diff --git a/_viash.yaml b/_viash.yaml index 121078b..4db24e1 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,5 +1,7 @@ +name: rnaseq + viash_version: 0.9.0 -version: v0.1.0 +version: v0.1.1 source: src target: target diff --git a/target/executable/bbmap_bbsplit/.config.vsh.yaml b/target/executable/bbmap_bbsplit/.config.vsh.yaml index c58bacd..4c5776f 100644 --- a/target/executable/bbmap_bbsplit/.config.vsh.yaml +++ b/target/executable/bbmap_bbsplit/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "bbmap_bbsplit" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -219,7 +219,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "docker" @@ -238,10 +238,11 @@ build_info: output: "target/executable/bbmap_bbsplit" executable: "target/executable/bbmap_bbsplit/bbmap_bbsplit" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -263,5 +264,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.1'" organization: "vsh" diff --git a/target/executable/bbmap_bbsplit/bbmap_bbsplit b/target/executable/bbmap_bbsplit/bbmap_bbsplit index b772a2b..06e072d 100755 --- a/target/executable/bbmap_bbsplit/bbmap_bbsplit +++ b/target/executable/bbmap_bbsplit/bbmap_bbsplit @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# bbmap_bbsplit v0.1.0 +# bbmap_bbsplit v0.1.1 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "bbmap_bbsplit v0.1.0" + echo "bbmap_bbsplit v0.1.1" echo "" echo "Split sequencing reads by mapping them to multiple references simultaneously." echo "" @@ -506,10 +506,10 @@ tar xzf BBMap_39.01.tar.gz && \ cp -r bbmap/* /usr/local/bin 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:28Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -645,7 +645,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bbmap_bbsplit v0.1.0" + echo "bbmap_bbsplit v0.1.1" exit ;; --id) @@ -852,7 +852,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/bbmap_bbsplit:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/bbmap_bbsplit:v0.1.1' fi # print dockerfile diff --git a/target/executable/bedtools_genomecov/.config.vsh.yaml b/target/executable/bedtools_genomecov/.config.vsh.yaml index d812d3e..92d7c76 100644 --- a/target/executable/bedtools_genomecov/.config.vsh.yaml +++ b/target/executable/bedtools_genomecov/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "bedtools_genomecov" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -159,7 +159,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "docker" @@ -178,10 +178,11 @@ build_info: output: "target/executable/bedtools_genomecov" executable: "target/executable/bedtools_genomecov/bedtools_genomecov" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -203,5 +204,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/bedtools_genomecov/bedtools_genomecov b/target/executable/bedtools_genomecov/bedtools_genomecov index 95fe81a..c3b80ec 100755 --- a/target/executable/bedtools_genomecov/bedtools_genomecov +++ b/target/executable/bedtools_genomecov/bedtools_genomecov @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "bedtools_genomecov v0.1.0" + echo "bedtools_genomecov v0.1.1" echo "" echo "Compute BEDGRAPH (-bg) summaries of feature coverage" echo "" @@ -481,10 +481,10 @@ mv bedtools.static /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.created="2024-10-04T11:21:40Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:23Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -620,7 +620,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bedtools_genomecov v0.1.0" + echo "bedtools_genomecov v0.1.1" exit ;; --strandedness) @@ -766,7 +766,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/bedtools_genomecov:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/bedtools_genomecov:v0.1.1' fi # print dockerfile diff --git a/target/executable/cat_additional_fasta/.config.vsh.yaml b/target/executable/cat_additional_fasta/.config.vsh.yaml index 562d475..bcb3e3b 100644 --- a/target/executable/cat_additional_fasta/.config.vsh.yaml +++ b/target/executable/cat_additional_fasta/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "cat_additional_fasta" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -169,7 +169,7 @@ engines: id: "docker" image: "python" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" entrypoint: [] cmd: null @@ -182,10 +182,11 @@ build_info: output: "target/executable/cat_additional_fasta" executable: "target/executable/cat_additional_fasta/cat_additional_fasta" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -207,5 +208,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/cat_additional_fasta/cat_additional_fasta b/target/executable/cat_additional_fasta/cat_additional_fasta index 67f75fa..6897757 100755 --- a/target/executable/cat_additional_fasta/cat_additional_fasta +++ b/target/executable/cat_additional_fasta/cat_additional_fasta @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "cat_additional_fasta v0.1.0" + echo "cat_additional_fasta v0.1.1" echo "" echo "Concatenate addional fasta file to reference FASTA and GTF files." echo "" @@ -480,10 +480,10 @@ function ViashDockerfile { FROM python:latest ENTRYPOINT [] 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:23Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -619,7 +619,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "cat_additional_fasta v0.1.0" + echo "cat_additional_fasta v0.1.1" exit ;; --fasta) @@ -776,7 +776,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/cat_additional_fasta:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/cat_additional_fasta:v0.1.1' fi # print dockerfile diff --git a/target/executable/cat_fastq/.config.vsh.yaml b/target/executable/cat_fastq/.config.vsh.yaml index 49a1a7c..1c861f2 100644 --- a/target/executable/cat_fastq/.config.vsh.yaml +++ b/target/executable/cat_fastq/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "cat_fastq" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -156,7 +156,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" entrypoint: [] cmd: null @@ -169,10 +169,11 @@ build_info: output: "target/executable/cat_fastq" executable: "target/executable/cat_fastq/cat_fastq" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -194,5 +195,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/cat_fastq/cat_fastq b/target/executable/cat_fastq/cat_fastq index d8deaa7..272e6c8 100755 --- a/target/executable/cat_fastq/cat_fastq +++ b/target/executable/cat_fastq/cat_fastq @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "cat_fastq v0.1.0" + echo "cat_fastq v0.1.1" echo "" echo "Concatenate multiple fastq files" echo "" @@ -472,10 +472,10 @@ function ViashDockerfile { FROM ubuntu:22.04 ENTRYPOINT [] 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:24Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -611,7 +611,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "cat_fastq v0.1.0" + echo "cat_fastq v0.1.1" exit ;; --read_1) @@ -758,7 +758,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/cat_fastq:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/cat_fastq:v0.1.1' fi # print dockerfile diff --git a/target/executable/deseq2_qc/.config.vsh.yaml b/target/executable/deseq2_qc/.config.vsh.yaml index 9e02358..091197d 100644 --- a/target/executable/deseq2_qc/.config.vsh.yaml +++ b/target/executable/deseq2_qc/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "deseq2_qc" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "input" arguments: @@ -207,7 +207,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -239,10 +239,11 @@ build_info: output: "target/executable/deseq2_qc" executable: "target/executable/deseq2_qc/deseq2_qc" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -264,5 +265,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/deseq2_qc/deseq2_qc b/target/executable/deseq2_qc/deseq2_qc index 46469d5..5b21753 100755 --- a/target/executable/deseq2_qc/deseq2_qc +++ b/target/executable/deseq2_qc/deseq2_qc @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "deseq2_qc v0.1.0" + echo "deseq2_qc v0.1.1" echo "" echo "run deseq2, perform pca, generate heatmaps and scatterplots for samples in the" 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")' 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:28Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "deseq2_qc v0.1.0" + echo "deseq2_qc v0.1.1" exit ;; --counts) @@ -831,7 +831,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/deseq2_qc:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/deseq2_qc:v0.1.1' fi # print dockerfile diff --git a/target/executable/dupradar/.config.vsh.yaml b/target/executable/dupradar/.config.vsh.yaml index 7ba30b8..45633c8 100644 --- a/target/executable/dupradar/.config.vsh.yaml +++ b/target/executable/dupradar/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "dupradar" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -244,7 +244,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -266,10 +266,11 @@ build_info: output: "target/executable/dupradar" executable: "target/executable/dupradar/dupradar" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -291,5 +292,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/dupradar/dupradar b/target/executable/dupradar/dupradar index b5ef31a..c95347d 100755 --- a/target/executable/dupradar/dupradar +++ b/target/executable/dupradar/dupradar @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "dupradar v0.1.0" + echo "dupradar v0.1.1" echo "" echo "Assessment of duplication rates in RNA-Seq datasets" 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")' 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:26Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -659,7 +659,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "dupradar v0.1.0" + echo "dupradar v0.1.1" exit ;; --id) @@ -882,7 +882,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/dupradar:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/dupradar:v0.1.1' fi # print dockerfile diff --git a/target/executable/fastqc/.config.vsh.yaml b/target/executable/fastqc/.config.vsh.yaml index 3243d7b..bd0681b 100644 --- a/target/executable/fastqc/.config.vsh.yaml +++ b/target/executable/fastqc/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "fastqc" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -180,7 +180,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -198,10 +198,11 @@ build_info: output: "target/executable/fastqc" executable: "target/executable/fastqc/fastqc" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -223,5 +224,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/fastqc/fastqc b/target/executable/fastqc/fastqc index 14b3083..c701310 100755 --- a/target/executable/fastqc/fastqc +++ b/target/executable/fastqc/fastqc @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "fastqc v0.1.0" + echo "fastqc v0.1.1" echo "" echo "Fastqc component, please see" 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/* 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:25Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -629,7 +629,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "fastqc v0.1.0" + echo "fastqc v0.1.1" exit ;; --paired) @@ -792,7 +792,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/fastqc:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/fastqc:v0.1.1' fi # print dockerfile diff --git a/target/executable/fq_subsample/.config.vsh.yaml b/target/executable/fq_subsample/.config.vsh.yaml index 43fc2ba..e25bf95 100644 --- a/target/executable/fq_subsample/.config.vsh.yaml +++ b/target/executable/fq_subsample/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "fq_subsample" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -153,7 +153,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "docker" @@ -177,10 +177,11 @@ build_info: output: "target/executable/fq_subsample" executable: "target/executable/fq_subsample/fq_subsample" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -202,5 +203,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/fq_subsample/fq_subsample b/target/executable/fq_subsample/fq_subsample index ea89340..9c3c6a0 100755 --- a/target/executable/fq_subsample/fq_subsample +++ b/target/executable/fq_subsample/fq_subsample @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "fq_subsample v0.1.0" + echo "fq_subsample v0.1.1" echo "" 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" @@ -485,10 +485,10 @@ cargo install --locked --path . && \ 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.created="2024-10-04T11:21:41Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:24Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -624,7 +624,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "fq_subsample v0.1.0" + echo "fq_subsample v0.1.1" exit ;; --input) @@ -765,7 +765,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/fq_subsample:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/fq_subsample:v0.1.1' fi # print dockerfile diff --git a/target/executable/getchromsizes/.config.vsh.yaml b/target/executable/getchromsizes/.config.vsh.yaml index 0ab5de3..ec5e543 100644 --- a/target/executable/getchromsizes/.config.vsh.yaml +++ b/target/executable/getchromsizes/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "getchromsizes" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -146,7 +146,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "docker" @@ -167,10 +167,11 @@ build_info: output: "target/executable/getchromsizes" executable: "target/executable/getchromsizes/getchromsizes" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -192,5 +193,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/getchromsizes/getchromsizes b/target/executable/getchromsizes/getchromsizes index 9b49cf8..1c80f46 100755 --- a/target/executable/getchromsizes/getchromsizes +++ b/target/executable/getchromsizes/getchromsizes @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "getchromsizes v0.1.0" + echo "getchromsizes v0.1.1" echo "" echo "Generates a FASTA file of chromosome sizes and a fasta index file." echo "" @@ -480,10 +480,10 @@ make && \ make install 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:23Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -619,7 +619,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "getchromsizes v0.1.0" + echo "getchromsizes v0.1.1" exit ;; --fasta) @@ -754,7 +754,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/getchromsizes:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/getchromsizes:v0.1.1' fi # print dockerfile diff --git a/target/executable/gtf2bed/.config.vsh.yaml b/target/executable/gtf2bed/.config.vsh.yaml index db3ec69..ff7fdbc 100644 --- a/target/executable/gtf2bed/.config.vsh.yaml +++ b/target/executable/gtf2bed/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "gtf2bed" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -127,7 +127,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -145,10 +145,11 @@ build_info: output: "target/executable/gtf2bed" executable: "target/executable/gtf2bed/gtf2bed" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -170,5 +171,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/gtf2bed/gtf2bed b/target/executable/gtf2bed/gtf2bed index e2f9da8..85599c0 100755 --- a/target/executable/gtf2bed/gtf2bed +++ b/target/executable/gtf2bed/gtf2bed @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "gtf2bed v0.1.0" + echo "gtf2bed v0.1.1" echo "" echo "Create BED annotation file from GTF." echo "" @@ -466,10 +466,10 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:24Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -605,7 +605,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "gtf2bed v0.1.0" + echo "gtf2bed v0.1.1" exit ;; --gtf) @@ -718,7 +718,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/gtf2bed:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/gtf2bed:v0.1.1' fi # print dockerfile diff --git a/target/executable/gtf_filter/.config.vsh.yaml b/target/executable/gtf_filter/.config.vsh.yaml index f8b255b..5503f11 100644 --- a/target/executable/gtf_filter/.config.vsh.yaml +++ b/target/executable/gtf_filter/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "gtf_filter" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -142,7 +142,7 @@ engines: id: "docker" image: "python" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" entrypoint: [] cmd: null @@ -155,10 +155,11 @@ build_info: output: "target/executable/gtf_filter" executable: "target/executable/gtf_filter/gtf_filter" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -180,5 +181,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/gtf_filter/gtf_filter b/target/executable/gtf_filter/gtf_filter index 61b6631..f7b1f88 100755 --- a/target/executable/gtf_filter/gtf_filter +++ b/target/executable/gtf_filter/gtf_filter @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "gtf_filter v0.1.0" + echo "gtf_filter v0.1.1" echo "" echo "Filters a GTF file based on sequence names in a FASTA file." echo "" @@ -470,10 +470,10 @@ function ViashDockerfile { FROM python:latest ENTRYPOINT [] 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:27Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -609,7 +609,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "gtf_filter v0.1.0" + echo "gtf_filter v0.1.1" exit ;; --fasta) @@ -738,7 +738,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/gtf_filter:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/gtf_filter:v0.1.1' fi # print dockerfile diff --git a/target/executable/gunzip/.config.vsh.yaml b/target/executable/gunzip/.config.vsh.yaml index c000ae3..0bb49dc 100644 --- a/target/executable/gunzip/.config.vsh.yaml +++ b/target/executable/gunzip/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "gunzip" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -126,7 +126,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -144,10 +144,11 @@ build_info: output: "target/executable/gunzip" executable: "target/executable/gunzip/gunzip" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -169,5 +170,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/gunzip/gunzip b/target/executable/gunzip/gunzip index 2b0d442..9bbb3f9 100755 --- a/target/executable/gunzip/gunzip +++ b/target/executable/gunzip/gunzip @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "gunzip v0.1.0" + echo "gunzip v0.1.1" echo "" echo "Compress or uncompress a file or list of files." echo "" @@ -466,10 +466,10 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:25Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -605,7 +605,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "gunzip v0.1.0" + echo "gunzip v0.1.1" exit ;; --input) @@ -718,7 +718,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/gunzip:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/gunzip:v0.1.1' fi # print dockerfile diff --git a/target/executable/kallisto/kallisto_index/.config.vsh.yaml b/target/executable/kallisto/kallisto_index/.config.vsh.yaml index 3dfe0b9..f38599e 100644 --- a/target/executable/kallisto/kallisto_index/.config.vsh.yaml +++ b/target/executable/kallisto/kallisto_index/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "kallisto_index" namespace: "kallisto" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -135,7 +135,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "docker" @@ -155,10 +155,11 @@ build_info: output: "target/executable/kallisto/kallisto_index" executable: "target/executable/kallisto/kallisto_index/kallisto_index" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -180,5 +181,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/kallisto/kallisto_index/kallisto_index b/target/executable/kallisto/kallisto_index/kallisto_index index b6bd819..31aa1cc 100755 --- a/target/executable/kallisto/kallisto_index/kallisto_index +++ b/target/executable/kallisto/kallisto_index/kallisto_index @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "kallisto_index v0.1.0" + echo "kallisto_index v0.1.1" echo "" echo "Create Kallisto index." echo "" @@ -471,10 +471,10 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \ mv kallisto/kallisto /usr/local/bin/ 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:28Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -610,7 +610,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "kallisto_index v0.1.0" + echo "kallisto_index v0.1.1" exit ;; --transcriptome_fasta) @@ -734,7 +734,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/kallisto/kallisto_index:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/kallisto/kallisto_index:v0.1.1' fi # print dockerfile diff --git a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml index 2ad005e..f55951e 100644 --- a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml +++ b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "kallisto_quant" namespace: "kallisto" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -233,7 +233,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "docker" @@ -253,10 +253,11 @@ build_info: output: "target/executable/kallisto/kallisto_quant" executable: "target/executable/kallisto/kallisto_quant/kallisto_quant" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -278,5 +279,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/kallisto/kallisto_quant/kallisto_quant b/target/executable/kallisto/kallisto_quant/kallisto_quant index 0ad601e..85921d9 100755 --- a/target/executable/kallisto/kallisto_quant/kallisto_quant +++ b/target/executable/kallisto/kallisto_quant/kallisto_quant @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "kallisto_quant v0.1.0" + echo "kallisto_quant v0.1.1" echo "" echo "Computes equivalence classes for reads and quantifies abundances." echo "" @@ -515,10 +515,10 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \ mv kallisto/kallisto /usr/local/bin/ 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:28Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -654,7 +654,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "kallisto_quant v0.1.0" + echo "kallisto_quant v0.1.1" exit ;; --input) @@ -883,7 +883,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/kallisto/kallisto_quant:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/kallisto/kallisto_quant:v0.1.1' fi # print dockerfile diff --git a/target/executable/multiqc_custom_biotype/.config.vsh.yaml b/target/executable/multiqc_custom_biotype/.config.vsh.yaml index 6cecf74..d2a4713 100644 --- a/target/executable/multiqc_custom_biotype/.config.vsh.yaml +++ b/target/executable/multiqc_custom_biotype/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "multiqc_custom_biotype" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -152,7 +152,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -173,10 +173,11 @@ build_info: output: "target/executable/multiqc_custom_biotype" executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -198,5 +199,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/multiqc_custom_biotype/multiqc_custom_biotype b/target/executable/multiqc_custom_biotype/multiqc_custom_biotype index 7557ea5..af30cde 100755 --- a/target/executable/multiqc_custom_biotype/multiqc_custom_biotype +++ b/target/executable/multiqc_custom_biotype/multiqc_custom_biotype @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "multiqc_custom_biotype v0.1.0" + echo "multiqc_custom_biotype v0.1.1" echo "" echo "Calculate features percentage for biotype counts" echo "" @@ -481,10 +481,10 @@ RUN apt-get update && \ RUN pip install --upgrade pip 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:25Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -620,7 +620,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "multiqc_custom_biotype v0.1.0" + echo "multiqc_custom_biotype v0.1.1" exit ;; --biocounts) @@ -766,7 +766,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/multiqc_custom_biotype:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/multiqc_custom_biotype:v0.1.1' fi # print dockerfile diff --git a/target/executable/picard_markduplicates/.config.vsh.yaml b/target/executable/picard_markduplicates/.config.vsh.yaml index 692f42e..da58325 100644 --- a/target/executable/picard_markduplicates/.config.vsh.yaml +++ b/target/executable/picard_markduplicates/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "picard_markduplicates" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -186,7 +186,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "docker" @@ -207,10 +207,11 @@ build_info: output: "target/executable/picard_markduplicates" executable: "target/executable/picard_markduplicates/picard_markduplicates" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -232,5 +233,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/picard_markduplicates/picard_markduplicates b/target/executable/picard_markduplicates/picard_markduplicates index dceadb0..1a4b6f7 100755 --- a/target/executable/picard_markduplicates/picard_markduplicates +++ b/target/executable/picard_markduplicates/picard_markduplicates @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "picard_markduplicates v0.1.0" + echo "picard_markduplicates v0.1.1" echo "" echo "Locate and tag duplicate reads in a BAM file" echo "" @@ -494,10 +494,10 @@ wget --no-check-certificate https://github.com/broadinstitute/picard/releases/do mv picard.jar /usr/local/bin 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:27Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -633,7 +633,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "picard_markduplicates v0.1.0" + echo "picard_markduplicates v0.1.1" exit ;; --bam) @@ -801,7 +801,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/picard_markduplicates:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/picard_markduplicates:v0.1.1' fi # print dockerfile diff --git a/target/executable/prepare_multiqc_input/.config.vsh.yaml b/target/executable/prepare_multiqc_input/.config.vsh.yaml index b373b47..18e79b8 100644 --- a/target/executable/prepare_multiqc_input/.config.vsh.yaml +++ b/target/executable/prepare_multiqc_input/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "prepare_multiqc_input" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -396,7 +396,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" entrypoint: [] cmd: null @@ -409,10 +409,11 @@ build_info: output: "target/executable/prepare_multiqc_input" executable: "target/executable/prepare_multiqc_input/prepare_multiqc_input" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -434,5 +435,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/prepare_multiqc_input/prepare_multiqc_input b/target/executable/prepare_multiqc_input/prepare_multiqc_input index 2d50ef5..e8a1a50 100755 --- a/target/executable/prepare_multiqc_input/prepare_multiqc_input +++ b/target/executable/prepare_multiqc_input/prepare_multiqc_input @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "prepare_multiqc_input v0.1.0" + echo "prepare_multiqc_input v0.1.1" echo "" echo "Prepare directory with all the input files for MultiQC." echo "" @@ -557,10 +557,10 @@ function ViashDockerfile { FROM ubuntu:22.04 ENTRYPOINT [] 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:25Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -696,7 +696,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "prepare_multiqc_input v0.1.0" + echo "prepare_multiqc_input v0.1.1" exit ;; --fail_trimming_multiqc) @@ -1311,7 +1311,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/prepare_multiqc_input:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/prepare_multiqc_input:v0.1.1' fi # print dockerfile diff --git a/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml b/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml index 78194b4..db0a0a0 100644 --- a/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml +++ b/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "preprocess_transcripts_fasta" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -125,7 +125,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" entrypoint: [] cmd: null @@ -138,10 +138,11 @@ build_info: output: "target/executable/preprocess_transcripts_fasta" executable: "target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -163,5 +164,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta b/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta index 7667657..e841321 100755 --- a/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta +++ b/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "preprocess_transcripts_fasta v0.1.0" + echo "preprocess_transcripts_fasta v0.1.1" echo "" echo "Process transcripts FASTA if GTF file is GENOCODE format" echo "" @@ -462,10 +462,10 @@ function ViashDockerfile { FROM ubuntu:22.04 ENTRYPOINT [] 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:24Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -601,7 +601,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "preprocess_transcripts_fasta v0.1.0" + echo "preprocess_transcripts_fasta v0.1.1" exit ;; --transcript_fasta) @@ -714,7 +714,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/preprocess_transcripts_fasta:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/preprocess_transcripts_fasta:v0.1.1' fi # print dockerfile diff --git a/target/executable/preseq_lcextrap/.config.vsh.yaml b/target/executable/preseq_lcextrap/.config.vsh.yaml index 8db2daf..b167402 100644 --- a/target/executable/preseq_lcextrap/.config.vsh.yaml +++ b/target/executable/preseq_lcextrap/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "preseq_lcextrap" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -146,7 +146,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -191,10 +191,11 @@ build_info: output: "target/executable/preseq_lcextrap" executable: "target/executable/preseq_lcextrap/preseq_lcextrap" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -216,5 +217,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/preseq_lcextrap/preseq_lcextrap b/target/executable/preseq_lcextrap/preseq_lcextrap index cc002ac..15bc863 100755 --- a/target/executable/preseq_lcextrap/preseq_lcextrap +++ b/target/executable/preseq_lcextrap/preseq_lcextrap @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "preseq_lcextrap v0.1.0" + echo "preseq_lcextrap v0.1.1" echo "" 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." @@ -495,10 +495,10 @@ mkdir build && cd build && \ make && make install && make HAVE_HTSLIB=1 all 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:25Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -634,7 +634,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "preseq_lcextrap v0.1.0" + echo "preseq_lcextrap v0.1.1" exit ;; --input) @@ -769,7 +769,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/preseq_lcextrap:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/preseq_lcextrap:v0.1.1' fi # print dockerfile diff --git a/target/executable/qualimap/.config.vsh.yaml b/target/executable/qualimap/.config.vsh.yaml index aa517e0..02d14c3 100644 --- a/target/executable/qualimap/.config.vsh.yaml +++ b/target/executable/qualimap/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "qualimap" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -237,7 +237,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -271,10 +271,11 @@ build_info: output: "target/executable/qualimap" executable: "target/executable/qualimap/qualimap" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -296,5 +297,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/qualimap/qualimap b/target/executable/qualimap/qualimap index aa9b76b..86eeba9 100755 --- a/target/executable/qualimap/qualimap +++ b/target/executable/qualimap/qualimap @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "qualimap v0.1.0" + echo "qualimap v0.1.1" echo "" echo "RNA-seq QC analysis using the qualimap" 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")' 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:25Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -676,7 +676,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "qualimap v0.1.0" + echo "qualimap v0.1.1" exit ;; --input) @@ -887,7 +887,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/qualimap:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/qualimap:v0.1.1' fi # print dockerfile diff --git a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml index b68472e..b121548 100644 --- a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml +++ b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "rsem_calculate_expression" namespace: "rsem" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -251,7 +251,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -299,10 +299,11 @@ build_info: output: "target/executable/rsem/rsem_calculate_expression" executable: "target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -324,5 +325,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression index 0379149..0141815 100755 --- a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression +++ b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression @@ -1,6 +1,6 @@ #!/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 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "rsem_calculate_expression v0.1.0" + echo "rsem_calculate_expression v0.1.1" echo "" echo "Calculate expression with RSEM." echo "" @@ -542,10 +542,10 @@ echo 'export PATH=$PATH:/usr/local/bin' >> ~/.bashrc && \ /bin/bash -c "source /etc/profile && source ~/.bashrc && echo $PATH && which STAR" 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:26Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -681,7 +681,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "rsem_calculate_expression v0.1.0" + echo "rsem_calculate_expression v0.1.1" exit ;; --id) @@ -921,7 +921,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rsem/rsem_calculate_expression:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rsem/rsem_calculate_expression:v0.1.1' fi # print dockerfile diff --git a/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml b/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml index b09832a..b27bab1 100644 --- a/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml +++ b/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "rsem_merge_counts" namespace: "rsem" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -169,7 +169,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" entrypoint: [] cmd: null @@ -182,10 +182,11 @@ build_info: output: "target/executable/rsem/rsem_merge_counts" executable: "target/executable/rsem/rsem_merge_counts/rsem_merge_counts" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -207,5 +208,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/rsem/rsem_merge_counts/rsem_merge_counts b/target/executable/rsem/rsem_merge_counts/rsem_merge_counts index a1a6b5a..1b67fa5 100755 --- a/target/executable/rsem/rsem_merge_counts/rsem_merge_counts +++ b/target/executable/rsem/rsem_merge_counts/rsem_merge_counts @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "rsem_merge_counts v0.1.0" + echo "rsem_merge_counts v0.1.1" echo "" echo "Merge the transcript quantification results obtained from rsem" echo "calculate-expression across all samples." @@ -483,10 +483,10 @@ function ViashDockerfile { FROM ubuntu:22.04 ENTRYPOINT [] 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:25Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -622,7 +622,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "rsem_merge_counts v0.1.0" + echo "rsem_merge_counts v0.1.1" exit ;; --counts_gene) @@ -779,7 +779,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rsem/rsem_merge_counts:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rsem/rsem_merge_counts:v0.1.1' fi # print dockerfile diff --git a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml index c09b25e..797f5d4 100644 --- a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "rseqc_bamstat" namespace: "rseqc" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -140,7 +140,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -163,10 +163,11 @@ build_info: output: "target/executable/rseqc/rseqc_bamstat" executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -188,5 +189,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat index 67bb26a..d92f0c5 100755 --- a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat +++ b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "rseqc_bamstat v0.1.0" + echo "rseqc_bamstat v0.1.1" echo "" echo "Generate statistics from a bam file." echo "" @@ -477,10 +477,10 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:27Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -616,7 +616,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "rseqc_bamstat v0.1.0" + echo "rseqc_bamstat v0.1.1" exit ;; --input) @@ -740,7 +740,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rseqc/rseqc_bamstat:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rseqc/rseqc_bamstat:v0.1.1' fi # print dockerfile diff --git a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml index 8a88899..a8f6e3a 100644 --- a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "rseqc_inferexperiment" namespace: "rseqc" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -163,7 +163,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -186,10 +186,11 @@ build_info: output: "target/executable/rseqc/rseqc_inferexperiment" executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -211,5 +212,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment index c2c7cb0..93686fd 100755 --- a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment +++ b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "rseqc_inferexperiment v0.1.0" + echo "rseqc_inferexperiment v0.1.1" echo "" echo "Infer strandedness from sequencing reads" echo "" @@ -487,10 +487,10 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:29Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -626,7 +626,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "rseqc_inferexperiment v0.1.0" + echo "rseqc_inferexperiment v0.1.1" exit ;; --input) @@ -772,7 +772,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rseqc/rseqc_inferexperiment:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rseqc/rseqc_inferexperiment:v0.1.1' fi # print dockerfile diff --git a/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml b/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml index 106fd6f..dc5ec7d 100644 --- a/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "rseqc_innerdistance" namespace: "rseqc" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -248,7 +248,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -272,10 +272,11 @@ build_info: output: "target/executable/rseqc/rseqc_innerdistance" executable: "target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -297,5 +298,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance b/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance index 43f421f..da42e7c 100755 --- a/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance +++ b/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "rseqc_innerdistance v0.1.0" + echo "rseqc_innerdistance v0.1.1" echo "" echo "Calculate inner distance between read pairs." echo "" @@ -529,10 +529,10 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:29Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -668,7 +668,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "rseqc_innerdistance v0.1.0" + echo "rseqc_innerdistance v0.1.1" exit ;; --input) @@ -891,7 +891,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rseqc/rseqc_innerdistance:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rseqc/rseqc_innerdistance:v0.1.1' fi # print dockerfile diff --git a/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml b/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml index fb743ed..4c65464 100644 --- a/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "rseqc_junctionannotation" namespace: "rseqc" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -236,7 +236,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -260,10 +260,11 @@ build_info: output: "target/executable/rseqc/rseqc_junctionannotation" executable: "target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -285,5 +286,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation b/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation index 8602fb7..56de435 100755 --- a/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation +++ b/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "rseqc_junctionannotation v0.1.0" + echo "rseqc_junctionannotation v0.1.1" echo "" echo "Compare detected splice junctions to reference gene model." echo "" @@ -519,10 +519,10 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:30Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -658,7 +658,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "rseqc_junctionannotation v0.1.0" + echo "rseqc_junctionannotation v0.1.1" exit ;; --input) @@ -870,7 +870,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rseqc/rseqc_junctionannotation:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rseqc/rseqc_junctionannotation:v0.1.1' fi # print dockerfile diff --git a/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml b/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml index c177ff4..e24a422 100644 --- a/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "rseqc_junctionsaturation" namespace: "rseqc" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -225,7 +225,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -249,10 +249,11 @@ build_info: output: "target/executable/rseqc/rseqc_junctionsaturation" executable: "target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -274,5 +275,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation b/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation index ec0cd42..c16b749 100755 --- a/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation +++ b/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "rseqc_junctionsaturation v0.1.0" + echo "rseqc_junctionsaturation v0.1.1" echo "" echo "Compare detected splice junctions to reference gene model." echo "" @@ -522,10 +522,10 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:27Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -661,7 +661,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "rseqc_junctionsaturation v0.1.0" + echo "rseqc_junctionsaturation v0.1.1" exit ;; --input) @@ -862,7 +862,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rseqc/rseqc_junctionsaturation:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rseqc/rseqc_junctionsaturation:v0.1.1' fi # print dockerfile diff --git a/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml b/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml index 68ee8bf..8e3570a 100644 --- a/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "rseqc_readdistribution" namespace: "rseqc" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -139,7 +139,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -162,10 +162,11 @@ build_info: output: "target/executable/rseqc/rseqc_readdistribution" executable: "target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -187,5 +188,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution b/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution index f72e0d3..f40ba33 100755 --- a/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution +++ b/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "rseqc_readdistribution v0.1.0" + echo "rseqc_readdistribution v0.1.1" echo "" echo "Calculate how mapped reads are distributed over genomic features." echo "" @@ -474,10 +474,10 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:28Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -613,7 +613,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "rseqc_readdistribution v0.1.0" + echo "rseqc_readdistribution v0.1.1" exit ;; --input) @@ -737,7 +737,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rseqc/rseqc_readdistribution:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rseqc/rseqc_readdistribution:v0.1.1' fi # print dockerfile diff --git a/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml b/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml index e424662..5d61374 100644 --- a/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "rseqc_readduplication" namespace: "rseqc" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -187,7 +187,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -211,10 +211,11 @@ build_info: output: "target/executable/rseqc/rseqc_readduplication" executable: "target/executable/rseqc/rseqc_readduplication/rseqc_readduplication" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -236,5 +237,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication b/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication index 524fb58..3c10b29 100755 --- a/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication +++ b/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "rseqc_readduplication v0.1.0" + echo "rseqc_readduplication v0.1.1" echo "" echo "Calculate read duplication rate." echo "" @@ -499,10 +499,10 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:26Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -638,7 +638,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "rseqc_readduplication v0.1.0" + echo "rseqc_readduplication v0.1.1" exit ;; --input) @@ -806,7 +806,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rseqc/rseqc_readduplication:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rseqc/rseqc_readduplication:v0.1.1' fi # print dockerfile diff --git a/target/executable/rseqc/rseqc_tin/.config.vsh.yaml b/target/executable/rseqc/rseqc_tin/.config.vsh.yaml index acf9174..c7bb08c 100644 --- a/target/executable/rseqc/rseqc_tin/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_tin/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "rseqc_tin" namespace: "rseqc" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -193,7 +193,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -214,10 +214,11 @@ build_info: output: "target/executable/rseqc/rseqc_tin" executable: "target/executable/rseqc/rseqc_tin/rseqc_tin" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -239,5 +240,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/rseqc/rseqc_tin/rseqc_tin b/target/executable/rseqc/rseqc_tin/rseqc_tin index 61ef225..c617606 100755 --- a/target/executable/rseqc/rseqc_tin/rseqc_tin +++ b/target/executable/rseqc/rseqc_tin/rseqc_tin @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "rseqc_tin v0.1.0" + echo "rseqc_tin v0.1.1" echo "" echo "Calculte TIN (transcript integrity number) from RNA-seq reads" echo "" @@ -501,10 +501,10 @@ RUN apt-get update && \ RUN pip3 install RSeQC 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:29Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -640,7 +640,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "rseqc_tin v0.1.0" + echo "rseqc_tin v0.1.1" exit ;; --bam_input) @@ -813,7 +813,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rseqc/rseqc_tin:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rseqc/rseqc_tin:v0.1.1' fi # print dockerfile diff --git a/target/executable/sortmerna/.config.vsh.yaml b/target/executable/sortmerna/.config.vsh.yaml index aad80d2..62268b7 100644 --- a/target/executable/sortmerna/.config.vsh.yaml +++ b/target/executable/sortmerna/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "sortmerna" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -179,7 +179,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "docker" @@ -198,10 +198,11 @@ build_info: output: "target/executable/sortmerna" executable: "target/executable/sortmerna/sortmerna" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -223,5 +224,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/sortmerna/sortmerna b/target/executable/sortmerna/sortmerna index c9a6ef7..c5fc435 100755 --- a/target/executable/sortmerna/sortmerna +++ b/target/executable/sortmerna/sortmerna @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "sortmerna v0.1.0" + echo "sortmerna v0.1.1" echo "" echo "Local sequence alignment tool for filtering, mapping and clustering. The main" 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 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:25Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -631,7 +631,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "sortmerna v0.1.0" + echo "sortmerna v0.1.1" exit ;; --paired) @@ -794,7 +794,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/sortmerna:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/sortmerna:v0.1.1' fi # print dockerfile diff --git a/target/executable/stringtie/.config.vsh.yaml b/target/executable/stringtie/.config.vsh.yaml index 7a58393..cbb5488 100644 --- a/target/executable/stringtie/.config.vsh.yaml +++ b/target/executable/stringtie/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "stringtie" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -196,7 +196,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "docker" @@ -216,10 +216,11 @@ build_info: output: "target/executable/stringtie" executable: "target/executable/stringtie/stringtie" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -241,5 +242,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/stringtie/stringtie b/target/executable/stringtie/stringtie index dee6930..73439d6 100755 --- a/target/executable/stringtie/stringtie +++ b/target/executable/stringtie/stringtie @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "stringtie v0.1.0" + echo "stringtie v0.1.1" echo "" echo "Transcript assembly and quantification for RNA-Seq" 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/ 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:26Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -635,7 +635,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "stringtie v0.1.0" + echo "stringtie v0.1.1" exit ;; --strandedness) @@ -825,7 +825,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/stringtie:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/stringtie:v0.1.1' fi # print dockerfile diff --git a/target/executable/summarizedexperiment/.config.vsh.yaml b/target/executable/summarizedexperiment/.config.vsh.yaml index 9187b55..3ad6cab 100644 --- a/target/executable/summarizedexperiment/.config.vsh.yaml +++ b/target/executable/summarizedexperiment/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "summarizedexperiment" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -175,7 +175,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -199,10 +199,11 @@ build_info: output: "target/executable/summarizedexperiment" executable: "target/executable/summarizedexperiment/summarizedexperiment" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -224,5 +225,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/summarizedexperiment/summarizedexperiment b/target/executable/summarizedexperiment/summarizedexperiment index 0be8cc8..26dc0ce 100755 --- a/target/executable/summarizedexperiment/summarizedexperiment +++ b/target/executable/summarizedexperiment/summarizedexperiment @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "summarizedexperiment v0.1.0" + echo "summarizedexperiment v0.1.1" echo "" echo "Create SummarizedExperiment object from Salmon counts" 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")' 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:24Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -626,7 +626,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "summarizedexperiment v0.1.0" + echo "summarizedexperiment v0.1.1" exit ;; --tpm_gene) @@ -805,7 +805,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/summarizedexperiment:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/summarizedexperiment:v0.1.1' fi # print dockerfile diff --git a/target/executable/trimgalore/.config.vsh.yaml b/target/executable/trimgalore/.config.vsh.yaml index f18c6ab..bf00bb4 100644 --- a/target/executable/trimgalore/.config.vsh.yaml +++ b/target/executable/trimgalore/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "trimgalore" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -770,7 +770,7 @@ engines: id: "docker" image: "quay.io/biocontainers/trim-galore:0.6.9--hdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "docker" @@ -788,10 +788,11 @@ build_info: output: "target/executable/trimgalore" executable: "target/executable/trimgalore/trimgalore" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -813,5 +814,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/trimgalore/trimgalore b/target/executable/trimgalore/trimgalore index 55a9c9b..6d29722 100755 --- a/target/executable/trimgalore/trimgalore +++ b/target/executable/trimgalore/trimgalore @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "trimgalore v0.1.0" + echo "trimgalore v0.1.1" echo "" echo "A wrapper tool around Cutadapt and FastQC to consistently apply quality and" 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 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.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -997,7 +997,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "trimgalore v0.1.0" + echo "trimgalore v0.1.1" exit ;; --input) @@ -1725,7 +1725,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/trimgalore:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/trimgalore:v0.1.1' fi # print dockerfile diff --git a/target/executable/tx2gene/.config.vsh.yaml b/target/executable/tx2gene/.config.vsh.yaml index bbcf4e9..0d0f307 100644 --- a/target/executable/tx2gene/.config.vsh.yaml +++ b/target/executable/tx2gene/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "tx2gene" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -170,7 +170,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -192,10 +192,11 @@ build_info: output: "target/executable/tx2gene" executable: "target/executable/tx2gene/tx2gene" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -217,5 +218,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/tx2gene/tx2gene b/target/executable/tx2gene/tx2gene index 9f65bf4..f5a061d 100755 --- a/target/executable/tx2gene/tx2gene +++ b/target/executable/tx2gene/tx2gene @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "tx2gene v0.1.0" + echo "tx2gene v0.1.1" echo "" echo "Get transcript id (tx) to gene names for tximport" echo "" @@ -487,10 +487,10 @@ RUN apt-get update && \ RUN pip install --upgrade pip 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:26Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -626,7 +626,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "tx2gene v0.1.0" + echo "tx2gene v0.1.1" exit ;; --quant_results) @@ -800,7 +800,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/tx2gene:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/tx2gene:v0.1.1' fi # print dockerfile diff --git a/target/executable/tximport/.config.vsh.yaml b/target/executable/tximport/.config.vsh.yaml index 4768b40..c29da73 100644 --- a/target/executable/tximport/.config.vsh.yaml +++ b/target/executable/tximport/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "tximport" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -218,7 +218,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -247,10 +247,11 @@ build_info: output: "target/executable/tximport" executable: "target/executable/tximport/tximport" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -272,5 +273,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/tximport/tximport b/target/executable/tximport/tximport index 2c70ae7..847b16b 100755 --- a/target/executable/tximport/tximport +++ b/target/executable/tximport/tximport @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "tximport v0.1.0" + echo "tximport v0.1.1" echo "" echo "Get dataframe linking transcript ID, gene ID, and gene name" 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")' 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:24Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -647,7 +647,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "tximport v0.1.0" + echo "tximport v0.1.1" exit ;; --quant_results) @@ -865,7 +865,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/tximport:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/tximport:v0.1.1' fi # print dockerfile diff --git a/target/executable/ucsc/bedclip/.config.vsh.yaml b/target/executable/ucsc/bedclip/.config.vsh.yaml index beea8cc..0c055e4 100644 --- a/target/executable/ucsc/bedclip/.config.vsh.yaml +++ b/target/executable/ucsc/bedclip/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedclip" namespace: "ucsc" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -141,7 +141,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -164,10 +164,11 @@ build_info: output: "target/executable/ucsc/bedclip" executable: "target/executable/ucsc/bedclip/bedclip" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -189,5 +190,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/ucsc/bedclip/bedclip b/target/executable/ucsc/bedclip/bedclip index a2a15ef..66081df 100755 --- a/target/executable/ucsc/bedclip/bedclip +++ b/target/executable/ucsc/bedclip/bedclip @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "bedclip v0.1.0" + echo "bedclip v0.1.1" echo "" echo "Remove lines from bed file that refer to off-chromosome locations" 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/ 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:28Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -612,7 +612,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bedclip v0.1.0" + echo "bedclip v0.1.1" exit ;; --input_bedgraph) @@ -736,7 +736,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/ucsc/bedclip:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/ucsc/bedclip:v0.1.1' fi # print dockerfile diff --git a/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml b/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml index 6dfcdd4..319c071 100644 --- a/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml +++ b/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedgraphtobigwig" namespace: "ucsc" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -141,7 +141,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -164,10 +164,11 @@ build_info: output: "target/executable/ucsc/bedgraphtobigwig" executable: "target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -189,5 +190,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig b/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig index cbc88fa..c6b7743 100755 --- a/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig +++ b/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "bedgraphtobigwig v0.1.0" + echo "bedgraphtobigwig v0.1.1" echo "" echo "Convert a bedGraph file to bigWig format" 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/ 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.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:29Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -612,7 +612,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "bedgraphtobigwig v0.1.0" + echo "bedgraphtobigwig v0.1.1" exit ;; --bedgraph) @@ -736,7 +736,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/ucsc/bedgraphtobigwig:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/ucsc/bedgraphtobigwig:v0.1.1' fi # print dockerfile diff --git a/target/executable/umitools/umitools_dedup/.config.vsh.yaml b/target/executable/umitools/umitools_dedup/.config.vsh.yaml index 980dabb..dd88018 100644 --- a/target/executable/umitools/umitools_dedup/.config.vsh.yaml +++ b/target/executable/umitools/umitools_dedup/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "umitools_dedup" namespace: "umitools" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -172,7 +172,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -195,10 +195,11 @@ build_info: output: "target/executable/umitools/umitools_dedup" executable: "target/executable/umitools/umitools_dedup/umitools_dedup" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -220,5 +221,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/umitools/umitools_dedup/umitools_dedup b/target/executable/umitools/umitools_dedup/umitools_dedup index 66abf8a..26b59e6 100755 --- a/target/executable/umitools/umitools_dedup/umitools_dedup +++ b/target/executable/umitools/umitools_dedup/umitools_dedup @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "umitools_dedup v0.1.0" + echo "umitools_dedup v0.1.1" echo "" echo "Deduplicate reads based on the mapping co-ordinate and the UMI attached to the" echo "read." @@ -489,10 +489,10 @@ RUN pip install --upgrade pip && \ 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.created="2024-10-04T11:21:56Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:28Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -628,7 +628,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "umitools_dedup v0.1.0" + echo "umitools_dedup v0.1.1" exit ;; --paired) @@ -785,7 +785,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/umitools/umitools_dedup:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/umitools/umitools_dedup:v0.1.1' fi # print dockerfile diff --git a/target/executable/umitools/umitools_extract/.config.vsh.yaml b/target/executable/umitools/umitools_extract/.config.vsh.yaml index 0796b28..23f39cf 100644 --- a/target/executable/umitools/umitools_extract/.config.vsh.yaml +++ b/target/executable/umitools/umitools_extract/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "umitools_extract" namespace: "umitools" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -230,7 +230,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -253,10 +253,11 @@ build_info: output: "target/executable/umitools/umitools_extract" executable: "target/executable/umitools/umitools_extract/umitools_extract" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -278,5 +279,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/umitools/umitools_extract/umitools_extract b/target/executable/umitools/umitools_extract/umitools_extract index 7d8fbab..af52d24 100755 --- a/target/executable/umitools/umitools_extract/umitools_extract +++ b/target/executable/umitools/umitools_extract/umitools_extract @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "umitools_extract v0.1.0" + echo "umitools_extract v0.1.1" echo "" 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" @@ -521,10 +521,10 @@ RUN pip install --upgrade pip && \ 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.created="2024-10-04T11:21:56Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:28Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -660,7 +660,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "umitools_extract v0.1.0" + echo "umitools_extract v0.1.1" exit ;; --paired) @@ -862,7 +862,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/umitools/umitools_extract:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/umitools/umitools_extract:v0.1.1' fi # print dockerfile diff --git a/target/executable/umitools_prepareforquant/.config.vsh.yaml b/target/executable/umitools_prepareforquant/.config.vsh.yaml index 028c4c4..8994ebe 100644 --- a/target/executable/umitools_prepareforquant/.config.vsh.yaml +++ b/target/executable/umitools_prepareforquant/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "umitools_prepareforquant" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -132,7 +132,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -156,10 +156,11 @@ build_info: output: "target/executable/umitools_prepareforquant" executable: "target/executable/umitools_prepareforquant/umitools_prepareforquant" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -181,5 +182,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/umitools_prepareforquant/umitools_prepareforquant b/target/executable/umitools_prepareforquant/umitools_prepareforquant index 5e6ba9b..5170883 100755 --- a/target/executable/umitools_prepareforquant/umitools_prepareforquant +++ b/target/executable/umitools_prepareforquant/umitools_prepareforquant @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "umitools_prepareforquant v0.1.0" + echo "umitools_prepareforquant v0.1.1" echo "" echo "Fix paired-end reads in name sorted BAM file to prepare for salmon" echo "quantification" @@ -473,10 +473,10 @@ RUN pip install --upgrade pip && \ 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.created="2024-10-04T11:21:58Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" -LABEL org.opencontainers.image.version="v0.1.0" +LABEL org.opencontainers.image.created="2024-10-17T16:18:27Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518" +LABEL org.opencontainers.image.version="v0.1.1" VIASHDOCKER fi @@ -612,7 +612,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "umitools_prepareforquant v0.1.0" + echo "umitools_prepareforquant v0.1.1" exit ;; --bam) @@ -736,7 +736,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/umitools_prepareforquant:v0.1.0' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/umitools_prepareforquant:v0.1.1' fi # print dockerfile diff --git a/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml b/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml index fb82133..0305d5f 100644 --- a/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml +++ b/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "genome_alignment_and_quant" namespace: "workflows" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -603,8 +603,8 @@ build_info: output: "target/executable/workflows/genome_alignment_and_quant" executable: "target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort" @@ -617,7 +617,8 @@ build_info: - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant" - "target/nextflow/rsem/rsem_calculate_expression" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -639,5 +640,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant b/target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant index b32dfec..c5469b7 100755 --- a/target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant +++ b/target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "genome_alignment_and_quant v0.1.0" + echo "genome_alignment_and_quant v0.1.1" echo "" echo "A viash sub-workflow for genome alignment and quantification stage of" echo "nf-core/rnaseq pipeline." @@ -401,7 +401,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "genome_alignment_and_quant v0.1.0" + echo "genome_alignment_and_quant v0.1.1" exit ;; --id) diff --git a/target/executable/workflows/merge_quant_results/.config.vsh.yaml b/target/executable/workflows/merge_quant_results/.config.vsh.yaml index 0087009..93b8ca3 100644 --- a/target/executable/workflows/merge_quant_results/.config.vsh.yaml +++ b/target/executable/workflows/merge_quant_results/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "merge_quant_results" namespace: "workflows" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -278,14 +278,15 @@ build_info: output: "target/executable/workflows/merge_quant_results" executable: "target/executable/workflows/merge_quant_results/merge_quant_results" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/tx2gene" - "target/nextflow/tximport" - "target/nextflow/summarizedexperiment" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -307,5 +308,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/workflows/merge_quant_results/merge_quant_results b/target/executable/workflows/merge_quant_results/merge_quant_results index 9a61c8c..65850b5 100755 --- a/target/executable/workflows/merge_quant_results/merge_quant_results +++ b/target/executable/workflows/merge_quant_results/merge_quant_results @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "merge_quant_results v0.1.0" + echo "merge_quant_results v0.1.1" echo "" echo "A sub-workflow to merge the counts obtained from salmon quant across all" echo "samples." @@ -267,7 +267,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "merge_quant_results v0.1.0" + echo "merge_quant_results v0.1.1" exit ;; --salmon_quant_results) diff --git a/target/executable/workflows/post_processing/.config.vsh.yaml b/target/executable/workflows/post_processing/.config.vsh.yaml index 2c7937a..6030b24 100644 --- a/target/executable/workflows/post_processing/.config.vsh.yaml +++ b/target/executable/workflows/post_processing/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "post_processing" namespace: "workflows" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -486,8 +486,8 @@ build_info: output: "target/executable/workflows/post_processing" executable: "target/executable/workflows/post_processing/post_processing" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/picard_markduplicates" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort" @@ -500,7 +500,8 @@ build_info: - "target/nextflow/ucsc/bedclip" - "target/nextflow/ucsc/bedgraphtobigwig" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -522,5 +523,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/workflows/post_processing/post_processing b/target/executable/workflows/post_processing/post_processing index f564fc9..8b91020 100755 --- a/target/executable/workflows/post_processing/post_processing +++ b/target/executable/workflows/post_processing/post_processing @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "post_processing v0.1.0" + echo "post_processing v0.1.1" echo "" echo "A viash sub-workflow for the post-processing stage of nf-core/rnaseq pipeline." echo "" @@ -350,7 +350,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "post_processing v0.1.0" + echo "post_processing v0.1.1" exit ;; --id) diff --git a/target/executable/workflows/pre_processing/.config.vsh.yaml b/target/executable/workflows/pre_processing/.config.vsh.yaml index 1dc571c..6b4bd55 100644 --- a/target/executable/workflows/pre_processing/.config.vsh.yaml +++ b/target/executable/workflows/pre_processing/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "pre_processing" namespace: "workflows" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Inputs" arguments: @@ -673,8 +673,8 @@ build_info: output: "target/executable/workflows/pre_processing" executable: "target/executable/workflows/pre_processing/pre_processing" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/fastqc" - "target/nextflow/umitools/umitools_extract" @@ -686,7 +686,8 @@ build_info: - "target/nextflow/fq_subsample" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -708,5 +709,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/workflows/pre_processing/pre_processing b/target/executable/workflows/pre_processing/pre_processing index 716f5b6..c84b65d 100755 --- a/target/executable/workflows/pre_processing/pre_processing +++ b/target/executable/workflows/pre_processing/pre_processing @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "pre_processing v0.1.0" + echo "pre_processing v0.1.1" echo "" echo "A subworkflow for the pre-processing stage of the nf-core/rnaseq pipeline." echo "" @@ -453,7 +453,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "pre_processing v0.1.0" + echo "pre_processing v0.1.1" exit ;; --id) diff --git a/target/executable/workflows/prepare_genome/.config.vsh.yaml b/target/executable/workflows/prepare_genome/.config.vsh.yaml index 6d91481..f349d97 100644 --- a/target/executable/workflows/prepare_genome/.config.vsh.yaml +++ b/target/executable/workflows/prepare_genome/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "prepare_genome" namespace: "workflows" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -496,8 +496,8 @@ build_info: output: "target/executable/workflows/prepare_genome" executable: "target/executable/workflows/prepare_genome/prepare_genome" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/gunzip" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread" @@ -513,7 +513,8 @@ build_info: - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index" - "target/nextflow/kallisto/kallisto_index" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -535,5 +536,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/workflows/prepare_genome/prepare_genome b/target/executable/workflows/prepare_genome/prepare_genome index 0cfe7e8..b905405 100755 --- a/target/executable/workflows/prepare_genome/prepare_genome +++ b/target/executable/workflows/prepare_genome/prepare_genome @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "prepare_genome v0.1.0" + echo "prepare_genome v0.1.1" echo "" echo "A subworkflow for preparing all the required genome references" echo "" @@ -354,7 +354,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "prepare_genome v0.1.0" + echo "prepare_genome v0.1.1" exit ;; --fasta) diff --git a/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml b/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml index 9d3df69..4923af5 100644 --- a/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml +++ b/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "pseudo_alignment_and_quant" namespace: "workflows" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -283,13 +283,14 @@ build_info: output: "target/executable/workflows/pseudo_alignment_and_quant" executable: "target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant" - "target/nextflow/kallisto/kallisto_quant" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -311,5 +312,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant b/target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant index 039580f..7d90e7b 100755 --- a/target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant +++ b/target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "pseudo_alignment_and_quant v0.1.0" + echo "pseudo_alignment_and_quant v0.1.1" echo "" echo "A viash sub-workflow for pseudo alignment and quantification stage of" echo "nf-core/rnaseq pipeline." @@ -279,7 +279,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "pseudo_alignment_and_quant v0.1.0" + echo "pseudo_alignment_and_quant v0.1.1" exit ;; --id) diff --git a/target/executable/workflows/quality_control/.config.vsh.yaml b/target/executable/workflows/quality_control/.config.vsh.yaml index 22a2110..bc435c8 100644 --- a/target/executable/workflows/quality_control/.config.vsh.yaml +++ b/target/executable/workflows/quality_control/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "quality_control" namespace: "workflows" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -1596,8 +1596,8 @@ build_info: output: "target/executable/workflows/quality_control" executable: "target/executable/workflows/quality_control/quality_control" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/rseqc/rseqc_bamstat" - "target/nextflow/rseqc/rseqc_inferexperiment" @@ -1618,7 +1618,8 @@ build_info: - "target/nextflow/rsem/rsem_merge_counts" - "target/nextflow/workflows/merge_quant_results" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -1640,5 +1641,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/workflows/quality_control/quality_control b/target/executable/workflows/quality_control/quality_control index 172bd6f..6fe832f 100755 --- a/target/executable/workflows/quality_control/quality_control +++ b/target/executable/workflows/quality_control/quality_control @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "quality_control v0.1.0" + echo "quality_control v0.1.1" echo "" echo "A subworkflow for the final quality control stage of the nf-core/rnaseq" echo "pipeline." @@ -834,7 +834,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "quality_control v0.1.0" + echo "quality_control v0.1.1" exit ;; --id) diff --git a/target/executable/workflows/rnaseq/.config.vsh.yaml b/target/executable/workflows/rnaseq/.config.vsh.yaml index 79c02d5..b6e5004 100644 --- a/target/executable/workflows/rnaseq/.config.vsh.yaml +++ b/target/executable/workflows/rnaseq/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "rnaseq" namespace: "workflows" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -2117,8 +2117,8 @@ build_info: output: "target/executable/workflows/rnaseq" executable: "target/executable/workflows/rnaseq/rnaseq" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/workflows/prepare_genome" - "target/nextflow/cat_fastq" @@ -2128,7 +2128,8 @@ build_info: - "target/nextflow/workflows/post_processing" - "target/nextflow/workflows/quality_control" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -2150,5 +2151,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/executable/workflows/rnaseq/rnaseq b/target/executable/workflows/rnaseq/rnaseq index f823219..0b1b939 100755 --- a/target/executable/workflows/rnaseq/rnaseq +++ b/target/executable/workflows/rnaseq/rnaseq @@ -1,6 +1,6 @@ #!/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 # 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 function ViashHelp { - echo "rnaseq v0.1.0" + echo "rnaseq v0.1.1" echo "" echo "A viash workflow for the nf-core/rnaseq pipeline." echo "" @@ -1093,7 +1093,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "rnaseq v0.1.0" + echo "rnaseq v0.1.1" exit ;; --id) diff --git a/target/nextflow/bbmap_bbsplit/.config.vsh.yaml b/target/nextflow/bbmap_bbsplit/.config.vsh.yaml index 1a9a98e..22c161c 100644 --- a/target/nextflow/bbmap_bbsplit/.config.vsh.yaml +++ b/target/nextflow/bbmap_bbsplit/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "bbmap_bbsplit" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -219,7 +219,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "docker" @@ -238,10 +238,11 @@ build_info: output: "target/nextflow/bbmap_bbsplit" executable: "target/nextflow/bbmap_bbsplit/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -263,5 +264,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/nextflow/bbmap_bbsplit/main.nf b/target/nextflow/bbmap_bbsplit/main.nf index 33a4455..43db1fb 100644 --- a/target/nextflow/bbmap_bbsplit/main.nf +++ b/target/nextflow/bbmap_bbsplit/main.nf @@ -1,4 +1,4 @@ -// 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 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2805,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "bbmap_bbsplit", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3082,7 +3082,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3104,11 +3104,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/bbmap_bbsplit", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3138,7 +3139,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3611,8 +3612,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/bbmap_bbsplit", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/bbmap_bbsplit", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/bbmap_bbsplit/nextflow.config b/target/nextflow/bbmap_bbsplit/nextflow.config index c9eaaea..9516b72 100644 --- a/target/nextflow/bbmap_bbsplit/nextflow.config +++ b/target/nextflow/bbmap_bbsplit/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'bbmap_bbsplit' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Split sequencing reads by mapping them to multiple references simultaneously.\n' } diff --git a/target/nextflow/bedtools_genomecov/.config.vsh.yaml b/target/nextflow/bedtools_genomecov/.config.vsh.yaml index 04a60d9..91c57af 100644 --- a/target/nextflow/bedtools_genomecov/.config.vsh.yaml +++ b/target/nextflow/bedtools_genomecov/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "bedtools_genomecov" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -159,7 +159,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "docker" @@ -178,10 +178,11 @@ build_info: output: "target/nextflow/bedtools_genomecov" executable: "target/nextflow/bedtools_genomecov/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -203,5 +204,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.1'" organization: "vsh" diff --git a/target/nextflow/bedtools_genomecov/main.nf b/target/nextflow/bedtools_genomecov/main.nf index 579f21a..ab234d1 100644 --- a/target/nextflow/bedtools_genomecov/main.nf +++ b/target/nextflow/bedtools_genomecov/main.nf @@ -1,4 +1,4 @@ -// bedtools_genomecov v0.1.0 +// bedtools_genomecov v0.1.1 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2805,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "bedtools_genomecov", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3009,7 +3009,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3031,11 +3031,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/bedtools_genomecov", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3065,7 +3066,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3493,8 +3494,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/bedtools_genomecov", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/bedtools_genomecov", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/bedtools_genomecov/nextflow.config b/target/nextflow/bedtools_genomecov/nextflow.config index 5e6c346..0af6e7f 100644 --- a/target/nextflow/bedtools_genomecov/nextflow.config +++ b/target/nextflow/bedtools_genomecov/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'bedtools_genomecov' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Compute BEDGRAPH (-bg) summaries of feature coverage' } diff --git a/target/nextflow/cat_additional_fasta/.config.vsh.yaml b/target/nextflow/cat_additional_fasta/.config.vsh.yaml index a8cd394..57df28d 100644 --- a/target/nextflow/cat_additional_fasta/.config.vsh.yaml +++ b/target/nextflow/cat_additional_fasta/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "cat_additional_fasta" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -169,7 +169,7 @@ engines: id: "docker" image: "python" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" entrypoint: [] cmd: null @@ -182,10 +182,11 @@ build_info: output: "target/nextflow/cat_additional_fasta" executable: "target/nextflow/cat_additional_fasta/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -207,5 +208,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/nextflow/cat_additional_fasta/main.nf b/target/nextflow/cat_additional_fasta/main.nf index 9825abe..5b05adc 100644 --- a/target/nextflow/cat_additional_fasta/main.nf +++ b/target/nextflow/cat_additional_fasta/main.nf @@ -1,4 +1,4 @@ -// 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 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2805,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "cat_additional_fasta", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3018,7 +3018,7 @@ meta = [ "id" : "docker", "image" : "python", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/" }, { @@ -3032,11 +3032,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/cat_additional_fasta", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3066,7 +3067,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3544,8 +3545,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/cat_additional_fasta", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/cat_additional_fasta", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/cat_additional_fasta/nextflow.config b/target/nextflow/cat_additional_fasta/nextflow.config index c1df99a..c0efdc2 100644 --- a/target/nextflow/cat_additional_fasta/nextflow.config +++ b/target/nextflow/cat_additional_fasta/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'cat_additional_fasta' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Concatenate addional fasta file to reference FASTA and GTF files.\n' } diff --git a/target/nextflow/cat_fastq/.config.vsh.yaml b/target/nextflow/cat_fastq/.config.vsh.yaml index 93b3f8c..3c5aa6d 100644 --- a/target/nextflow/cat_fastq/.config.vsh.yaml +++ b/target/nextflow/cat_fastq/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "cat_fastq" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -156,7 +156,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" entrypoint: [] cmd: null @@ -169,10 +169,11 @@ build_info: output: "target/nextflow/cat_fastq" executable: "target/nextflow/cat_fastq/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -194,5 +195,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.1'" organization: "vsh" diff --git a/target/nextflow/cat_fastq/main.nf b/target/nextflow/cat_fastq/main.nf index c650041..0f601da 100644 --- a/target/nextflow/cat_fastq/main.nf +++ b/target/nextflow/cat_fastq/main.nf @@ -1,4 +1,4 @@ -// cat_fastq v0.1.0 +// cat_fastq v0.1.1 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2805,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "cat_fastq", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3009,7 +3009,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/" }, { @@ -3023,11 +3023,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/cat_fastq", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3057,7 +3058,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3479,8 +3480,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/cat_fastq", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/cat_fastq", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/cat_fastq/nextflow.config b/target/nextflow/cat_fastq/nextflow.config index 8ccc791..eb5a388 100644 --- a/target/nextflow/cat_fastq/nextflow.config +++ b/target/nextflow/cat_fastq/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'cat_fastq' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Concatenate multiple fastq files' } diff --git a/target/nextflow/deseq2_qc/.config.vsh.yaml b/target/nextflow/deseq2_qc/.config.vsh.yaml index 0126dfd..88498e3 100644 --- a/target/nextflow/deseq2_qc/.config.vsh.yaml +++ b/target/nextflow/deseq2_qc/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "deseq2_qc" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "input" arguments: @@ -207,7 +207,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -239,10 +239,11 @@ build_info: output: "target/nextflow/deseq2_qc" executable: "target/nextflow/deseq2_qc/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -264,5 +265,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/nextflow/deseq2_qc/main.nf b/target/nextflow/deseq2_qc/main.nf index 61dbf77..f702f37 100644 --- a/target/nextflow/deseq2_qc/main.nf +++ b/target/nextflow/deseq2_qc/main.nf @@ -1,4 +1,4 @@ -// 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 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2805,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "deseq2_qc", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "input", @@ -3070,7 +3070,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3112,11 +3112,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/deseq2_qc", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3146,7 +3147,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3601,8 +3602,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/deseq2_qc", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/deseq2_qc", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/deseq2_qc/nextflow.config b/target/nextflow/deseq2_qc/nextflow.config index 20283cc..fb6d541 100644 --- a/target/nextflow/deseq2_qc/nextflow.config +++ b/target/nextflow/deseq2_qc/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'deseq2_qc' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'run deseq2, perform pca, generate heatmaps and scatterplots for samples in the counts files\n' } diff --git a/target/nextflow/dupradar/.config.vsh.yaml b/target/nextflow/dupradar/.config.vsh.yaml index 8d9b09a..6cf2d95 100644 --- a/target/nextflow/dupradar/.config.vsh.yaml +++ b/target/nextflow/dupradar/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "dupradar" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -244,7 +244,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -266,10 +266,11 @@ build_info: output: "target/nextflow/dupradar" executable: "target/nextflow/dupradar/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -291,5 +292,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.1'" organization: "vsh" diff --git a/target/nextflow/dupradar/main.nf b/target/nextflow/dupradar/main.nf index d171bd7..c0069a5 100644 --- a/target/nextflow/dupradar/main.nf +++ b/target/nextflow/dupradar/main.nf @@ -1,4 +1,4 @@ -// dupradar v0.1.0 +// dupradar v0.1.1 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2805,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "dupradar", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3106,7 +3106,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3136,11 +3136,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/dupradar", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3170,7 +3171,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3608,8 +3609,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/dupradar", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/dupradar", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/dupradar/nextflow.config b/target/nextflow/dupradar/nextflow.config index 271471f..8679dd8 100644 --- a/target/nextflow/dupradar/nextflow.config +++ b/target/nextflow/dupradar/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'dupradar' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Assessment of duplication rates in RNA-Seq datasets\n' } diff --git a/target/nextflow/fastqc/.config.vsh.yaml b/target/nextflow/fastqc/.config.vsh.yaml index a6adc46..b11125a 100644 --- a/target/nextflow/fastqc/.config.vsh.yaml +++ b/target/nextflow/fastqc/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "fastqc" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -180,7 +180,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -198,10 +198,11 @@ build_info: output: "target/nextflow/fastqc" executable: "target/nextflow/fastqc/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -223,5 +224,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/nextflow/fastqc/main.nf b/target/nextflow/fastqc/main.nf index 264e60b..6091dfd 100644 --- a/target/nextflow/fastqc/main.nf +++ b/target/nextflow/fastqc/main.nf @@ -1,4 +1,4 @@ -// fastqc v0.1.0 +// fastqc v0.1.1 // // 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 @@ -2805,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "fastqc", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3033,7 +3033,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3056,11 +3056,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/fastqc", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3090,7 +3091,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3535,8 +3536,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/fastqc", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/fastqc", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/fastqc/nextflow.config b/target/nextflow/fastqc/nextflow.config index eccbd33..8313799 100644 --- a/target/nextflow/fastqc/nextflow.config +++ b/target/nextflow/fastqc/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'fastqc' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Fastqc component, please see https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. This component can take one or more files (by means of shell globbing) or a complete directory.\n' } diff --git a/target/nextflow/fq_subsample/.config.vsh.yaml b/target/nextflow/fq_subsample/.config.vsh.yaml index cc5106c..0536264 100644 --- a/target/nextflow/fq_subsample/.config.vsh.yaml +++ b/target/nextflow/fq_subsample/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "fq_subsample" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -153,7 +153,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "docker" @@ -177,10 +177,11 @@ build_info: output: "target/nextflow/fq_subsample" executable: "target/nextflow/fq_subsample/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -202,5 +203,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.1'" organization: "vsh" diff --git a/target/nextflow/fq_subsample/main.nf b/target/nextflow/fq_subsample/main.nf index 58050a3..8c774e2 100644 --- a/target/nextflow/fq_subsample/main.nf +++ b/target/nextflow/fq_subsample/main.nf @@ -1,4 +1,4 @@ -// fq_subsample v0.1.0 +// fq_subsample v0.1.1 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2805,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "fq_subsample", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3002,7 +3002,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3027,11 +3027,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/fq_subsample", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3061,7 +3062,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3486,8 +3487,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/fq_subsample", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/fq_subsample", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/fq_subsample/nextflow.config b/target/nextflow/fq_subsample/nextflow.config index 2992f55..b9a04d1 100644 --- a/target/nextflow/fq_subsample/nextflow.config +++ b/target/nextflow/fq_subsample/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'fq_subsample' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'fq subsample outputs a subset of records from single or paired FASTQ files. This requires a seed (--seed) to be set in ext.args\n' } diff --git a/target/nextflow/getchromsizes/.config.vsh.yaml b/target/nextflow/getchromsizes/.config.vsh.yaml index f52214c..276272f 100644 --- a/target/nextflow/getchromsizes/.config.vsh.yaml +++ b/target/nextflow/getchromsizes/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "getchromsizes" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -146,7 +146,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "docker" @@ -167,10 +167,11 @@ build_info: output: "target/nextflow/getchromsizes" executable: "target/nextflow/getchromsizes/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -192,5 +193,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/nextflow/getchromsizes/main.nf b/target/nextflow/getchromsizes/main.nf index 0887fff..c9c8839 100644 --- a/target/nextflow/getchromsizes/main.nf +++ b/target/nextflow/getchromsizes/main.nf @@ -1,4 +1,4 @@ -// getchromsizes v0.1.0 +// getchromsizes v0.1.1 // // 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 @@ -2805,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "getchromsizes", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -2991,7 +2991,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3013,11 +3013,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/getchromsizes", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3047,7 +3048,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3458,8 +3459,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/getchromsizes", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/getchromsizes", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/getchromsizes/nextflow.config b/target/nextflow/getchromsizes/nextflow.config index c35e15b..083e89e 100644 --- a/target/nextflow/getchromsizes/nextflow.config +++ b/target/nextflow/getchromsizes/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'getchromsizes' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Generates a FASTA file of chromosome sizes and a fasta index file.\n' } diff --git a/target/nextflow/gtf2bed/.config.vsh.yaml b/target/nextflow/gtf2bed/.config.vsh.yaml index ea534d7..0a8d5a0 100644 --- a/target/nextflow/gtf2bed/.config.vsh.yaml +++ b/target/nextflow/gtf2bed/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "gtf2bed" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -127,7 +127,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -145,10 +145,11 @@ build_info: output: "target/nextflow/gtf2bed" executable: "target/nextflow/gtf2bed/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -170,5 +171,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.1'" organization: "vsh" diff --git a/target/nextflow/gtf2bed/main.nf b/target/nextflow/gtf2bed/main.nf index 082c423..96af03e 100644 --- a/target/nextflow/gtf2bed/main.nf +++ b/target/nextflow/gtf2bed/main.nf @@ -1,4 +1,4 @@ -// gtf2bed v0.1.0 +// gtf2bed v0.1.1 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2805,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "gtf2bed", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -2972,7 +2972,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -2995,11 +2995,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/gtf2bed", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3029,7 +3030,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3434,8 +3435,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/gtf2bed", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/gtf2bed", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/gtf2bed/nextflow.config b/target/nextflow/gtf2bed/nextflow.config index 8007fc4..67e8fb1 100644 --- a/target/nextflow/gtf2bed/nextflow.config +++ b/target/nextflow/gtf2bed/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'gtf2bed' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Create BED annotation file from GTF.\n' } diff --git a/target/nextflow/gtf_filter/.config.vsh.yaml b/target/nextflow/gtf_filter/.config.vsh.yaml index 297cace..ce2eb42 100644 --- a/target/nextflow/gtf_filter/.config.vsh.yaml +++ b/target/nextflow/gtf_filter/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "gtf_filter" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -142,7 +142,7 @@ engines: id: "docker" image: "python" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" entrypoint: [] cmd: null @@ -155,10 +155,11 @@ build_info: output: "target/nextflow/gtf_filter" executable: "target/nextflow/gtf_filter/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -180,5 +181,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/nextflow/gtf_filter/main.nf b/target/nextflow/gtf_filter/main.nf index 917c4c7..f76d5d5 100644 --- a/target/nextflow/gtf_filter/main.nf +++ b/target/nextflow/gtf_filter/main.nf @@ -1,4 +1,4 @@ -// 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 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2805,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "gtf_filter", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -2989,7 +2989,7 @@ meta = [ "id" : "docker", "image" : "python", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/" }, { @@ -3003,11 +3003,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/gtf_filter", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3037,7 +3038,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3493,8 +3494,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/gtf_filter", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/gtf_filter", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/gtf_filter/nextflow.config b/target/nextflow/gtf_filter/nextflow.config index 57f08e7..d97db65 100644 --- a/target/nextflow/gtf_filter/nextflow.config +++ b/target/nextflow/gtf_filter/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'gtf_filter' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Filters a GTF file based on sequence names in a FASTA file.\n' } diff --git a/target/nextflow/gunzip/.config.vsh.yaml b/target/nextflow/gunzip/.config.vsh.yaml index e904567..cfc86f4 100644 --- a/target/nextflow/gunzip/.config.vsh.yaml +++ b/target/nextflow/gunzip/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "gunzip" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -126,7 +126,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -144,10 +144,11 @@ build_info: output: "target/nextflow/gunzip" executable: "target/nextflow/gunzip/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -169,5 +170,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.1'" organization: "vsh" diff --git a/target/nextflow/gunzip/main.nf b/target/nextflow/gunzip/main.nf index 1151b1a..2681692 100644 --- a/target/nextflow/gunzip/main.nf +++ b/target/nextflow/gunzip/main.nf @@ -1,4 +1,4 @@ -// gunzip v0.1.0 +// gunzip v0.1.1 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2805,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "gunzip", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -2969,7 +2969,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -2992,11 +2992,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/gunzip", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3026,7 +3027,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3437,8 +3438,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/gunzip", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/gunzip", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/gunzip/nextflow.config b/target/nextflow/gunzip/nextflow.config index e6ce83a..3ab32ef 100644 --- a/target/nextflow/gunzip/nextflow.config +++ b/target/nextflow/gunzip/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'gunzip' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Compress or uncompress a file or list of files.\n' } diff --git a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml index 63d2c8e..d81ffc7 100644 --- a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml +++ b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "kallisto_index" namespace: "kallisto" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -135,7 +135,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "docker" @@ -155,10 +155,11 @@ build_info: output: "target/nextflow/kallisto/kallisto_index" executable: "target/nextflow/kallisto/kallisto_index/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -180,5 +181,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/nextflow/kallisto/kallisto_index/main.nf b/target/nextflow/kallisto/kallisto_index/main.nf index 07ff0fd..d8399a6 100644 --- a/target/nextflow/kallisto/kallisto_index/main.nf +++ b/target/nextflow/kallisto/kallisto_index/main.nf @@ -1,4 +1,4 @@ -// 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 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "kallisto_index", "namespace" : "kallisto", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -2980,7 +2980,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3002,11 +3002,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/kallisto/kallisto_index", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3036,7 +3037,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3445,8 +3446,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/kallisto/kallisto_index", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/kallisto/kallisto_index", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/kallisto/kallisto_index/nextflow.config b/target/nextflow/kallisto/kallisto_index/nextflow.config index 12f5f02..6611b7c 100644 --- a/target/nextflow/kallisto/kallisto_index/nextflow.config +++ b/target/nextflow/kallisto/kallisto_index/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'kallisto/kallisto_index' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Create Kallisto index.\n' } diff --git a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml index b24179a..02a8012 100644 --- a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml +++ b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "kallisto_quant" namespace: "kallisto" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -233,7 +233,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "docker" @@ -253,10 +253,11 @@ build_info: output: "target/nextflow/kallisto/kallisto_quant" executable: "target/nextflow/kallisto/kallisto_quant/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -278,5 +279,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.1'" organization: "vsh" diff --git a/target/nextflow/kallisto/kallisto_quant/main.nf b/target/nextflow/kallisto/kallisto_quant/main.nf index f85ac61..174aeb9 100644 --- a/target/nextflow/kallisto/kallisto_quant/main.nf +++ b/target/nextflow/kallisto/kallisto_quant/main.nf @@ -1,4 +1,4 @@ -// kallisto_quant v0.1.0 +// kallisto_quant v0.1.1 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "kallisto_quant", "namespace" : "kallisto", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3092,7 +3092,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3114,11 +3114,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/kallisto/kallisto_quant", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3148,7 +3149,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3598,8 +3599,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/kallisto/kallisto_quant", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/kallisto/kallisto_quant", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/kallisto/kallisto_quant/nextflow.config b/target/nextflow/kallisto/kallisto_quant/nextflow.config index f767733..d0e9b49 100644 --- a/target/nextflow/kallisto/kallisto_quant/nextflow.config +++ b/target/nextflow/kallisto/kallisto_quant/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'kallisto/kallisto_quant' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Computes equivalence classes for reads and quantifies abundances.\n' } diff --git a/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml b/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml index 864a524..17491e5 100644 --- a/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml +++ b/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "multiqc_custom_biotype" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -152,7 +152,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -173,10 +173,11 @@ build_info: output: "target/nextflow/multiqc_custom_biotype" executable: "target/nextflow/multiqc_custom_biotype/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -198,5 +199,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/nextflow/multiqc_custom_biotype/main.nf b/target/nextflow/multiqc_custom_biotype/main.nf index c02e457..23ac055 100644 --- a/target/nextflow/multiqc_custom_biotype/main.nf +++ b/target/nextflow/multiqc_custom_biotype/main.nf @@ -1,4 +1,4 @@ -// 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 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2805,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "multiqc_custom_biotype", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -2997,7 +2997,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3025,11 +3025,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/multiqc_custom_biotype", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3059,7 +3060,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3473,8 +3474,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/multiqc_custom_biotype", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/multiqc_custom_biotype", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/multiqc_custom_biotype/nextflow.config b/target/nextflow/multiqc_custom_biotype/nextflow.config index 8f0a455..e190493 100644 --- a/target/nextflow/multiqc_custom_biotype/nextflow.config +++ b/target/nextflow/multiqc_custom_biotype/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'multiqc_custom_biotype' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Calculate features percentage for biotype counts' } diff --git a/target/nextflow/picard_markduplicates/.config.vsh.yaml b/target/nextflow/picard_markduplicates/.config.vsh.yaml index f69c977..1683e7d 100644 --- a/target/nextflow/picard_markduplicates/.config.vsh.yaml +++ b/target/nextflow/picard_markduplicates/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "picard_markduplicates" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -186,7 +186,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "docker" @@ -207,10 +207,11 @@ build_info: output: "target/nextflow/picard_markduplicates" executable: "target/nextflow/picard_markduplicates/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -232,5 +233,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.1'" organization: "vsh" diff --git a/target/nextflow/picard_markduplicates/main.nf b/target/nextflow/picard_markduplicates/main.nf index 94e838b..cf7063b 100644 --- a/target/nextflow/picard_markduplicates/main.nf +++ b/target/nextflow/picard_markduplicates/main.nf @@ -1,4 +1,4 @@ -// picard_markduplicates v0.1.0 +// picard_markduplicates v0.1.1 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2805,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "picard_markduplicates", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3038,7 +3038,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3063,11 +3063,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/picard_markduplicates", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3097,7 +3098,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3519,8 +3520,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/picard_markduplicates", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/picard_markduplicates", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/picard_markduplicates/nextflow.config b/target/nextflow/picard_markduplicates/nextflow.config index a7e7149..f4cab69 100644 --- a/target/nextflow/picard_markduplicates/nextflow.config +++ b/target/nextflow/picard_markduplicates/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'picard_markduplicates' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Locate and tag duplicate reads in a BAM file\n' } diff --git a/target/nextflow/prepare_multiqc_input/.config.vsh.yaml b/target/nextflow/prepare_multiqc_input/.config.vsh.yaml index c430d24..71433bf 100644 --- a/target/nextflow/prepare_multiqc_input/.config.vsh.yaml +++ b/target/nextflow/prepare_multiqc_input/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "prepare_multiqc_input" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -396,7 +396,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" entrypoint: [] cmd: null @@ -409,10 +409,11 @@ build_info: output: "target/nextflow/prepare_multiqc_input" executable: "target/nextflow/prepare_multiqc_input/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -434,5 +435,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/nextflow/prepare_multiqc_input/main.nf b/target/nextflow/prepare_multiqc_input/main.nf index f92dee0..992eb52 100644 --- a/target/nextflow/prepare_multiqc_input/main.nf +++ b/target/nextflow/prepare_multiqc_input/main.nf @@ -1,4 +1,4 @@ -// 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 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2805,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "prepare_multiqc_input", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3263,7 +3263,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/" }, { @@ -3277,11 +3277,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/prepare_multiqc_input", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3311,7 +3312,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3816,8 +3817,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/prepare_multiqc_input", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/prepare_multiqc_input", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/prepare_multiqc_input/nextflow.config b/target/nextflow/prepare_multiqc_input/nextflow.config index 35cf4b6..240811f 100644 --- a/target/nextflow/prepare_multiqc_input/nextflow.config +++ b/target/nextflow/prepare_multiqc_input/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'prepare_multiqc_input' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Prepare directory with all the input files for MultiQC.\n' } diff --git a/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml b/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml index 2738b1b..e398561 100644 --- a/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml +++ b/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "preprocess_transcripts_fasta" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -125,7 +125,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" entrypoint: [] cmd: null @@ -138,10 +138,11 @@ build_info: output: "target/nextflow/preprocess_transcripts_fasta" executable: "target/nextflow/preprocess_transcripts_fasta/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -163,5 +164,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.1'" organization: "vsh" diff --git a/target/nextflow/preprocess_transcripts_fasta/main.nf b/target/nextflow/preprocess_transcripts_fasta/main.nf index eea3cfb..330c160 100644 --- a/target/nextflow/preprocess_transcripts_fasta/main.nf +++ b/target/nextflow/preprocess_transcripts_fasta/main.nf @@ -1,4 +1,4 @@ -// preprocess_transcripts_fasta v0.1.0 +// preprocess_transcripts_fasta v0.1.1 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2805,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "preprocess_transcripts_fasta", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -2968,7 +2968,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/" }, { @@ -2982,11 +2982,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/preprocess_transcripts_fasta", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3016,7 +3017,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3427,8 +3428,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/preprocess_transcripts_fasta", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/preprocess_transcripts_fasta", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/preprocess_transcripts_fasta/nextflow.config b/target/nextflow/preprocess_transcripts_fasta/nextflow.config index e03288e..9903d33 100644 --- a/target/nextflow/preprocess_transcripts_fasta/nextflow.config +++ b/target/nextflow/preprocess_transcripts_fasta/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'preprocess_transcripts_fasta' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Process transcripts FASTA if GTF file is GENOCODE format\n' } diff --git a/target/nextflow/preseq_lcextrap/.config.vsh.yaml b/target/nextflow/preseq_lcextrap/.config.vsh.yaml index 6bf5ebe..a13ac97 100644 --- a/target/nextflow/preseq_lcextrap/.config.vsh.yaml +++ b/target/nextflow/preseq_lcextrap/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "preseq_lcextrap" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -146,7 +146,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -191,10 +191,11 @@ build_info: output: "target/nextflow/preseq_lcextrap" executable: "target/nextflow/preseq_lcextrap/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -216,5 +217,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/nextflow/preseq_lcextrap/main.nf b/target/nextflow/preseq_lcextrap/main.nf index f8c4c28..689667c 100644 --- a/target/nextflow/preseq_lcextrap/main.nf +++ b/target/nextflow/preseq_lcextrap/main.nf @@ -1,4 +1,4 @@ -// 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 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2805,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "preseq_lcextrap", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -2992,7 +2992,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3035,11 +3035,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/preseq_lcextrap", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3069,7 +3070,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3500,8 +3501,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/preseq_lcextrap", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/preseq_lcextrap", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/preseq_lcextrap/nextflow.config b/target/nextflow/preseq_lcextrap/nextflow.config index d37019e..781ff32 100644 --- a/target/nextflow/preseq_lcextrap/nextflow.config +++ b/target/nextflow/preseq_lcextrap/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'preseq_lcextrap' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Computing the expected future yield of distinct reads and bounds on the number of total distinct reads in the library and the associated confidence intervals.' } diff --git a/target/nextflow/qualimap/.config.vsh.yaml b/target/nextflow/qualimap/.config.vsh.yaml index 6bd5c3d..5048497 100644 --- a/target/nextflow/qualimap/.config.vsh.yaml +++ b/target/nextflow/qualimap/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "qualimap" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -237,7 +237,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -271,10 +271,11 @@ build_info: output: "target/nextflow/qualimap" executable: "target/nextflow/qualimap/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -296,5 +297,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.1'" organization: "vsh" diff --git a/target/nextflow/qualimap/main.nf b/target/nextflow/qualimap/main.nf index 69d65cf..69ae7af 100644 --- a/target/nextflow/qualimap/main.nf +++ b/target/nextflow/qualimap/main.nf @@ -1,4 +1,4 @@ -// qualimap v0.1.0 +// qualimap v0.1.1 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2805,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "qualimap", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3100,7 +3100,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3144,11 +3144,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/qualimap", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3178,7 +3179,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3606,8 +3607,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/qualimap", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/qualimap", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/qualimap/nextflow.config b/target/nextflow/qualimap/nextflow.config index 2e94683..f4ac616 100644 --- a/target/nextflow/qualimap/nextflow.config +++ b/target/nextflow/qualimap/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'qualimap' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'RNA-seq QC analysis using the qualimap \n' } diff --git a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml index f640c7d..c35ee8a 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "rsem_calculate_expression" namespace: "rsem" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -251,7 +251,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -299,10 +299,11 @@ build_info: output: "target/nextflow/rsem/rsem_calculate_expression" executable: "target/nextflow/rsem/rsem_calculate_expression/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -324,5 +325,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/nextflow/rsem/rsem_calculate_expression/main.nf b/target/nextflow/rsem/rsem_calculate_expression/main.nf index f394405..bc08631 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/main.nf +++ b/target/nextflow/rsem/rsem_calculate_expression/main.nf @@ -1,4 +1,4 @@ -// 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 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "rsem_calculate_expression", "namespace" : "rsem", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3117,7 +3117,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3163,11 +3163,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rsem/rsem_calculate_expression", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3197,7 +3198,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3647,8 +3648,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/rsem/rsem_calculate_expression", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/rsem/rsem_calculate_expression", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/rsem/rsem_calculate_expression/nextflow.config b/target/nextflow/rsem/rsem_calculate_expression/nextflow.config index 5623294..8844d15 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/nextflow.config +++ b/target/nextflow/rsem/rsem_calculate_expression/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'rsem/rsem_calculate_expression' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Calculate expression with RSEM.\n' } diff --git a/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml b/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml index 76e0f6c..057d5db 100644 --- a/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "rsem_merge_counts" namespace: "rsem" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -169,7 +169,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" entrypoint: [] cmd: null @@ -182,10 +182,11 @@ build_info: output: "target/nextflow/rsem/rsem_merge_counts" executable: "target/nextflow/rsem/rsem_merge_counts/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -207,5 +208,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.1'" organization: "vsh" diff --git a/target/nextflow/rsem/rsem_merge_counts/main.nf b/target/nextflow/rsem/rsem_merge_counts/main.nf index 4ee6a29..88a8575 100644 --- a/target/nextflow/rsem/rsem_merge_counts/main.nf +++ b/target/nextflow/rsem/rsem_merge_counts/main.nf @@ -1,4 +1,4 @@ -// rsem_merge_counts v0.1.0 +// rsem_merge_counts v0.1.1 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "rsem_merge_counts", "namespace" : "rsem", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3014,7 +3014,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/" }, { @@ -3028,11 +3028,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rsem/rsem_merge_counts", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3062,7 +3063,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3494,8 +3495,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/rsem/rsem_merge_counts", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/rsem/rsem_merge_counts", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/rsem/rsem_merge_counts/nextflow.config b/target/nextflow/rsem/rsem_merge_counts/nextflow.config index f6cc7fd..b4409ec 100644 --- a/target/nextflow/rsem/rsem_merge_counts/nextflow.config +++ b/target/nextflow/rsem/rsem_merge_counts/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'rsem/rsem_merge_counts' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Merge the transcript quantification results obtained from rsem calculate-expression across all samples.\n' } diff --git a/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml index f7aeb11..239b2de 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "rseqc_bamstat" namespace: "rseqc" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -140,7 +140,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -163,10 +163,11 @@ build_info: output: "target/nextflow/rseqc/rseqc_bamstat" executable: "target/nextflow/rseqc/rseqc_bamstat/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -188,5 +189,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/nextflow/rseqc/rseqc_bamstat/main.nf b/target/nextflow/rseqc/rseqc_bamstat/main.nf index 86ffe55..d020bc2 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/main.nf +++ b/target/nextflow/rseqc/rseqc_bamstat/main.nf @@ -1,4 +1,4 @@ -// 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 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "rseqc_bamstat", "namespace" : "rseqc", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -2985,7 +2985,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3016,11 +3016,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_bamstat", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3050,7 +3051,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3459,8 +3460,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/rseqc/rseqc_bamstat", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/rseqc/rseqc_bamstat", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/rseqc/rseqc_bamstat/nextflow.config b/target/nextflow/rseqc/rseqc_bamstat/nextflow.config index df0ba21..8178a50 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/nextflow.config +++ b/target/nextflow/rseqc/rseqc_bamstat/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'rseqc/rseqc_bamstat' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Generate statistics from a bam file.\n' } diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml index 1a3be9a..3cccb4d 100644 --- a/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "rseqc_inferexperiment" namespace: "rseqc" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -163,7 +163,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -186,10 +186,11 @@ build_info: output: "target/nextflow/rseqc/rseqc_inferexperiment" executable: "target/nextflow/rseqc/rseqc_inferexperiment/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -211,5 +212,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.1'" organization: "vsh" diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/main.nf b/target/nextflow/rseqc/rseqc_inferexperiment/main.nf index 481dafc..787d899 100644 --- a/target/nextflow/rseqc/rseqc_inferexperiment/main.nf +++ b/target/nextflow/rseqc/rseqc_inferexperiment/main.nf @@ -1,4 +1,4 @@ -// rseqc_inferexperiment v0.1.0 +// rseqc_inferexperiment v0.1.1 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "rseqc_inferexperiment", "namespace" : "rseqc", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3013,7 +3013,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3044,11 +3044,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_inferexperiment", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3078,7 +3079,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3491,8 +3492,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/rseqc/rseqc_inferexperiment", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/rseqc/rseqc_inferexperiment", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/nextflow.config b/target/nextflow/rseqc/rseqc_inferexperiment/nextflow.config index b737f70..1e6b12d 100644 --- a/target/nextflow/rseqc/rseqc_inferexperiment/nextflow.config +++ b/target/nextflow/rseqc/rseqc_inferexperiment/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'rseqc/rseqc_inferexperiment' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Infer strandedness from sequencing reads\n' } diff --git a/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml index bbfffc2..eef1e97 100644 --- a/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "rseqc_innerdistance" namespace: "rseqc" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -248,7 +248,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -272,10 +272,11 @@ build_info: output: "target/nextflow/rseqc/rseqc_innerdistance" executable: "target/nextflow/rseqc/rseqc_innerdistance/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -297,5 +298,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/nextflow/rseqc/rseqc_innerdistance/main.nf b/target/nextflow/rseqc/rseqc_innerdistance/main.nf index 82641a6..d9d09f5 100644 --- a/target/nextflow/rseqc/rseqc_innerdistance/main.nf +++ b/target/nextflow/rseqc/rseqc_innerdistance/main.nf @@ -1,4 +1,4 @@ -// 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 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "rseqc_innerdistance", "namespace" : "rseqc", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3105,7 +3105,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3137,11 +3137,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_innerdistance", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3171,7 +3172,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3604,8 +3605,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/rseqc/rseqc_innerdistance", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/rseqc/rseqc_innerdistance", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/rseqc/rseqc_innerdistance/nextflow.config b/target/nextflow/rseqc/rseqc_innerdistance/nextflow.config index a582da4..48b0a3a 100644 --- a/target/nextflow/rseqc/rseqc_innerdistance/nextflow.config +++ b/target/nextflow/rseqc/rseqc_innerdistance/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'rseqc/rseqc_innerdistance' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Calculate inner distance between read pairs. \n' } diff --git a/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml index 8f21b47..7e14b21 100644 --- a/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "rseqc_junctionannotation" namespace: "rseqc" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -236,7 +236,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -260,10 +260,11 @@ build_info: output: "target/nextflow/rseqc/rseqc_junctionannotation" executable: "target/nextflow/rseqc/rseqc_junctionannotation/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -285,5 +286,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.1'" organization: "vsh" diff --git a/target/nextflow/rseqc/rseqc_junctionannotation/main.nf b/target/nextflow/rseqc/rseqc_junctionannotation/main.nf index 6907db9..5372497 100644 --- a/target/nextflow/rseqc/rseqc_junctionannotation/main.nf +++ b/target/nextflow/rseqc/rseqc_junctionannotation/main.nf @@ -1,4 +1,4 @@ -// rseqc_junctionannotation v0.1.0 +// rseqc_junctionannotation v0.1.1 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "rseqc_junctionannotation", "namespace" : "rseqc", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3096,7 +3096,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3128,11 +3128,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_junctionannotation", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3162,7 +3163,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3591,8 +3592,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/rseqc/rseqc_junctionannotation", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/rseqc/rseqc_junctionannotation", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/rseqc/rseqc_junctionannotation/nextflow.config b/target/nextflow/rseqc/rseqc_junctionannotation/nextflow.config index dfb15d4..51871c9 100644 --- a/target/nextflow/rseqc/rseqc_junctionannotation/nextflow.config +++ b/target/nextflow/rseqc/rseqc_junctionannotation/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'rseqc/rseqc_junctionannotation' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Compare detected splice junctions to reference gene model.\n' } diff --git a/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml index e06945e..aea7b18 100644 --- a/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "rseqc_junctionsaturation" namespace: "rseqc" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -225,7 +225,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -249,10 +249,11 @@ build_info: output: "target/nextflow/rseqc/rseqc_junctionsaturation" executable: "target/nextflow/rseqc/rseqc_junctionsaturation/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -274,5 +275,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf b/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf index 9daea77..de5fbf8 100644 --- a/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf +++ b/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf @@ -1,4 +1,4 @@ -// 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 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "rseqc_junctionsaturation", "namespace" : "rseqc", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3081,7 +3081,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3113,11 +3113,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_junctionsaturation", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3147,7 +3148,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3574,8 +3575,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/rseqc/rseqc_junctionsaturation", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/rseqc/rseqc_junctionsaturation", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/rseqc/rseqc_junctionsaturation/nextflow.config b/target/nextflow/rseqc/rseqc_junctionsaturation/nextflow.config index 074edc3..fa912cb 100644 --- a/target/nextflow/rseqc/rseqc_junctionsaturation/nextflow.config +++ b/target/nextflow/rseqc/rseqc_junctionsaturation/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'rseqc/rseqc_junctionsaturation' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Compare detected splice junctions to reference gene model.\n' } diff --git a/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml index 8c8bdd4..eabacfb 100644 --- a/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "rseqc_readdistribution" namespace: "rseqc" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -139,7 +139,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -162,10 +162,11 @@ build_info: output: "target/nextflow/rseqc/rseqc_readdistribution" executable: "target/nextflow/rseqc/rseqc_readdistribution/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -187,5 +188,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.1'" organization: "vsh" diff --git a/target/nextflow/rseqc/rseqc_readdistribution/main.nf b/target/nextflow/rseqc/rseqc_readdistribution/main.nf index 6c2a68c..f83b52c 100644 --- a/target/nextflow/rseqc/rseqc_readdistribution/main.nf +++ b/target/nextflow/rseqc/rseqc_readdistribution/main.nf @@ -1,4 +1,4 @@ -// rseqc_readdistribution v0.1.0 +// rseqc_readdistribution v0.1.1 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "rseqc_readdistribution", "namespace" : "rseqc", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -2986,7 +2986,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3017,11 +3017,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_readdistribution", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3051,7 +3052,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3460,8 +3461,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/rseqc/rseqc_readdistribution", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/rseqc/rseqc_readdistribution", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/rseqc/rseqc_readdistribution/nextflow.config b/target/nextflow/rseqc/rseqc_readdistribution/nextflow.config index 2cda6d4..50f6aa4 100644 --- a/target/nextflow/rseqc/rseqc_readdistribution/nextflow.config +++ b/target/nextflow/rseqc/rseqc_readdistribution/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'rseqc/rseqc_readdistribution' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Calculate how mapped reads are distributed over genomic features.\n' } diff --git a/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml index be7be69..cd3a315 100644 --- a/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "rseqc_readduplication" namespace: "rseqc" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -187,7 +187,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -211,10 +211,11 @@ build_info: output: "target/nextflow/rseqc/rseqc_readduplication" executable: "target/nextflow/rseqc/rseqc_readduplication/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -236,5 +237,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/nextflow/rseqc/rseqc_readduplication/main.nf b/target/nextflow/rseqc/rseqc_readduplication/main.nf index 280b856..b14a080 100644 --- a/target/nextflow/rseqc/rseqc_readduplication/main.nf +++ b/target/nextflow/rseqc/rseqc_readduplication/main.nf @@ -1,4 +1,4 @@ -// 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 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "rseqc_readduplication", "namespace" : "rseqc", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3039,7 +3039,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3071,11 +3071,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_readduplication", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3105,7 +3106,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3526,8 +3527,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/rseqc/rseqc_readduplication", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/rseqc/rseqc_readduplication", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/rseqc/rseqc_readduplication/nextflow.config b/target/nextflow/rseqc/rseqc_readduplication/nextflow.config index df632d9..6fb9016 100644 --- a/target/nextflow/rseqc/rseqc_readduplication/nextflow.config +++ b/target/nextflow/rseqc/rseqc_readduplication/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'rseqc/rseqc_readduplication' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Calculate read duplication rate.\n' } diff --git a/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml index 8a85963..9af08f4 100644 --- a/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "rseqc_tin" namespace: "rseqc" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -193,7 +193,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -214,10 +214,11 @@ build_info: output: "target/nextflow/rseqc/rseqc_tin" executable: "target/nextflow/rseqc/rseqc_tin/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -239,5 +240,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.1'" organization: "vsh" diff --git a/target/nextflow/rseqc/rseqc_tin/main.nf b/target/nextflow/rseqc/rseqc_tin/main.nf index 106537b..ad04f35 100644 --- a/target/nextflow/rseqc/rseqc_tin/main.nf +++ b/target/nextflow/rseqc/rseqc_tin/main.nf @@ -1,4 +1,4 @@ -// rseqc_tin v0.1.0 +// rseqc_tin v0.1.1 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "rseqc_tin", "namespace" : "rseqc", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3047,7 +3047,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3076,11 +3076,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_tin", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3110,7 +3111,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3545,8 +3546,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/rseqc/rseqc_tin", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/rseqc/rseqc_tin", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/rseqc/rseqc_tin/nextflow.config b/target/nextflow/rseqc/rseqc_tin/nextflow.config index 3366739..9eeddea 100644 --- a/target/nextflow/rseqc/rseqc_tin/nextflow.config +++ b/target/nextflow/rseqc/rseqc_tin/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'rseqc/rseqc_tin' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Calculte TIN (transcript integrity number) from RNA-seq reads\n' } diff --git a/target/nextflow/sortmerna/.config.vsh.yaml b/target/nextflow/sortmerna/.config.vsh.yaml index 96c0d58..8c11b20 100644 --- a/target/nextflow/sortmerna/.config.vsh.yaml +++ b/target/nextflow/sortmerna/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "sortmerna" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -179,7 +179,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "docker" @@ -198,10 +198,11 @@ build_info: output: "target/nextflow/sortmerna" executable: "target/nextflow/sortmerna/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -223,5 +224,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/nextflow/sortmerna/main.nf b/target/nextflow/sortmerna/main.nf index e2b6bb0..94309d8 100644 --- a/target/nextflow/sortmerna/main.nf +++ b/target/nextflow/sortmerna/main.nf @@ -1,4 +1,4 @@ -// sortmerna v0.1.0 +// sortmerna v0.1.1 // // 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 @@ -2805,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "sortmerna", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3028,7 +3028,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3050,11 +3050,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/sortmerna", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3084,7 +3085,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3529,8 +3530,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/sortmerna", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/sortmerna", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/sortmerna/nextflow.config b/target/nextflow/sortmerna/nextflow.config index 9f010b6..5603a43 100644 --- a/target/nextflow/sortmerna/nextflow.config +++ b/target/nextflow/sortmerna/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'sortmerna' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Local sequence alignment tool for filtering, mapping and clustering. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data. SortMeRNA takes as input files of reads (fasta, fastq, fasta.gz, fastq.gz) and one or multiple rRNA database file(s), and sorts apart aligned and rejected reads into two files.\n' } diff --git a/target/nextflow/stringtie/.config.vsh.yaml b/target/nextflow/stringtie/.config.vsh.yaml index 87c0bd7..6484e6d 100644 --- a/target/nextflow/stringtie/.config.vsh.yaml +++ b/target/nextflow/stringtie/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "stringtie" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -196,7 +196,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "docker" @@ -216,10 +216,11 @@ build_info: output: "target/nextflow/stringtie" executable: "target/nextflow/stringtie/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -241,5 +242,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.1'" organization: "vsh" diff --git a/target/nextflow/stringtie/main.nf b/target/nextflow/stringtie/main.nf index c5ac323..4ae6e7b 100644 --- a/target/nextflow/stringtie/main.nf +++ b/target/nextflow/stringtie/main.nf @@ -1,4 +1,4 @@ -// stringtie v0.1.0 +// stringtie v0.1.1 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2805,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "stringtie", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3051,7 +3051,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3073,11 +3073,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/stringtie", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3107,7 +3108,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3539,8 +3540,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/stringtie", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/stringtie", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/stringtie/nextflow.config b/target/nextflow/stringtie/nextflow.config index bfda49e..fe47bd1 100644 --- a/target/nextflow/stringtie/nextflow.config +++ b/target/nextflow/stringtie/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'stringtie' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Transcript assembly and quantification for RNA-Seq\n' } diff --git a/target/nextflow/summarizedexperiment/.config.vsh.yaml b/target/nextflow/summarizedexperiment/.config.vsh.yaml index ff952ca..3b77495 100644 --- a/target/nextflow/summarizedexperiment/.config.vsh.yaml +++ b/target/nextflow/summarizedexperiment/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "summarizedexperiment" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -175,7 +175,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -199,10 +199,11 @@ build_info: output: "target/nextflow/summarizedexperiment" executable: "target/nextflow/summarizedexperiment/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -224,5 +225,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/nextflow/summarizedexperiment/main.nf b/target/nextflow/summarizedexperiment/main.nf index 99cc530..6ba3d50 100644 --- a/target/nextflow/summarizedexperiment/main.nf +++ b/target/nextflow/summarizedexperiment/main.nf @@ -1,4 +1,4 @@ -// summarizedexperiment v0.1.0 +// summarizedexperiment v0.1.1 // // 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 @@ -2805,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "summarizedexperiment", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3022,7 +3022,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3054,11 +3054,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/summarizedexperiment", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3088,7 +3089,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3512,8 +3513,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/summarizedexperiment", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/summarizedexperiment", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/summarizedexperiment/nextflow.config b/target/nextflow/summarizedexperiment/nextflow.config index 441d515..93efd5a 100644 --- a/target/nextflow/summarizedexperiment/nextflow.config +++ b/target/nextflow/summarizedexperiment/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'summarizedexperiment' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Create SummarizedExperiment object from Salmon counts' } diff --git a/target/nextflow/trimgalore/.config.vsh.yaml b/target/nextflow/trimgalore/.config.vsh.yaml index b621ac9..0af246d 100644 --- a/target/nextflow/trimgalore/.config.vsh.yaml +++ b/target/nextflow/trimgalore/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "trimgalore" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -770,7 +770,7 @@ engines: id: "docker" image: "quay.io/biocontainers/trim-galore:0.6.9--hdfd78af_0" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "docker" @@ -788,10 +788,11 @@ build_info: output: "target/nextflow/trimgalore" executable: "target/nextflow/trimgalore/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -813,5 +814,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.1'" organization: "vsh" diff --git a/target/nextflow/trimgalore/main.nf b/target/nextflow/trimgalore/main.nf index 423c8cb..67978cd 100644 --- a/target/nextflow/trimgalore/main.nf +++ b/target/nextflow/trimgalore/main.nf @@ -1,4 +1,4 @@ -// trimgalore v0.1.0 +// trimgalore v0.1.1 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2805,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "trimgalore", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3554,7 +3554,7 @@ meta = [ "id" : "docker", "image" : "quay.io/biocontainers/trim-galore:0.6.9--hdfd78af_0", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3576,11 +3576,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/trimgalore", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3610,7 +3611,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -4172,8 +4173,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/trimgalore", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/trimgalore", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/trimgalore/nextflow.config b/target/nextflow/trimgalore/nextflow.config index 55b60b2..5b9c7ac 100644 --- a/target/nextflow/trimgalore/nextflow.config +++ b/target/nextflow/trimgalore/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'trimgalore' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files. \n' } diff --git a/target/nextflow/tx2gene/.config.vsh.yaml b/target/nextflow/tx2gene/.config.vsh.yaml index c18d94a..7b36716 100644 --- a/target/nextflow/tx2gene/.config.vsh.yaml +++ b/target/nextflow/tx2gene/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "tx2gene" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -170,7 +170,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -192,10 +192,11 @@ build_info: output: "target/nextflow/tx2gene" executable: "target/nextflow/tx2gene/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -217,5 +218,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/nextflow/tx2gene/main.nf b/target/nextflow/tx2gene/main.nf index 224f2ec..3011c57 100644 --- a/target/nextflow/tx2gene/main.nf +++ b/target/nextflow/tx2gene/main.nf @@ -1,4 +1,4 @@ -// tx2gene v0.1.0 +// tx2gene v0.1.1 // // 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 @@ -2805,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "tx2gene", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3020,7 +3020,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3049,11 +3049,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/tx2gene", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3083,7 +3084,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3512,8 +3513,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/tx2gene", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/tx2gene", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/tx2gene/nextflow.config b/target/nextflow/tx2gene/nextflow.config index 2e4fc42..2b04f9e 100644 --- a/target/nextflow/tx2gene/nextflow.config +++ b/target/nextflow/tx2gene/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'tx2gene' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Get transcript id (tx) to gene names for tximport' } diff --git a/target/nextflow/tximport/.config.vsh.yaml b/target/nextflow/tximport/.config.vsh.yaml index 09b5f45..60633c2 100644 --- a/target/nextflow/tximport/.config.vsh.yaml +++ b/target/nextflow/tximport/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "tximport" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -218,7 +218,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -247,10 +247,11 @@ build_info: output: "target/nextflow/tximport" executable: "target/nextflow/tximport/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -272,5 +273,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.1'" organization: "vsh" diff --git a/target/nextflow/tximport/main.nf b/target/nextflow/tximport/main.nf index 32ab726..dc59b82 100644 --- a/target/nextflow/tximport/main.nf +++ b/target/nextflow/tximport/main.nf @@ -1,4 +1,4 @@ -// tximport v0.1.0 +// tximport v0.1.1 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2805,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "tximport", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3076,7 +3076,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3114,11 +3114,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/tximport", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3148,7 +3149,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3580,8 +3581,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/tximport", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/tximport", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/tximport/nextflow.config b/target/nextflow/tximport/nextflow.config index 13be46b..f58744e 100644 --- a/target/nextflow/tximport/nextflow.config +++ b/target/nextflow/tximport/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'tximport' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Get dataframe linking transcript ID, gene ID, and gene name' } diff --git a/target/nextflow/ucsc/bedclip/.config.vsh.yaml b/target/nextflow/ucsc/bedclip/.config.vsh.yaml index 4f55293..e82fe90 100644 --- a/target/nextflow/ucsc/bedclip/.config.vsh.yaml +++ b/target/nextflow/ucsc/bedclip/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedclip" namespace: "ucsc" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -141,7 +141,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -164,10 +164,11 @@ build_info: output: "target/nextflow/ucsc/bedclip" executable: "target/nextflow/ucsc/bedclip/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -189,5 +190,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/nextflow/ucsc/bedclip/main.nf b/target/nextflow/ucsc/bedclip/main.nf index db82ecc..8dae3e5 100644 --- a/target/nextflow/ucsc/bedclip/main.nf +++ b/target/nextflow/ucsc/bedclip/main.nf @@ -1,4 +1,4 @@ -// bedclip v0.1.0 +// bedclip v0.1.1 // // 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 @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bedclip", "namespace" : "ucsc", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -2988,7 +2988,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3018,11 +3018,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/ucsc/bedclip", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3052,7 +3053,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3458,8 +3459,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/ucsc/bedclip", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/ucsc/bedclip", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/ucsc/bedclip/nextflow.config b/target/nextflow/ucsc/bedclip/nextflow.config index 73d0a6d..886dc83 100644 --- a/target/nextflow/ucsc/bedclip/nextflow.config +++ b/target/nextflow/ucsc/bedclip/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'ucsc/bedclip' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Remove lines from bed file that refer to off-chromosome locations' } diff --git a/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml b/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml index 320319b..d63e6b3 100644 --- a/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml +++ b/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "bedgraphtobigwig" namespace: "ucsc" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -141,7 +141,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -164,10 +164,11 @@ build_info: output: "target/nextflow/ucsc/bedgraphtobigwig" executable: "target/nextflow/ucsc/bedgraphtobigwig/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -189,5 +190,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.1'" organization: "vsh" diff --git a/target/nextflow/ucsc/bedgraphtobigwig/main.nf b/target/nextflow/ucsc/bedgraphtobigwig/main.nf index 871851c..675e4a3 100644 --- a/target/nextflow/ucsc/bedgraphtobigwig/main.nf +++ b/target/nextflow/ucsc/bedgraphtobigwig/main.nf @@ -1,4 +1,4 @@ -// bedgraphtobigwig v0.1.0 +// bedgraphtobigwig v0.1.1 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "bedgraphtobigwig", "namespace" : "ucsc", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -2988,7 +2988,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3018,11 +3018,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/ucsc/bedgraphtobigwig", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3052,7 +3053,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3458,8 +3459,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/ucsc/bedgraphtobigwig", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/ucsc/bedgraphtobigwig", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/ucsc/bedgraphtobigwig/nextflow.config b/target/nextflow/ucsc/bedgraphtobigwig/nextflow.config index 0334457..905c0eb 100644 --- a/target/nextflow/ucsc/bedgraphtobigwig/nextflow.config +++ b/target/nextflow/ucsc/bedgraphtobigwig/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'ucsc/bedgraphtobigwig' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Convert a bedGraph file to bigWig format' } diff --git a/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml b/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml index 8b50cc7..2729ead 100644 --- a/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml +++ b/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "umitools_dedup" namespace: "umitools" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -172,7 +172,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -195,10 +195,11 @@ build_info: output: "target/nextflow/umitools/umitools_dedup" executable: "target/nextflow/umitools/umitools_dedup/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -220,5 +221,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/nextflow/umitools/umitools_dedup/main.nf b/target/nextflow/umitools/umitools_dedup/main.nf index 1c4e63b..48b919e 100644 --- a/target/nextflow/umitools/umitools_dedup/main.nf +++ b/target/nextflow/umitools/umitools_dedup/main.nf @@ -1,4 +1,4 @@ -// 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 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "umitools_dedup", "namespace" : "umitools", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3023,7 +3023,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3054,11 +3054,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/umitools/umitools_dedup", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3088,7 +3089,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3513,8 +3514,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/umitools/umitools_dedup", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/umitools/umitools_dedup", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/umitools/umitools_dedup/nextflow.config b/target/nextflow/umitools/umitools_dedup/nextflow.config index 1c9b7ee..5ebbd30 100644 --- a/target/nextflow/umitools/umitools_dedup/nextflow.config +++ b/target/nextflow/umitools/umitools_dedup/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'umitools/umitools_dedup' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.\n' } diff --git a/target/nextflow/umitools/umitools_extract/.config.vsh.yaml b/target/nextflow/umitools/umitools_extract/.config.vsh.yaml index 435c322..4110278 100644 --- a/target/nextflow/umitools/umitools_extract/.config.vsh.yaml +++ b/target/nextflow/umitools/umitools_extract/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "umitools_extract" namespace: "umitools" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -230,7 +230,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -253,10 +253,11 @@ build_info: output: "target/nextflow/umitools/umitools_extract" executable: "target/nextflow/umitools/umitools_extract/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -278,5 +279,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.1'" organization: "vsh" diff --git a/target/nextflow/umitools/umitools_extract/main.nf b/target/nextflow/umitools/umitools_extract/main.nf index dae9481..e2a1ef7 100644 --- a/target/nextflow/umitools/umitools_extract/main.nf +++ b/target/nextflow/umitools/umitools_extract/main.nf @@ -1,4 +1,4 @@ -// umitools_extract v0.1.0 +// umitools_extract v0.1.1 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "umitools_extract", "namespace" : "umitools", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3088,7 +3088,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3119,11 +3119,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/umitools/umitools_extract", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3153,7 +3154,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3619,8 +3620,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/umitools/umitools_extract", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/umitools/umitools_extract", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/umitools/umitools_extract/nextflow.config b/target/nextflow/umitools/umitools_extract/nextflow.config index 766650a..a4017c3 100644 --- a/target/nextflow/umitools/umitools_extract/nextflow.config +++ b/target/nextflow/umitools/umitools_extract/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'umitools/umitools_extract' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes. See https://umi-tools.readthedocs.io/en/latest/ for more information.\nThis component flexible removes UMI sequences from fastq reads. UMIs are removed and appended to the read name.\nThis component extracts UMI barcode from a read and add it to the read name, leaving any sample barcode in place\n' } diff --git a/target/nextflow/umitools_prepareforquant/.config.vsh.yaml b/target/nextflow/umitools_prepareforquant/.config.vsh.yaml index 4edf9ae..dadf252 100644 --- a/target/nextflow/umitools_prepareforquant/.config.vsh.yaml +++ b/target/nextflow/umitools_prepareforquant/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "umitools_prepareforquant" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -132,7 +132,7 @@ engines: id: "docker" image: "ubuntu:22.04" target_registry: "images.viash-hub.com" - target_tag: "v0.1.0" + target_tag: "v0.1.1" namespace_separator: "/" setup: - type: "apt" @@ -156,10 +156,11 @@ build_info: output: "target/nextflow/umitools_prepareforquant" executable: "target/nextflow/umitools_prepareforquant/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -181,5 +182,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".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" diff --git a/target/nextflow/umitools_prepareforquant/main.nf b/target/nextflow/umitools_prepareforquant/main.nf index 0b4a1de..af37541 100644 --- a/target/nextflow/umitools_prepareforquant/main.nf +++ b/target/nextflow/umitools_prepareforquant/main.nf @@ -1,4 +1,4 @@ -// 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 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2805,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "umitools_prepareforquant", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -2975,7 +2975,7 @@ meta = [ "id" : "docker", "image" : "ubuntu:22.04", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.1.0", + "target_tag" : "v0.1.1", "namespace_separator" : "/", "setup" : [ { @@ -3007,11 +3007,12 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/umitools_prepareforquant", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3041,7 +3042,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } @@ -3450,8 +3451,8 @@ meta["defaults"] = [ directives: readJsonBlob('''{ "container" : { "registry" : "images.viash-hub.com", - "image" : "vsh/umitools_prepareforquant", - "tag" : "v0.1.0" + "image" : "vsh/rnaseq/umitools_prepareforquant", + "tag" : "v0.1.1" }, "tag" : "$id" }'''), diff --git a/target/nextflow/umitools_prepareforquant/nextflow.config b/target/nextflow/umitools_prepareforquant/nextflow.config index c78f35f..887ecd8 100644 --- a/target/nextflow/umitools_prepareforquant/nextflow.config +++ b/target/nextflow/umitools_prepareforquant/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'umitools_prepareforquant' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'Fix paired-end reads in name sorted BAM file to prepare for salmon quantification' } diff --git a/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml b/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml index 70cdec6..90d0729 100644 --- a/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml +++ b/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "genome_alignment_and_quant" namespace: "workflows" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -603,8 +603,8 @@ build_info: output: "target/nextflow/workflows/genome_alignment_and_quant" executable: "target/nextflow/workflows/genome_alignment_and_quant/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" dependencies: - "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" @@ -617,7 +617,8 @@ build_info: - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant" - "target/nextflow/rsem/rsem_calculate_expression" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -639,5 +640,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.1'" organization: "vsh" diff --git a/target/nextflow/workflows/genome_alignment_and_quant/main.nf b/target/nextflow/workflows/genome_alignment_and_quant/main.nf index 727a44e..e8616e1 100644 --- a/target/nextflow/workflows/genome_alignment_and_quant/main.nf +++ b/target/nextflow/workflows/genome_alignment_and_quant/main.nf @@ -1,4 +1,4 @@ -// genome_alignment_and_quant v0.1.0 +// genome_alignment_and_quant v0.1.1 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "genome_alignment_and_quant", "namespace" : "workflows", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3531,11 +3531,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/genome_alignment_and_quant", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3565,7 +3566,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } diff --git a/target/nextflow/workflows/genome_alignment_and_quant/nextflow.config b/target/nextflow/workflows/genome_alignment_and_quant/nextflow.config index 4a0eb9c..4be4ccf 100644 --- a/target/nextflow/workflows/genome_alignment_and_quant/nextflow.config +++ b/target/nextflow/workflows/genome_alignment_and_quant/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/genome_alignment_and_quant' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'A viash sub-workflow for genome alignment and quantification stage of nf-core/rnaseq pipeline.\n' } diff --git a/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml b/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml index e5bb889..7080b8b 100644 --- a/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml +++ b/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "merge_quant_results" namespace: "workflows" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -278,14 +278,15 @@ build_info: output: "target/nextflow/workflows/merge_quant_results" executable: "target/nextflow/workflows/merge_quant_results/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/tx2gene" - "target/nextflow/tximport" - "target/nextflow/summarizedexperiment" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -307,5 +308,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.1'" organization: "vsh" diff --git a/target/nextflow/workflows/merge_quant_results/main.nf b/target/nextflow/workflows/merge_quant_results/main.nf index f65ed33..48f158a 100644 --- a/target/nextflow/workflows/merge_quant_results/main.nf +++ b/target/nextflow/workflows/merge_quant_results/main.nf @@ -1,4 +1,4 @@ -// merge_quant_results v0.1.0 +// merge_quant_results v0.1.1 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "merge_quant_results", "namespace" : "workflows", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3149,11 +3149,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/merge_quant_results", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3183,7 +3184,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } diff --git a/target/nextflow/workflows/merge_quant_results/nextflow.config b/target/nextflow/workflows/merge_quant_results/nextflow.config index b85b790..37968d1 100644 --- a/target/nextflow/workflows/merge_quant_results/nextflow.config +++ b/target/nextflow/workflows/merge_quant_results/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/merge_quant_results' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'A sub-workflow to merge the counts obtained from salmon quant across all samples.' } diff --git a/target/nextflow/workflows/post_processing/.config.vsh.yaml b/target/nextflow/workflows/post_processing/.config.vsh.yaml index 62452d9..4bc1e0e 100644 --- a/target/nextflow/workflows/post_processing/.config.vsh.yaml +++ b/target/nextflow/workflows/post_processing/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "post_processing" namespace: "workflows" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -486,8 +486,8 @@ build_info: output: "target/nextflow/workflows/post_processing" executable: "target/nextflow/workflows/post_processing/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/picard_markduplicates" - "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/bedgraphtobigwig" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -522,5 +523,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.1'" organization: "vsh" diff --git a/target/nextflow/workflows/post_processing/main.nf b/target/nextflow/workflows/post_processing/main.nf index fb77fcd..72a6371 100644 --- a/target/nextflow/workflows/post_processing/main.nf +++ b/target/nextflow/workflows/post_processing/main.nf @@ -1,4 +1,4 @@ -// post_processing v0.1.0 +// post_processing v0.1.1 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "post_processing", "namespace" : "workflows", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3397,11 +3397,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/post_processing", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3431,7 +3432,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } diff --git a/target/nextflow/workflows/post_processing/nextflow.config b/target/nextflow/workflows/post_processing/nextflow.config index 776a891..d4b321d 100644 --- a/target/nextflow/workflows/post_processing/nextflow.config +++ b/target/nextflow/workflows/post_processing/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/post_processing' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'A viash sub-workflow for the post-processing stage of nf-core/rnaseq pipeline.\n' } diff --git a/target/nextflow/workflows/pre_processing/.config.vsh.yaml b/target/nextflow/workflows/pre_processing/.config.vsh.yaml index be70d37..9751294 100644 --- a/target/nextflow/workflows/pre_processing/.config.vsh.yaml +++ b/target/nextflow/workflows/pre_processing/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "pre_processing" namespace: "workflows" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Inputs" arguments: @@ -673,8 +673,8 @@ build_info: output: "target/nextflow/workflows/pre_processing" executable: "target/nextflow/workflows/pre_processing/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/fastqc" - "target/nextflow/umitools/umitools_extract" @@ -686,7 +686,8 @@ build_info: - "target/nextflow/fq_subsample" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -708,5 +709,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.1'" organization: "vsh" diff --git a/target/nextflow/workflows/pre_processing/main.nf b/target/nextflow/workflows/pre_processing/main.nf index a651615..753e298 100644 --- a/target/nextflow/workflows/pre_processing/main.nf +++ b/target/nextflow/workflows/pre_processing/main.nf @@ -1,4 +1,4 @@ -// pre_processing v0.1.0 +// pre_processing v0.1.1 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "pre_processing", "namespace" : "workflows", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Inputs", @@ -3626,11 +3626,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/pre_processing", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3660,7 +3661,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } diff --git a/target/nextflow/workflows/pre_processing/nextflow.config b/target/nextflow/workflows/pre_processing/nextflow.config index 177ded8..6b2e623 100644 --- a/target/nextflow/workflows/pre_processing/nextflow.config +++ b/target/nextflow/workflows/pre_processing/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/pre_processing' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'A subworkflow for the pre-processing stage of the nf-core/rnaseq pipeline.\n' } diff --git a/target/nextflow/workflows/prepare_genome/.config.vsh.yaml b/target/nextflow/workflows/prepare_genome/.config.vsh.yaml index 40b4872..65995d6 100644 --- a/target/nextflow/workflows/prepare_genome/.config.vsh.yaml +++ b/target/nextflow/workflows/prepare_genome/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "prepare_genome" namespace: "workflows" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -496,8 +496,8 @@ build_info: output: "target/nextflow/workflows/prepare_genome" executable: "target/nextflow/workflows/prepare_genome/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/gunzip" - "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/nextflow/kallisto/kallisto_index" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -535,5 +536,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.1'" organization: "vsh" diff --git a/target/nextflow/workflows/prepare_genome/main.nf b/target/nextflow/workflows/prepare_genome/main.nf index 80fa34a..01bfbc6 100644 --- a/target/nextflow/workflows/prepare_genome/main.nf +++ b/target/nextflow/workflows/prepare_genome/main.nf @@ -1,4 +1,4 @@ -// prepare_genome v0.1.0 +// prepare_genome v0.1.1 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "prepare_genome", "namespace" : "workflows", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3407,11 +3407,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/prepare_genome", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3441,7 +3442,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } diff --git a/target/nextflow/workflows/prepare_genome/nextflow.config b/target/nextflow/workflows/prepare_genome/nextflow.config index 056965b..e271dc5 100644 --- a/target/nextflow/workflows/prepare_genome/nextflow.config +++ b/target/nextflow/workflows/prepare_genome/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/prepare_genome' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'A subworkflow for preparing all the required genome references\n' } diff --git a/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml b/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml index 433b60f..df7a801 100644 --- a/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml +++ b/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "pseudo_alignment_and_quant" namespace: "workflows" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -283,13 +283,14 @@ build_info: output: "target/nextflow/workflows/pseudo_alignment_and_quant" executable: "target/nextflow/workflows/pseudo_alignment_and_quant/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant" - "target/nextflow/kallisto/kallisto_quant" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -311,5 +312,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.1'" organization: "vsh" diff --git a/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf b/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf index b0f9868..0fa23e7 100644 --- a/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf +++ b/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf @@ -1,4 +1,4 @@ -// pseudo_alignment_and_quant v0.1.0 +// pseudo_alignment_and_quant v0.1.1 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "pseudo_alignment_and_quant", "namespace" : "workflows", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -3143,11 +3143,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/pseudo_alignment_and_quant", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -3177,7 +3178,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } diff --git a/target/nextflow/workflows/pseudo_alignment_and_quant/nextflow.config b/target/nextflow/workflows/pseudo_alignment_and_quant/nextflow.config index 3023ed0..a9c663e 100644 --- a/target/nextflow/workflows/pseudo_alignment_and_quant/nextflow.config +++ b/target/nextflow/workflows/pseudo_alignment_and_quant/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/pseudo_alignment_and_quant' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'A viash sub-workflow for pseudo alignment and quantification stage of nf-core/rnaseq pipeline.\n' } diff --git a/target/nextflow/workflows/quality_control/.config.vsh.yaml b/target/nextflow/workflows/quality_control/.config.vsh.yaml index 6db3b15..ecf9eca 100644 --- a/target/nextflow/workflows/quality_control/.config.vsh.yaml +++ b/target/nextflow/workflows/quality_control/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "quality_control" namespace: "workflows" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -1596,8 +1596,8 @@ build_info: output: "target/nextflow/workflows/quality_control" executable: "target/nextflow/workflows/quality_control/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/rseqc/rseqc_bamstat" - "target/nextflow/rseqc/rseqc_inferexperiment" @@ -1618,7 +1618,8 @@ build_info: - "target/nextflow/rsem/rsem_merge_counts" - "target/nextflow/workflows/merge_quant_results" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -1640,5 +1641,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.1'" organization: "vsh" diff --git a/target/nextflow/workflows/quality_control/main.nf b/target/nextflow/workflows/quality_control/main.nf index be6de30..8d0cf29 100644 --- a/target/nextflow/workflows/quality_control/main.nf +++ b/target/nextflow/workflows/quality_control/main.nf @@ -1,4 +1,4 @@ -// quality_control v0.1.0 +// quality_control v0.1.1 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "quality_control", "namespace" : "workflows", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -4676,11 +4676,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/quality_control", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -4710,7 +4711,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } diff --git a/target/nextflow/workflows/quality_control/nextflow.config b/target/nextflow/workflows/quality_control/nextflow.config index c0ed49d..8a63b94 100644 --- a/target/nextflow/workflows/quality_control/nextflow.config +++ b/target/nextflow/workflows/quality_control/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/quality_control' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'A subworkflow for the final quality control stage of the nf-core/rnaseq pipeline.\n' } diff --git a/target/nextflow/workflows/rnaseq/.config.vsh.yaml b/target/nextflow/workflows/rnaseq/.config.vsh.yaml index 29f3f1a..32e858e 100644 --- a/target/nextflow/workflows/rnaseq/.config.vsh.yaml +++ b/target/nextflow/workflows/rnaseq/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "rnaseq" namespace: "workflows" -version: "v0.1.0" +version: "v0.1.1" argument_groups: - name: "Input" arguments: @@ -2117,8 +2117,8 @@ build_info: output: "target/nextflow/workflows/rnaseq" executable: "target/nextflow/workflows/rnaseq/main.nf" viash_version: "0.9.0" - git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa" - git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518" + git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/workflows/prepare_genome" - "target/nextflow/cat_fastq" @@ -2128,7 +2128,8 @@ build_info: - "target/nextflow/workflows/post_processing" - "target/nextflow/workflows/quality_control" package_config: - version: "v0.1.0" + name: "rnaseq" + version: "v0.1.1" info: test_resources: - path: "gs://viash-hub-test-data/rnaseq/v1" @@ -2150,5 +2151,5 @@ package_config: \ := '$id'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + - ".engines[.type == 'docker'].target_tag := 'v0.1.1'" organization: "vsh" diff --git a/target/nextflow/workflows/rnaseq/main.nf b/target/nextflow/workflows/rnaseq/main.nf index ad3a5e2..742b3a8 100644 --- a/target/nextflow/workflows/rnaseq/main.nf +++ b/target/nextflow/workflows/rnaseq/main.nf @@ -1,4 +1,4 @@ -// rnaseq v0.1.0 +// rnaseq v0.1.1 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "rnaseq", "namespace" : "workflows", - "version" : "v0.1.0", + "version" : "v0.1.1", "argument_groups" : [ { "name" : "Input", @@ -5283,11 +5283,12 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/rnaseq", "viash_version" : "0.9.0", - "git_commit" : "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa", - "git_remote" : "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq" + "git_commit" : "0f49a3ff62687a68af3e43608224d922a5fad518", + "git_remote" : "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq" }, "package_config" : { - "version" : "v0.1.0", + "name" : "rnaseq", + "version" : "v0.1.1", "info" : { "test_resources" : [ { @@ -5317,7 +5318,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.1.0'" + ".engines[.type == 'docker'].target_tag := 'v0.1.1'" ], "organization" : "vsh" } diff --git a/target/nextflow/workflows/rnaseq/nextflow.config b/target/nextflow/workflows/rnaseq/nextflow.config index d38e8fe..c4c8aef 100644 --- a/target/nextflow/workflows/rnaseq/nextflow.config +++ b/target/nextflow/workflows/rnaseq/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'workflows/rnaseq' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.1.0' + version = 'v0.1.1' description = 'A viash workflow for the nf-core/rnaseq pipeline.\n' }