updated workflow

src/primingprob/PrimingProb_process.nf

@@ -6,10 +6,11 @@ params.output = "/Users/kegany44/Master/PythonCourse/Issue_4/scrna-seq-simulatio
 
 
 log.info """\
-         R I B L A S T      P I P E L I N E    
+         PRIMING PROBABILITY PIPELINE    
          ===================================
          transcripts: ${params.transcripts}
          primers    : ${params.primers}
+         output     : ${params.output}
          """
          .stripIndent()
 

src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.err

-/Users/kegany44/Master/PythonCourse/Issue_4/scrna-seq-simulation/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.sh: line 2: RIblast: command not found

src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.run

-#!/bin/bash
-# NEXTFLOW TASK: RIblast_interaction
-set -e
-set -u
-NXF_DEBUG=${NXF_DEBUG:=0}; [[ $NXF_DEBUG > 1 ]] && set -x
-NXF_ENTRY=${1:-nxf_main}
-
-
-nxf_date() {
-    local ts=$(date +%s%3N);
-    if [[ ${#ts} == 10 ]]; then echo ${ts}000
-    elif [[ $ts == *%3N ]]; then echo ${ts/\%3N/000}
-    elif [[ $ts == *3N ]]; then echo ${ts/3N/000}
-    elif [[ ${#ts} == 13 ]]; then echo $ts
-    else echo "Unexpected timestamp value: $ts"; exit 1
-    fi
-}
-
-nxf_env() {
-    echo '============= task environment ============='
-    env | sort | sed "s/\(.*\)AWS\(.*\)=\(.\{6\}\).*/\1AWS\2=\3xxxxxxxxxxxxx/"
-    echo '============= task output =================='
-}
-
-nxf_kill() {
-    declare -a children
-    while read P PP;do
-        children[$PP]+=" $P"
-    done < <(ps -e -o pid= -o ppid=)
-
-    kill_all() {
-        [[ $1 != $$ ]] && kill $1 2>/dev/null || true
-        for i in ${children[$1]:=}; do kill_all $i; done
-    }
-
-    kill_all $1
-}
-
-nxf_mktemp() {
-    local base=${1:-/tmp}
-    if [[ $(uname) = Darwin ]]; then mktemp -d $base/nxf.XXXXXXXXXX
-    else TMPDIR="$base" mktemp -d -t nxf.XXXXXXXXXX
-    fi
-}
-
-on_exit() {
-    exit_status=${nxf_main_ret:=$?}
-    printf $exit_status > /Users/kegany44/Master/PythonCourse/Issue_4/scrna-seq-simulation/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.exitcode
-    set +u
-    [[ "$tee1" ]] && kill $tee1 2>/dev/null
-    [[ "$tee2" ]] && kill $tee2 2>/dev/null
-    [[ "$ctmp" ]] && rm -rf $ctmp || true
-    exit $exit_status
-}
-
-on_term() {
-    set +e
-    [[ "$pid" ]] && nxf_kill $pid
-}
-
-nxf_launch() {
-    /bin/bash -ue /Users/kegany44/Master/PythonCourse/Issue_4/scrna-seq-simulation/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.sh
-}
-
-nxf_stage() {
-    true
-    # stage input files
-    rm -f transcript.fasta
-    rm -f primer.fasta
-    ln -s /Users/kegany44/Master/PythonCourse/Issue_4/scrna-seq-simulation/inputs/transcript.fasta transcript.fasta
-    ln -s /Users/kegany44/Master/PythonCourse/Issue_4/scrna-seq-simulation/inputs/primer.fasta primer.fasta
-}
-
-nxf_unstage() {
-    true
-    [[ ${nxf_main_ret:=0} != 0 ]] && return
-}
-
-nxf_main() {
-    trap on_exit EXIT
-    trap on_term TERM INT USR2
-    trap '' USR1
-
-    [[ "${NXF_CHDIR:-}" ]] && cd "$NXF_CHDIR"
-    NXF_SCRATCH=''
-    [[ $NXF_DEBUG > 0 ]] && nxf_env
-    touch /Users/kegany44/Master/PythonCourse/Issue_4/scrna-seq-simulation/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.begin
-    set +u
-    set -u
-    [[ $NXF_SCRATCH ]] && echo "nxf-scratch-dir $HOSTNAME:$NXF_SCRATCH" && cd $NXF_SCRATCH
-    nxf_stage
-
-    set +e
-    local ctmp=$(set +u; nxf_mktemp /dev/shm 2>/dev/null || nxf_mktemp $TMPDIR)
-    local cout=$ctmp/.command.out; mkfifo $cout
-    local cerr=$ctmp/.command.err; mkfifo $cerr
-    tee .command.out < $cout &
-    tee1=$!
-    tee .command.err < $cerr >&2 &
-    tee2=$!
-    ( nxf_launch ) >$cout 2>$cerr &
-    pid=$!
-    wait $pid || nxf_main_ret=$?
-    wait $tee1 $tee2
-    nxf_unstage
-}
-
-$NXF_ENTRY

src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.sh

-#!/bin/bash -ue
-RIblast db -i transcript.fasta -o test_db
-RIblast ris -i primer.fasta -o Energies.txt -d test_db

src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.exitcode

-127
\ No newline at end of file

src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/primer.fasta

-/Users/kegany44/Master/PythonCourse/Issue_4/scrna-seq-simulation/inputs/primer.fasta
\ No newline at end of file

src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/transcript.fasta

-/Users/kegany44/Master/PythonCourse/Issue_4/scrna-seq-simulation/inputs/transcript.fasta
\ No newline at end of file