Adding wrapper files

README.md

@@ -1 +1,3 @@
 # broad-variant-pipeline-tool
+
+NOTE: The Docker container needed to run this tool must be obtained from the Broad after signing MTA

broad_variant_pipeline.sh

@@ -0,0 +1,50 @@
+#!/bin/bash
+export INDIVIDUAL_ID=$1
+export BAM_TUMOR=$2
+export BAM_TUMOR_BAI=$3
+export BAM_NORMAL=$4
+export BAM_NORMAL_BAI=$5
+export REF_DIR=$6
+export FINALRESULTSDIR=`readlink -f $7`
+
+ln -s $BAM_TUMOR tumor.bam
+ln -s $BAM_TUMOR_BAI tumor.bam.bai
+ln -s $BAM_NORMAL normal.bam
+ln -s $BAM_NORMAL_BAI normal.bam.bai
+
+ln -s $REF_DIR /cga/fh/pcawg_pipeline/refdata
+
+PIPELINE=/cga/fh/pcawg_pipeline/pipelines/pcawg_pipeline_v5.py
+
+export PIPETTE_SERVER_DIR=/cga/fh/pcawg_pipeline/utils/pipette_server
+
+export COMMDIR=$FINALRESULTSDIR/jobResults_pipette/status
+#OUTDIR contains the intermediate files
+export OUTDIR=$FINALRESULTSDIR/jobResults_pipette/jobs/$INDIVIDUAL_ID
+#FINALRESULTSDIR contains all the files that should be kept after the pipeline completes
+#export FINALRESULTSDIR=/cga/fh/pcawg_pipeline/jobResults_pipette/results
+
+rm -rf $COMMDIR
+mkdir -p $COMMDIR
+
+set -e
+
+python3 $PIPETTE_SERVER_DIR/pipetteSynchronousRunner.py $COMMDIR $OUTDIR $PIPELINE $COMMDIR $OUTDIR $INDIVIDUAL_ID `pwd`/tumor.bam `pwd`/normal.bam # > run.out 2> run.err
+
+find $OUTDIR -name pipette.module.usage.txt  | xargs  sh -c 'for f; do cat "$f" ; done' true |sort | uniq > $FINALRESULTSDIR/summary.usage.txt
+
+mkdir $FINALRESULTSDIR/gnos_vcfs
+#cp $OUTDIR/links_for_gnos/*/*.vcf.gz $FINALRESULTSDIR/gnos_vcfs/
+cp $FINALRESULTSDIR/jobResults_pipette/jobs/*/links_for_gnos/tabix_dRanger/*.broad-dRanger.DATECODE.somatic.sv.vcf.gz broad-dRanger.DATECODE.somatic.sv.vcf.gz
+cp $FINALRESULTSDIR/jobResults_pipette/jobs/*/links_for_gnos/tabix_merge_sv_vcf/*.broad-dRanger_snowman.DATECODE.somatic.sv.vcf.gz broad-dRanger_snowman.DATECODE.somatic.sv.vcf.gz
+cp $FINALRESULTSDIR/jobResults_pipette/jobs/*/links_for_gnos/tabix_mutect/*.broad-mutect.DATECODE.somatic.snv_mnv.vcf.gz broad-mutect.DATECODE.somatic.snv_mnv.vcf.gz
+cp $FINALRESULTSDIR/jobResults_pipette/jobs/*/links_for_gnos/tabix_snowman_germline_indel/*.broad-snowman.DATECODE.germline.indel.vcf.gz broad-snowman.DATECODE.germline.indel.vcf.gz
+cp $FINALRESULTSDIR/jobResults_pipette/jobs/*/links_for_gnos/tabix_snowman_germline_sv/*.broad-snowman.DATECODE.germline.sv.vcf.gz broad-snowman.DATECODE.germline.sv.vcf.gz
+cp $FINALRESULTSDIR/jobResults_pipette/jobs/*/links_for_gnos/tabix_snowman_somatic_indel/*.broad-snowman.DATECODE.somatic.indel.vcf.gz broad-snowman.DATECODE.somatic.indel.vcf.gz
+cp $FINALRESULTSDIR/jobResults_pipette/jobs/*/links_for_gnos/tabix_snowman_somatic_sv/*.broad-snowman.DATECODE.somatic.sv.vcf.gz broad-snowman.DATECODE.somatic.sv.vcf.gz
+
+#collect the file outputs for return back to Broad
+tar -cvhf $FINALRESULTSDIR/broad.tar.gz $OUTDIR/links_for_broad
+
+#display any failing modules
+cat summary.usage.txt

broad_variant_pipeline.xml

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+<tool id="broad_variant_pipline" name="BroadVariantPipeline" version="1.0.0">
+    <description></description>
+    <requirements>
+        <!-- This docker image is closed source and must be obtained seperately -->
+        <container type="docker">broad_variant_pipeline</container>
+    </requirements>
+    <command interpreter="bash">
+broad_variant_pipeline.sh ${sample_id} ${tumor_bam} ${tumor_bam.metadata.bam_index} ${normal_bam} ${normal_bam.metadata.bam_index} ${broad_ref_dir} ./
+    </command>
+
+    <inputs>
+        <param name="sample_id" type="text" label="Sample Name"/>
+        <param name="tumor_bam" type="data" format="bam" label="Tumor BAM file"/>
+        <param name="normal_bam" type="data" format="bam" label="Normal BAM file"/>
+        <param name="broad_ref_dir" type="select" label="Broad Reference Directory">
+            <options from_file="broad_ref_dir.loc">
+                <column name="name" index="0"/>
+                <column name="value" index="1"/>
+            </options>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="dRanger" format="vcf_bgzip" label="broad-dRanger.DATECODE.somatic.sv.vcf.gz" from_work_dir="broad-dRanger.DATECODE.somatic.sv.vcf.gz"/>
+        <data name="mutect" format="vcf_bgzip" label="broad-mutect.DATECODE.somatic.snv_mnv.vcf.gz" from_work_dir="broad-mutect.DATECODE.somatic.snv_mnv.vcf.gz"/>
+        <data name="snowman_dRanger" format="vcf_bgzip" label="broad-dRanger_snowman.DATECODE.somatic.sv.vcf.gz" from_work_dir="broad-dRanger_snowman.DATECODE.somatic.sv.vcf.gz"/>
+        <data name="snowman_germline_indel" format="vcf_bgzip" label="broad-snowman.DATECODE.germline.indel.vcf.gz" from_work_dir="broad-snowman.DATECODE.germline.indel.vcf.gz"/>
+        <data name="snowman_germline_sv" format="vcf_bgzip" label="broad-snowman.DATECODE.germline.sv.vcf.gz" from_work_dir="broad-snowman.DATECODE.germline.sv.vcf.gz"/>
+        <data name="snowman_somatic_indel" format="vcf_bgzip" label="broad-snowman.DATECODE.somatic.indel.vcf.gz" from_work_dir="broad-snowman.DATECODE.somatic.indel.vcf.gz"/>
+        <data name="snowman_somatic_sv" format="vcf_bgzip" label="broad-snowman.DATECODE.somatic.sv.vcf.gz" from_work_dir="broad-snowman.DATECODE.somatic.sv.vcf.gz"/>
+        <data format="data" name="broad_output" label="broad.tar.gz" from_work_dir="broad.tar.gz"/>
+    </outputs>
+    <stdio>
+        <exit_code range="1:" level="fatal" />
+    </stdio>
+    <help>
+If you want help, you've come to the wrong place
+  </help>
+</tool>