From 4c591824695e5fb340b0e25d2c253eb76bdb8ac6 Mon Sep 17 00:00:00 2001
From: Melvin Alappat <melvin.alappat@unibas.ch>
Date: Thu, 30 Dec 2021 14:44:03 +0100
Subject: [PATCH] updated workflow
---
src/primingprob/PrimingProb_process.nf | 3 +-
.../.command.begin | 0
.../.command.err | 1 -
.../.command.out | 0
.../.command.run | 108 ------------------
.../.command.sh | 3 -
.../e44fcf5a9b873853ca63a43b531eb0/.exitcode | 1 -
.../primer.fasta | 1 -
.../transcript.fasta | 1 -
9 files changed, 2 insertions(+), 116 deletions(-)
delete mode 100644 src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.begin
delete mode 100644 src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.err
delete mode 100644 src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.out
delete mode 100644 src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.run
delete mode 100644 src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.sh
delete mode 100644 src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.exitcode
delete mode 120000 src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/primer.fasta
delete mode 120000 src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/transcript.fasta
diff --git a/src/primingprob/PrimingProb_process.nf b/src/primingprob/PrimingProb_process.nf
index 59ba2a9..1f170e5 100644
--- a/src/primingprob/PrimingProb_process.nf
+++ b/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 : ${params.output}
"""
.stripIndent()
diff --git a/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.begin b/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.begin
deleted file mode 100644
index e69de29..0000000
diff --git a/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.err b/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.err
deleted file mode 100644
index 49b6c12..0000000
--- a/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.err
+++ /dev/null
@@ -1 +0,0 @@
-/Users/kegany44/Master/PythonCourse/Issue_4/scrna-seq-simulation/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.sh: line 2: RIblast: command not found
diff --git a/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.out b/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.out
deleted file mode 100644
index e69de29..0000000
diff --git a/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.run b/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.run
deleted file mode 100644
index f21b88e..0000000
--- a/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.run
+++ /dev/null
@@ -1,108 +0,0 @@
-#!/bin/bash
-# NEXTFLOW TASK: RIblast_interaction
-set -e
-set -u
-NXF_DEBUG=${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
diff --git a/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.sh b/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.sh
deleted file mode 100644
index ea89100..0000000
--- a/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.command.sh
+++ /dev/null
@@ -1,3 +0,0 @@
-#!/bin/bash -ue
-RIblast db -i transcript.fasta -o test_db
-RIblast ris -i primer.fasta -o Energies.txt -d test_db
diff --git a/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.exitcode b/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.exitcode
deleted file mode 100644
index 405e057..0000000
--- a/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/.exitcode
+++ /dev/null
@@ -1 +0,0 @@
-127
\ No newline at end of file
diff --git a/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/primer.fasta b/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/primer.fasta
deleted file mode 120000
index 3c8fce8..0000000
--- a/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/primer.fasta
+++ /dev/null
@@ -1 +0,0 @@
-/Users/kegany44/Master/PythonCourse/Issue_4/scrna-seq-simulation/inputs/primer.fasta
\ No newline at end of file
diff --git a/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/transcript.fasta b/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/transcript.fasta
deleted file mode 120000
index cbf803b..0000000
--- a/src/primingprob/bin/work/36/e44fcf5a9b873853ca63a43b531eb0/transcript.fasta
+++ /dev/null
@@ -1 +0,0 @@
-/Users/kegany44/Master/PythonCourse/Issue_4/scrna-seq-simulation/inputs/transcript.fasta
\ No newline at end of file
--
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