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Build branch main with version main (a2e8c5d)

Browse Source 
Build pipeline: viash-hub.craftbox.main-fvsn9

Source commit: a2e8c5d12d

Source message: Add concat_text component (#4)

* Add concat_text component
* Minor cleanup
* Update src/concat_text/config.vsh.yaml
* Update in line with most of Dries' comments
* Don't claim to cleanup if it ain't happening...
* Add authorship
* Avoid using deprecated Viash variable

---------

Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
This commit is contained in:
CI
2024-07-24 08:39:04 +00:00
parent a0733101ff
commit f57725a0fd
19 changed files with 5532 additions and 10 deletions
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11
src/_authors/dries_schaumont.yaml Normal file
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name: Dries Schaumont
info:
links:
email: dries@data-intuitive.com
github: DriesSchaumont
orcid: "0000-0002-4389-0440"
linkedin: dries-schaumont
organizations:
- name: Data Intuitive
href: https://www.data-intuitive.com
role: Data Scientist

9
src/_authors/toni_verbeiren.yaml Normal file
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name: Toni Verbeiren
info:
links:
github: tverbeiren
linkedin: verbeiren
organizations:
- name: Data Intuitive
href: https://www.data-intuitive.com
role: Data Scientist and CEO

56
src/concat_text/config.vsh.yaml Normal file
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@@ -0,0 +1,56 @@
name: concat_text
description: |
Concatenate a number of text files, handle gzipped text files gracefully and
optionally gzip the output text file.
This component is useful for concatening fastq files from different lanes, for instance.
authors:
- __merge__: /src/_authors/toni_verbeiren.yaml
roles: [ author, maintainer ]
- __merge__: /src/_authors/dries_schaumont.yaml
roles: [ reviewer ]
info:
improvements: |
This component could be improved in 2 ways:
1. Allow for a mix of zipped and plain input files
2. Allow to specify a compression algorithm for the output
argument_groups:
- name: Input arguments
arguments:
- name: --input
description: A list of (gzipped) text files.
type: file
multiple: true
required: true
example: input?.txt.gz
- name: Output arguments
arguments:
- name: "--gzip_output"
type: boolean_true
description: Should the output be zipped?
- name: --output
description: File to write the output to, optionally gzipped.
type: file
direction: output
example: output.txt
resources:
- type: bash_script
path: script.sh
test_resources:
- type: bash_script
path: test.sh
engines:
- type: docker
image: alpine:latest
setup:
- type: apk
packages:
- bash
- procps
- file
runners:
- type: executable
- type: nextflow

34
src/concat_text/script.sh Normal file
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@@ -0,0 +1,34 @@
#!/usr/bin/env bash
set -euo pipefail
TMPDIR=$(mktemp -d "$meta_temp_dir/concat_text-XXXXXX")
function clean_up {
[[ -d "$TMPDIR" ]] && rm -r "$TMPDIR"
}
trap clean_up EXIT
par_input="$(echo "$par_input" | tr ';' ' ')"
echo -n ">> Check if input is gzipped... "
set +eo pipefail
file $par_input | grep -q 'gzip'
is_zipped="$?"
set -euo pipefail
[[ "$is_zipped" == "0" ]] && echo "yes" || echo "no"
if [[ "$is_zipped" == "0" ]]; then
echo ">> zcat gzipped files"
zcat $par_input > $TMPDIR/contents
else
echo ">> cat plain files"
cat $par_input > $TMPDIR/contents
fi
if [ "$par_gzip_output" == true ]; then
echo ">> Zip output file"
gzip $TMPDIR/contents
mv $TMPDIR/contents.gz $par_output
else
mv $TMPDIR/contents $par_output
fi

70
src/concat_text/test.sh Normal file
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@@ -0,0 +1,70 @@
#!/usr/bin/env bash
set -euo pipefail
echo ">> Creating test input files file[1-3].txt"
INPUT_FILE_1="file1.txt"
INPUT_FILE_2="file2.txt"
INPUT_FILE_3="file3.txt"
echo "one" > "$INPUT_FILE_1"
echo "two" > "$INPUT_FILE_2"
echo "three" > "$INPUT_FILE_3"
echo ">> Created input files"
echo ">> Creating zipped versions at file[1-3].txt.gz"
gzip -k $INPUT_FILE_1
gzip -k $INPUT_FILE_2
gzip -k $INPUT_FILE_3
echo ">> Creating expected output file expected_output.txt and zipped version"
cat > "expected_output.txt" <<EOF
one
two
three
EOF
gzip -k "expected_output.txt"
echo ">> Run component on 3 plain input files, plain output"
$meta_executable \
--input "$INPUT_FILE_1;$INPUT_FILE_2;$INPUT_FILE_3" \
--output "output1.txt"
[[ ! -f "output1.txt" ]] \
&& echo "Output file output1.txt not found!" && exit 1
[[ $(cmp "output1.txt" "expected_output.txt") ]] \
&& echo "Output file output1.txt is not as expected!" && exit 1
echo ">> Run component on 3 zipped input files, plain output"
$meta_executable \
--input "$INPUT_FILE_1.gz;$INPUT_FILE_2.gz;$INPUT_FILE_3.gz" \
--output "output2.txt"
[[ ! -f "output2.txt" ]] \
&& echo "Output file output2.txt not found!" && exit 1
[[ $(cmp "output2.txt" "expected_output.txt") ]] \
&& echo "Output file output2.txt is not as expected!" && exit 1
echo ">> Run component on 3 plain input files, zipped output"
$meta_executable \
--input "$INPUT_FILE_1;$INPUT_FILE_2;$INPUT_FILE_3" \
--output "output3.txt.gz" \
--gzip_output
[[ ! -f "output3.txt.gz" ]] \
&& echo "Output file output3.txt.gz not found!" && exit 1
[[ $(cmp "output3.txt.gz" "expected_output.txt.gz") ]] \
&& echo "Output file output3.txt.gz is not as expected!" && exit 1
echo ">> Run component on 3 zipped input files, zipped output"
$meta_executable \
--input "$INPUT_FILE_1.gz;$INPUT_FILE_2.gz;$INPUT_FILE_3.gz" \
--output "output4.txt.gz" \
--gzip_output
[[ ! -f "output4.txt.gz" ]] \
&& echo "Output file output4.txt.gz not found!" && exit 1
[[ $(cmp "output4.txt.gz" "expected_output.txt.gz") ]] \
&& echo "Output file output4.txt.gz is not as expected!" && exit 1
echo ">> Tests done"

197
target/executable/concat_text/.config.vsh.yaml Normal file
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name: "concat_text"
version: "main"
authors:
- name: "Toni Verbeiren"
roles:
- "author"
- "maintainer"
info:
links:
github: "tverbeiren"
linkedin: "verbeiren"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Scientist and CEO"
- name: "Dries Schaumont"
roles:
- "reviewer"
info:
links:
email: "dries@data-intuitive.com"
github: "DriesSchaumont"
orcid: "0000-0002-4389-0440"
linkedin: "dries-schaumont"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Scientist"
argument_groups:
- name: "Input arguments"
arguments:
- type: "file"
name: "--input"
description: "A list of (gzipped) text files."
info: null
example:
- "input?.txt.gz"
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: true
multiple_sep: ";"
- name: "Output arguments"
arguments:
- type: "boolean_true"
name: "--gzip_output"
description: "Should the output be zipped?"
info: null
direction: "input"
- type: "file"
name: "--output"
description: "File to write the output to, optionally gzipped."
info: null
example:
- "output.txt"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
resources:
- type: "bash_script"
path: "script.sh"
is_executable: true
description: "Concatenate a number of text files, handle gzipped text files gracefully\
\ and\noptionally gzip the output text file.\n\nThis component is useful for concatening\
\ fastq files from different lanes, for instance.\n"
test_resources:
- type: "bash_script"
path: "test.sh"
is_executable: true
info:
improvements: "This component could be improved in 2 ways:\n 1. Allow for a mix\
\ of zipped and plain input files\n 2. Allow to specify a compression algorithm\
\ for the output\n"
status: "enabled"
requirements:
commands:
- "ps"
license: "MIT"
links:
repository: "https://github.com/viash-hub/craftbox"
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: "docker"
id: "docker"
image: "alpine:latest"
target_registry: "images.viash-hub.com"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "apk"
packages:
- "bash"
- "procps"
- "file"
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/concat_text/config.vsh.yaml"
runner: "executable"
engine: "docker|native"
output: "target/executable/concat_text"
executable: "target/executable/concat_text/concat_text"
viash_version: "0.9.0-RC6"
git_commit: "a2e8c5d12d55e072f829bc184be03e21893cb524"
git_remote: "https://github.com/viash-hub/craftbox"
package_config:
name: "craftbox"
version: "main"
description: "A collection of custom-tailored scripts and applied tools.\n"
info: null
viash_version: "0.9.0-RC6"
source: "src"
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "scripts"
- "custom"
- "implementations"
license: "MIT"
organization: "vsh"
links:
repository: "https://github.com/viash-hub/craftbox"
issue_tracker: "https://github.com/viash-hub/craftbox/issues"

1134
target/executable/concat_text/concat_text Executable file
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2
target/executable/csv2fasta/.config.vsh.yaml
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@@ -222,7 +222,7 @@ build_info:
output: "target/executable/csv2fasta"
executable: "target/executable/csv2fasta/csv2fasta"
viash_version: "0.9.0-RC6"
git_commit: "781f66883977e37a849f228ee1dffddbb7acdf32"
git_commit: "a2e8c5d12d55e072f829bc184be03e21893cb524"
git_remote: "https://github.com/viash-hub/craftbox"
package_config:
name: "craftbox"

4
target/executable/csv2fasta/csv2fasta
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@@ -524,9 +524,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "dnaio"
LABEL org.opencontainers.image.description="Companion container for running component csv2fasta"
LABEL org.opencontainers.image.created="2024-06-26T12:28:10Z"
LABEL org.opencontainers.image.created="2024-07-24T08:32:31Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
LABEL org.opencontainers.image.revision="781f66883977e37a849f228ee1dffddbb7acdf32"
LABEL org.opencontainers.image.revision="a2e8c5d12d55e072f829bc184be03e21893cb524"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

2
target/executable/untar/.config.vsh.yaml
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@@ -147,7 +147,7 @@ build_info:
output: "target/executable/untar"
executable: "target/executable/untar/untar"
viash_version: "0.9.0-RC6"
git_commit: "781f66883977e37a849f228ee1dffddbb7acdf32"
git_commit: "a2e8c5d12d55e072f829bc184be03e21893cb524"
git_remote: "https://github.com/viash-hub/craftbox"
package_config:
name: "craftbox"

4
target/executable/untar/untar
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@@ -475,9 +475,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component untar"
LABEL org.opencontainers.image.created="2024-06-26T12:28:10Z"
LABEL org.opencontainers.image.created="2024-07-24T08:32:31Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/craftbox"
LABEL org.opencontainers.image.revision="781f66883977e37a849f228ee1dffddbb7acdf32"
LABEL org.opencontainers.image.revision="a2e8c5d12d55e072f829bc184be03e21893cb524"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

197
target/nextflow/concat_text/.config.vsh.yaml Normal file
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@@ -0,0 +1,197 @@
name: "concat_text"
version: "main"
authors:
- name: "Toni Verbeiren"
roles:
- "author"
- "maintainer"
info:
links:
github: "tverbeiren"
linkedin: "verbeiren"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Scientist and CEO"
- name: "Dries Schaumont"
roles:
- "reviewer"
info:
links:
email: "dries@data-intuitive.com"
github: "DriesSchaumont"
orcid: "0000-0002-4389-0440"
linkedin: "dries-schaumont"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Scientist"
argument_groups:
- name: "Input arguments"
arguments:
- type: "file"
name: "--input"
description: "A list of (gzipped) text files."
info: null
example:
- "input?.txt.gz"
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: true
multiple_sep: ";"
- name: "Output arguments"
arguments:
- type: "boolean_true"
name: "--gzip_output"
description: "Should the output be zipped?"
info: null
direction: "input"
- type: "file"
name: "--output"
description: "File to write the output to, optionally gzipped."
info: null
example:
- "output.txt"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
resources:
- type: "bash_script"
path: "script.sh"
is_executable: true
description: "Concatenate a number of text files, handle gzipped text files gracefully\
\ and\noptionally gzip the output text file.\n\nThis component is useful for concatening\
\ fastq files from different lanes, for instance.\n"
test_resources:
- type: "bash_script"
path: "test.sh"
is_executable: true
info:
improvements: "This component could be improved in 2 ways:\n 1. Allow for a mix\
\ of zipped and plain input files\n 2. Allow to specify a compression algorithm\
\ for the output\n"
status: "enabled"
requirements:
commands:
- "ps"
license: "MIT"
links:
repository: "https://github.com/viash-hub/craftbox"
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: "docker"
id: "docker"
image: "alpine:latest"
target_registry: "images.viash-hub.com"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "apk"
packages:
- "bash"
- "procps"
- "file"
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/concat_text/config.vsh.yaml"
runner: "nextflow"
engine: "docker|native"
output: "target/nextflow/concat_text"
executable: "target/nextflow/concat_text/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "a2e8c5d12d55e072f829bc184be03e21893cb524"
git_remote: "https://github.com/viash-hub/craftbox"
package_config:
name: "craftbox"
version: "main"
description: "A collection of custom-tailored scripts and applied tools.\n"
info: null
viash_version: "0.9.0-RC6"
source: "src"
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "scripts"
- "custom"
- "implementations"
license: "MIT"
organization: "vsh"
links:
repository: "https://github.com/viash-hub/craftbox"
issue_tracker: "https://github.com/viash-hub/craftbox/issues"

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126
target/nextflow/concat_text/nextflow.config Normal file
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@@ -0,0 +1,126 @@
manifest {
name = 'concat_text'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'main'
description = 'Concatenate a number of text files, handle gzipped text files gracefully and\noptionally gzip the output text file.\n\nThis component is useful for concatening fastq files from different lanes, for instance.\n'
author = 'Toni Verbeiren, Dries Schaumont'
}
process.container = 'nextflow/bash:latest'
// detect tempdir
tempDir = java.nio.file.Paths.get(
System.getenv('NXF_TEMP') ?:
System.getenv('VIASH_TEMP') ?:
System.getenv('TEMPDIR') ?:
System.getenv('TMPDIR') ?:
'/tmp'
).toAbsolutePath()
profiles {
no_publish {
process {
withName: '.*' {
publishDir = [
enabled: false
]
}
}
}
mount_temp {
docker.temp = tempDir
podman.temp = tempDir
charliecloud.temp = tempDir
}
docker {
docker.enabled = true
// docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
podman {
podman.enabled = true
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
shifter {
shifter.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
}
charliecloud {
charliecloud.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
}
}
process{
withLabel: mem1gb { memory = 1000000000.B }
withLabel: mem2gb { memory = 2000000000.B }
withLabel: mem5gb { memory = 5000000000.B }
withLabel: mem10gb { memory = 10000000000.B }
withLabel: mem20gb { memory = 20000000000.B }
withLabel: mem50gb { memory = 50000000000.B }
withLabel: mem100gb { memory = 100000000000.B }
withLabel: mem200gb { memory = 200000000000.B }
withLabel: mem500gb { memory = 500000000000.B }
withLabel: mem1tb { memory = 1000000000000.B }
withLabel: mem2tb { memory = 2000000000000.B }
withLabel: mem5tb { memory = 5000000000000.B }
withLabel: mem10tb { memory = 10000000000000.B }
withLabel: mem20tb { memory = 20000000000000.B }
withLabel: mem50tb { memory = 50000000000000.B }
withLabel: mem100tb { memory = 100000000000000.B }
withLabel: mem200tb { memory = 200000000000000.B }
withLabel: mem500tb { memory = 500000000000000.B }
withLabel: mem1gib { memory = 1073741824.B }
withLabel: mem2gib { memory = 2147483648.B }
withLabel: mem4gib { memory = 4294967296.B }
withLabel: mem8gib { memory = 8589934592.B }
withLabel: mem16gib { memory = 17179869184.B }
withLabel: mem32gib { memory = 34359738368.B }
withLabel: mem64gib { memory = 68719476736.B }
withLabel: mem128gib { memory = 137438953472.B }
withLabel: mem256gib { memory = 274877906944.B }
withLabel: mem512gib { memory = 549755813888.B }
withLabel: mem1tib { memory = 1099511627776.B }
withLabel: mem2tib { memory = 2199023255552.B }
withLabel: mem4tib { memory = 4398046511104.B }
withLabel: mem8tib { memory = 8796093022208.B }
withLabel: mem16tib { memory = 17592186044416.B }
withLabel: mem32tib { memory = 35184372088832.B }
withLabel: mem64tib { memory = 70368744177664.B }
withLabel: mem128tib { memory = 140737488355328.B }
withLabel: mem256tib { memory = 281474976710656.B }
withLabel: mem512tib { memory = 562949953421312.B }
withLabel: cpu1 { cpus = 1 }
withLabel: cpu2 { cpus = 2 }
withLabel: cpu5 { cpus = 5 }
withLabel: cpu10 { cpus = 10 }
withLabel: cpu20 { cpus = 20 }
withLabel: cpu50 { cpus = 50 }
withLabel: cpu100 { cpus = 100 }
withLabel: cpu200 { cpus = 200 }
withLabel: cpu500 { cpus = 500 }
withLabel: cpu1000 { cpus = 1000 }
}

106
target/nextflow/concat_text/nextflow_schema.json Normal file
View File

@@ -0,0 +1,106 @@
{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "concat_text",
"description": "Concatenate a number of text files, handle gzipped text files gracefully and\noptionally gzip the output text file.\n\nThis component is useful for concatening fastq files from different lanes, for instance.\n",
"type": "object",
"definitions": {
"input arguments" : {
"title": "Input arguments",
"type": "object",
"description": "No description",
"properties": {
"input": {
"type":
"string",
"description": "Type: List of `file`, required, example: `input?.txt.gz`, multiple_sep: `\":\"`. A list of (gzipped) text files",
"help_text": "Type: List of `file`, required, example: `input?.txt.gz`, multiple_sep: `\":\"`. A list of (gzipped) text files."
}
}
},
"output arguments" : {
"title": "Output arguments",
"type": "object",
"description": "No description",
"properties": {
"gzip_output": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Should the output be zipped?",
"help_text": "Type: `boolean_true`, default: `false`. Should the output be zipped?"
,
"default": "False"
}
,
"output": {
"type":
"string",
"description": "Type: `file`, default: `$id.$key.output.txt`, example: `output.txt`. File to write the output to, optionally gzipped",
"help_text": "Type: `file`, default: `$id.$key.output.txt`, example: `output.txt`. File to write the output to, optionally gzipped."
,
"default": "$id.$key.output.txt"
}
}
},
"nextflow input-output arguments" : {
"title": "Nextflow input-output arguments",
"type": "object",
"description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
"properties": {
"publish_dir": {
"type":
"string",
"description": "Type: `string`, required, example: `output/`. Path to an output directory",
"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
}
,
"param_list": {
"type":
"string",
"description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
"help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
"hidden": true
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/input arguments"
},
{
"$ref": "#/definitions/output arguments"
},
{
"$ref": "#/definitions/nextflow input-output arguments"
}
]
}

2
target/nextflow/csv2fasta/.config.vsh.yaml
View File

@@ -222,7 +222,7 @@ build_info:
output: "target/nextflow/csv2fasta"
executable: "target/nextflow/csv2fasta/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "781f66883977e37a849f228ee1dffddbb7acdf32"
git_commit: "a2e8c5d12d55e072f829bc184be03e21893cb524"
git_remote: "https://github.com/viash-hub/craftbox"
package_config:
name: "craftbox"

2
target/nextflow/csv2fasta/main.nf
View File

@@ -3041,7 +3041,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/csv2fasta",
"viash_version" : "0.9.0-RC6",
"git_commit" : "781f66883977e37a849f228ee1dffddbb7acdf32",
"git_commit" : "a2e8c5d12d55e072f829bc184be03e21893cb524",
"git_remote" : "https://github.com/viash-hub/craftbox"
},
"package_config" : {

2
target/nextflow/untar/.config.vsh.yaml
View File

@@ -147,7 +147,7 @@ build_info:
output: "target/nextflow/untar"
executable: "target/nextflow/untar/main.nf"
viash_version: "0.9.0-RC6"
git_commit: "781f66883977e37a849f228ee1dffddbb7acdf32"
git_commit: "a2e8c5d12d55e072f829bc184be03e21893cb524"
git_remote: "https://github.com/viash-hub/craftbox"
package_config:
name: "craftbox"

2
target/nextflow/untar/main.nf
View File

@@ -2962,7 +2962,7 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/untar",
"viash_version" : "0.9.0-RC6",
"git_commit" : "781f66883977e37a849f228ee1dffddbb7acdf32",
"git_commit" : "a2e8c5d12d55e072f829bc184be03e21893cb524",
"git_remote" : "https://github.com/viash-hub/craftbox"
},
"package_config" : {