<
-        set -e
-        mkdir -p $(dirname ~{outputJson})
-        python <<CODE
-        import json
-        import yaml
-        with open("~{yaml}", "r") as input_yaml:
-            sample_config = yaml.load(input_yaml)
-
-        sample_rg_lists = []
-        for sample in sample_config["samples"]:
-            new_sample = {"readgroups": [], "id": sample['id']}
-            for library in sample["libraries"]:
-                for readgroup in library["readgroups"]:
-                    new_readgroup = {'lib_id': library['id'], 'id': readgroup['id']}
-                    # Having a nested "reads" struct does not make any sense.
-                    new_readgroup.update(readgroup["reads"])
-                    new_sample['readgroups'].append(new_readgroup)
-            sample_rg_lists.append(new_sample)
-        sample_mod_config = {"samples": sample_rg_lists}
-        with open("~{outputJson}", "w") as output_json:
-            json.dump(sample_mod_config, output_json)
-        CODE
-    >>>
-
-    output {
-        File json = outputJson
-    }
-
-    runtime {
-        docker: dockerImage
-    }
-}
 
 task StringArrayMd5 {
     input {
@@ -202,7 +161,8 @@ task YamlToJson {
     input {
         File yaml
         String outputJson = basename(yaml, "\.ya?ml$") + ".json"
-        String dockerImage = "biowdl/pyyaml:3.13-py37-slim"
+        # biowdl-input-converter has python and pyyaml.
+        String dockerImage = "quay.io/biocontainers/biowdl-input-converter:0.1.0--py_0"
     }
     command {
         set -e