feat: upgrade to GATK 4.3.0 for gcnv calling (#218)

snappy_wrappers/wrappers/gcnv/annotate_gc/wrapper.py

@@ -5,7 +5,6 @@
 
 from snakemake.shell import shell
 
-
 # Pick the target BED file to use.  If it goes by the name "default" then we
 # simply take the one at xhmm/path_target_interval_list.  Otherwise, we
 # have to go through the list in xhmm/path_target_interval_list_mapping.
@@ -31,8 +30,8 @@
 gatk AnnotateIntervals \
     --interval-merging-rule OVERLAPPING_ONLY \
     --mappability-track {map_bed} \
-    -R {snakemake.config[static_data_config][reference][path]} \
-    -L {snakemake.input.interval_list} \
-    -O {snakemake.output.tsv}
+    --reference {snakemake.config[static_data_config][reference][path]} \
+    --intervals {snakemake.input.interval_list} \
+    --output {snakemake.output.tsv}
 """
 )

snappy_wrappers/wrappers/gcnv/contig_ploidy/wrapper.py

@@ -9,6 +9,8 @@
 export TMPDIR=$(mktemp -d)
 trap "rm -rf $TMPDIR" ERR EXIT
 
+export MKL_NUM_THREADS={snakemake.threads}
+export OMP_NUM_THREADS={snakemake.threads}
 export THEANO_FLAGS="base_compiledir=$TMPDIR/theano_compile_dir"
 
 PRIORS=$TMPDIR/ploidy_priors.tsv

snappy_wrappers/wrappers/gcnv/contig_ploidy_case_mode/environment.yaml

@@ -0,0 +1 @@
+../environment.yaml

snappy_wrappers/wrappers/gcnv/environment.yaml

@@ -1,8 +1,42 @@
 channels:
   - conda-forge
   - bioconda
+  - file:///data/gpfs-1/scratch/users/holtgrem_c/art/LinuxArtifacts/packages
 dependencies:
-  - gatk4 ==4.1.7.0
-  - gcnvkernel ==0.7
+  - gatk4 ==4.3.0.0
   - bcftools
   - htslib
+  - parallel
+  # the hard to install gcnvkernel
+  - gcnvkernel ==0.8
+  # gcnvkernel dependencies
+  - conda-forge::python =3.6.10
+  - pip =20.0.2
+  - conda-forge::mkl =2019.5
+  - conda-forge::mkl-service =2.3.0
+  - conda-forge::numpy =1.17.5
+  - conda-forge::theano =1.0.4
+  - defaults::tensorflow =1.15.0
+  - conda-forge::scipy =1.0.0
+  - conda-forge::pymc3 =3.1
+  - conda-forge::h5py =2.10.0 
+  - conda-forge::keras =2.2.4
+  - defaults::intel-openmp =2019.4
+  - conda-forge::scikit-learn =0.23.1
+  - conda-forge::matplotlib =3.2.1
+  - conda-forge::pandas =1.0.3
+  - conda-forge::typing_extensions =4.1.1
+  - conda-forge::dill =0.3.4
+  - r-base =3.6.2
+  - r-data.table =1.12.8
+  - r-dplyr =0.8.5
+  - r-getopt =1.20.3
+  - r-ggplot2 =3.3.0
+  - r-gplots =3.0.3
+  - r-gsalib =2.1
+  - r-optparse =1.6.4
+  - r-backports =1.1.10
+  - biopython =1.76
+  - pyvcf =0.6.8
+  - bioconda::pysam =0.15.3
+

snappy_wrappers/wrappers/gcnv/filter_intervals/wrapper.py

@@ -21,8 +21,6 @@
     r"""
 set -x
 
-
-
 gatk --java-options "-Xmx{mem_jvm}m" \
     FilterIntervals \
     --intervals {snakemake.input.interval_list} \

snappy_wrappers/wrappers/gcnv/post_germline_calls_case_mode/environment.yaml

@@ -0,0 +1 @@
+../environment.yaml