Commit be83f64f authored by Xavier Grand's avatar Xavier Grand
Browse files

Modif bedtools module pour fonction closest

parent e27e275a
......@@ -16,7 +16,7 @@
# limitations under the License.
[[ "$NXF_DEBUG" == 'x' ]] && set -x
NXF_VER=${NXF_VER:-'21.04.3'}
NXF_VER=${NXF_VER:-'21.10.6'}
NXF_ORG=${NXF_ORG:-'nextflow-io'}
NXF_HOME=${NXF_HOME:-$HOME/.nextflow}
NXF_PROT=${NXF_PROT:-'https'}
......@@ -24,6 +24,7 @@ NXF_BASE=${NXF_BASE:-$NXF_PROT://www.nextflow.io/releases}
NXF_TEMP=${NXF_TEMP:-$TMPDIR}
NXF_DIST=${NXF_DIST:-$NXF_HOME/framework}
NXF_CLI="$0 $@"
NXF_CLI_OPTS=${NXF_CLI_OPTS:-}
export NXF_CLI
export NXF_ORG
......@@ -98,10 +99,10 @@ function resolve_link() {
realpath "$1"
elif command -v readlink &>/dev/null; then
local target="$1"
cd $(dirname $target); target=$(basename $target)
cd "$(dirname "$target")"; target="$(basename "$target")"
while [ -L "$target" ]; do
target="$(readlink "$target")"
cd $(dirname $target); target=$(basename $target)
cd "$(dirname "$target")"; target="$(basename "$target")"
done
echo "$(cd "$(dirname "$target")"; pwd -P)/$target"
else
......@@ -196,6 +197,10 @@ dockerize=''
declare -a jvmopts=()
declare -a args=("$@")
declare -a commands=(clone config drop help history info ls pull run view node console kuberun)
# $NXF_CLI_OPTS allow to pass arbitrary cli opts via the environment
# note: do not wrap with quotes because the variable can be used to specify more than on option separate by blanks
[ "$NXF_CLI_OPTS" ] && args+=($NXF_CLI_OPTS)
cmd=''
while [[ $# != 0 ]]; do
case $1 in
......@@ -333,8 +338,8 @@ else
version_check="^(1.7|1.8)"
version_message="Java 7 or 8"
else
version_check="^(1.8|9|10|11|12|13|14|15)"
version_message="Java 8 or later"
version_check="^(1.8|9|10|11|12|13|14|15|16|17)"
version_message="Java 8 or later (up to 17)"
fi
if [[ ! $JAVA_VER =~ $version_check ]]; then
echo_red "ERROR: Cannot find Java or it's a wrong version -- please make sure that $version_message is installed"
......@@ -345,8 +350,8 @@ else
fi
exit 1
fi
if [[ ! $JAVA_VER =~ ^(1.8|9|10|11|12|13|14|15) ]]; then
echo_yellow "NOTE: Nextflow is not tested with Java $JAVA_VER -- It's recommended the use of version 8 up to 15\n"
if [[ ! $JAVA_VER =~ ^(1.8|9|10|11|12|13|14|15|16|17) ]]; then
echo_yellow "NOTE: Nextflow is not tested with Java $JAVA_VER -- It's recommended the use of version 8 up to 17\n"
elif [[ ! $JAVA_VER =~ ^(1.8|9|10|11) && $NXF_MODE == ignite ]]; then
echo_yellow "WARN: Apache Ignite executor is not tested with Java $JAVA_VER -- It's recommended the use of version 8 up to 11\n"
fi
......@@ -373,7 +378,7 @@ fi
[[ "$JAVA_HOME" ]] && JAVA_OPTS+=(-Dcapsule.java.home="$JAVA_HOME")
[[ "$CAPSULE_LOG" ]] && JAVA_OPTS+=(-Dcapsule.log=$CAPSULE_LOG)
[[ "$CAPSULE_RESET" ]] && JAVA_OPTS+=(-Dcapsule.reset=true)
[[ "$cmd" != "run" && "$cmd" != "node" ]] && JAVA_OPTS+=(-XX:+TieredCompilation -XX:TieredStopAtLevel=1)
[[ "$cmd" != "run" && "$cmd" != "node" ]] && JAVA_OPTS+=(-XX:+TieredCompilation -XX:TieredStopAtLevel=1 -Dcom.sun.security.enableAIAcaIssuers=true)
[[ "$NXF_OPTS" ]] && JAVA_OPTS+=($NXF_OPTS)
[[ "$NXF_CLASSPATH" ]] && export NXF_CLASSPATH
[[ "$NXF_GRAB" ]] && export NXF_GRAB
......@@ -422,18 +427,21 @@ else
LAUNCH_FILE="${NXF_LAUNCHER}/classpath-$(env_md5)"
fi
if [ -s "$LAUNCH_FILE" ] && [ "$LAUNCH_FILE" -nt "$NXF_BIN" ]; then
launcher=($(cat "$LAUNCH_FILE"))
declare -a launcher="($(cat "$LAUNCH_FILE"))"
else
# otherwise run the capsule and get the result classpath in the 'launcher' and save it to a file
cli=($("$JAVA_CMD" "${JAVA_OPTS[@]}" -jar "$NXF_BIN"))
[[ $? -ne 0 ]] && echo_red 'Unable to initialize nextflow environment' && exit 1
if [[ "$JAVA_VER" =~ ^(9|10|11|12|13|14|15) ]]; then
if [[ "$JAVA_VER" =~ ^(9|10|11|12|13|14|15|16|17) ]]; then
launcher=("${cli[@]:0:1}")
launcher+=(--add-opens=java.base/java.lang=ALL-UNNAMED)
launcher+=(--add-opens=java.base/java.io=ALL-UNNAMED)
launcher+=(--add-opens=java.base/java.nio=ALL-UNNAMED)
launcher+=(--add-opens=java.base/java.net=ALL-UNNAMED)
launcher+=(--add-opens=java.base/java.util=ALL-UNNAMED)
launcher+=(--add-opens=java.base/java.util.concurrent.locks=ALL-UNNAMED)
launcher+=(--add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED)
launcher+=(--add-opens=java.base/java.nio.file.spi=ALL-UNNAMED)
launcher+=(--add-opens=java.base/sun.nio.ch=ALL-UNNAMED)
launcher+=(--add-opens=java.base/sun.nio.fs=ALL-UNNAMED)
......@@ -442,7 +450,6 @@ else
launcher+=(--add-opens=java.base/sun.net.www.protocol.ftp=ALL-UNNAMED)
launcher+=(--add-opens=java.base/sun.net.www.protocol.file=ALL-UNNAMED)
launcher+=(--add-opens=java.base/jdk.internal.misc=ALL-UNNAMED)
launcher+=(--illegal-access=deny)
launcher+=("${cli[@]:1}")
else
launcher=("${cli[@]}")
......
......@@ -215,6 +215,8 @@ process nearestExon_To_Peak {
script:
"""
bedtools closest -d -a ${bed} -b ${exons} > ${bed_id}_nearestExon.bed
bedtools closest -a ${exons} -b ${bed} -D a -iu > ${bed_id}_nearestExon.bed
bedtools closest -a ${exons} -b ${bed} -D a -id >> ${bed_id}_nearestExon.bed
bedtools sort -i ${bed_id}_nearestExon.bed > ${bed_id}_Distance_To_Exons_FasterDB_sorted.bed
"""
}
\ No newline at end of file
......@@ -14,7 +14,10 @@ Channel
fastq_files = fastq1
.concat(fastq2)
.groupBy
.set { fastq_files }
println(fastq_files)
/*
idx_genome = "${params.idx}*.bt2"
......
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