diff --git a/nextflow b/nextflow
deleted file mode 100755
index 603960e2483eeee204814dd3c56a4fa4a1562b47..0000000000000000000000000000000000000000
--- a/nextflow
+++ /dev/null
@@ -1,447 +0,0 @@
-#!/usr/bin/env bash
-#
-# Copyright 2020-2022, Seqera Labs
-# Copyright 2013-2019, Centre for Genomic Regulation (CRG)
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-[[ "$NXF_DEBUG" == 'x' ]] && set -x
-NXF_VER=${NXF_VER:-'22.10.3'}
-NXF_ORG=${NXF_ORG:-'nextflow-io'}
-NXF_HOME=${NXF_HOME:-$HOME/.nextflow}
-NXF_PROT=${NXF_PROT:-'https'}
-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
-export NXF_HOME
-
-if [[ $TERM && $TERM != 'dumb' ]]; then
-if command -v tput &>/dev/null; then
-GREEN=$(tput setaf 2; tput bold)
-YELLOW=$(tput setaf 3)
-RED=$(tput setaf 1)
-NORMAL=$(tput sgr0)
-fi
-fi
-
-function echo_red() {
- >&2 echo -e "$RED$*$NORMAL"
-}
-
-function echo_green() {
- echo -e "$GREEN$*$NORMAL"
-}
-
-function echo_yellow() {
- >&2 echo -e "$YELLOW$*$NORMAL"
-}
-
-function die() {
- echo_red "$*"
- exit 1
-}
-
-function get_abs_filename() {
- echo "$(cd "$(dirname "$1")" && pwd)/$(basename "$1")"
-}
-
-function get() {
- if command -v curl &>/dev/null; then
- GET="curl -fsSL '$1' -o '$2'"
- elif command -v wget &>/dev/null; then
- GET="wget -q '$1' -O '$2'"
- else
- echo_red "ERROR: Cannot find 'curl' nor 'wget' utility -- please install one of them"
- exit 1
- fi
-
- printf "Downloading nextflow dependencies. It may require a few seconds, please wait .. "
- eval $GET; status=$?
- printf "\r\033[K"
- if [ $status -ne 0 ]; then
- echo_red "ERROR: Cannot download nextflow required file -- make sure you can connect to the internet"
- echo ""
- echo "Alternatively you can try to download this file:"
- echo " $1"
- echo ""
- echo "and save it as:"
- echo " ${3:-$2}"
- echo ""
- exit 1
- fi
-}
-
-function make_temp() {
- local base=${NXF_TEMP:=$PWD}
- if [ "$(uname)" = 'Darwin' ]; then mktemp "${base}/nxf-tmp.XXXXXX" || exit $?
- else mktemp -t nxf-tmp.XXXXXX -p "${base}" || exit $?
- fi
-}
-
-function resolve_link() {
- [[ ! -f $1 ]] && exit 1
- if command -v realpath &>/dev/null; then
- realpath "$1"
- elif command -v readlink &>/dev/null; then
- local target="$1"
- cd "$(dirname "$target")"; target="$(basename "$target")"
- while [ -L "$target" ]; do
- target="$(readlink "$target")"
- cd "$(dirname "$target")"; target="$(basename "$target")"
- done
- echo "$(cd "$(dirname "$target")"; pwd -P)/$target"
- else
- echo_yellow "WARN: Neither \`realpath\` nor \`readlink\` command can be found"
- exit 1
- fi
-}
-
-function current_ver() {
- [[ $NXF_EDGE == 1 ]] && printf 'edge' || printf 'latest'
-}
-
-function install() {
- local tmpfile=$(make_temp)
- local version=$(set +u; [[ $NXF_VER ]] && printf "v$NXF_VER" || current_ver)
- local action="a=${2:-default}"
- get "$NXF_BASE/$version/nextflow?$action" "$tmpfile" "$1" || exit $?
- mv "$tmpfile" "$1" || exit $?
- chmod +x "$1" || exit $?
- bash "$1" -download || exit $?
- echo ''
- echo -e $'Nextflow installation completed. Please note:'
- echo -e $'- the executable file `nextflow` has been created in the folder:' $(dirname $1)
- if [[ ! "$PATH" =~ (^|:)"$(dirname $1)"(:|$) ]]; then
- echo -e $'- you may complete the installation by moving it to a directory in your $PATH'
- fi
- echo ''
-}
-
-function launch_nextflow() {
- # the launch command line
- local cmdline=()
- # remove leading and trailing double-quotes
- for x in "${launcher[@]}"; do
- x="${x%\"}"
- x="${x#\"}"
- cmdline+=("$x")
- done
-
- if [[ "$bg" ]]; then
- local pid_file="${NXF_PID_FILE:-.nextflow.pid}"
- cmdline+=("${args[@]}")
- exec "${cmdline[@]}" &
- disown
- echo $! > "$pid_file"
- exit 0
- fi
-
- cmdline+=("${args[@]}")
- exec "${cmdline[@]}"
- exit 1
-}
-
-# check self-install
-if [ "$0" = "bash" ] || [[ "$0" =~ .*/bash ]]; then
- if [ -d nextflow ]; then
- echo 'Please note:'
- echo "- The install procedure needs to create a file named 'nextflow' in this folder, but a directory with this name already exists."
- echo "- Please renamed/delete that directory, or execute the Nextflow install procedure in another folder."
- echo ''
- exit 1
- fi
- install "$PWD/nextflow" install
- exit 0
-fi
-
-# clean up env
-# see https://github.com/nextflow-io/nextflow/issues/1716
-unset JAVA_TOOL_OPTIONS
-
-# parse the command line
-bg=''
-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 $1 in
- -D*)
- if [[ ! "$cmd" ]]; then
- jvmopts+=("$1")
- fi
- ;;
- -d|-dockerize)
- if [[ ! "$cmd" && ! -f /.nextflow/dockerized ]]; then
- dockerize=1
- fi
- ;;
- -bg)
- if [[ ! -f /.nextflow/dockerized ]]; then
- bg=1
- fi
- ;;
- -download)
- if [[ ! "$cmd" ]]; then
- rm -rf "$NXF_DIST/$NXF_VER" || exit $?
- bash "$0" -version || exit $?
- exit 0
- fi
- ;;
- -self-update|self-update)
- if [[ ! "$cmd" ]]; then
- [[ -z $NXF_EDGE && $NXF_VER = *-edge ]] && NXF_EDGE=1
- unset NXF_VER
- install "$0" update
- exit 0
- fi
- ;;
- *)
- [[ $1 && $1 != -* && ! "$cmd" && ${commands[*]} =~ $1 ]] && cmd=$1
- ;;
- esac
- shift
-done
-
-NXF_DOCKER_OPTS=${NXF_DOCKER_OPTS:=''}
-if [[ "$dockerize" ]]; then
- if [[ "$bg" ]]; then detach='--detach '; else detach=''; fi
- NXF_ASSETS=${NXF_ASSETS:-${NXF_HOME:-$HOME/.nextflow}/assets}
- mkdir -p "$NXF_ASSETS"
- exec docker run $detach --rm --net host \
- -e NXF_ANSI_LOG=false \
- -e USER -e HOME -e NXF_ASSETS=$NXF_ASSETS -e NXF_USRMAP=$(id -u) -e NXF_DOCKER_OPTS='-u $(id -u)' \
- -v /var/run/docker.sock:/var/run/docker.sock \
- -v $HOME:$HOME:ro,Z -v $NXF_ASSETS:$NXF_ASSETS:Z -v $PWD:$PWD:Z -w $PWD $NXF_DOCKER_OPTS \
- nextflow/nextflow:$NXF_VER nextflow "${args[@]}"
- exit 1
-fi
-
-CAPSULE_LOG=${CAPSULE_LOG:=''}
-CAPSULE_RESET=${CAPSULE_RESET:=''}
-CAPSULE_CACHE_DIR=${CAPSULE_CACHE_DIR:="$NXF_HOME/capsule"}
-
-NXF_PACK=one
-NXF_MODE=${NXF_MODE:-''}
-NXF_JAR=${NXF_JAR:-nextflow-$NXF_VER-$NXF_PACK.jar}
-NXF_BIN=${NXF_BIN:-$NXF_DIST/$NXF_VER/$NXF_JAR}
-NXF_PATH=$(dirname "$NXF_BIN")
-NXF_URL=${NXF_URL:-$NXF_BASE/v$NXF_VER/$NXF_JAR}
-NXF_GRAB=${NXF_GRAB:-''}
-NXF_CLASSPATH=${NXF_CLASSPATH:-''}
-NXF_HOST=${HOSTNAME:-localhost}
-[[ $NXF_LAUNCHER ]] || NXF_LAUNCHER=${NXF_HOME}/tmp/launcher/nextflow-${NXF_PACK}_${NXF_VER}/${NXF_HOST}
-
-# Determine the path to this file
-if [[ $NXF_PACK = all ]]; then
- NXF_BIN=$(which "$0" 2>/dev/null)
- [ $? -gt 0 -a -f "$0" ] && NXF_BIN="./$0"
-fi
-
-# use nextflow custom java home path
-if [[ "$NXF_JAVA_HOME" ]]; then
- JAVA_HOME="$NXF_JAVA_HOME"
- unset JAVA_CMD
-fi
-# Determine the Java command to use to start the JVM.
-if [ ! -x "$JAVA_CMD" ] ; then
- if [ -d "$JAVA_HOME" ] ; then
- if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
- # IBM's JDK on AIX uses strange locations for the executables
- JAVA_CMD="$JAVA_HOME/jre/sh/java"
- else
- JAVA_CMD="$JAVA_HOME/bin/java"
- fi
- elif [ -x /usr/libexec/java_home ]; then
- JAVA_CMD="$(/usr/libexec/java_home -v 1.8+)/bin/java"
- else
- JAVA_CMD="$(which java)" || JAVA_CMD=java
- fi
-fi
-
-# Retrieve the java version from a NF local file
-JAVA_KEY="$NXF_HOME/tmp/ver/$(resolve_link "$JAVA_CMD" | sed 's@/@.@g')"
-if [ -f "$JAVA_KEY" ]; then
- JAVA_VER="$(cat "$JAVA_KEY")"
-else
- JAVA_VER="$("$JAVA_CMD" $NXF_OPTS -version 2>&1)"
- if [ $? -ne 0 ]; then
- echo_red "${JAVA_VER:-Failed to launch the Java virtual machine}"
- echo_yellow "NOTE: Nextflow is trying to use the Java VM defined by the following environment variables:\n JAVA_CMD: $JAVA_CMD\n NXF_OPTS: $NXF_OPTS\n"
- exit 1
- fi
- JAVA_VER=$(echo "$JAVA_VER" | awk '/version/ {gsub(/"/, "", $3); print $3}')
- # check NF version
- if [[ ! $NXF_VER =~ ([0-9]+)\.([0-9]+)\.([0-9].*) ]]; then
- echo_red "Not a valid Nextflow version: $NXF_VER"
- exit 1
- fi
- major=${BASH_REMATCH[1]}
- minor=${BASH_REMATCH[2]}
- # legacy version - Java 7/8 only
- if [ $major -eq 0 ] && [ $minor -lt 26 ]; then
- version_check="^(1.7|1.8)"
- version_message="Java 7 or 8"
- else
- version_check="^(1.8|9|10|11|12|13|14|15|16|17|18)"
- version_message="Java 8 or later (up to 18)"
- fi
- if [[ ! $JAVA_VER =~ $version_check ]]; then
- echo_red "ERROR: Cannot find Java or it's a wrong version -- please make sure that $version_message is installed"
- if [[ "$NXF_JAVA_HOME" ]]; then
- echo_yellow "NOTE: Nextflow is trying to use the Java VM defined by the following environment variables:\n JAVA_CMD: $JAVA_CMD\n NXF_JAVA_HOME: $NXF_JAVA_HOME\n"
- else
- echo_yellow "NOTE: Nextflow is trying to use the Java VM defined by the following environment variables:\n JAVA_CMD: $JAVA_CMD\n JAVA_HOME: $JAVA_HOME\n"
- fi
- exit 1
- fi
- if [[ ! $JAVA_VER =~ ^(11|12|13|14|15|16|17|18) ]]; then
- echo_yellow "NOTE: Nextflow is not tested with Java $JAVA_VER -- It's recommended the use of version 11 up to 18\n"
- fi
- mkdir -p $(dirname "$JAVA_KEY")
- [[ -f $JAVA_VER ]] && echo $JAVA_VER > "$JAVA_KEY"
-fi
-
-# Verify nextflow jar is available
-if [ ! -f "$NXF_BIN" ]; then
- [ -f "$NXF_PATH" ] && rm "$NXF_PATH"
- mkdir -p "$NXF_PATH" || exit $?
- tmpfile=$(make_temp)
- get "$NXF_URL" "$tmpfile" "$NXF_BIN"
- mv "$tmpfile" "$NXF_BIN"
-fi
-
-COLUMNS=${COLUMNS:-`tty -s && tput cols 2>/dev/null || true`}
-declare -a JAVA_OPTS=()
-JAVA_OPTS+=(-Dfile.encoding=UTF-8 -Dcapsule.trampoline -Dcapsule.java.cmd="$JAVA_CMD" -Dcom.sun.security.enableAIAcaIssuers=true)
-if [[ $cmd == console ]]; then bg=1;
-else JAVA_OPTS+=(-Djava.awt.headless=true)
-fi
-
-[[ "$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)
-[[ "$NXF_OPTS" ]] && JAVA_OPTS+=($NXF_OPTS)
-[[ "$NXF_CLASSPATH" ]] && export NXF_CLASSPATH
-[[ "$NXF_GRAB" ]] && export NXF_GRAB
-[[ "$COLUMNS" ]] && export COLUMNS
-[[ "$NXF_TEMP" ]] && JAVA_OPTS+=(-Djava.io.tmpdir="$NXF_TEMP")
-[[ "${jvmopts[@]}" ]] && JAVA_OPTS+=("${jvmopts[@]}")
-export JAVA_CMD
-export CAPSULE_CACHE_DIR
-export NXF_PLUGINS_DIR
-export NXF_PLUGINS_MODE
-export NXF_PLUGINS_DEFAULT
-export NXF_PACK
-
-# lookup the a `md5` command
-if hash md5sum 2>/dev/null; then MD5=md5sum;
-elif hash gmd5sum 2>/dev/null; then MD5=gmd5sum;
-elif hash md5 2>/dev/null; then MD5=md5;
-else MD5=''
-fi
-
-# when no md5 command is available fallback on default execution
-if [ ! "$MD5" ] || [ "$CAPSULE_RESET" ]; then
- launcher=($("$JAVA_CMD" "${JAVA_OPTS[@]}" -jar "$NXF_BIN"))
- launch_nextflow
- exit 1
-fi
-
-# creates a md5 unique for the given variables
-env_md5() {
-cat <<EOF | $MD5 | cut -f1 -d' '
-$JAVA_CMD
-$JAVA_VER
-${JAVA_OPTS[@]}
-$NXF_HOME
-$NXF_VER
-$NXF_OPTS
-$NXF_GRAB
-$NXF_CLASSPATH
-$NXF_JVM_ARGS
-EOF
-}
-
-# checked if a cached classpath file exists and it newer that the nextflow boot jar file
-if [[ -f /.nextflow/dockerized ]]; then
- LAUNCH_FILE=/.nextflow/launch-classpath
-else
- LAUNCH_FILE="${NXF_LAUNCHER}/classpath-$(env_md5)"
-fi
-if [ -s "$LAUNCH_FILE" ] && [ "$LAUNCH_FILE" -nt "$NXF_BIN" ]; then
- declare -a launcher="($(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"))
- [[ $? -ne 0 ]] && echo_red 'Unable to initialize nextflow environment' && exit 1
-
- # first string between double quotes is the full path to java, also blank spaces are included
- # remainder string are arguments
- # we extract first part into `cmd_base`` and remainder into `cmd_tail`` and convert them to array as previous version
- cmd_pattern='"([^"]*)"(.*)'
- [[ "${cli[@]}" =~ $cmd_pattern ]]
- cmd_base=(${BASH_REMATCH[1]})
- cmd_tail=(${BASH_REMATCH[2]})
-
- if [[ "$JAVA_VER" =~ ^(9|10|11|12|13|14|15|16|17|18) ]]; then
- launcher="${cmd_base[@]}"
- launcher+=(--add-opens=java.base/java.lang=ALL-UNNAMED)
- launcher+=(--add-opens=java.base/java.io=ALL-UNNAMED)
- launcher+=(--add-opens=java.base/java.nio=ALL-UNNAMED)
- launcher+=(--add-opens=java.base/java.net=ALL-UNNAMED)
- launcher+=(--add-opens=java.base/java.util=ALL-UNNAMED)
- launcher+=(--add-opens=java.base/java.util.concurrent.locks=ALL-UNNAMED)
- launcher+=(--add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED)
- launcher+=(--add-opens=java.base/java.nio.file.spi=ALL-UNNAMED)
- launcher+=(--add-opens=java.base/sun.nio.ch=ALL-UNNAMED)
- launcher+=(--add-opens=java.base/sun.nio.fs=ALL-UNNAMED)
- launcher+=(--add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED)
- launcher+=(--add-opens=java.base/sun.net.www.protocol.https=ALL-UNNAMED)
- launcher+=(--add-opens=java.base/sun.net.www.protocol.ftp=ALL-UNNAMED)
- launcher+=(--add-opens=java.base/sun.net.www.protocol.file=ALL-UNNAMED)
- launcher+=(--add-opens=java.base/jdk.internal.misc=ALL-UNNAMED)
- [[ "$NXF_JVM_ARGS" ]] && launcher+=($NXF_JVM_ARGS)
- launcher+=("${cmd_tail[@]}")
- else
- launcher="${cmd_base[@]}"
- [[ "$NXF_JVM_ARGS" ]] && launcher+=($NXF_JVM_ARGS)
- launcher+=("${cmd_tail[@]}")
- fi
-
- # Don't show errors if the LAUNCH_FILE can't be created
- if mkdir -p "${NXF_LAUNCHER}" 2>/dev/null; then
- STR=''
- for x in "${launcher[@]}"; do
- [[ "$x" != "\"-Duser.dir=$PWD\"" ]] && STR+="$x "
- done
- printf "$STR">"$LAUNCH_FILE"
- else
- echo_yellow "Warning: Couldn't create cached classpath folder: $NXF_LAUNCHER -- Maybe NXF_HOME is not writable?"
- fi
-
-fi
-
-# finally run it
-launch_nextflow
diff --git a/src/.docker_modules/r-bolero/1.0/Dockerfile b/src/.docker_modules/r-bolero/1.0/Dockerfile
index de41dda18442e36277830e2e2035e3e503b815e0..e5169402aea8580c37efdbc8997e9f31e1522a2f 100644
--- a/src/.docker_modules/r-bolero/1.0/Dockerfile
+++ b/src/.docker_modules/r-bolero/1.0/Dockerfile
@@ -3,7 +3,14 @@ LABEL AUTHOR="Alia Rifki"
LABEL MAINTAINER="Xavier Grand <xavier.grand@inserm.fr>"
LABEL build_date="2023-05-26"
-## Copy all Rscript files
+
+RUN apt-get update \
+ && apt-get install -y --no-install-recommends \
+ libcurl4-openssl-dev \
+ libssl-dev \
+ procps
+
+## copy Rscript files
COPY ./*.R .
## Install packages
diff --git a/src/.docker_modules/r-docher-test/1.0/Dockerfile b/src/.docker_modules/r-docher-test/1.0/Dockerfile
deleted file mode 100644
index 9c3fa5cf773c6b44ed8f61a56acc5924df3edfcd..0000000000000000000000000000000000000000
--- a/src/.docker_modules/r-docher-test/1.0/Dockerfile
+++ /dev/null
@@ -1,9 +0,0 @@
-FROM rocker/r-base:4.2.3
-
-## copy Rscript files
-COPY ./*.R .
-
-RUN Rscript install_pkgs.R
-
-# command to run on container start
-CMD [ "bash" ]
\ No newline at end of file
diff --git a/src/.docker_modules/r-docher-test/1.0/install_pkgs.R b/src/.docker_modules/r-docher-test/1.0/install_pkgs.R
deleted file mode 100644
index 20def570d4eea82c9488e92f888efacef4a94f6b..0000000000000000000000000000000000000000
--- a/src/.docker_modules/r-docher-test/1.0/install_pkgs.R
+++ /dev/null
@@ -1,6 +0,0 @@
-#!/bin/Rscript
-# Packages installation:
-list.of.packages <- c("BiocManager", "ggplot2", "dplyr", "reshape2",
- "RColorBrewer", "R.utils")
-new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
-if(length(new.packages)) install.packages(new.packages, dependencies = T)
\ No newline at end of file
diff --git a/src/.docker_modules/r-docher-test/1.0/start_positions_individuals_2.R b/src/.docker_modules/r-docher-test/1.0/start_positions_individuals_2.R
deleted file mode 100755
index 0ba0f18208c4c186d152aad9bb2add79a41ace12..0000000000000000000000000000000000000000
--- a/src/.docker_modules/r-docher-test/1.0/start_positions_individuals_2.R
+++ /dev/null
@@ -1,202 +0,0 @@
-#!/bin/Rscript
-library(dplyr)
-library(ggplot2)
-library(tidyverse)
-library(RColorBrewer)
-library(conflicted)
-#résolution de conflits entre les bibliothèques dplyr et stats
-conflict_prefer("filter", "dplyr")
-conflict_prefer("lag", "dplyr")
-
-# Load Start_positions_count files:
-
-list_file <- list.files(path=".",
- pattern="*.txt",
- all.files=FALSE,
- full.names=FALSE)
-file_to_load <- paste0("./", list_file[1])
-filename <- strsplit(list_file[1], split = "[.]")[[1]][1]
-
-sam_bc01 <- read.table(file_to_load, header = F)
-sam_bc01[3] <- rep(filename, length(sam_bc01[,1]))
-
-# Function to parse and arrange data:
-
-parsingData <- function(df) {
- binsize <- 10
- pos <- as.data.frame(table(df[,2]))
- colnames(pos)[1] <- "Start"
-
- Start <- as.data.frame(as.factor(seq(0, 3300)))
- colnames(Start)[1] = "Start"
-
- tmp <- dplyr::left_join(Start, pos)
- tmp[is.na(tmp)] <- 0
-
- tmp$Start <- as.numeric(tmp$Start)
-
- df2 <- as_tibble(tmp) %>%
- mutate(bin = round(Start/binsize)*binsize) %>%
- group_by(bin) %>%
- summarize(nb_reads = sum(Freq, na.rm = T))
- df2[is.na(df2)] <- 0
- df2[3] <- rep(df[1,3], length(df2$bin))
- colnames(df2) <- c("Start_position", "nb_reads", "Barcode")
- df2
-}
-
-df_parsed <- parsingData(sam_bc01)
-
-ggplot(df_parsed, aes(Start_position, nb_reads)) +
- geom_area(alpha = 0.5, fill = "blue") +
- scale_y_sqrt() +
- facet_wrap(facets = vars(df_parsed$Barcode)) +
- theme_light()+
- scale_x_continuous(breaks = c(0, 127, 1114, 1490, 2554, 2732, 2907, 3421),
- label = c("1692", "1819", "2806", "EcoRI", "1065",
- "1243", "1418", "1932")) +
- theme(axis.text.x = element_text(angle = 45)
- )
-
-ggsave(paste0(filename,".jpg"),
- plot = last_plot(),
- scale = 2,
- width = 1920,
- height = 1080,
- units = "px",
- dpi = 300,
-)
-
-# Classify reads based on start-position:
-
-# Separate preCore & pg:
-classify_reads <- function(read_info) {
- if (read_info <= 103) {
- promoter <- "preCore"
- }
- else if (read_info >= 117 &
- read_info <= 276) {
- promoter <- "pgRNA"
- }
- else if (read_info >= 1106 &
- read_info <= 1221 ) {
- promoter <- "preS1"
- }
- else if (read_info >= 1455 &
- read_info <= 1632 ) {
- promoter <- "preS2/S"
- }
- else if (read_info >= 2550 &
- read_info <= 2968 ) {
- promoter <- "HBx"
- }
- else promoter <- "Undefined"
-}
-
-colnames(sam_bc01) <- c("read_ID", "start_position", "barcode")
-sam_bc01$promoter <- sapply(sam_bc01$start_position,
- classify_reads)
-
-write.table(sam_bc01,
- file = "classification_of_reads_per_RNA.txt",
- quote = FALSE,
- sep = "\t",
- row.names = FALSE)
-
-# Compute Reads number per promoters:
-list_name_samples <- list(filename)
-
-count_promoter_reads <- function(barcode, df) {
- tmpdf <- as.data.frame(df)
- tmpdf <- tmpdf[tmpdf$Barcode == barcode,]
- preCore <- sum(tmpdf$nb_reads[tmpdf$Start_position <= 103])
- pgRNA <- sum(tmpdf$nb_reads[tmpdf$Start_position >= 117 &
- tmpdf$Start_position <= 276])
- preS1 <- sum(tmpdf$nb_reads[tmpdf$Start_position >= 1106 &
- tmpdf$Start_position <= 1221])
- preS2S <- sum(tmpdf$nb_reads[tmpdf$Start_position >= 1455 &
- tmpdf$Start_position <= 1632])
- HBx <- sum(tmpdf$nb_reads[tmpdf$Start_position >= 2550 &
- tmpdf$Start_position <= 2968])
- total <- sum(preCore, pgRNA, preS1, preS2S, HBx)
- res <- c(preCore/total*100, pgRNA/total*100, preS1/total*100,
- preS2S/total*100, HBx/total*100, total)
- return(res)
-}
-
-abscount_promoter_reads <- function(barcode, df) {
- tmpdf <- as.data.frame(df)
- tmpdf <- tmpdf[tmpdf$Barcode == barcode,]
- preCore <- sum(tmpdf$nb_reads[tmpdf$Start_position <= 103])
- pgRNA <- sum(tmpdf$nb_reads[tmpdf$Start_position >= 117 &
- tmpdf$Start_position <= 276])
- preS1 <- sum(tmpdf$nb_reads[tmpdf$Start_position >= 1106 &
- tmpdf$Start_position <= 1221])
- preS2S <- sum(tmpdf$nb_reads[tmpdf$Start_position >= 1455 &
- tmpdf$Start_position <= 1632])
- HBx <- sum(tmpdf$nb_reads[tmpdf$Start_position >= 2550 &
- tmpdf$Start_position <= 2968])
- total <- sum(preCore, pgRNA, preS1, preS2S, HBx)
- res <- c(preCore, pgRNA, preS1, preS2S,
- HBx, total)
- return(res)
-}
-
-promoters <- factor(c("preCore", "pgRNA", "preS1", "preS2/S", "HBx"),
- levels = c("preCore", "pgRNA", "preS1", "preS2/S", "HBx"))
-
-abs_count_reads <- data.frame()
-abs_count_reads <- sapply(list_name_samples,
- abscount_promoter_reads,
- df_parsed)
-abs_count_reads <- cbind(c(as.vector(promoters),"total"), abs_count_reads)
-colnames(abs_count_reads) <- c("promoter", "read_number")
-
-write.table(abs_count_reads,
- file = "Count_reads_per_promoter.tsv",
- quote = FALSE,
- sep = "\t",
- row.names = FALSE)
-
-resultats_start_promoters <- lapply(list_name_samples,
- count_promoter_reads,
- df_parsed)
-
-resultats_start_promoters <- as.data.frame(do.call(cbind,
- resultats_start_promoters))
-totalCountSample <- as.data.frame(resultats_start_promoters[6,])
-colnames(totalCountSample) <- c(filename)
-resultats_start_promoters <- as.data.frame(resultats_start_promoters[1:5,])
-colnames(resultats_start_promoters) <- as.vector(list_name_samples)
-resultats_start_promoters <- cbind(promoters, resultats_start_promoters)
-formated_start_promoters <- pivot_longer(resultats_start_promoters,
- cols = c(filename),
- names_to = "Barcodes",
- values_to = "nb_reads")
-
-mycolors <- colorRampPalette(brewer.pal(10, "Paired"))(10)
-mycolors5 <- c("#712E80", "#006695", "#3B9746", "#1F4F25", "#F5751A")
-mycolors6 <- c("#A6CEE3", "#3362ff", "#33c5ff", "#6A3D9A", "#d60000")
-
-plot_camembert <- function(barcode, df, tot) {
- camembert <- ggplot(df[df$Barcodes == barcode,], aes(x = barcode,
- y = nb_reads,
- fill=promoters)) +
- geom_col() +
- coord_polar("y") +
- scale_fill_manual(values = mycolors5) +
- labs(title = paste0("#reads = ", tot[1,barcode]), x=element_blank(), y=element_blank()) +
- theme_light()
-
- print(camembert)
-
- ggsave(filename = paste0("./Reads_start_promoters_", barcode, "_camembert.jpg"),
- plot = last_plot(),
- scale = 1,
- width = 1920,
- height = 1080,
- units = "px",
- dpi = 300)
-}
-
-lapply(list_name_samples, plot_camembert, formated_start_promoters, totalCountSample)
diff --git a/src/bolero.nf b/src/bolero.nf
index d4192a41c658f36cda5f9c17d4d19f78f2293e61..a2bbe2f522eb712b238495d7c2c4d73f489f825a 100755
--- a/src/bolero.nf
+++ b/src/bolero.nf
@@ -185,6 +185,12 @@ if(!params.skipBC) {
}
}
+
+include { control_basecalling } from "./nf_modules/pycoqc/main.nf"
+include { control_bam } from "./nf_modules/pycoqc/main.nf"
+// include { barecode } from "./nf_modules/barecode/main.nf"
+include { pycoqc } from "./nf_modules/pycoqc/main.nf"
+include { barcoding_cpu } from "./nf_modules/ont-guppy/main.nf"
include { control_basecalling } from "./nf_modules/pycoqc/main.nf"
include { control_bam } from "./nf_modules/pycoqc/main.nf"
include { concatenate } from "./nf_modules/seqkit/main.nf"
@@ -274,6 +280,14 @@ workflow {
sort_index_bam(hbv_genome.out.bam)
control_bam(ss.collect(), sort_index_bam.out.indexed_bam)
+ sort_index_bam.out.indexed_bam
+ .flatten()
+ .filter(~/.*bam$/)
+ .collect()
+ .set{bam_path}
+
+ //control_bam(ss, bam_path)
+
//###################### START POSITIONS #######################
start_position_counts(sort_index_bam.out.indexed_bam)
diff --git a/src/nextflow.config b/src/nextflow.config
index b1b3d869f5e4a396140dc867f48037ef5ecc0eaf..a875c043d3caf61e7add727548c82a8ab4561165 100755
--- a/src/nextflow.config
+++ b/src/nextflow.config
@@ -140,6 +140,41 @@ profiles {
}
}
}
+ pollux {
+ singularity.enabled = true
+ singularity.cacheDir = "./bin/"
+ singularity.runOptions = "--bind /data,/home"
+ process {
+ errorStrategy = 'finish'
+ memory = '256GB'
+ withLabel: big_mem_mono_cpus {
+ cpus = 1
+ }
+ withLabel: big_mem_multi_cpus {
+ cpus = 16
+ }
+ withLabel: small_mem_mono_cpus {
+ cpus = 1
+ memory = '2GB'
+ }
+ withLabel: small_mem_multi_cpus {
+ cpus = 8
+ memory = '2GB'
+ }
+ withLabel: mid_mem_mono_cpus {
+ cpus = 1
+ memory = '8GB'
+ }
+ withLabel: mid_mem_multi_cpus {
+ cpus = 8
+ memory = '8GB'
+ }
+ withLabel: gpus {
+ maxForks = 1
+ containerOptions = '--nv'
+ }
+ }
+ }
psmn {
charliecloud.enabled = true
charliecloud.cacheDir = "/Xnfs/abc/charliecloud"
diff --git a/src/nextflow_XGR.config b/src/nextflow_XGR.config
deleted file mode 100755
index 9675a552d7e6c191b5880ccffe18e0d866ceb19c..0000000000000000000000000000000000000000
--- a/src/nextflow_XGR.config
+++ /dev/null
@@ -1,191 +0,0 @@
-nextflowVersion = '>=20'
-
-manifest {
- homePage = 'https://gitbio.ens-lyon.fr/LBMC/nextflow'
- description = 'pipeline to '
- mainScript = 'main.nf'
- version = '0.0.0'
-}
-
-report {
- enabled = true
- file = "$baseDir/../results/report.html"
-}
-
-profiles {
- docker {
- docker.temp = "auto"
- docker.enabled = true
- process {
- errorStrategy = 'finish'
- memory = '24GB'
- withLabel: big_mem_mono_cpus {
- cpus = 1
- }
- withLabel: big_mem_multi_cpus {
- cpus = 16
- }
- withLabel: small_mem_mono_cpus {
- cpus = 1
- memory = '2GB'
- }
- withLabel: small_mem_multi_cpus {
- cpus = 16
- memory = '2GB'
- }
- withLabel: mid_mem_mono_cpus {
- cpus = 1
- memory = '8GB'
- }
- withLabel: mid_mem_multi_cpus {
- cpus = 16
- memory = '8GB'
- }
- }
- }
- podman {
- podman.enabled = true
- process {
- errorStrategy = 'finish'
- memory = '16GB'
- withLabel: big_mem_mono_cpus {
- cpus = 1
- }
- withLabel: big_mem_multi_cpus {
- cpus = 4
- }
- withLabel: small_mem_mono_cpus {
- cpus = 1
- memory = '2GB'
- }
- withLabel: small_mem_multi_cpus {
- cpus = 4
- memory = '2GB'
- }
- withLabel: mid_mem_mono_cpus {
- cpus = 1
- memory = '8GB'
- }
- withLabel: mid_mem_multi_cpus {
- cpus = 4
- memory = '8GB'
- }
- }
- }
- singularity {
- singularity.enabled = true
- singularity.cacheDir = "./bin/"
- singularity.bind = "/home"
- process {
- errorStrategy = 'finish'
- memory = '16GB'
- withLabel: big_mem_mono_cpus {
- cpus = 1
- }
- withLabel: big_mem_multi_cpus {
- cpus = 16
- }
- withLabel: small_mem_mono_cpus {
- cpus = 1
- memory = '4GB'
- }
- withLabel: small_mem_multi_cpus {
- cpus = 16
- memory = '4GB'
- }
- withLabel: mid_mem_mono_cpus {
- cpus = 1
- memory = '8GB'
- }
- withLabel: mid_mem_multi_cpus {
- cpus = 8
- memory = '8GB'
- }
- }
- }
- psmn {
- charliecloud.enabled = true
- charliecloud.cacheDir = "/Xnfs/abc/charliecloud"
- charliecloud.runOptions = "--bind /scratch:/scratch --bind /Xnfs:/Xnfs"
- process{
- errorStrategy = { sleep(Math.pow(2, task.attempt) * 200 as long); return 'retry' }
- maxRetries = 3
- withLabel: big_mem_mono_cpus {
- executor = "slurm"
- cpus = 1
- memory = "128GB"
- time = "24h"
- clusterOptions = "--partition=Lake"
- }
- withLabel: big_mem_multi_cpus {
- executor = "slurm"
- cpus = 32
- memory = "192GB"
- time = "24h"
- clusterOptions = "--partition=Lake"
- }
- withLabel: small_mem_mono_cpus {
- executor = "slurm"
- cpus = 1
- memory = "16GB"
- time = "24h"
- clusterOptions = "--partition=Lake"
- }
- withLabel: small_mem_multi_cpus {
- executor = "slurm"
- cpus = 32
- memory = "16GB"
- time = "24h"
- clusterOptions = "--partition=Lake"
- }
- }
- }
- ccin2p3 {
- singularity.enabled = true
- singularity.cacheDir = "$baseDir/../bin/"
- singularity.runOptions = "--bind /pbs,/sps,/scratch,/tmp"
- process{
- maxRetries = 3
- withLabel: big_mem_mono_cpus {
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "slurm"
- clusterOptions = "--licenses=sps"
- cpus = 1
- memory = "8GB"
- queue = "htc"
- }
- withLabel: big_mem_multi_cpus {
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "slurm"
- clusterOptions = "--licenses=sps"
- cpus = 1
- memory = "8GB"
- queue = "htc"
- }
- withLabel: small_mem_mono_cpus {
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "slurm"
- clusterOptions = "--licenses=sps"
- cpus = 1
- memory = "8GB"
- queue = "htc"
- }
- withLabel: small_mem_multi_cpus {
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "slurm"
- clusterOptions = "--licenses=sps"
- cpus = 1
- memory = "8GB"
- queue = "htc"
- }
- }
- }
-}
diff --git a/src/nf_modules/guppy-gpu/main.nf b/src/nf_modules/guppy-gpu/main.nf
index 5bf73ce4ac5ae84e7326269aa93902d92cc47d11..e22083b78209b3af8b865f13f504219cb0dea1b7 100755
--- a/src/nf_modules/guppy-gpu/main.nf
+++ b/src/nf_modules/guppy-gpu/main.nf
@@ -50,4 +50,4 @@ guppy_basecaller --compress_fastq \
--num_callers ${params.num_callers} \
--chunks_per_runner ${params.chunks_per_runner}
"""
-}
\ No newline at end of file
+}
diff --git a/src/nf_modules/ont-guppy/main.nf b/src/nf_modules/ont-guppy/main.nf
index de5119cd1d5d799707156263f29da14ff365a4d5..63ab494aeb9b00eee18caaae19141619551b6625 100644
--- a/src/nf_modules/ont-guppy/main.nf
+++ b/src/nf_modules/ont-guppy/main.nf
@@ -176,5 +176,4 @@ guppy_barcoder \
--trim_adapters \
--compress_fastq
"""
-}
-
+}
\ No newline at end of file