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Build branch v0.1 with version v0.1.1 (0f49a3f)

Browse Source 
Build pipeline: vsh-ci-dev-w9454

Source commit: 0f49a3ff62

Source message: Bump version to v0.1.1
This commit is contained in:
CI
2024-10-17 17:31:01 +00:00
parent 69e0b1ebaf
commit 3e6bb670c5
246 changed files with 1539 additions and 1390 deletions
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4
_viash.yaml
View File

@@ -1,5 +1,7 @@
name: rnaseq
viash_version: 0.9.0 viash_version: 0.9.0
version: v0.1.0 version: v0.1.1
source: src source: src
target: target target: target

13
target/executable/bbmap_bbsplit/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "bbmap_bbsplit" name: "bbmap_bbsplit"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -219,7 +219,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "docker" - type: "docker"
@@ -238,10 +238,11 @@ build_info:
output: "target/executable/bbmap_bbsplit" output: "target/executable/bbmap_bbsplit"
executable: "target/executable/bbmap_bbsplit/bbmap_bbsplit" executable: "target/executable/bbmap_bbsplit/bbmap_bbsplit"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -263,5 +264,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/bbmap_bbsplit/bbmap_bbsplit
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@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# bbmap_bbsplit v0.1.0 # bbmap_bbsplit v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "bbmap_bbsplit v0.1.0" echo "bbmap_bbsplit v0.1.1"
echo "" echo ""
echo "Split sequencing reads by mapping them to multiple references simultaneously." echo "Split sequencing reads by mapping them to multiple references simultaneously."
echo "" echo ""
@@ -506,10 +506,10 @@ tar xzf BBMap_39.01.tar.gz && \
cp -r bbmap/* /usr/local/bin cp -r bbmap/* /usr/local/bin
LABEL org.opencontainers.image.description="Companion container for running component bbmap_bbsplit" LABEL org.opencontainers.image.description="Companion container for running component bbmap_bbsplit"
LABEL org.opencontainers.image.created="2024-10-04T11:21:39Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:28Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -645,7 +645,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "bbmap_bbsplit v0.1.0" echo "bbmap_bbsplit v0.1.1"
exit exit
;; ;;
--id) --id)
@@ -852,7 +852,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/bbmap_bbsplit:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/bbmap_bbsplit:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/bedtools_genomecov/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "bedtools_genomecov" name: "bedtools_genomecov"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -159,7 +159,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "docker" - type: "docker"
@@ -178,10 +178,11 @@ build_info:
output: "target/executable/bedtools_genomecov" output: "target/executable/bedtools_genomecov"
executable: "target/executable/bedtools_genomecov/bedtools_genomecov" executable: "target/executable/bedtools_genomecov/bedtools_genomecov"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -203,5 +204,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/bedtools_genomecov/bedtools_genomecov
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# bedtools_genomecov v0.1.0 # bedtools_genomecov v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "bedtools_genomecov v0.1.0" echo "bedtools_genomecov v0.1.1"
echo "" echo ""
echo "Compute BEDGRAPH (-bg) summaries of feature coverage" echo "Compute BEDGRAPH (-bg) summaries of feature coverage"
echo "" echo ""
@@ -481,10 +481,10 @@ mv bedtools.static /usr/local/bin/bedtools && \
chmod a+x /usr/local/bin/bedtools chmod a+x /usr/local/bin/bedtools
LABEL org.opencontainers.image.description="Companion container for running component bedtools_genomecov" LABEL org.opencontainers.image.description="Companion container for running component bedtools_genomecov"
LABEL org.opencontainers.image.created="2024-10-04T11:21:40Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:23Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -620,7 +620,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "bedtools_genomecov v0.1.0" echo "bedtools_genomecov v0.1.1"
exit exit
;; ;;
--strandedness) --strandedness)
@@ -766,7 +766,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/bedtools_genomecov:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/bedtools_genomecov:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/cat_additional_fasta/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "cat_additional_fasta" name: "cat_additional_fasta"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -169,7 +169,7 @@ engines:
id: "docker" id: "docker"
image: "python" image: "python"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
entrypoint: [] entrypoint: []
cmd: null cmd: null
@@ -182,10 +182,11 @@ build_info:
output: "target/executable/cat_additional_fasta" output: "target/executable/cat_additional_fasta"
executable: "target/executable/cat_additional_fasta/cat_additional_fasta" executable: "target/executable/cat_additional_fasta/cat_additional_fasta"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -207,5 +208,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/cat_additional_fasta/cat_additional_fasta
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# cat_additional_fasta v0.1.0 # cat_additional_fasta v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "cat_additional_fasta v0.1.0" echo "cat_additional_fasta v0.1.1"
echo "" echo ""
echo "Concatenate addional fasta file to reference FASTA and GTF files." echo "Concatenate addional fasta file to reference FASTA and GTF files."
echo "" echo ""
@@ -480,10 +480,10 @@ function ViashDockerfile {
FROM python:latest FROM python:latest
ENTRYPOINT [] ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component cat_additional_fasta" LABEL org.opencontainers.image.description="Companion container for running component cat_additional_fasta"
LABEL org.opencontainers.image.created="2024-10-04T11:21:48Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:23Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -619,7 +619,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "cat_additional_fasta v0.1.0" echo "cat_additional_fasta v0.1.1"
exit exit
;; ;;
--fasta) --fasta)
@@ -776,7 +776,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/cat_additional_fasta:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/cat_additional_fasta:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/cat_fastq/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "cat_fastq" name: "cat_fastq"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -156,7 +156,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
entrypoint: [] entrypoint: []
cmd: null cmd: null
@@ -169,10 +169,11 @@ build_info:
output: "target/executable/cat_fastq" output: "target/executable/cat_fastq"
executable: "target/executable/cat_fastq/cat_fastq" executable: "target/executable/cat_fastq/cat_fastq"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -194,5 +195,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/cat_fastq/cat_fastq
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# cat_fastq v0.1.0 # cat_fastq v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "cat_fastq v0.1.0" echo "cat_fastq v0.1.1"
echo "" echo ""
echo "Concatenate multiple fastq files" echo "Concatenate multiple fastq files"
echo "" echo ""
@@ -472,10 +472,10 @@ function ViashDockerfile {
FROM ubuntu:22.04 FROM ubuntu:22.04
ENTRYPOINT [] ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component cat_fastq" LABEL org.opencontainers.image.description="Companion container for running component cat_fastq"
LABEL org.opencontainers.image.created="2024-10-04T11:21:48Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:24Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -611,7 +611,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "cat_fastq v0.1.0" echo "cat_fastq v0.1.1"
exit exit
;; ;;
--read_1) --read_1)
@@ -758,7 +758,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/cat_fastq:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/cat_fastq:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/deseq2_qc/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "deseq2_qc" name: "deseq2_qc"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "input" - name: "input"
arguments: arguments:
@@ -207,7 +207,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "apt" - type: "apt"
@@ -239,10 +239,11 @@ build_info:
output: "target/executable/deseq2_qc" output: "target/executable/deseq2_qc"
executable: "target/executable/deseq2_qc/deseq2_qc" executable: "target/executable/deseq2_qc/deseq2_qc"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -264,5 +265,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/deseq2_qc/deseq2_qc
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# deseq2_qc v0.1.0 # deseq2_qc v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "deseq2_qc v0.1.0" echo "deseq2_qc v0.1.1"
echo "" echo ""
echo "run deseq2, perform pca, generate heatmaps and scatterplots for samples in the" echo "run deseq2, perform pca, generate heatmaps and scatterplots for samples in the"
echo "counts files" echo "counts files"
@@ -502,10 +502,10 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
Rscript -e 'remotes::install_url(c("https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz"), repos = "https://cran.rstudio.com")' Rscript -e 'remotes::install_url(c("https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz"), repos = "https://cran.rstudio.com")'
LABEL org.opencontainers.image.description="Companion container for running component deseq2_qc" LABEL org.opencontainers.image.description="Companion container for running component deseq2_qc"
LABEL org.opencontainers.image.created="2024-10-04T11:21:58Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:28Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "deseq2_qc v0.1.0" echo "deseq2_qc v0.1.1"
exit exit
;; ;;
--counts) --counts)
@@ -831,7 +831,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/deseq2_qc:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/deseq2_qc:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/dupradar/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "dupradar" name: "dupradar"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -244,7 +244,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "apt" - type: "apt"
@@ -266,10 +266,11 @@ build_info:
output: "target/executable/dupradar" output: "target/executable/dupradar"
executable: "target/executable/dupradar/dupradar" executable: "target/executable/dupradar/dupradar"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -291,5 +292,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/dupradar/dupradar
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# dupradar v0.1.0 # dupradar v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "dupradar v0.1.0" echo "dupradar v0.1.1"
echo "" echo ""
echo "Assessment of duplication rates in RNA-Seq datasets" echo "Assessment of duplication rates in RNA-Seq datasets"
echo "" echo ""
@@ -520,10 +520,10 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.pa
Rscript -e 'if (!requireNamespace("dupRadar", quietly = TRUE)) BiocManager::install("dupRadar")' Rscript -e 'if (!requireNamespace("dupRadar", quietly = TRUE)) BiocManager::install("dupRadar")'
LABEL org.opencontainers.image.description="Companion container for running component dupradar" LABEL org.opencontainers.image.description="Companion container for running component dupradar"
LABEL org.opencontainers.image.created="2024-10-04T11:21:49Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:26Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -659,7 +659,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "dupradar v0.1.0" echo "dupradar v0.1.1"
exit exit
;; ;;
--id) --id)
@@ -882,7 +882,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/dupradar:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/dupradar:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/fastqc/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "fastqc" name: "fastqc"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -180,7 +180,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "apt" - type: "apt"
@@ -198,10 +198,11 @@ build_info:
output: "target/executable/fastqc" output: "target/executable/fastqc"
executable: "target/executable/fastqc/fastqc" executable: "target/executable/fastqc/fastqc"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -223,5 +224,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/fastqc/fastqc
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# fastqc v0.1.0 # fastqc v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "fastqc v0.1.0" echo "fastqc v0.1.1"
echo "" echo ""
echo "Fastqc component, please see" echo "Fastqc component, please see"
echo "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. This component can" echo "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. This component can"
@@ -490,10 +490,10 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/* rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component fastqc" LABEL org.opencontainers.image.description="Companion container for running component fastqc"
LABEL org.opencontainers.image.created="2024-10-04T11:21:41Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:25Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -629,7 +629,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "fastqc v0.1.0" echo "fastqc v0.1.1"
exit exit
;; ;;
--paired) --paired)
@@ -792,7 +792,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/fastqc:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/fastqc:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/fq_subsample/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "fq_subsample" name: "fq_subsample"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -153,7 +153,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "docker" - type: "docker"
@@ -177,10 +177,11 @@ build_info:
output: "target/executable/fq_subsample" output: "target/executable/fq_subsample"
executable: "target/executable/fq_subsample/fq_subsample" executable: "target/executable/fq_subsample/fq_subsample"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -202,5 +203,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/fq_subsample/fq_subsample
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# fq_subsample v0.1.0 # fq_subsample v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "fq_subsample v0.1.0" echo "fq_subsample v0.1.1"
echo "" echo ""
echo "fq subsample outputs a subset of records from single or paired FASTQ files. This" echo "fq subsample outputs a subset of records from single or paired FASTQ files. This"
echo "requires a seed (--seed) to be set in ext.args" echo "requires a seed (--seed) to be set in ext.args"
@@ -485,10 +485,10 @@ cargo install --locked --path . && \
mv /usr/local/fq/target/release/fq /usr/local/bin/ mv /usr/local/fq/target/release/fq /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component fq_subsample" LABEL org.opencontainers.image.description="Companion container for running component fq_subsample"
LABEL org.opencontainers.image.created="2024-10-04T11:21:41Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:24Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -624,7 +624,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "fq_subsample v0.1.0" echo "fq_subsample v0.1.1"
exit exit
;; ;;
--input) --input)
@@ -765,7 +765,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/fq_subsample:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/fq_subsample:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/getchromsizes/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "getchromsizes" name: "getchromsizes"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -146,7 +146,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "docker" - type: "docker"
@@ -167,10 +167,11 @@ build_info:
output: "target/executable/getchromsizes" output: "target/executable/getchromsizes"
executable: "target/executable/getchromsizes/getchromsizes" executable: "target/executable/getchromsizes/getchromsizes"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -192,5 +193,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/getchromsizes/getchromsizes
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# getchromsizes v0.1.0 # getchromsizes v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "getchromsizes v0.1.0" echo "getchromsizes v0.1.1"
echo "" echo ""
echo "Generates a FASTA file of chromosome sizes and a fasta index file." echo "Generates a FASTA file of chromosome sizes and a fasta index file."
echo "" echo ""
@@ -480,10 +480,10 @@ make && \
make install make install
LABEL org.opencontainers.image.description="Companion container for running component getchromsizes" LABEL org.opencontainers.image.description="Companion container for running component getchromsizes"
LABEL org.opencontainers.image.created="2024-10-04T11:21:41Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:23Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -619,7 +619,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "getchromsizes v0.1.0" echo "getchromsizes v0.1.1"
exit exit
;; ;;
--fasta) --fasta)
@@ -754,7 +754,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/getchromsizes:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/getchromsizes:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/gtf2bed/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "gtf2bed" name: "gtf2bed"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -127,7 +127,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "apt" - type: "apt"
@@ -145,10 +145,11 @@ build_info:
output: "target/executable/gtf2bed" output: "target/executable/gtf2bed"
executable: "target/executable/gtf2bed/gtf2bed" executable: "target/executable/gtf2bed/gtf2bed"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -170,5 +171,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/gtf2bed/gtf2bed
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# gtf2bed v0.1.0 # gtf2bed v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "gtf2bed v0.1.0" echo "gtf2bed v0.1.1"
echo "" echo ""
echo "Create BED annotation file from GTF." echo "Create BED annotation file from GTF."
echo "" echo ""
@@ -466,10 +466,10 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/* rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component gtf2bed" LABEL org.opencontainers.image.description="Companion container for running component gtf2bed"
LABEL org.opencontainers.image.created="2024-10-04T11:21:54Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:24Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -605,7 +605,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "gtf2bed v0.1.0" echo "gtf2bed v0.1.1"
exit exit
;; ;;
--gtf) --gtf)
@@ -718,7 +718,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/gtf2bed:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/gtf2bed:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/gtf_filter/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "gtf_filter" name: "gtf_filter"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -142,7 +142,7 @@ engines:
id: "docker" id: "docker"
image: "python" image: "python"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
entrypoint: [] entrypoint: []
cmd: null cmd: null
@@ -155,10 +155,11 @@ build_info:
output: "target/executable/gtf_filter" output: "target/executable/gtf_filter"
executable: "target/executable/gtf_filter/gtf_filter" executable: "target/executable/gtf_filter/gtf_filter"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -180,5 +181,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/gtf_filter/gtf_filter
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# gtf_filter v0.1.0 # gtf_filter v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "gtf_filter v0.1.0" echo "gtf_filter v0.1.1"
echo "" echo ""
echo "Filters a GTF file based on sequence names in a FASTA file." echo "Filters a GTF file based on sequence names in a FASTA file."
echo "" echo ""
@@ -470,10 +470,10 @@ function ViashDockerfile {
FROM python:latest FROM python:latest
ENTRYPOINT [] ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component gtf_filter" LABEL org.opencontainers.image.description="Companion container for running component gtf_filter"
LABEL org.opencontainers.image.created="2024-10-04T11:21:57Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:27Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -609,7 +609,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "gtf_filter v0.1.0" echo "gtf_filter v0.1.1"
exit exit
;; ;;
--fasta) --fasta)
@@ -738,7 +738,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/gtf_filter:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/gtf_filter:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/gunzip/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "gunzip" name: "gunzip"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -126,7 +126,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "apt" - type: "apt"
@@ -144,10 +144,11 @@ build_info:
output: "target/executable/gunzip" output: "target/executable/gunzip"
executable: "target/executable/gunzip/gunzip" executable: "target/executable/gunzip/gunzip"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -169,5 +170,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/gunzip/gunzip
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# gunzip v0.1.0 # gunzip v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "gunzip v0.1.0" echo "gunzip v0.1.1"
echo "" echo ""
echo "Compress or uncompress a file or list of files." echo "Compress or uncompress a file or list of files."
echo "" echo ""
@@ -466,10 +466,10 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/* rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component gunzip" LABEL org.opencontainers.image.description="Companion container for running component gunzip"
LABEL org.opencontainers.image.created="2024-10-04T11:21:42Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:25Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -605,7 +605,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "gunzip v0.1.0" echo "gunzip v0.1.1"
exit exit
;; ;;
--input) --input)
@@ -718,7 +718,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/gunzip:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/gunzip:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/kallisto/kallisto_index/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "kallisto_index" name: "kallisto_index"
namespace: "kallisto" namespace: "kallisto"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -135,7 +135,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "docker" - type: "docker"
@@ -155,10 +155,11 @@ build_info:
output: "target/executable/kallisto/kallisto_index" output: "target/executable/kallisto/kallisto_index"
executable: "target/executable/kallisto/kallisto_index/kallisto_index" executable: "target/executable/kallisto/kallisto_index/kallisto_index"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -180,5 +181,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/kallisto/kallisto_index/kallisto_index
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# kallisto_index v0.1.0 # kallisto_index v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "kallisto_index v0.1.0" echo "kallisto_index v0.1.1"
echo "" echo ""
echo "Create Kallisto index." echo "Create Kallisto index."
echo "" echo ""
@@ -471,10 +471,10 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \
mv kallisto/kallisto /usr/local/bin/ mv kallisto/kallisto /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_index" LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_index"
LABEL org.opencontainers.image.created="2024-10-04T11:21:55Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:28Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -610,7 +610,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "kallisto_index v0.1.0" echo "kallisto_index v0.1.1"
exit exit
;; ;;
--transcriptome_fasta) --transcriptome_fasta)
@@ -734,7 +734,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/kallisto/kallisto_index:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/kallisto/kallisto_index:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/kallisto/kallisto_quant/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "kallisto_quant" name: "kallisto_quant"
namespace: "kallisto" namespace: "kallisto"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -233,7 +233,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "docker" - type: "docker"
@@ -253,10 +253,11 @@ build_info:
output: "target/executable/kallisto/kallisto_quant" output: "target/executable/kallisto/kallisto_quant"
executable: "target/executable/kallisto/kallisto_quant/kallisto_quant" executable: "target/executable/kallisto/kallisto_quant/kallisto_quant"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -278,5 +279,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/kallisto/kallisto_quant/kallisto_quant
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# kallisto_quant v0.1.0 # kallisto_quant v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "kallisto_quant v0.1.0" echo "kallisto_quant v0.1.1"
echo "" echo ""
echo "Computes equivalence classes for reads and quantifies abundances." echo "Computes equivalence classes for reads and quantifies abundances."
echo "" echo ""
@@ -515,10 +515,10 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \
mv kallisto/kallisto /usr/local/bin/ mv kallisto/kallisto /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_quant" LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_quant"
LABEL org.opencontainers.image.created="2024-10-04T11:21:55Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:28Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -654,7 +654,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "kallisto_quant v0.1.0" echo "kallisto_quant v0.1.1"
exit exit
;; ;;
--input) --input)
@@ -883,7 +883,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/kallisto/kallisto_quant:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/kallisto/kallisto_quant:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/multiqc_custom_biotype/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "multiqc_custom_biotype" name: "multiqc_custom_biotype"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -152,7 +152,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "apt" - type: "apt"
@@ -173,10 +173,11 @@ build_info:
output: "target/executable/multiqc_custom_biotype" output: "target/executable/multiqc_custom_biotype"
executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype" executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -198,5 +199,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/multiqc_custom_biotype/multiqc_custom_biotype
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# multiqc_custom_biotype v0.1.0 # multiqc_custom_biotype v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "multiqc_custom_biotype v0.1.0" echo "multiqc_custom_biotype v0.1.1"
echo "" echo ""
echo "Calculate features percentage for biotype counts" echo "Calculate features percentage for biotype counts"
echo "" echo ""
@@ -481,10 +481,10 @@ RUN apt-get update && \
RUN pip install --upgrade pip RUN pip install --upgrade pip
LABEL org.opencontainers.image.description="Companion container for running component multiqc_custom_biotype" LABEL org.opencontainers.image.description="Companion container for running component multiqc_custom_biotype"
LABEL org.opencontainers.image.created="2024-10-04T11:21:50Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:25Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -620,7 +620,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "multiqc_custom_biotype v0.1.0" echo "multiqc_custom_biotype v0.1.1"
exit exit
;; ;;
--biocounts) --biocounts)
@@ -766,7 +766,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/multiqc_custom_biotype:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/multiqc_custom_biotype:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/picard_markduplicates/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "picard_markduplicates" name: "picard_markduplicates"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -186,7 +186,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "docker" - type: "docker"
@@ -207,10 +207,11 @@ build_info:
output: "target/executable/picard_markduplicates" output: "target/executable/picard_markduplicates"
executable: "target/executable/picard_markduplicates/picard_markduplicates" executable: "target/executable/picard_markduplicates/picard_markduplicates"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -232,5 +233,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/picard_markduplicates/picard_markduplicates
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# picard_markduplicates v0.1.0 # picard_markduplicates v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "picard_markduplicates v0.1.0" echo "picard_markduplicates v0.1.1"
echo "" echo ""
echo "Locate and tag duplicate reads in a BAM file" echo "Locate and tag duplicate reads in a BAM file"
echo "" echo ""
@@ -494,10 +494,10 @@ wget --no-check-certificate https://github.com/broadinstitute/picard/releases/do
mv picard.jar /usr/local/bin mv picard.jar /usr/local/bin
LABEL org.opencontainers.image.description="Companion container for running component picard_markduplicates" LABEL org.opencontainers.image.description="Companion container for running component picard_markduplicates"
LABEL org.opencontainers.image.created="2024-10-04T11:21:57Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:27Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -633,7 +633,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "picard_markduplicates v0.1.0" echo "picard_markduplicates v0.1.1"
exit exit
;; ;;
--bam) --bam)
@@ -801,7 +801,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/picard_markduplicates:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/picard_markduplicates:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/prepare_multiqc_input/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "prepare_multiqc_input" name: "prepare_multiqc_input"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -396,7 +396,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
entrypoint: [] entrypoint: []
cmd: null cmd: null
@@ -409,10 +409,11 @@ build_info:
output: "target/executable/prepare_multiqc_input" output: "target/executable/prepare_multiqc_input"
executable: "target/executable/prepare_multiqc_input/prepare_multiqc_input" executable: "target/executable/prepare_multiqc_input/prepare_multiqc_input"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -434,5 +435,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/prepare_multiqc_input/prepare_multiqc_input
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# prepare_multiqc_input v0.1.0 # prepare_multiqc_input v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "prepare_multiqc_input v0.1.0" echo "prepare_multiqc_input v0.1.1"
echo "" echo ""
echo "Prepare directory with all the input files for MultiQC." echo "Prepare directory with all the input files for MultiQC."
echo "" echo ""
@@ -557,10 +557,10 @@ function ViashDockerfile {
FROM ubuntu:22.04 FROM ubuntu:22.04
ENTRYPOINT [] ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component prepare_multiqc_input" LABEL org.opencontainers.image.description="Companion container for running component prepare_multiqc_input"
LABEL org.opencontainers.image.created="2024-10-04T11:21:53Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:25Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -696,7 +696,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "prepare_multiqc_input v0.1.0" echo "prepare_multiqc_input v0.1.1"
exit exit
;; ;;
--fail_trimming_multiqc) --fail_trimming_multiqc)
@@ -1311,7 +1311,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/prepare_multiqc_input:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/prepare_multiqc_input:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/preprocess_transcripts_fasta/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "preprocess_transcripts_fasta" name: "preprocess_transcripts_fasta"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -125,7 +125,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
entrypoint: [] entrypoint: []
cmd: null cmd: null
@@ -138,10 +138,11 @@ build_info:
output: "target/executable/preprocess_transcripts_fasta" output: "target/executable/preprocess_transcripts_fasta"
executable: "target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta" executable: "target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -163,5 +164,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# preprocess_transcripts_fasta v0.1.0 # preprocess_transcripts_fasta v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "preprocess_transcripts_fasta v0.1.0" echo "preprocess_transcripts_fasta v0.1.1"
echo "" echo ""
echo "Process transcripts FASTA if GTF file is GENOCODE format" echo "Process transcripts FASTA if GTF file is GENOCODE format"
echo "" echo ""
@@ -462,10 +462,10 @@ function ViashDockerfile {
FROM ubuntu:22.04 FROM ubuntu:22.04
ENTRYPOINT [] ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component preprocess_transcripts_fasta" LABEL org.opencontainers.image.description="Companion container for running component preprocess_transcripts_fasta"
LABEL org.opencontainers.image.created="2024-10-04T11:21:52Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:24Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -601,7 +601,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "preprocess_transcripts_fasta v0.1.0" echo "preprocess_transcripts_fasta v0.1.1"
exit exit
;; ;;
--transcript_fasta) --transcript_fasta)
@@ -714,7 +714,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/preprocess_transcripts_fasta:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/preprocess_transcripts_fasta:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/preseq_lcextrap/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "preseq_lcextrap" name: "preseq_lcextrap"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -146,7 +146,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "apt" - type: "apt"
@@ -191,10 +191,11 @@ build_info:
output: "target/executable/preseq_lcextrap" output: "target/executable/preseq_lcextrap"
executable: "target/executable/preseq_lcextrap/preseq_lcextrap" executable: "target/executable/preseq_lcextrap/preseq_lcextrap"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -216,5 +217,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/preseq_lcextrap/preseq_lcextrap
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# preseq_lcextrap v0.1.0 # preseq_lcextrap v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "preseq_lcextrap v0.1.0" echo "preseq_lcextrap v0.1.1"
echo "" echo ""
echo "Computing the expected future yield of distinct reads and bounds on the number" echo "Computing the expected future yield of distinct reads and bounds on the number"
echo "of total distinct reads in the library and the associated confidence intervals." echo "of total distinct reads in the library and the associated confidence intervals."
@@ -495,10 +495,10 @@ mkdir build && cd build && \
make && make install && make HAVE_HTSLIB=1 all make && make install && make HAVE_HTSLIB=1 all
LABEL org.opencontainers.image.description="Companion container for running component preseq_lcextrap" LABEL org.opencontainers.image.description="Companion container for running component preseq_lcextrap"
LABEL org.opencontainers.image.created="2024-10-04T11:21:42Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:25Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -634,7 +634,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "preseq_lcextrap v0.1.0" echo "preseq_lcextrap v0.1.1"
exit exit
;; ;;
--input) --input)
@@ -769,7 +769,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/preseq_lcextrap:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/preseq_lcextrap:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/qualimap/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "qualimap" name: "qualimap"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -237,7 +237,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "apt" - type: "apt"
@@ -271,10 +271,11 @@ build_info:
output: "target/executable/qualimap" output: "target/executable/qualimap"
executable: "target/executable/qualimap/qualimap" executable: "target/executable/qualimap/qualimap"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -296,5 +297,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/qualimap/qualimap
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# qualimap v0.1.0 # qualimap v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "qualimap v0.1.0" echo "qualimap v0.1.1"
echo "" echo ""
echo "RNA-seq QC analysis using the qualimap" echo "RNA-seq QC analysis using the qualimap"
echo "" echo ""
@@ -537,10 +537,10 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
Rscript -e 'remotes::install_cran(c("optparse"), repos = "https://cran.rstudio.com")' Rscript -e 'remotes::install_cran(c("optparse"), repos = "https://cran.rstudio.com")'
LABEL org.opencontainers.image.description="Companion container for running component qualimap" LABEL org.opencontainers.image.description="Companion container for running component qualimap"
LABEL org.opencontainers.image.created="2024-10-04T11:21:40Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:25Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -676,7 +676,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "qualimap v0.1.0" echo "qualimap v0.1.1"
exit exit
;; ;;
--input) --input)
@@ -887,7 +887,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/qualimap:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/qualimap:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "rsem_calculate_expression" name: "rsem_calculate_expression"
namespace: "rsem" namespace: "rsem"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -251,7 +251,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "apt" - type: "apt"
@@ -299,10 +299,11 @@ build_info:
output: "target/executable/rsem/rsem_calculate_expression" output: "target/executable/rsem/rsem_calculate_expression"
executable: "target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression" executable: "target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -324,5 +325,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# rsem_calculate_expression v0.1.0 # rsem_calculate_expression v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "rsem_calculate_expression v0.1.0" echo "rsem_calculate_expression v0.1.1"
echo "" echo ""
echo "Calculate expression with RSEM." echo "Calculate expression with RSEM."
echo "" echo ""
@@ -542,10 +542,10 @@ echo 'export PATH=$PATH:/usr/local/bin' >> ~/.bashrc && \
/bin/bash -c "source /etc/profile && source ~/.bashrc && echo $PATH && which STAR" /bin/bash -c "source /etc/profile && source ~/.bashrc && echo $PATH && which STAR"
LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_calculate_expression" LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_calculate_expression"
LABEL org.opencontainers.image.created="2024-10-04T11:21:55Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:26Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -681,7 +681,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "rsem_calculate_expression v0.1.0" echo "rsem_calculate_expression v0.1.1"
exit exit
;; ;;
--id) --id)
@@ -921,7 +921,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rsem/rsem_calculate_expression:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rsem/rsem_calculate_expression:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/rsem/rsem_merge_counts/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "rsem_merge_counts" name: "rsem_merge_counts"
namespace: "rsem" namespace: "rsem"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -169,7 +169,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
entrypoint: [] entrypoint: []
cmd: null cmd: null
@@ -182,10 +182,11 @@ build_info:
output: "target/executable/rsem/rsem_merge_counts" output: "target/executable/rsem/rsem_merge_counts"
executable: "target/executable/rsem/rsem_merge_counts/rsem_merge_counts" executable: "target/executable/rsem/rsem_merge_counts/rsem_merge_counts"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -207,5 +208,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/rsem/rsem_merge_counts/rsem_merge_counts
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# rsem_merge_counts v0.1.0 # rsem_merge_counts v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "rsem_merge_counts v0.1.0" echo "rsem_merge_counts v0.1.1"
echo "" echo ""
echo "Merge the transcript quantification results obtained from rsem" echo "Merge the transcript quantification results obtained from rsem"
echo "calculate-expression across all samples." echo "calculate-expression across all samples."
@@ -483,10 +483,10 @@ function ViashDockerfile {
FROM ubuntu:22.04 FROM ubuntu:22.04
ENTRYPOINT [] ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_merge_counts" LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_merge_counts"
LABEL org.opencontainers.image.created="2024-10-04T11:21:54Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:25Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -622,7 +622,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "rsem_merge_counts v0.1.0" echo "rsem_merge_counts v0.1.1"
exit exit
;; ;;
--counts_gene) --counts_gene)
@@ -779,7 +779,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rsem/rsem_merge_counts:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rsem/rsem_merge_counts:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "rseqc_bamstat" name: "rseqc_bamstat"
namespace: "rseqc" namespace: "rseqc"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -140,7 +140,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "apt" - type: "apt"
@@ -163,10 +163,11 @@ build_info:
output: "target/executable/rseqc/rseqc_bamstat" output: "target/executable/rseqc/rseqc_bamstat"
executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat" executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -188,5 +189,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/rseqc/rseqc_bamstat/rseqc_bamstat
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# rseqc_bamstat v0.1.0 # rseqc_bamstat v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "rseqc_bamstat v0.1.0" echo "rseqc_bamstat v0.1.1"
echo "" echo ""
echo "Generate statistics from a bam file." echo "Generate statistics from a bam file."
echo "" echo ""
@@ -477,10 +477,10 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC" pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_bamstat" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_bamstat"
LABEL org.opencontainers.image.created="2024-10-04T11:21:52Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:27Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -616,7 +616,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "rseqc_bamstat v0.1.0" echo "rseqc_bamstat v0.1.1"
exit exit
;; ;;
--input) --input)
@@ -740,7 +740,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rseqc/rseqc_bamstat:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rseqc/rseqc_bamstat:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "rseqc_inferexperiment" name: "rseqc_inferexperiment"
namespace: "rseqc" namespace: "rseqc"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -163,7 +163,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "apt" - type: "apt"
@@ -186,10 +186,11 @@ build_info:
output: "target/executable/rseqc/rseqc_inferexperiment" output: "target/executable/rseqc/rseqc_inferexperiment"
executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment" executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -211,5 +212,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# rseqc_inferexperiment v0.1.0 # rseqc_inferexperiment v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "rseqc_inferexperiment v0.1.0" echo "rseqc_inferexperiment v0.1.1"
echo "" echo ""
echo "Infer strandedness from sequencing reads" echo "Infer strandedness from sequencing reads"
echo "" echo ""
@@ -487,10 +487,10 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC" pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_inferexperiment" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_inferexperiment"
LABEL org.opencontainers.image.created="2024-10-04T11:21:50Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:29Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -626,7 +626,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "rseqc_inferexperiment v0.1.0" echo "rseqc_inferexperiment v0.1.1"
exit exit
;; ;;
--input) --input)
@@ -772,7 +772,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rseqc/rseqc_inferexperiment:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rseqc/rseqc_inferexperiment:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "rseqc_innerdistance" name: "rseqc_innerdistance"
namespace: "rseqc" namespace: "rseqc"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -248,7 +248,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "apt" - type: "apt"
@@ -272,10 +272,11 @@ build_info:
output: "target/executable/rseqc/rseqc_innerdistance" output: "target/executable/rseqc/rseqc_innerdistance"
executable: "target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance" executable: "target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -297,5 +298,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# rseqc_innerdistance v0.1.0 # rseqc_innerdistance v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "rseqc_innerdistance v0.1.0" echo "rseqc_innerdistance v0.1.1"
echo "" echo ""
echo "Calculate inner distance between read pairs." echo "Calculate inner distance between read pairs."
echo "" echo ""
@@ -529,10 +529,10 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC" pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_innerdistance" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_innerdistance"
LABEL org.opencontainers.image.created="2024-10-04T11:21:52Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:29Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -668,7 +668,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "rseqc_innerdistance v0.1.0" echo "rseqc_innerdistance v0.1.1"
exit exit
;; ;;
--input) --input)
@@ -891,7 +891,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rseqc/rseqc_innerdistance:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rseqc/rseqc_innerdistance:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "rseqc_junctionannotation" name: "rseqc_junctionannotation"
namespace: "rseqc" namespace: "rseqc"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -236,7 +236,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "apt" - type: "apt"
@@ -260,10 +260,11 @@ build_info:
output: "target/executable/rseqc/rseqc_junctionannotation" output: "target/executable/rseqc/rseqc_junctionannotation"
executable: "target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation" executable: "target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -285,5 +286,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# rseqc_junctionannotation v0.1.0 # rseqc_junctionannotation v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "rseqc_junctionannotation v0.1.0" echo "rseqc_junctionannotation v0.1.1"
echo "" echo ""
echo "Compare detected splice junctions to reference gene model." echo "Compare detected splice junctions to reference gene model."
echo "" echo ""
@@ -519,10 +519,10 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC" pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionannotation" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionannotation"
LABEL org.opencontainers.image.created="2024-10-04T11:21:51Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:30Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -658,7 +658,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "rseqc_junctionannotation v0.1.0" echo "rseqc_junctionannotation v0.1.1"
exit exit
;; ;;
--input) --input)
@@ -870,7 +870,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rseqc/rseqc_junctionannotation:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rseqc/rseqc_junctionannotation:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "rseqc_junctionsaturation" name: "rseqc_junctionsaturation"
namespace: "rseqc" namespace: "rseqc"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -225,7 +225,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "apt" - type: "apt"
@@ -249,10 +249,11 @@ build_info:
output: "target/executable/rseqc/rseqc_junctionsaturation" output: "target/executable/rseqc/rseqc_junctionsaturation"
executable: "target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation" executable: "target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -274,5 +275,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# rseqc_junctionsaturation v0.1.0 # rseqc_junctionsaturation v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "rseqc_junctionsaturation v0.1.0" echo "rseqc_junctionsaturation v0.1.1"
echo "" echo ""
echo "Compare detected splice junctions to reference gene model." echo "Compare detected splice junctions to reference gene model."
echo "" echo ""
@@ -522,10 +522,10 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC" pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionsaturation" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionsaturation"
LABEL org.opencontainers.image.created="2024-10-04T11:21:51Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:27Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -661,7 +661,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "rseqc_junctionsaturation v0.1.0" echo "rseqc_junctionsaturation v0.1.1"
exit exit
;; ;;
--input) --input)
@@ -862,7 +862,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rseqc/rseqc_junctionsaturation:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rseqc/rseqc_junctionsaturation:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "rseqc_readdistribution" name: "rseqc_readdistribution"
namespace: "rseqc" namespace: "rseqc"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -139,7 +139,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "apt" - type: "apt"
@@ -162,10 +162,11 @@ build_info:
output: "target/executable/rseqc/rseqc_readdistribution" output: "target/executable/rseqc/rseqc_readdistribution"
executable: "target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution" executable: "target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -187,5 +188,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# rseqc_readdistribution v0.1.0 # rseqc_readdistribution v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "rseqc_readdistribution v0.1.0" echo "rseqc_readdistribution v0.1.1"
echo "" echo ""
echo "Calculate how mapped reads are distributed over genomic features." echo "Calculate how mapped reads are distributed over genomic features."
echo "" echo ""
@@ -474,10 +474,10 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC" pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readdistribution" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readdistribution"
LABEL org.opencontainers.image.created="2024-10-04T11:21:52Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:28Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -613,7 +613,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "rseqc_readdistribution v0.1.0" echo "rseqc_readdistribution v0.1.1"
exit exit
;; ;;
--input) --input)
@@ -737,7 +737,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rseqc/rseqc_readdistribution:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rseqc/rseqc_readdistribution:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "rseqc_readduplication" name: "rseqc_readduplication"
namespace: "rseqc" namespace: "rseqc"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -187,7 +187,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "apt" - type: "apt"
@@ -211,10 +211,11 @@ build_info:
output: "target/executable/rseqc/rseqc_readduplication" output: "target/executable/rseqc/rseqc_readduplication"
executable: "target/executable/rseqc/rseqc_readduplication/rseqc_readduplication" executable: "target/executable/rseqc/rseqc_readduplication/rseqc_readduplication"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -236,5 +237,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/rseqc/rseqc_readduplication/rseqc_readduplication
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# rseqc_readduplication v0.1.0 # rseqc_readduplication v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "rseqc_readduplication v0.1.0" echo "rseqc_readduplication v0.1.1"
echo "" echo ""
echo "Calculate read duplication rate." echo "Calculate read duplication rate."
echo "" echo ""
@@ -499,10 +499,10 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC" pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readduplication" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readduplication"
LABEL org.opencontainers.image.created="2024-10-04T11:21:50Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:26Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -638,7 +638,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "rseqc_readduplication v0.1.0" echo "rseqc_readduplication v0.1.1"
exit exit
;; ;;
--input) --input)
@@ -806,7 +806,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rseqc/rseqc_readduplication:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rseqc/rseqc_readduplication:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/rseqc/rseqc_tin/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "rseqc_tin" name: "rseqc_tin"
namespace: "rseqc" namespace: "rseqc"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -193,7 +193,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "apt" - type: "apt"
@@ -214,10 +214,11 @@ build_info:
output: "target/executable/rseqc/rseqc_tin" output: "target/executable/rseqc/rseqc_tin"
executable: "target/executable/rseqc/rseqc_tin/rseqc_tin" executable: "target/executable/rseqc/rseqc_tin/rseqc_tin"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -239,5 +240,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/rseqc/rseqc_tin/rseqc_tin
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# rseqc_tin v0.1.0 # rseqc_tin v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "rseqc_tin v0.1.0" echo "rseqc_tin v0.1.1"
echo "" echo ""
echo "Calculte TIN (transcript integrity number) from RNA-seq reads" echo "Calculte TIN (transcript integrity number) from RNA-seq reads"
echo "" echo ""
@@ -501,10 +501,10 @@ RUN apt-get update && \
RUN pip3 install RSeQC RUN pip3 install RSeQC
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_tin" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_tin"
LABEL org.opencontainers.image.created="2024-10-04T11:21:50Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:29Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -640,7 +640,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "rseqc_tin v0.1.0" echo "rseqc_tin v0.1.1"
exit exit
;; ;;
--bam_input) --bam_input)
@@ -813,7 +813,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rseqc/rseqc_tin:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rseqc/rseqc_tin:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/sortmerna/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "sortmerna" name: "sortmerna"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -179,7 +179,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "docker" - type: "docker"
@@ -198,10 +198,11 @@ build_info:
output: "target/executable/sortmerna" output: "target/executable/sortmerna"
executable: "target/executable/sortmerna/sortmerna" executable: "target/executable/sortmerna/sortmerna"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -223,5 +224,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/sortmerna/sortmerna
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# sortmerna v0.1.0 # sortmerna v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "sortmerna v0.1.0" echo "sortmerna v0.1.1"
echo "" echo ""
echo "Local sequence alignment tool for filtering, mapping and clustering. The main" echo "Local sequence alignment tool for filtering, mapping and clustering. The main"
echo "application of SortMeRNA is filtering rRNA from metatranscriptomic data." echo "application of SortMeRNA is filtering rRNA from metatranscriptomic data."
@@ -492,10 +492,10 @@ wget --no-check-certificate https://github.com/sortmerna/sortmerna/releases/down
bash sortmerna-4.3.6-Linux.sh --skip-license bash sortmerna-4.3.6-Linux.sh --skip-license
LABEL org.opencontainers.image.description="Companion container for running component sortmerna" LABEL org.opencontainers.image.description="Companion container for running component sortmerna"
LABEL org.opencontainers.image.created="2024-10-04T11:21:57Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:25Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -631,7 +631,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "sortmerna v0.1.0" echo "sortmerna v0.1.1"
exit exit
;; ;;
--paired) --paired)
@@ -794,7 +794,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/sortmerna:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/sortmerna:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/stringtie/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "stringtie" name: "stringtie"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -196,7 +196,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "docker" - type: "docker"
@@ -216,10 +216,11 @@ build_info:
output: "target/executable/stringtie" output: "target/executable/stringtie"
executable: "target/executable/stringtie/stringtie" executable: "target/executable/stringtie/stringtie"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -241,5 +242,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/stringtie/stringtie
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# stringtie v0.1.0 # stringtie v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "stringtie v0.1.0" echo "stringtie v0.1.1"
echo "" echo ""
echo "Transcript assembly and quantification for RNA-Seq" echo "Transcript assembly and quantification for RNA-Seq"
echo "" echo ""
@@ -496,10 +496,10 @@ tar -xzf stringtie-2.2.1.Linux_x86_64.tar.gz && \
cp stringtie-2.2.1.Linux_x86_64/stringtie /usr/local/bin/ cp stringtie-2.2.1.Linux_x86_64/stringtie /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component stringtie" LABEL org.opencontainers.image.description="Companion container for running component stringtie"
LABEL org.opencontainers.image.created="2024-10-04T11:21:54Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:26Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -635,7 +635,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "stringtie v0.1.0" echo "stringtie v0.1.1"
exit exit
;; ;;
--strandedness) --strandedness)
@@ -825,7 +825,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/stringtie:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/stringtie:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/summarizedexperiment/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "summarizedexperiment" name: "summarizedexperiment"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -175,7 +175,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "apt" - type: "apt"
@@ -199,10 +199,11 @@ build_info:
output: "target/executable/summarizedexperiment" output: "target/executable/summarizedexperiment"
executable: "target/executable/summarizedexperiment/summarizedexperiment" executable: "target/executable/summarizedexperiment/summarizedexperiment"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -224,5 +225,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/summarizedexperiment/summarizedexperiment
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# summarizedexperiment v0.1.0 # summarizedexperiment v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "summarizedexperiment v0.1.0" echo "summarizedexperiment v0.1.1"
echo "" echo ""
echo "Create SummarizedExperiment object from Salmon counts" echo "Create SummarizedExperiment object from Salmon counts"
echo "" echo ""
@@ -487,10 +487,10 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.pa
Rscript -e 'if (!requireNamespace("tximeta", quietly = TRUE)) BiocManager::install("tximeta")' Rscript -e 'if (!requireNamespace("tximeta", quietly = TRUE)) BiocManager::install("tximeta")'
LABEL org.opencontainers.image.description="Companion container for running component summarizedexperiment" LABEL org.opencontainers.image.description="Companion container for running component summarizedexperiment"
LABEL org.opencontainers.image.created="2024-10-04T11:21:58Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:24Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -626,7 +626,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "summarizedexperiment v0.1.0" echo "summarizedexperiment v0.1.1"
exit exit
;; ;;
--tpm_gene) --tpm_gene)
@@ -805,7 +805,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/summarizedexperiment:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/summarizedexperiment:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/trimgalore/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "trimgalore" name: "trimgalore"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -770,7 +770,7 @@ engines:
id: "docker" id: "docker"
image: "quay.io/biocontainers/trim-galore:0.6.9--hdfd78af_0" image: "quay.io/biocontainers/trim-galore:0.6.9--hdfd78af_0"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "docker" - type: "docker"
@@ -788,10 +788,11 @@ build_info:
output: "target/executable/trimgalore" output: "target/executable/trimgalore"
executable: "target/executable/trimgalore/trimgalore" executable: "target/executable/trimgalore/trimgalore"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -813,5 +814,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

14
target/executable/trimgalore/trimgalore
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# trimgalore v0.1.0 # trimgalore v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "trimgalore v0.1.0" echo "trimgalore v0.1.1"
echo "" echo ""
echo "A wrapper tool around Cutadapt and FastQC to consistently apply quality and" echo "A wrapper tool around Cutadapt and FastQC to consistently apply quality and"
echo "adapter trimming to FastQ files." echo "adapter trimming to FastQ files."
@@ -858,10 +858,10 @@ ENTRYPOINT []
RUN echo "TrimGalore: `trim_galore --version | sed -n 's/.*version\s\+\([0-9]\+\.[0-9]\+\.[0-9]\+\).*/\1/p'`" > /var/software_versions.txt RUN echo "TrimGalore: `trim_galore --version | sed -n 's/.*version\s\+\([0-9]\+\.[0-9]\+\.[0-9]\+\).*/\1/p'`" > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component trimgalore" LABEL org.opencontainers.image.description="Companion container for running component trimgalore"
LABEL org.opencontainers.image.created="2024-10-04T11:21:56Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:28Z"
LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore" LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -997,7 +997,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "trimgalore v0.1.0" echo "trimgalore v0.1.1"
exit exit
;; ;;
--input) --input)
@@ -1725,7 +1725,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/trimgalore:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/trimgalore:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/tx2gene/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "tx2gene" name: "tx2gene"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -170,7 +170,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "apt" - type: "apt"
@@ -192,10 +192,11 @@ build_info:
output: "target/executable/tx2gene" output: "target/executable/tx2gene"
executable: "target/executable/tx2gene/tx2gene" executable: "target/executable/tx2gene/tx2gene"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -217,5 +218,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/tx2gene/tx2gene
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# tx2gene v0.1.0 # tx2gene v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "tx2gene v0.1.0" echo "tx2gene v0.1.1"
echo "" echo ""
echo "Get transcript id (tx) to gene names for tximport" echo "Get transcript id (tx) to gene names for tximport"
echo "" echo ""
@@ -487,10 +487,10 @@ RUN apt-get update && \
RUN pip install --upgrade pip RUN pip install --upgrade pip
LABEL org.opencontainers.image.description="Companion container for running component tx2gene" LABEL org.opencontainers.image.description="Companion container for running component tx2gene"
LABEL org.opencontainers.image.created="2024-10-04T11:21:53Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:26Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -626,7 +626,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "tx2gene v0.1.0" echo "tx2gene v0.1.1"
exit exit
;; ;;
--quant_results) --quant_results)
@@ -800,7 +800,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/tx2gene:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/tx2gene:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/tximport/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "tximport" name: "tximport"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -218,7 +218,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "apt" - type: "apt"
@@ -247,10 +247,11 @@ build_info:
output: "target/executable/tximport" output: "target/executable/tximport"
executable: "target/executable/tximport/tximport" executable: "target/executable/tximport/tximport"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -272,5 +273,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/tximport/tximport
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# tximport v0.1.0 # tximport v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "tximport v0.1.0" echo "tximport v0.1.1"
echo "" echo ""
echo "Get dataframe linking transcript ID, gene ID, and gene name" echo "Get dataframe linking transcript ID, gene ID, and gene name"
echo "" echo ""
@@ -508,10 +508,10 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
Rscript -e 'remotes::install_cran(c("jsonlite"), repos = "https://cran.rstudio.com")' Rscript -e 'remotes::install_cran(c("jsonlite"), repos = "https://cran.rstudio.com")'
LABEL org.opencontainers.image.description="Companion container for running component tximport" LABEL org.opencontainers.image.description="Companion container for running component tximport"
LABEL org.opencontainers.image.created="2024-10-04T11:21:48Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:24Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -647,7 +647,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "tximport v0.1.0" echo "tximport v0.1.1"
exit exit
;; ;;
--quant_results) --quant_results)
@@ -865,7 +865,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/tximport:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/tximport:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/ucsc/bedclip/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "bedclip" name: "bedclip"
namespace: "ucsc" namespace: "ucsc"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -141,7 +141,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "apt" - type: "apt"
@@ -164,10 +164,11 @@ build_info:
output: "target/executable/ucsc/bedclip" output: "target/executable/ucsc/bedclip"
executable: "target/executable/ucsc/bedclip/bedclip" executable: "target/executable/ucsc/bedclip/bedclip"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -189,5 +190,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/ucsc/bedclip/bedclip
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# bedclip v0.1.0 # bedclip v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "bedclip v0.1.0" echo "bedclip v0.1.1"
echo "" echo ""
echo "Remove lines from bed file that refer to off-chromosome locations" echo "Remove lines from bed file that refer to off-chromosome locations"
echo "" echo ""
@@ -473,10 +473,10 @@ RUN apt-get update && \
RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedClip /usr/local/bin/ RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedClip /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component ucsc bedclip" LABEL org.opencontainers.image.description="Companion container for running component ucsc bedclip"
LABEL org.opencontainers.image.created="2024-10-04T11:21:49Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:28Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -612,7 +612,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "bedclip v0.1.0" echo "bedclip v0.1.1"
exit exit
;; ;;
--input_bedgraph) --input_bedgraph)
@@ -736,7 +736,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/ucsc/bedclip:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/ucsc/bedclip:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "bedgraphtobigwig" name: "bedgraphtobigwig"
namespace: "ucsc" namespace: "ucsc"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -141,7 +141,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "apt" - type: "apt"
@@ -164,10 +164,11 @@ build_info:
output: "target/executable/ucsc/bedgraphtobigwig" output: "target/executable/ucsc/bedgraphtobigwig"
executable: "target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig" executable: "target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -189,5 +190,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# bedgraphtobigwig v0.1.0 # bedgraphtobigwig v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "bedgraphtobigwig v0.1.0" echo "bedgraphtobigwig v0.1.1"
echo "" echo ""
echo "Convert a bedGraph file to bigWig format" echo "Convert a bedGraph file to bigWig format"
echo "" echo ""
@@ -473,10 +473,10 @@ RUN apt-get update && \
RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedGraphToBigWig /usr/local/bin/ RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedGraphToBigWig /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component ucsc bedgraphtobigwig" LABEL org.opencontainers.image.description="Companion container for running component ucsc bedgraphtobigwig"
LABEL org.opencontainers.image.created="2024-10-04T11:21:49Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:29Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -612,7 +612,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "bedgraphtobigwig v0.1.0" echo "bedgraphtobigwig v0.1.1"
exit exit
;; ;;
--bedgraph) --bedgraph)
@@ -736,7 +736,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/ucsc/bedgraphtobigwig:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/ucsc/bedgraphtobigwig:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/umitools/umitools_dedup/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "umitools_dedup" name: "umitools_dedup"
namespace: "umitools" namespace: "umitools"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -172,7 +172,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "apt" - type: "apt"
@@ -195,10 +195,11 @@ build_info:
output: "target/executable/umitools/umitools_dedup" output: "target/executable/umitools/umitools_dedup"
executable: "target/executable/umitools/umitools_dedup/umitools_dedup" executable: "target/executable/umitools/umitools_dedup/umitools_dedup"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -220,5 +221,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/umitools/umitools_dedup/umitools_dedup
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# umitools_dedup v0.1.0 # umitools_dedup v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "umitools_dedup v0.1.0" echo "umitools_dedup v0.1.1"
echo "" echo ""
echo "Deduplicate reads based on the mapping co-ordinate and the UMI attached to the" echo "Deduplicate reads based on the mapping co-ordinate and the UMI attached to the"
echo "read." echo "read."
@@ -489,10 +489,10 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "umi_tools" pip install --upgrade --no-cache-dir "umi_tools"
LABEL org.opencontainers.image.description="Companion container for running component umitools umitools_dedup" LABEL org.opencontainers.image.description="Companion container for running component umitools umitools_dedup"
LABEL org.opencontainers.image.created="2024-10-04T11:21:56Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:28Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -628,7 +628,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "umitools_dedup v0.1.0" echo "umitools_dedup v0.1.1"
exit exit
;; ;;
--paired) --paired)
@@ -785,7 +785,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/umitools/umitools_dedup:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/umitools/umitools_dedup:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/umitools/umitools_extract/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "umitools_extract" name: "umitools_extract"
namespace: "umitools" namespace: "umitools"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -230,7 +230,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "apt" - type: "apt"
@@ -253,10 +253,11 @@ build_info:
output: "target/executable/umitools/umitools_extract" output: "target/executable/umitools/umitools_extract"
executable: "target/executable/umitools/umitools_extract/umitools_extract" executable: "target/executable/umitools/umitools_extract/umitools_extract"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -278,5 +279,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/umitools/umitools_extract/umitools_extract
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# umitools_extract v0.1.0 # umitools_extract v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "umitools_extract v0.1.0" echo "umitools_extract v0.1.1"
echo "" echo ""
echo "UMI-tools contains tools for dealing with Unique Molecular Identifiers" echo "UMI-tools contains tools for dealing with Unique Molecular Identifiers"
echo "(UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes. See" echo "(UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes. See"
@@ -521,10 +521,10 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "umi_tools" pip install --upgrade --no-cache-dir "umi_tools"
LABEL org.opencontainers.image.description="Companion container for running component umitools umitools_extract" LABEL org.opencontainers.image.description="Companion container for running component umitools umitools_extract"
LABEL org.opencontainers.image.created="2024-10-04T11:21:56Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:28Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -660,7 +660,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "umitools_extract v0.1.0" echo "umitools_extract v0.1.1"
exit exit
;; ;;
--paired) --paired)
@@ -862,7 +862,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/umitools/umitools_extract:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/umitools/umitools_extract:v0.1.1'
fi fi
# print dockerfile # print dockerfile

13
target/executable/umitools_prepareforquant/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "umitools_prepareforquant" name: "umitools_prepareforquant"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -132,7 +132,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "apt" - type: "apt"
@@ -156,10 +156,11 @@ build_info:
output: "target/executable/umitools_prepareforquant" output: "target/executable/umitools_prepareforquant"
executable: "target/executable/umitools_prepareforquant/umitools_prepareforquant" executable: "target/executable/umitools_prepareforquant/umitools_prepareforquant"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -181,5 +182,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

16
target/executable/umitools_prepareforquant/umitools_prepareforquant
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# umitools_prepareforquant v0.1.0 # umitools_prepareforquant v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "umitools_prepareforquant v0.1.0" echo "umitools_prepareforquant v0.1.1"
echo "" echo ""
echo "Fix paired-end reads in name sorted BAM file to prepare for salmon" echo "Fix paired-end reads in name sorted BAM file to prepare for salmon"
echo "quantification" echo "quantification"
@@ -473,10 +473,10 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "umi_tools" "pysam" pip install --upgrade --no-cache-dir "umi_tools" "pysam"
LABEL org.opencontainers.image.description="Companion container for running component umitools_prepareforquant" LABEL org.opencontainers.image.description="Companion container for running component umitools_prepareforquant"
LABEL org.opencontainers.image.created="2024-10-04T11:21:58Z" LABEL org.opencontainers.image.created="2024-10-17T16:18:27Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
LABEL org.opencontainers.image.version="v0.1.0" LABEL org.opencontainers.image.version="v0.1.1"
VIASHDOCKER VIASHDOCKER
fi fi
@@ -612,7 +612,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "umitools_prepareforquant v0.1.0" echo "umitools_prepareforquant v0.1.1"
exit exit
;; ;;
--bam) --bam)
@@ -736,7 +736,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id # determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/umitools_prepareforquant:v0.1.0' VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/umitools_prepareforquant:v0.1.1'
fi fi
# print dockerfile # print dockerfile

11
target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "genome_alignment_and_quant" name: "genome_alignment_and_quant"
namespace: "workflows" namespace: "workflows"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -603,8 +603,8 @@ build_info:
output: "target/executable/workflows/genome_alignment_and_quant" output: "target/executable/workflows/genome_alignment_and_quant"
executable: "target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant" executable: "target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
dependencies: dependencies:
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort"
@@ -617,7 +617,8 @@ build_info:
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant"
- "target/nextflow/rsem/rsem_calculate_expression" - "target/nextflow/rsem/rsem_calculate_expression"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -639,5 +640,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

6
target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# genome_alignment_and_quant v0.1.0 # genome_alignment_and_quant v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "genome_alignment_and_quant v0.1.0" echo "genome_alignment_and_quant v0.1.1"
echo "" echo ""
echo "A viash sub-workflow for genome alignment and quantification stage of" echo "A viash sub-workflow for genome alignment and quantification stage of"
echo "nf-core/rnaseq pipeline." echo "nf-core/rnaseq pipeline."
@@ -401,7 +401,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "genome_alignment_and_quant v0.1.0" echo "genome_alignment_and_quant v0.1.1"
exit exit
;; ;;
--id) --id)

11
target/executable/workflows/merge_quant_results/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "merge_quant_results" name: "merge_quant_results"
namespace: "workflows" namespace: "workflows"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -278,14 +278,15 @@ build_info:
output: "target/executable/workflows/merge_quant_results" output: "target/executable/workflows/merge_quant_results"
executable: "target/executable/workflows/merge_quant_results/merge_quant_results" executable: "target/executable/workflows/merge_quant_results/merge_quant_results"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
dependencies: dependencies:
- "target/nextflow/tx2gene" - "target/nextflow/tx2gene"
- "target/nextflow/tximport" - "target/nextflow/tximport"
- "target/nextflow/summarizedexperiment" - "target/nextflow/summarizedexperiment"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -307,5 +308,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

6
target/executable/workflows/merge_quant_results/merge_quant_results
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# merge_quant_results v0.1.0 # merge_quant_results v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "merge_quant_results v0.1.0" echo "merge_quant_results v0.1.1"
echo "" echo ""
echo "A sub-workflow to merge the counts obtained from salmon quant across all" echo "A sub-workflow to merge the counts obtained from salmon quant across all"
echo "samples." echo "samples."
@@ -267,7 +267,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "merge_quant_results v0.1.0" echo "merge_quant_results v0.1.1"
exit exit
;; ;;
--salmon_quant_results) --salmon_quant_results)

11
target/executable/workflows/post_processing/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "post_processing" name: "post_processing"
namespace: "workflows" namespace: "workflows"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -486,8 +486,8 @@ build_info:
output: "target/executable/workflows/post_processing" output: "target/executable/workflows/post_processing"
executable: "target/executable/workflows/post_processing/post_processing" executable: "target/executable/workflows/post_processing/post_processing"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
dependencies: dependencies:
- "target/nextflow/picard_markduplicates" - "target/nextflow/picard_markduplicates"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort"
@@ -500,7 +500,8 @@ build_info:
- "target/nextflow/ucsc/bedclip" - "target/nextflow/ucsc/bedclip"
- "target/nextflow/ucsc/bedgraphtobigwig" - "target/nextflow/ucsc/bedgraphtobigwig"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -522,5 +523,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

6
target/executable/workflows/post_processing/post_processing
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# post_processing v0.1.0 # post_processing v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "post_processing v0.1.0" echo "post_processing v0.1.1"
echo "" echo ""
echo "A viash sub-workflow for the post-processing stage of nf-core/rnaseq pipeline." echo "A viash sub-workflow for the post-processing stage of nf-core/rnaseq pipeline."
echo "" echo ""
@@ -350,7 +350,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "post_processing v0.1.0" echo "post_processing v0.1.1"
exit exit
;; ;;
--id) --id)

11
target/executable/workflows/pre_processing/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "pre_processing" name: "pre_processing"
namespace: "workflows" namespace: "workflows"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Inputs" - name: "Inputs"
arguments: arguments:
@@ -673,8 +673,8 @@ build_info:
output: "target/executable/workflows/pre_processing" output: "target/executable/workflows/pre_processing"
executable: "target/executable/workflows/pre_processing/pre_processing" executable: "target/executable/workflows/pre_processing/pre_processing"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
dependencies: dependencies:
- "target/nextflow/fastqc" - "target/nextflow/fastqc"
- "target/nextflow/umitools/umitools_extract" - "target/nextflow/umitools/umitools_extract"
@@ -686,7 +686,8 @@ build_info:
- "target/nextflow/fq_subsample" - "target/nextflow/fq_subsample"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -708,5 +709,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

6
target/executable/workflows/pre_processing/pre_processing
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# pre_processing v0.1.0 # pre_processing v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "pre_processing v0.1.0" echo "pre_processing v0.1.1"
echo "" echo ""
echo "A subworkflow for the pre-processing stage of the nf-core/rnaseq pipeline." echo "A subworkflow for the pre-processing stage of the nf-core/rnaseq pipeline."
echo "" echo ""
@@ -453,7 +453,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "pre_processing v0.1.0" echo "pre_processing v0.1.1"
exit exit
;; ;;
--id) --id)

11
target/executable/workflows/prepare_genome/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "prepare_genome" name: "prepare_genome"
namespace: "workflows" namespace: "workflows"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -496,8 +496,8 @@ build_info:
output: "target/executable/workflows/prepare_genome" output: "target/executable/workflows/prepare_genome"
executable: "target/executable/workflows/prepare_genome/prepare_genome" executable: "target/executable/workflows/prepare_genome/prepare_genome"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
dependencies: dependencies:
- "target/nextflow/gunzip" - "target/nextflow/gunzip"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread"
@@ -513,7 +513,8 @@ build_info:
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index"
- "target/nextflow/kallisto/kallisto_index" - "target/nextflow/kallisto/kallisto_index"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -535,5 +536,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

6
target/executable/workflows/prepare_genome/prepare_genome
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# prepare_genome v0.1.0 # prepare_genome v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "prepare_genome v0.1.0" echo "prepare_genome v0.1.1"
echo "" echo ""
echo "A subworkflow for preparing all the required genome references" echo "A subworkflow for preparing all the required genome references"
echo "" echo ""
@@ -354,7 +354,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "prepare_genome v0.1.0" echo "prepare_genome v0.1.1"
exit exit
;; ;;
--fasta) --fasta)

11
target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "pseudo_alignment_and_quant" name: "pseudo_alignment_and_quant"
namespace: "workflows" namespace: "workflows"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -283,13 +283,14 @@ build_info:
output: "target/executable/workflows/pseudo_alignment_and_quant" output: "target/executable/workflows/pseudo_alignment_and_quant"
executable: "target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant" executable: "target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
dependencies: dependencies:
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant"
- "target/nextflow/kallisto/kallisto_quant" - "target/nextflow/kallisto/kallisto_quant"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -311,5 +312,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

6
target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# pseudo_alignment_and_quant v0.1.0 # pseudo_alignment_and_quant v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "pseudo_alignment_and_quant v0.1.0" echo "pseudo_alignment_and_quant v0.1.1"
echo "" echo ""
echo "A viash sub-workflow for pseudo alignment and quantification stage of" echo "A viash sub-workflow for pseudo alignment and quantification stage of"
echo "nf-core/rnaseq pipeline." echo "nf-core/rnaseq pipeline."
@@ -279,7 +279,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "pseudo_alignment_and_quant v0.1.0" echo "pseudo_alignment_and_quant v0.1.1"
exit exit
;; ;;
--id) --id)

11
target/executable/workflows/quality_control/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "quality_control" name: "quality_control"
namespace: "workflows" namespace: "workflows"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -1596,8 +1596,8 @@ build_info:
output: "target/executable/workflows/quality_control" output: "target/executable/workflows/quality_control"
executable: "target/executable/workflows/quality_control/quality_control" executable: "target/executable/workflows/quality_control/quality_control"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
dependencies: dependencies:
- "target/nextflow/rseqc/rseqc_bamstat" - "target/nextflow/rseqc/rseqc_bamstat"
- "target/nextflow/rseqc/rseqc_inferexperiment" - "target/nextflow/rseqc/rseqc_inferexperiment"
@@ -1618,7 +1618,8 @@ build_info:
- "target/nextflow/rsem/rsem_merge_counts" - "target/nextflow/rsem/rsem_merge_counts"
- "target/nextflow/workflows/merge_quant_results" - "target/nextflow/workflows/merge_quant_results"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -1640,5 +1641,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

6
target/executable/workflows/quality_control/quality_control
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# quality_control v0.1.0 # quality_control v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "quality_control v0.1.0" echo "quality_control v0.1.1"
echo "" echo ""
echo "A subworkflow for the final quality control stage of the nf-core/rnaseq" echo "A subworkflow for the final quality control stage of the nf-core/rnaseq"
echo "pipeline." echo "pipeline."
@@ -834,7 +834,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "quality_control v0.1.0" echo "quality_control v0.1.1"
exit exit
;; ;;
--id) --id)

11
target/executable/workflows/rnaseq/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "rnaseq" name: "rnaseq"
namespace: "workflows" namespace: "workflows"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -2117,8 +2117,8 @@ build_info:
output: "target/executable/workflows/rnaseq" output: "target/executable/workflows/rnaseq"
executable: "target/executable/workflows/rnaseq/rnaseq" executable: "target/executable/workflows/rnaseq/rnaseq"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
dependencies: dependencies:
- "target/nextflow/workflows/prepare_genome" - "target/nextflow/workflows/prepare_genome"
- "target/nextflow/cat_fastq" - "target/nextflow/cat_fastq"
@@ -2128,7 +2128,8 @@ build_info:
- "target/nextflow/workflows/post_processing" - "target/nextflow/workflows/post_processing"
- "target/nextflow/workflows/quality_control" - "target/nextflow/workflows/quality_control"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -2150,5 +2151,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

6
target/executable/workflows/rnaseq/rnaseq
View File

@@ -1,6 +1,6 @@
#!/usr/bin/env bash #!/usr/bin/env bash
# rnaseq v0.1.0 # rnaseq v0.1.1
# #
# This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # 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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
# ViashHelp: Display helpful explanation about this executable # ViashHelp: Display helpful explanation about this executable
function ViashHelp { function ViashHelp {
echo "rnaseq v0.1.0" echo "rnaseq v0.1.1"
echo "" echo ""
echo "A viash workflow for the nf-core/rnaseq pipeline." echo "A viash workflow for the nf-core/rnaseq pipeline."
echo "" echo ""
@@ -1093,7 +1093,7 @@ while [[ $# -gt 0 ]]; do
shift 1 shift 1
;; ;;
--version) --version)
echo "rnaseq v0.1.0" echo "rnaseq v0.1.1"
exit exit
;; ;;
--id) --id)

13
target/nextflow/bbmap_bbsplit/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "bbmap_bbsplit" name: "bbmap_bbsplit"
version: "v0.1.0" version: "v0.1.1"
argument_groups: argument_groups:
- name: "Input" - name: "Input"
arguments: arguments:
@@ -219,7 +219,7 @@ engines:
id: "docker" id: "docker"
image: "ubuntu:22.04" image: "ubuntu:22.04"
target_registry: "images.viash-hub.com" target_registry: "images.viash-hub.com"
target_tag: "v0.1.0" target_tag: "v0.1.1"
namespace_separator: "/" namespace_separator: "/"
setup: setup:
- type: "docker" - type: "docker"
@@ -238,10 +238,11 @@ build_info:
output: "target/nextflow/bbmap_bbsplit" output: "target/nextflow/bbmap_bbsplit"
executable: "target/nextflow/bbmap_bbsplit/main.nf" executable: "target/nextflow/bbmap_bbsplit/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
package_config: package_config:
version: "v0.1.0" name: "rnaseq"
version: "v0.1.1"
info: info:
test_resources: test_resources:
- path: "gs://viash-hub-test-data/rnaseq/v1" - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -263,5 +264,5 @@ package_config:
\ := '$id'\n" \ := '$id'\n"
- ".engines += { type: \"native\" }" - ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.1.0'" - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
organization: "vsh" organization: "vsh"

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