fix: adjustment of manta wrapper for sv_calling_wgs

snappy_wrappers/wrappers/manta/germline_targeted/wrapper.py

@@ -75,6 +75,8 @@
 cp -ra $workdir/results $outdir
 rm -rf $workdir
 
+sleep 1min  # for good measure
+
 pushd $outdir
 tar czf results.tar.gz results
 ln -sr results/variants/diploidSV.vcf.gz $(basename {snakemake.output.vcf})

snappy_wrappers/wrappers/manta/germline_wgs/wrapper.py

@@ -1,26 +1,65 @@
-# -*- coding: utf-8 -*-
-"""Wrapper for running Manta in germline variant calling mode on WGS data
-"""
+from snakemake import shell
 
-from snakemake.shell import shell
+__author__ = "Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>"
 
-__author__ = "Manuel Holtgrewe"
-__email__ = "manuel.holtgrewe@bih-charite.de"
+DEF_HELPER_FUNCS = r"""
+compute-md5()
+{
+    if [[ $# -ne 2 ]]; then
+        >&2 echo "Invalid number of arguments: $#"
+        exit 1
+    fi
+    md5sum $1 \
+    | awk '{ gsub(/.*\//, "", $2); print; }' \
+    > $2
+}
+"""
 
 shell(
     r"""
-# -----------------------------------------------------------------------------
-# Redirect stderr to log file by default and enable printing executed commands
-exec 2> >(tee -a "{snakemake.log}")
 set -x
-# -----------------------------------------------------------------------------
+
+# Write files for reproducibility -----------------------------------------------------------------
+
+{DEF_HELPER_FUNCS}
+
+# Write out information about conda and save a copy of the wrapper with picked variables
+# as well as the environment.yaml file.
+conda list >{snakemake.log.conda_list}
+conda info >{snakemake.log.conda_info}
+compute-md5 {snakemake.log.conda_list} {snakemake.log.conda_list_md5}
+compute-md5 {snakemake.log.conda_info} {snakemake.log.conda_info_md5}
+cp {__real_file__} {snakemake.log.wrapper}
+compute-md5 {snakemake.log.wrapper} {snakemake.log.wrapper_md5}
+cp $(dirname {__file__})/environment.yaml {snakemake.log.env_yaml}
+compute-md5 {snakemake.log.env_yaml} {snakemake.log.env_yaml_md5}
+
+# Also pipe stderr to log file --------------------------------------------------------------------
+
+if [[ -n "{snakemake.log.log}" ]]; then
+    if [[ "$(set +e; tty; set -e)" != "" ]]; then
+        rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log})
+        exec 2> >(tee -a "{snakemake.log.log}" >&2)
+    else
+        rm -f "{snakemake.log.log}" && mkdir -p $(dirname {snakemake.log.log})
+        echo "No tty, logging disabled" >"{snakemake.log.log}"
+    fi
+fi
+
+# Create auto-cleaned temporary directory
+export TMPDIR=$(mktemp -d)
+trap "rm -rf $TMPDIR" EXIT
+
+# Run actual tools --------------------------------------------------------------------------------
 
 basedir=$(dirname $(dirname {snakemake.output.vcf}))
 workdir=$basedir/work
 outdir=$basedir/out
 
 # Ensure the working directory is removed, configManta.py will bail out if it already exists
 trap "rm -rf \"$workdir\"" EXIT
+# Clear out $outdir, there may be some old files remaining that are not governed by Snakemake
+rm -rf $outdir/*
 
 configManta.py \
     --referenceFasta {snakemake.config[static_data_config][reference][path]} \
@@ -35,6 +74,8 @@
 cp -ra $workdir/results $outdir
 rm -rf $workdir
 
+sleep 1min  # for good measure
+
 pushd $outdir
 tar czf results.tar.gz results
 ln -sr results/variants/diploidSV.vcf.gz $(basename {snakemake.output.vcf})
@@ -43,9 +84,28 @@
     $(basename {snakemake.output.vcf} .vcf.gz).candidates.vcf.gz
 ln -sr results/variants/candidateSV.vcf.gz.tbi \
     $(basename {snakemake.output.vcf} .vcf.gz).candidates.vcf.gz.tbi
+popd
+
+# Compute MD5 sums on output files
+compute-md5 {snakemake.output.vcf} {snakemake.output.vcf_md5}
+compute-md5 {snakemake.output.vcf_tbi} {snakemake.output.vcf_tbi_md5}
+
+# Create output links -----------------------------------------------------------------------------
 
-for f in results.tar.gz *.vcf.gz *.tbi; do
-    md5sum $f >$f.md5
+for path in {snakemake.output.output_links}; do
+  dst=$path
+  src=work/${{dst#output/}}
+  ln -sr $src $dst
 done
 """
 )
+
+# Compute MD5 sums of logs.
+shell(
+    r"""
+{DEF_HELPER_FUNCS}
+
+sleep 1s  # try to wait for log file flush
+compute-md5 {snakemake.log.log} {snakemake.log.log_md5}
+"""
+)