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Build branch main with version main (1e1ffb3)

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Build pipeline: vsh-ci-dev-jsbwk

Source commit: 1e1ffb315f

Source message: Merge pull request #17 from viash-hub/add_biobox_modules

- Migrate a number of components to biobox
- Fix tests
- Reduce size of test resources
- Prepare for Viash Hub
This commit is contained in:
CI
2024-09-13 07:41:13 +00:00
commit 1ebb61f1e8
557 changed files with 430700 additions and 0 deletions
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304
target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml Normal file
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name: "pseudo_alignment_and_quant"
namespace: "workflows"
version: "main"
argument_groups:
- name: "Input"
arguments:
- type: "string"
name: "--id"
description: "ID of the sample."
info: null
example:
- "foo"
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--fastq_1"
alternatives:
- "-i"
description: "Path to the sample (or read 1 of paired end sample)."
info: null
example:
- "input.fastq.gz"
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--fastq_2"
description: "Path to read 2 of the sample."
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--strandedness"
description: "Sample strand-specificity. Must be one of unstranded, forward, or\
\ reverse"
info: null
required: false
choices:
- "forward"
- "reverse"
- "unstranded"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--gtf"
description: "GTF file"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--transcript_fasta"
description: "Fasta file of the reference transcriptome."
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--pseudo_aligner"
description: "Specifies the pseudo aligner to use - available options are 'salmon'.\
\ Runs in addition to '--aligner'."
info: null
default:
- "false"
required: false
choices:
- "salmon"
- "kallisto"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--salmon_index"
description: "Salmon index"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--kallisto_index"
description: "Kallisto index"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--lib_type"
description: "Override library type inferred based on strandedness defined in\
\ meta object"
info: null
default:
- ""
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--kallisto_quant_fragment_length"
description: "For single-end mode only, the estimated average fragment length\
\ to use for quantification with Kallisto."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--kallisto_quant_fragment_length_sd"
description: "For single-end mode only, the estimated standard deviation of the\
\ fragment length for quantification with Kallisto."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Output"
arguments:
- type: "file"
name: "--pseudo_multiqc"
info: null
default:
- "$id.quant.log"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--quant_out_dir"
info: null
default:
- "$id.salmon_quant"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--salmon_quant_results_file"
info: null
default:
- "$id.quant.sf"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--kallisto_quant_results_file"
info: null
default:
- "$id.abundance.tsv"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
resources:
- type: "nextflow_script"
path: "main.nf"
is_executable: true
entrypoint: "run_wf"
description: "A viash sub-workflow for pseudo alignment and quantification stage of\
\ nf-core/rnaseq pipeline.\n"
info: null
status: "enabled"
requirements:
commands:
- "ps"
dependencies:
- name: "salmon/salmon_quant"
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.1"
- name: "kallisto/kallisto_quant"
repository:
type: "local"
repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.1"
runners:
- type: "executable"
id: "executable"
docker_setup_strategy: "ifneedbepullelsecachedbuild"
- type: "nextflow"
id: "nextflow"
directives:
tag: "$id"
auto:
simplifyInput: true
simplifyOutput: false
transcript: false
publish: false
config:
labels:
mem1gb: "memory = 1000000000.B"
mem2gb: "memory = 2000000000.B"
mem5gb: "memory = 5000000000.B"
mem10gb: "memory = 10000000000.B"
mem20gb: "memory = 20000000000.B"
mem50gb: "memory = 50000000000.B"
mem100gb: "memory = 100000000000.B"
mem200gb: "memory = 200000000000.B"
mem500gb: "memory = 500000000000.B"
mem1tb: "memory = 1000000000000.B"
mem2tb: "memory = 2000000000000.B"
mem5tb: "memory = 5000000000000.B"
mem10tb: "memory = 10000000000000.B"
mem20tb: "memory = 20000000000000.B"
mem50tb: "memory = 50000000000000.B"
mem100tb: "memory = 100000000000000.B"
mem200tb: "memory = 200000000000000.B"
mem500tb: "memory = 500000000000000.B"
mem1gib: "memory = 1073741824.B"
mem2gib: "memory = 2147483648.B"
mem4gib: "memory = 4294967296.B"
mem8gib: "memory = 8589934592.B"
mem16gib: "memory = 17179869184.B"
mem32gib: "memory = 34359738368.B"
mem64gib: "memory = 68719476736.B"
mem128gib: "memory = 137438953472.B"
mem256gib: "memory = 274877906944.B"
mem512gib: "memory = 549755813888.B"
mem1tib: "memory = 1099511627776.B"
mem2tib: "memory = 2199023255552.B"
mem4tib: "memory = 4398046511104.B"
mem8tib: "memory = 8796093022208.B"
mem16tib: "memory = 17592186044416.B"
mem32tib: "memory = 35184372088832.B"
mem64tib: "memory = 70368744177664.B"
mem128tib: "memory = 140737488355328.B"
mem256tib: "memory = 281474976710656.B"
mem512tib: "memory = 562949953421312.B"
cpu1: "cpus = 1"
cpu2: "cpus = 2"
cpu5: "cpus = 5"
cpu10: "cpus = 10"
cpu20: "cpus = 20"
cpu50: "cpus = 50"
cpu100: "cpus = 100"
cpu200: "cpus = 200"
cpu500: "cpus = 500"
cpu1000: "cpus = 1000"
debug: false
container: "docker"
engines:
- type: "native"
id: "native"
build_info:
config: "src/workflows/pseudo_alignment_and_quant/config.vsh.yaml"
runner: "executable"
engine: "native"
output: "target/executable/workflows/pseudo_alignment_and_quant"
executable: "target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant"
viash_version: "0.9.0"
git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
git_remote: "https://github.com/viash-hub/rnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/salmon/salmon_quant"
- "target/nextflow/kallisto/kallisto_quant"
package_config:
version: "main"
info:
test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1"
dest: "testData"
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag\
\ := '$id'\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'main'"
organization: "vsh"

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target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant Executable file
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#!/usr/bin/env bash
# pseudo_alignment_and_quant main
#
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
# work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
# Intuitive.
#
# The component may contain files which fall under a different license. The
# authors of this component should specify the license in the header of such
# files, or include a separate license file detailing the licenses of all included
# files.
set -e
if [ -z "$VIASH_TEMP" ]; then
VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMPDIR}
VIASH_TEMP=${VIASH_TEMP:-$VIASH_TEMPDIR}
VIASH_TEMP=${VIASH_TEMP:-$VIASH_TMP}
VIASH_TEMP=${VIASH_TEMP:-$TMPDIR}
VIASH_TEMP=${VIASH_TEMP:-$TMP}
VIASH_TEMP=${VIASH_TEMP:-$TEMPDIR}
VIASH_TEMP=${VIASH_TEMP:-$TEMP}
VIASH_TEMP=${VIASH_TEMP:-/tmp}
fi
# define helper functions
# ViashQuote: put quotes around non flag values
# $1 : unquoted string
# return : possibly quoted string
# examples:
# ViashQuote --foo # returns --foo
# ViashQuote bar # returns 'bar'
# Viashquote --foo=bar # returns --foo='bar'
function ViashQuote {
if [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+=.+$ ]]; then
echo "$1" | sed "s#=\(.*\)#='\1'#"
elif [[ "$1" =~ ^-+[a-zA-Z0-9_\-]+$ ]]; then
echo "$1"
else
echo "'$1'"
fi
}
# ViashRemoveFlags: Remove leading flag
# $1 : string with a possible leading flag
# return : string without possible leading flag
# examples:
# ViashRemoveFlags --foo=bar # returns bar
function ViashRemoveFlags {
echo "$1" | sed 's/^--*[a-zA-Z0-9_\-]*=//'
}
# ViashSourceDir: return the path of a bash file, following symlinks
# usage : ViashSourceDir ${BASH_SOURCE[0]}
# $1 : Should always be set to ${BASH_SOURCE[0]}
# returns : The absolute path of the bash file
function ViashSourceDir {
local source="$1"
while [ -h "$source" ]; do
local dir="$( cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd )"
source="$(readlink "$source")"
[[ $source != /* ]] && source="$dir/$source"
done
cd -P "$( dirname "$source" )" >/dev/null 2>&1 && pwd
}
# ViashFindTargetDir: return the path of the '.build.yaml' file, following symlinks
# usage : ViashFindTargetDir 'ScriptPath'
# $1 : The location from where to start the upward search
# returns : The absolute path of the '.build.yaml' file
function ViashFindTargetDir {
local source="$1"
while [[ "$source" != "" && ! -e "$source/.build.yaml" ]]; do
source=${source%/*}
done
echo $source
}
# see https://en.wikipedia.org/wiki/Syslog#Severity_level
VIASH_LOGCODE_EMERGENCY=0
VIASH_LOGCODE_ALERT=1
VIASH_LOGCODE_CRITICAL=2
VIASH_LOGCODE_ERROR=3
VIASH_LOGCODE_WARNING=4
VIASH_LOGCODE_NOTICE=5
VIASH_LOGCODE_INFO=6
VIASH_LOGCODE_DEBUG=7
VIASH_VERBOSITY=$VIASH_LOGCODE_NOTICE
# ViashLog: Log events depending on the verbosity level
# usage: ViashLog 1 alert Oh no something went wrong!
# $1: required verbosity level
# $2: display tag
# $3+: messages to display
# stdout: Your input, prepended by '[$2] '.
function ViashLog {
local required_level="$1"
local display_tag="$2"
shift 2
if [ $VIASH_VERBOSITY -ge $required_level ]; then
>&2 echo "[$display_tag]" "$@"
fi
}
# ViashEmergency: log events when the system is unstable
# usage: ViashEmergency Oh no something went wrong.
# stdout: Your input, prepended by '[emergency] '.
function ViashEmergency {
ViashLog $VIASH_LOGCODE_EMERGENCY emergency "$@"
}
# ViashAlert: log events when actions must be taken immediately (e.g. corrupted system database)
# usage: ViashAlert Oh no something went wrong.
# stdout: Your input, prepended by '[alert] '.
function ViashAlert {
ViashLog $VIASH_LOGCODE_ALERT alert "$@"
}
# ViashCritical: log events when a critical condition occurs
# usage: ViashCritical Oh no something went wrong.
# stdout: Your input, prepended by '[critical] '.
function ViashCritical {
ViashLog $VIASH_LOGCODE_CRITICAL critical "$@"
}
# ViashError: log events when an error condition occurs
# usage: ViashError Oh no something went wrong.
# stdout: Your input, prepended by '[error] '.
function ViashError {
ViashLog $VIASH_LOGCODE_ERROR error "$@"
}
# ViashWarning: log potentially abnormal events
# usage: ViashWarning Something may have gone wrong.
# stdout: Your input, prepended by '[warning] '.
function ViashWarning {
ViashLog $VIASH_LOGCODE_WARNING warning "$@"
}
# ViashNotice: log significant but normal events
# usage: ViashNotice This just happened.
# stdout: Your input, prepended by '[notice] '.
function ViashNotice {
ViashLog $VIASH_LOGCODE_NOTICE notice "$@"
}
# ViashInfo: log normal events
# usage: ViashInfo This just happened.
# stdout: Your input, prepended by '[info] '.
function ViashInfo {
ViashLog $VIASH_LOGCODE_INFO info "$@"
}
# ViashDebug: log all events, for debugging purposes
# usage: ViashDebug This just happened.
# stdout: Your input, prepended by '[debug] '.
function ViashDebug {
ViashLog $VIASH_LOGCODE_DEBUG debug "$@"
}
# find source folder of this component
VIASH_META_RESOURCES_DIR=`ViashSourceDir ${BASH_SOURCE[0]}`
# find the root of the built components & dependencies
VIASH_TARGET_DIR=`ViashFindTargetDir $VIASH_META_RESOURCES_DIR`
# define meta fields
VIASH_META_NAME="pseudo_alignment_and_quant"
VIASH_META_FUNCTIONALITY_NAME="pseudo_alignment_and_quant"
VIASH_META_EXECUTABLE="$VIASH_META_RESOURCES_DIR/$VIASH_META_NAME"
VIASH_META_CONFIG="$VIASH_META_RESOURCES_DIR/.config.vsh.yaml"
VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable
function ViashHelp {
echo "pseudo_alignment_and_quant main"
echo ""
echo "A viash sub-workflow for pseudo alignment and quantification stage of"
echo "nf-core/rnaseq pipeline."
echo ""
echo "Input:"
echo " --id"
echo " type: string, required parameter"
echo " example: foo"
echo " ID of the sample."
echo ""
echo " -i, --fastq_1"
echo " type: file, required parameter, file must exist"
echo " example: input.fastq.gz"
echo " Path to the sample (or read 1 of paired end sample)."
echo ""
echo " --fastq_2"
echo " type: file, file must exist"
echo " Path to read 2 of the sample."
echo ""
echo " --strandedness"
echo " type: string"
echo " choices: [ forward, reverse, unstranded ]"
echo " Sample strand-specificity. Must be one of unstranded, forward, or"
echo " reverse"
echo ""
echo " --gtf"
echo " type: file, file must exist"
echo " GTF file"
echo ""
echo " --transcript_fasta"
echo " type: file, file must exist"
echo " Fasta file of the reference transcriptome."
echo ""
echo " --pseudo_aligner"
echo " type: string"
echo " default: false"
echo " choices: [ salmon, kallisto ]"
echo " Specifies the pseudo aligner to use - available options are 'salmon'."
echo " Runs in addition to '--aligner'."
echo ""
echo " --salmon_index"
echo " type: file, file must exist"
echo " Salmon index"
echo ""
echo " --kallisto_index"
echo " type: file, file must exist"
echo " Kallisto index"
echo ""
echo " --lib_type"
echo " type: string"
echo " default:"
echo " Override library type inferred based on strandedness defined in meta"
echo " object"
echo ""
echo " --kallisto_quant_fragment_length"
echo " type: integer"
echo " For single-end mode only, the estimated average fragment length to use"
echo " for quantification with Kallisto."
echo ""
echo " --kallisto_quant_fragment_length_sd"
echo " type: integer"
echo " For single-end mode only, the estimated standard deviation of the"
echo " fragment length for quantification with Kallisto."
echo ""
echo "Output:"
echo " --pseudo_multiqc"
echo " type: file, output, file must exist"
echo " default: \$id.quant.log"
echo ""
echo " --quant_out_dir"
echo " type: file, output, file must exist"
echo " default: \$id.salmon_quant"
echo ""
echo " --salmon_quant_results_file"
echo " type: file, output, file must exist"
echo " default: \$id.quant.sf"
echo ""
echo " --kallisto_quant_results_file"
echo " type: file, output, file must exist"
echo " default: \$id.abundance.tsv"
}
# initialise variables
VIASH_MODE='run'
VIASH_ENGINE_ID='native'
# initialise array
VIASH_POSITIONAL_ARGS=''
while [[ $# -gt 0 ]]; do
case "$1" in
-h|--help)
ViashHelp
exit
;;
---v|---verbose)
let "VIASH_VERBOSITY=VIASH_VERBOSITY+1"
shift 1
;;
---verbosity)
VIASH_VERBOSITY="$2"
shift 2
;;
---verbosity=*)
VIASH_VERBOSITY="$(ViashRemoveFlags "$1")"
shift 1
;;
--version)
echo "pseudo_alignment_and_quant main"
exit
;;
--id)
[ -n "$VIASH_PAR_ID" ] && ViashError Bad arguments for option \'--id\': \'$VIASH_PAR_ID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_ID="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --id. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--id=*)
[ -n "$VIASH_PAR_ID" ] && ViashError Bad arguments for option \'--id=*\': \'$VIASH_PAR_ID\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_ID=$(ViashRemoveFlags "$1")
shift 1
;;
--fastq_1)
[ -n "$VIASH_PAR_FASTQ_1" ] && ViashError Bad arguments for option \'--fastq_1\': \'$VIASH_PAR_FASTQ_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_FASTQ_1="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --fastq_1. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--fastq_1=*)
[ -n "$VIASH_PAR_FASTQ_1" ] && ViashError Bad arguments for option \'--fastq_1=*\': \'$VIASH_PAR_FASTQ_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_FASTQ_1=$(ViashRemoveFlags "$1")
shift 1
;;
-i)
[ -n "$VIASH_PAR_FASTQ_1" ] && ViashError Bad arguments for option \'-i\': \'$VIASH_PAR_FASTQ_1\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_FASTQ_1="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to -i. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--fastq_2)
[ -n "$VIASH_PAR_FASTQ_2" ] && ViashError Bad arguments for option \'--fastq_2\': \'$VIASH_PAR_FASTQ_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_FASTQ_2="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --fastq_2. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--fastq_2=*)
[ -n "$VIASH_PAR_FASTQ_2" ] && ViashError Bad arguments for option \'--fastq_2=*\': \'$VIASH_PAR_FASTQ_2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_FASTQ_2=$(ViashRemoveFlags "$1")
shift 1
;;
--strandedness)
[ -n "$VIASH_PAR_STRANDEDNESS" ] && ViashError Bad arguments for option \'--strandedness\': \'$VIASH_PAR_STRANDEDNESS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_STRANDEDNESS="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --strandedness. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--strandedness=*)
[ -n "$VIASH_PAR_STRANDEDNESS" ] && ViashError Bad arguments for option \'--strandedness=*\': \'$VIASH_PAR_STRANDEDNESS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_STRANDEDNESS=$(ViashRemoveFlags "$1")
shift 1
;;
--gtf)
[ -n "$VIASH_PAR_GTF" ] && ViashError Bad arguments for option \'--gtf\': \'$VIASH_PAR_GTF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_GTF="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --gtf. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--gtf=*)
[ -n "$VIASH_PAR_GTF" ] && ViashError Bad arguments for option \'--gtf=*\': \'$VIASH_PAR_GTF\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_GTF=$(ViashRemoveFlags "$1")
shift 1
;;
--transcript_fasta)
[ -n "$VIASH_PAR_TRANSCRIPT_FASTA" ] && ViashError Bad arguments for option \'--transcript_fasta\': \'$VIASH_PAR_TRANSCRIPT_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_TRANSCRIPT_FASTA="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --transcript_fasta. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--transcript_fasta=*)
[ -n "$VIASH_PAR_TRANSCRIPT_FASTA" ] && ViashError Bad arguments for option \'--transcript_fasta=*\': \'$VIASH_PAR_TRANSCRIPT_FASTA\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_TRANSCRIPT_FASTA=$(ViashRemoveFlags "$1")
shift 1
;;
--pseudo_aligner)
[ -n "$VIASH_PAR_PSEUDO_ALIGNER" ] && ViashError Bad arguments for option \'--pseudo_aligner\': \'$VIASH_PAR_PSEUDO_ALIGNER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_PSEUDO_ALIGNER="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --pseudo_aligner. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--pseudo_aligner=*)
[ -n "$VIASH_PAR_PSEUDO_ALIGNER" ] && ViashError Bad arguments for option \'--pseudo_aligner=*\': \'$VIASH_PAR_PSEUDO_ALIGNER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_PSEUDO_ALIGNER=$(ViashRemoveFlags "$1")
shift 1
;;
--salmon_index)
[ -n "$VIASH_PAR_SALMON_INDEX" ] && ViashError Bad arguments for option \'--salmon_index\': \'$VIASH_PAR_SALMON_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SALMON_INDEX="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --salmon_index. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--salmon_index=*)
[ -n "$VIASH_PAR_SALMON_INDEX" ] && ViashError Bad arguments for option \'--salmon_index=*\': \'$VIASH_PAR_SALMON_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SALMON_INDEX=$(ViashRemoveFlags "$1")
shift 1
;;
--kallisto_index)
[ -n "$VIASH_PAR_KALLISTO_INDEX" ] && ViashError Bad arguments for option \'--kallisto_index\': \'$VIASH_PAR_KALLISTO_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_KALLISTO_INDEX="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --kallisto_index. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--kallisto_index=*)
[ -n "$VIASH_PAR_KALLISTO_INDEX" ] && ViashError Bad arguments for option \'--kallisto_index=*\': \'$VIASH_PAR_KALLISTO_INDEX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_KALLISTO_INDEX=$(ViashRemoveFlags "$1")
shift 1
;;
--lib_type)
[ -n "$VIASH_PAR_LIB_TYPE" ] && ViashError Bad arguments for option \'--lib_type\': \'$VIASH_PAR_LIB_TYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_LIB_TYPE="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --lib_type. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--lib_type=*)
[ -n "$VIASH_PAR_LIB_TYPE" ] && ViashError Bad arguments for option \'--lib_type=*\': \'$VIASH_PAR_LIB_TYPE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_LIB_TYPE=$(ViashRemoveFlags "$1")
shift 1
;;
--kallisto_quant_fragment_length)
[ -n "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH" ] && ViashError Bad arguments for option \'--kallisto_quant_fragment_length\': \'$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --kallisto_quant_fragment_length. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--kallisto_quant_fragment_length=*)
[ -n "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH" ] && ViashError Bad arguments for option \'--kallisto_quant_fragment_length=*\': \'$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH=$(ViashRemoveFlags "$1")
shift 1
;;
--kallisto_quant_fragment_length_sd)
[ -n "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD" ] && ViashError Bad arguments for option \'--kallisto_quant_fragment_length_sd\': \'$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --kallisto_quant_fragment_length_sd. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--kallisto_quant_fragment_length_sd=*)
[ -n "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD" ] && ViashError Bad arguments for option \'--kallisto_quant_fragment_length_sd=*\': \'$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD=$(ViashRemoveFlags "$1")
shift 1
;;
--pseudo_multiqc)
[ -n "$VIASH_PAR_PSEUDO_MULTIQC" ] && ViashError Bad arguments for option \'--pseudo_multiqc\': \'$VIASH_PAR_PSEUDO_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_PSEUDO_MULTIQC="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --pseudo_multiqc. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--pseudo_multiqc=*)
[ -n "$VIASH_PAR_PSEUDO_MULTIQC" ] && ViashError Bad arguments for option \'--pseudo_multiqc=*\': \'$VIASH_PAR_PSEUDO_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_PSEUDO_MULTIQC=$(ViashRemoveFlags "$1")
shift 1
;;
--quant_out_dir)
[ -n "$VIASH_PAR_QUANT_OUT_DIR" ] && ViashError Bad arguments for option \'--quant_out_dir\': \'$VIASH_PAR_QUANT_OUT_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_QUANT_OUT_DIR="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --quant_out_dir. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--quant_out_dir=*)
[ -n "$VIASH_PAR_QUANT_OUT_DIR" ] && ViashError Bad arguments for option \'--quant_out_dir=*\': \'$VIASH_PAR_QUANT_OUT_DIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_QUANT_OUT_DIR=$(ViashRemoveFlags "$1")
shift 1
;;
--salmon_quant_results_file)
[ -n "$VIASH_PAR_SALMON_QUANT_RESULTS_FILE" ] && ViashError Bad arguments for option \'--salmon_quant_results_file\': \'$VIASH_PAR_SALMON_QUANT_RESULTS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SALMON_QUANT_RESULTS_FILE="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --salmon_quant_results_file. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--salmon_quant_results_file=*)
[ -n "$VIASH_PAR_SALMON_QUANT_RESULTS_FILE" ] && ViashError Bad arguments for option \'--salmon_quant_results_file=*\': \'$VIASH_PAR_SALMON_QUANT_RESULTS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SALMON_QUANT_RESULTS_FILE=$(ViashRemoveFlags "$1")
shift 1
;;
--kallisto_quant_results_file)
[ -n "$VIASH_PAR_KALLISTO_QUANT_RESULTS_FILE" ] && ViashError Bad arguments for option \'--kallisto_quant_results_file\': \'$VIASH_PAR_KALLISTO_QUANT_RESULTS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_KALLISTO_QUANT_RESULTS_FILE="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --kallisto_quant_results_file. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--kallisto_quant_results_file=*)
[ -n "$VIASH_PAR_KALLISTO_QUANT_RESULTS_FILE" ] && ViashError Bad arguments for option \'--kallisto_quant_results_file=*\': \'$VIASH_PAR_KALLISTO_QUANT_RESULTS_FILE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_KALLISTO_QUANT_RESULTS_FILE=$(ViashRemoveFlags "$1")
shift 1
;;
---engine)
VIASH_ENGINE_ID="$2"
shift 2
;;
---engine=*)
VIASH_ENGINE_ID="$(ViashRemoveFlags "$1")"
shift 1
;;
---cpus)
[ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_META_CPUS="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to ---cpus. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
---cpus=*)
[ -n "$VIASH_META_CPUS" ] && ViashError Bad arguments for option \'---cpus=*\': \'$VIASH_META_CPUS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_META_CPUS=$(ViashRemoveFlags "$1")
shift 1
;;
---memory)
[ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_META_MEMORY="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to ---memory. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
---memory=*)
[ -n "$VIASH_META_MEMORY" ] && ViashError Bad arguments for option \'---memory=*\': \'$VIASH_META_MEMORY\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_META_MEMORY=$(ViashRemoveFlags "$1")
shift 1
;;
*) # positional arg or unknown option
# since the positional args will be eval'd, can we always quote, instead of using ViashQuote
VIASH_POSITIONAL_ARGS="$VIASH_POSITIONAL_ARGS '$1'"
[[ $1 == -* ]] && ViashWarning $1 looks like a parameter but is not a defined parameter and will instead be treated as a positional argument. Use "--help" to get more information on the parameters.
shift # past argument
;;
esac
done
# parse positional parameters
eval set -- $VIASH_POSITIONAL_ARGS
if [ "$VIASH_ENGINE_ID" == "native" ] ; then
VIASH_ENGINE_TYPE='native'
else
ViashError "Engine '$VIASH_ENGINE_ID' is not recognized. Options are: native."
exit 1
fi
# setting computational defaults
# helper function for parsing memory strings
function ViashMemoryAsBytes {
local memory=`echo "$1" | tr '[:upper:]' '[:lower:]' | tr -d '[:space:]'`
local memory_regex='^([0-9]+)([kmgtp]i?b?|b)$'
if [[ $memory =~ $memory_regex ]]; then
local number=${memory/[^0-9]*/}
local symbol=${memory/*[0-9]/}
case $symbol in
b) memory_b=$number ;;
kb|k) memory_b=$(( $number * 1000 )) ;;
mb|m) memory_b=$(( $number * 1000 * 1000 )) ;;
gb|g) memory_b=$(( $number * 1000 * 1000 * 1000 )) ;;
tb|t) memory_b=$(( $number * 1000 * 1000 * 1000 * 1000 )) ;;
pb|p) memory_b=$(( $number * 1000 * 1000 * 1000 * 1000 * 1000 )) ;;
kib|ki) memory_b=$(( $number * 1024 )) ;;
mib|mi) memory_b=$(( $number * 1024 * 1024 )) ;;
gib|gi) memory_b=$(( $number * 1024 * 1024 * 1024 )) ;;
tib|ti) memory_b=$(( $number * 1024 * 1024 * 1024 * 1024 )) ;;
pib|pi) memory_b=$(( $number * 1024 * 1024 * 1024 * 1024 * 1024 )) ;;
esac
echo "$memory_b"
fi
}
# compute memory in different units
if [ ! -z ${VIASH_META_MEMORY+x} ]; then
VIASH_META_MEMORY_B=`ViashMemoryAsBytes $VIASH_META_MEMORY`
# do not define other variables if memory_b is an empty string
if [ ! -z "$VIASH_META_MEMORY_B" ]; then
VIASH_META_MEMORY_KB=$(( ($VIASH_META_MEMORY_B+999) / 1000 ))
VIASH_META_MEMORY_MB=$(( ($VIASH_META_MEMORY_KB+999) / 1000 ))
VIASH_META_MEMORY_GB=$(( ($VIASH_META_MEMORY_MB+999) / 1000 ))
VIASH_META_MEMORY_TB=$(( ($VIASH_META_MEMORY_GB+999) / 1000 ))
VIASH_META_MEMORY_PB=$(( ($VIASH_META_MEMORY_TB+999) / 1000 ))
VIASH_META_MEMORY_KIB=$(( ($VIASH_META_MEMORY_B+1023) / 1024 ))
VIASH_META_MEMORY_MIB=$(( ($VIASH_META_MEMORY_KIB+1023) / 1024 ))
VIASH_META_MEMORY_GIB=$(( ($VIASH_META_MEMORY_MIB+1023) / 1024 ))
VIASH_META_MEMORY_TIB=$(( ($VIASH_META_MEMORY_GIB+1023) / 1024 ))
VIASH_META_MEMORY_PIB=$(( ($VIASH_META_MEMORY_TIB+1023) / 1024 ))
else
# unset memory if string is empty
unset $VIASH_META_MEMORY_B
fi
fi
# unset nproc if string is empty
if [ -z "$VIASH_META_CPUS" ]; then
unset $VIASH_META_CPUS
fi
# check whether required parameters exist
if [ -z ${VIASH_PAR_ID+x} ]; then
ViashError '--id' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
if [ -z ${VIASH_PAR_FASTQ_1+x} ]; then
ViashError '--fastq_1' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
if [ -z ${VIASH_META_NAME+x} ]; then
ViashError 'name' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
if [ -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then
ViashError 'functionality_name' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
if [ -z ${VIASH_META_RESOURCES_DIR+x} ]; then
ViashError 'resources_dir' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
if [ -z ${VIASH_META_EXECUTABLE+x} ]; then
ViashError 'executable' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
if [ -z ${VIASH_META_CONFIG+x} ]; then
ViashError 'config' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
if [ -z ${VIASH_META_TEMP_DIR+x} ]; then
ViashError 'temp_dir' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
# filling in defaults
if [ -z ${VIASH_PAR_PSEUDO_ALIGNER+x} ]; then
VIASH_PAR_PSEUDO_ALIGNER="false"
fi
if [ -z ${VIASH_PAR_LIB_TYPE+x} ]; then
VIASH_PAR_LIB_TYPE=""
fi
if [ -z ${VIASH_PAR_PSEUDO_MULTIQC+x} ]; then
VIASH_PAR_PSEUDO_MULTIQC="\$id.quant.log"
fi
if [ -z ${VIASH_PAR_QUANT_OUT_DIR+x} ]; then
VIASH_PAR_QUANT_OUT_DIR="\$id.salmon_quant"
fi
if [ -z ${VIASH_PAR_SALMON_QUANT_RESULTS_FILE+x} ]; then
VIASH_PAR_SALMON_QUANT_RESULTS_FILE="\$id.quant.sf"
fi
if [ -z ${VIASH_PAR_KALLISTO_QUANT_RESULTS_FILE+x} ]; then
VIASH_PAR_KALLISTO_QUANT_RESULTS_FILE="\$id.abundance.tsv"
fi
# check whether required files exist
if [ ! -z "$VIASH_PAR_FASTQ_1" ] && [ ! -e "$VIASH_PAR_FASTQ_1" ]; then
ViashError "Input file '$VIASH_PAR_FASTQ_1' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_FASTQ_2" ] && [ ! -e "$VIASH_PAR_FASTQ_2" ]; then
ViashError "Input file '$VIASH_PAR_FASTQ_2' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_GTF" ] && [ ! -e "$VIASH_PAR_GTF" ]; then
ViashError "Input file '$VIASH_PAR_GTF' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_TRANSCRIPT_FASTA" ] && [ ! -e "$VIASH_PAR_TRANSCRIPT_FASTA" ]; then
ViashError "Input file '$VIASH_PAR_TRANSCRIPT_FASTA' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_SALMON_INDEX" ] && [ ! -e "$VIASH_PAR_SALMON_INDEX" ]; then
ViashError "Input file '$VIASH_PAR_SALMON_INDEX' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_KALLISTO_INDEX" ] && [ ! -e "$VIASH_PAR_KALLISTO_INDEX" ]; then
ViashError "Input file '$VIASH_PAR_KALLISTO_INDEX' does not exist."
exit 1
fi
# check whether parameters values are of the right type
if [[ -n "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH" ]]; then
if ! [[ "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH" =~ ^[-+]?[0-9]+$ ]]; then
ViashError '--kallisto_quant_fragment_length' has to be an integer. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD" ]]; then
if ! [[ "$VIASH_PAR_KALLISTO_QUANT_FRAGMENT_LENGTH_SD" =~ ^[-+]?[0-9]+$ ]]; then
ViashError '--kallisto_quant_fragment_length_sd' has to be an integer. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_CPUS" ]]; then
if ! [[ "$VIASH_META_CPUS" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'cpus' has to be an integer. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_B" ]]; then
if ! [[ "$VIASH_META_MEMORY_B" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_b' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_KB" ]]; then
if ! [[ "$VIASH_META_MEMORY_KB" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_kb' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_MB" ]]; then
if ! [[ "$VIASH_META_MEMORY_MB" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_mb' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_GB" ]]; then
if ! [[ "$VIASH_META_MEMORY_GB" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_gb' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_TB" ]]; then
if ! [[ "$VIASH_META_MEMORY_TB" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_tb' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_PB" ]]; then
if ! [[ "$VIASH_META_MEMORY_PB" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_pb' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_KIB" ]]; then
if ! [[ "$VIASH_META_MEMORY_KIB" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_kib' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_MIB" ]]; then
if ! [[ "$VIASH_META_MEMORY_MIB" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_mib' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_GIB" ]]; then
if ! [[ "$VIASH_META_MEMORY_GIB" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_gib' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_TIB" ]]; then
if ! [[ "$VIASH_META_MEMORY_TIB" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_tib' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_META_MEMORY_PIB" ]]; then
if ! [[ "$VIASH_META_MEMORY_PIB" =~ ^[-+]?[0-9]+$ ]]; then
ViashError 'memory_pib' has to be a long. Use "--help" to get more information on the parameters.
exit 1
fi
fi
# check whether value is belongs to a set of choices
if [ ! -z "$VIASH_PAR_STRANDEDNESS" ]; then
VIASH_PAR_STRANDEDNESS_CHOICES=("forward;reverse;unstranded")
IFS=';'
set -f
if ! [[ ";${VIASH_PAR_STRANDEDNESS_CHOICES[*]};" =~ ";$VIASH_PAR_STRANDEDNESS;" ]]; then
ViashError '--strandedness' specified value of \'$VIASH_PAR_STRANDEDNESS\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
exit 1
fi
set +f
unset IFS
fi
if [ ! -z "$VIASH_PAR_PSEUDO_ALIGNER" ]; then
VIASH_PAR_PSEUDO_ALIGNER_CHOICES=("salmon;kallisto")
IFS=';'
set -f
if ! [[ ";${VIASH_PAR_PSEUDO_ALIGNER_CHOICES[*]};" =~ ";$VIASH_PAR_PSEUDO_ALIGNER;" ]]; then
ViashError '--pseudo_aligner' specified value of \'$VIASH_PAR_PSEUDO_ALIGNER\' is not in the list of allowed values. Use "--help" to get more information on the parameters.
exit 1
fi
set +f
unset IFS
fi
# create parent directories of output files, if so desired
if [ ! -z "$VIASH_PAR_PSEUDO_MULTIQC" ] && [ ! -d "$(dirname "$VIASH_PAR_PSEUDO_MULTIQC")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_PSEUDO_MULTIQC")"
fi
if [ ! -z "$VIASH_PAR_QUANT_OUT_DIR" ] && [ ! -d "$(dirname "$VIASH_PAR_QUANT_OUT_DIR")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_QUANT_OUT_DIR")"
fi
if [ ! -z "$VIASH_PAR_SALMON_QUANT_RESULTS_FILE" ] && [ ! -d "$(dirname "$VIASH_PAR_SALMON_QUANT_RESULTS_FILE")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_SALMON_QUANT_RESULTS_FILE")"
fi
if [ ! -z "$VIASH_PAR_KALLISTO_QUANT_RESULTS_FILE" ] && [ ! -d "$(dirname "$VIASH_PAR_KALLISTO_QUANT_RESULTS_FILE")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_KALLISTO_QUANT_RESULTS_FILE")"
fi
if [ "$VIASH_ENGINE_ID" == "native" ] ; then
if [ "$VIASH_MODE" == "run" ]; then
VIASH_CMD="bash"
else
ViashError "Engine '$VIASH_ENGINE_ID' does not support mode '$VIASH_MODE'."
exit 1
fi
fi
# set dependency paths
VIASH_DEP_KALLISTO_KALLISTO_QUANT="$VIASH_META_RESOURCES_DIR/../../../nextflow/kallisto/kallisto_quant/main.nf"
VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.1/nextflow/salmon/salmon_quant/main.nf"
ViashDebug "Running command: $(echo $VIASH_CMD)"
cat << VIASHEOF | eval $VIASH_CMD
set -e
tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-pseudo_alignment_and_quant-XXXXXX").nf
function clean_up {
rm "\$tempscript"
}
function interrupt {
echo -e "\nCTRL-C Pressed..."
exit 1
}
trap clean_up EXIT
trap interrupt INT SIGINT
cat > "\$tempscript" << 'VIASHMAIN'
//// VIASH START
// The following code has been auto-generated by Viash.
//// VIASH END
workflow run_wf {
take:
input_ch
main:
output_ch = input_ch
| map { id, state ->
def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
def paired = input.size() == 2
[ id, state + [ paired: paired, input: input ] ]
}
// Infer lib-type for salmon quant
| map { id, state ->
def lib_type = (state.paired) ?
(
(state.strandedness == "forward") ?
"ISF" :
(
(state.strandedness == "reverse") ? "ISR" : "IU"
)
)
: (
(state.strandedness == "forward") ?
"SF" :
(
(state.strandedness == "reverse") ? "SR" : "U"
)
)
[ id, state + [lib_type: lib_type] ]
}
// Count reads from BAM alignments using Salmon
| salmon_quant.run (
runIf: { id, state -> state.pseudo_aligner == 'salmon' },
fromState: { id, state ->
def unmated_reads = !state.paired ? state.fastq_1 : null
def mates1 = state.paired ? state.fastq_1 : null
def mates2 = state.paired ? state.fastq_2 : null
[ unmated_reads: unmated_reads,
mates1: mates1,
mates2: mates2,
gene_map: state.gtf,
index: state.salmon_index,
lib_type: state.lib_type ]
},
toState: [
"quant_results_dir": "output",
"salmon_quant_results_file": "quant_results"
]
)
| kallisto_quant.run (
runIf: { id, state -> state.pseudo_aligner == 'kallisto'},
fromState: [
"input": "input",
"paired": "paired",
"gtf": "gtf",
"index": "kallisto_index",
"fragment_length": "kallisto_quant_fragment_length",
"fragment_length_sd": "kallisto_quant_fragment_length_sd"
],
toState: [
"quant_out_dir": "output",
"kallisto_quant_results_file": "quant_results_file",
"pseudo_multiqc": "log"
]
)
| map { id, state ->
def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() }
[ id, mod_state ]
}
| setState (
[ "pseudo_multiqc": "quant_results",
"quant_out_dir": "quant_out_dir",
"salmon_quant_results_file": "salmon_quant_results_file",
"kallisto_quant_results_file": "kallisto_quant_results_file" ]
)
emit:
output_ch
}
VIASHMAIN
nextflow run . -main-script "\$tempscript" &
wait "\$!"
VIASHEOF
# check whether required files exist
if [ ! -z "$VIASH_PAR_PSEUDO_MULTIQC" ] && [ ! -e "$VIASH_PAR_PSEUDO_MULTIQC" ]; then
ViashError "Output file '$VIASH_PAR_PSEUDO_MULTIQC' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_QUANT_OUT_DIR" ] && [ ! -e "$VIASH_PAR_QUANT_OUT_DIR" ]; then
ViashError "Output file '$VIASH_PAR_QUANT_OUT_DIR' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_SALMON_QUANT_RESULTS_FILE" ] && [ ! -e "$VIASH_PAR_SALMON_QUANT_RESULTS_FILE" ]; then
ViashError "Output file '$VIASH_PAR_SALMON_QUANT_RESULTS_FILE' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_KALLISTO_QUANT_RESULTS_FILE" ] && [ ! -e "$VIASH_PAR_KALLISTO_QUANT_RESULTS_FILE" ]; then
ViashError "Output file '$VIASH_PAR_KALLISTO_QUANT_RESULTS_FILE' does not exist."
exit 1
fi
exit 0