diff --git a/assets/methods_description_template.yml b/src/assets/methods_description_template.yml similarity index 100% rename from assets/methods_description_template.yml rename to src/assets/methods_description_template.yml diff --git a/assets/multiqc/biotypes_header.txt b/src/assets/multiqc/biotypes_header.txt similarity index 100% rename from assets/multiqc/biotypes_header.txt rename to src/assets/multiqc/biotypes_header.txt diff --git a/assets/multiqc/deseq2_clustering_header.txt b/src/assets/multiqc/deseq2_clustering_header.txt similarity index 100% rename from assets/multiqc/deseq2_clustering_header.txt rename to src/assets/multiqc/deseq2_clustering_header.txt diff --git a/assets/multiqc/deseq2_pca_header.txt b/src/assets/multiqc/deseq2_pca_header.txt similarity index 100% rename from assets/multiqc/deseq2_pca_header.txt rename to src/assets/multiqc/deseq2_pca_header.txt diff --git a/assets/multiqc_config.yml b/src/assets/multiqc_config.yml similarity index 100% rename from assets/multiqc_config.yml rename to src/assets/multiqc_config.yml diff --git a/assets/rrna-db-defaults.txt b/src/assets/rrna-db-defaults.txt similarity index 100% rename from assets/rrna-db-defaults.txt rename to src/assets/rrna-db-defaults.txt diff --git a/src/deseq2_qc/config.vsh.yaml b/src/deseq2_qc/config.vsh.yaml index 7d845cb..dd3cb6c 100644 --- a/src/deseq2_qc/config.vsh.yaml +++ b/src/deseq2_qc/config.vsh.yaml @@ -5,14 +5,14 @@ info: paths: [modules/local/deseq2_qc.nf] last_sha: 92b2a7857de1dda9d1c19a088941fc81e2976ff7 description: | - Run DESeq2, perform PCA, generate heatmaps and scatterplots for samples in the counts files + run deseq2, perform pca, generate heatmaps and scatterplots for samples in the counts files argument_groups: -- name: "Input" +- name: "input" arguments: - name: "--counts" type: file - description: Count file matrix where rows are genes and columns are samples + description: count file matrix where rows are genes and columns are samples - name: "--pca_header_multiqc" type: file default: assets/multiqc/deseq2_pca_header.txt @@ -50,13 +50,16 @@ resources: path: script.sh # copied from https://github.com/nf-core/rnaseq/blob/3.12.0/bin/deseq2_qc.r - path: deseq2_qc.r + # Add proper default headers as part of the component + - path: /src/assets/multiqc/deseq2_pca_header.txt + dest: assets/multiqc/deseq2_pca_header.txt + - path: /src/assets/multiqc/deseq2_clustering_header.txt + dest: assets/multiqc/deseq2_clustering_header.txt test_resources: - type: bash_script path: test.sh - path: /testData/unit_test_resources/counts.tsv - - path: /assets/multiqc/deseq2_pca_header.txt - - path: /assets/multiqc/deseq2_clustering_header.txt engines: - type: docker @@ -70,4 +73,4 @@ engines: url: https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz runners: - type: executable - - type: nextflow \ No newline at end of file + - type: nextflow diff --git a/src/deseq2_qc/test.sh b/src/deseq2_qc/test.sh index b103247..d610ccc 100644 --- a/src/deseq2_qc/test.sh +++ b/src/deseq2_qc/test.sh @@ -5,8 +5,6 @@ echo "> Running $meta_functionality_name" "$meta_executable" \ --counts $meta_resources_dir/counts.tsv \ - --pca_header_multiqc $meta_resources_dir/deseq2_pca_header.txt \ - --clustering_header_multiqc $meta_resources_dir/deseq2_clustering_header.txt \ --extra_args "--id_col 1 --sample_suffix '' --outprefix deseq2 --count_col 2" \ --extra_args2 "test" \ --deseq2_output "deseq2/" \ @@ -25,4 +23,4 @@ echo ">> Check whether output exists" [ ! -f "sample.dists_mqc.tsv" ] && echo "sample.dists_mqc.tsv was not created" && exit 1 [ ! -s "sample.dists_mqc.tsv" ] && echo "sample.dists_mqc.tsv is empty" && exit 1 -exit 0 \ No newline at end of file +exit 0 diff --git a/src/multiqc_custom_biotype/config.vsh.yaml b/src/multiqc_custom_biotype/config.vsh.yaml index 9e6c75c..46859b8 100644 --- a/src/multiqc_custom_biotype/config.vsh.yaml +++ b/src/multiqc_custom_biotype/config.vsh.yaml @@ -33,6 +33,9 @@ resources: path: script.sh # Copied from https://github.com/nf-core/rnaseq/blob/3.12.0/bin/mqc_features_stat.py - path: mqc_features_stat.py + # Include the header for the biotypes in the component + - path: /src/assets/multiqc/biotypes_header.txt + dest: assets/multiqc/biotypes_header.txt engines: - type: docker @@ -43,4 +46,4 @@ engines: - type: python runners: - type: executable - - type: nextflow \ No newline at end of file + - type: nextflow diff --git a/src/workflows/quality_control/config.vsh.yaml b/src/workflows/quality_control/config.vsh.yaml index 63ccddb..f41741c 100644 --- a/src/workflows/quality_control/config.vsh.yaml +++ b/src/workflows/quality_control/config.vsh.yaml @@ -101,7 +101,7 @@ argument_groups: description: Specify if the GTF annotation is in GENCODE format. - name: "--biotypes_header" type: file - default: assets/multiqc/biotypes_header.txt + default: src/assets/multiqc/biotypes_header.txt - name: "--biotype" type: string description: Biotype value to use while appending entries to GTF file when additional fasta file is provided. @@ -243,10 +243,10 @@ argument_groups: type: boolean - name: "--pca_header_multiqc" type: file - default: assets/multiqc/deseq2_pca_header.txt + default: src/assets/multiqc/deseq2_pca_header.txt - name: "--clustering_header_multiqc" type: file - default: assets/multiqc/deseq2_clustering_header.txt + default: src/assets/multiqc/deseq2_clustering_header.txt - name: "--deseq2_vst" type: boolean description: Use vst transformation instead of rlog with DESeq2 diff --git a/src/workflows/rnaseq/config.vsh.yaml b/src/workflows/rnaseq/config.vsh.yaml index 0060fda..774d901 100644 --- a/src/workflows/rnaseq/config.vsh.yaml +++ b/src/workflows/rnaseq/config.vsh.yaml @@ -129,7 +129,7 @@ argument_groups: - name: "--ribo_database_manifest" type: file description: Text file containing paths to fasta files (one per line) that will be used to create the database for SortMeRNA. - default: assets/rrna-db-defaults.txt + default: src/assets/rrna-db-defaults.txt - name: UMI options arguments: @@ -310,10 +310,10 @@ argument_groups: default: '-verbose -seed 1 -seg_len 100000000' - name: "--pca_header_multiqc" type: file - default: assets/multiqc/deseq2_pca_header.txt + default: src/assets/multiqc/deseq2_pca_header.txt - name: "--clustering_header_multiqc" type: file - default: assets/multiqc/deseq2_clustering_header.txt + default: src/assets/multiqc/deseq2_clustering_header.txt - name: "--deseq2_vst" type: boolean default: true @@ -336,12 +336,12 @@ argument_groups: arguments: - name: "--multiqc_custom_config" type: file - default: assets/multiqc_config.yml + default: src/assets/multiqc_config.yml - name: "--multiqc_title" type: string - name: "--multiqc_methods_description" type: file - default: assets/methods_description_template.yml + default: src/assets/methods_description_template.yml - name: Output arguments: diff --git a/target/executable/bbmap_bbsplit/.config.vsh.yaml b/target/executable/bbmap_bbsplit/.config.vsh.yaml index 3b2b4fb..2ba28ab 100644 --- a/target/executable/bbmap_bbsplit/.config.vsh.yaml +++ b/target/executable/bbmap_bbsplit/.config.vsh.yaml @@ -238,8 +238,8 @@ build_info: output: "target/executable/bbmap_bbsplit" executable: "target/executable/bbmap_bbsplit/bbmap_bbsplit" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/bbmap_bbsplit/bbmap_bbsplit b/target/executable/bbmap_bbsplit/bbmap_bbsplit index 4baaebb..6b462d4 100755 --- a/target/executable/bbmap_bbsplit/bbmap_bbsplit +++ b/target/executable/bbmap_bbsplit/bbmap_bbsplit @@ -506,9 +506,9 @@ 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="2024-10-01T10:01:50Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:05Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/bedtools_genomecov/.config.vsh.yaml b/target/executable/bedtools_genomecov/.config.vsh.yaml index c4be6f4..ba75e9d 100644 --- a/target/executable/bedtools_genomecov/.config.vsh.yaml +++ b/target/executable/bedtools_genomecov/.config.vsh.yaml @@ -178,8 +178,8 @@ build_info: output: "target/executable/bedtools_genomecov" executable: "target/executable/bedtools_genomecov/bedtools_genomecov" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/bedtools_genomecov/bedtools_genomecov b/target/executable/bedtools_genomecov/bedtools_genomecov index e8bf0e2..f627a14 100755 --- a/target/executable/bedtools_genomecov/bedtools_genomecov +++ b/target/executable/bedtools_genomecov/bedtools_genomecov @@ -481,9 +481,9 @@ 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="2024-10-01T10:01:51Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:05Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/cat_additional_fasta/.config.vsh.yaml b/target/executable/cat_additional_fasta/.config.vsh.yaml index a57bed6..a334e37 100644 --- a/target/executable/cat_additional_fasta/.config.vsh.yaml +++ b/target/executable/cat_additional_fasta/.config.vsh.yaml @@ -182,8 +182,8 @@ build_info: output: "target/executable/cat_additional_fasta" executable: "target/executable/cat_additional_fasta/cat_additional_fasta" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/cat_additional_fasta/cat_additional_fasta b/target/executable/cat_additional_fasta/cat_additional_fasta index b9fca31..95da18e 100755 --- a/target/executable/cat_additional_fasta/cat_additional_fasta +++ b/target/executable/cat_additional_fasta/cat_additional_fasta @@ -480,9 +480,9 @@ function ViashDockerfile { FROM python:latest ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component cat_additional_fasta" -LABEL org.opencontainers.image.created="2024-10-01T10:01:59Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:13Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/cat_fastq/.config.vsh.yaml b/target/executable/cat_fastq/.config.vsh.yaml index e7933c0..77b1bde 100644 --- a/target/executable/cat_fastq/.config.vsh.yaml +++ b/target/executable/cat_fastq/.config.vsh.yaml @@ -169,8 +169,8 @@ build_info: output: "target/executable/cat_fastq" executable: "target/executable/cat_fastq/cat_fastq" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/cat_fastq/cat_fastq b/target/executable/cat_fastq/cat_fastq index fcc9253..811ac76 100755 --- a/target/executable/cat_fastq/cat_fastq +++ b/target/executable/cat_fastq/cat_fastq @@ -472,9 +472,9 @@ function ViashDockerfile { FROM ubuntu:22.04 ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component cat_fastq" -LABEL org.opencontainers.image.created="2024-10-01T10:01:59Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:13Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/deseq2_qc/.config.vsh.yaml b/target/executable/deseq2_qc/.config.vsh.yaml index 7080a65..ce2a890 100644 --- a/target/executable/deseq2_qc/.config.vsh.yaml +++ b/target/executable/deseq2_qc/.config.vsh.yaml @@ -1,11 +1,11 @@ name: "deseq2_qc" version: "main" argument_groups: -- name: "Input" +- name: "input" arguments: - type: "file" name: "--counts" - description: "Count file matrix where rows are genes and columns are samples" + description: "count file matrix where rows are genes and columns are samples" info: null must_exist: true create_parent: true @@ -104,7 +104,13 @@ resources: is_executable: true - type: "file" path: "deseq2_qc.r" -description: "Run DESeq2, perform PCA, generate heatmaps and scatterplots for samples\ +- type: "file" + path: "assets/multiqc/deseq2_pca_header.txt" + dest: "assets/multiqc/deseq2_pca_header.txt" +- type: "file" + path: "assets/multiqc/deseq2_clustering_header.txt" + dest: "assets/multiqc/deseq2_clustering_header.txt" +description: "run deseq2, perform pca, generate heatmaps and scatterplots for samples\ \ in the counts files\n" test_resources: - type: "bash_script" @@ -112,10 +118,6 @@ test_resources: is_executable: true - type: "file" path: "counts.tsv" -- type: "file" - path: "deseq2_pca_header.txt" -- type: "file" - path: "deseq2_clustering_header.txt" info: migration_info: git_repo: "https://github.com/nf-core/rnaseq.git" @@ -237,8 +239,8 @@ build_info: output: "target/executable/deseq2_qc" executable: "target/executable/deseq2_qc/deseq2_qc" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/deseq2_qc/assets/multiqc/deseq2_clustering_header.txt b/target/executable/deseq2_qc/assets/multiqc/deseq2_clustering_header.txt new file mode 100644 index 0000000..04e10ef --- /dev/null +++ b/target/executable/deseq2_qc/assets/multiqc/deseq2_clustering_header.txt @@ -0,0 +1,12 @@ +#id: 'deseq2_clustering' +#section_name: 'DESeq2 sample similarity' +#description: "is generated from clustering by Euclidean distances between +# DESeq2 +# rlog values for each sample +# in the deseq2_qc.r script." +#plot_type: 'heatmap' +#anchor: 'deseq2_clustering' +#pconfig: +# title: 'DESeq2: Heatmap of the sample-to-sample distances' +# xlab: True +# reverseColors: True diff --git a/target/executable/deseq2_qc/assets/multiqc/deseq2_pca_header.txt b/target/executable/deseq2_qc/assets/multiqc/deseq2_pca_header.txt new file mode 100644 index 0000000..2599732 --- /dev/null +++ b/target/executable/deseq2_qc/assets/multiqc/deseq2_pca_header.txt @@ -0,0 +1,11 @@ +#id: 'deseq2_pca' +#section_name: 'DESeq2 PCA plot' +#description: "PCA plot between samples in the experiment. +# These values are calculated using DESeq2 +# in the deseq2_qc.r script." +#plot_type: 'scatter' +#anchor: 'deseq2_pca' +#pconfig: +# title: 'DESeq2: Principal component plot' +# xlab: PC1 +# ylab: PC2 diff --git a/target/executable/deseq2_qc/deseq2_qc b/target/executable/deseq2_qc/deseq2_qc index 8711d25..3857d81 100755 --- a/target/executable/deseq2_qc/deseq2_qc +++ b/target/executable/deseq2_qc/deseq2_qc @@ -173,13 +173,13 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" function ViashHelp { echo "deseq2_qc main" echo "" - echo "Run DESeq2, perform PCA, generate heatmaps and scatterplots for samples in the" + echo "run deseq2, perform pca, generate heatmaps and scatterplots for samples in the" echo "counts files" echo "" - echo "Input:" + echo "input:" echo " --counts" echo " type: file, file must exist" - echo " Count file matrix where rows are genes and columns are samples" + echo " count file matrix where rows are genes and columns are samples" echo "" echo " --pca_header_multiqc" echo " type: file, file must exist" @@ -502,9 +502,9 @@ 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="2024-10-01T10:02:10Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:25Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/dupradar/.config.vsh.yaml b/target/executable/dupradar/.config.vsh.yaml index 9a3e8b1..0d9e3d0 100644 --- a/target/executable/dupradar/.config.vsh.yaml +++ b/target/executable/dupradar/.config.vsh.yaml @@ -266,8 +266,8 @@ build_info: output: "target/executable/dupradar" executable: "target/executable/dupradar/dupradar" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/dupradar/dupradar b/target/executable/dupradar/dupradar index 34feab1..3a4256c 100755 --- a/target/executable/dupradar/dupradar +++ b/target/executable/dupradar/dupradar @@ -520,9 +520,9 @@ 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="2024-10-01T10:02:01Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:14Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/fastqc/.config.vsh.yaml b/target/executable/fastqc/.config.vsh.yaml index 7eca36e..422f610 100644 --- a/target/executable/fastqc/.config.vsh.yaml +++ b/target/executable/fastqc/.config.vsh.yaml @@ -198,8 +198,8 @@ build_info: output: "target/executable/fastqc" executable: "target/executable/fastqc/fastqc" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/fastqc/fastqc b/target/executable/fastqc/fastqc index 0fa3e28..863672a 100755 --- a/target/executable/fastqc/fastqc +++ b/target/executable/fastqc/fastqc @@ -490,9 +490,9 @@ 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="2024-10-01T10:01:52Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:06Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/fq_subsample/.config.vsh.yaml b/target/executable/fq_subsample/.config.vsh.yaml index b8d1e13..1a48d8b 100644 --- a/target/executable/fq_subsample/.config.vsh.yaml +++ b/target/executable/fq_subsample/.config.vsh.yaml @@ -177,8 +177,8 @@ build_info: output: "target/executable/fq_subsample" executable: "target/executable/fq_subsample/fq_subsample" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/fq_subsample/fq_subsample b/target/executable/fq_subsample/fq_subsample index b812f86..0b7fc07 100755 --- a/target/executable/fq_subsample/fq_subsample +++ b/target/executable/fq_subsample/fq_subsample @@ -485,9 +485,9 @@ 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="2024-10-01T10:01:51Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:06Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/getchromsizes/.config.vsh.yaml b/target/executable/getchromsizes/.config.vsh.yaml index 23676e4..cc06e31 100644 --- a/target/executable/getchromsizes/.config.vsh.yaml +++ b/target/executable/getchromsizes/.config.vsh.yaml @@ -167,8 +167,8 @@ build_info: output: "target/executable/getchromsizes" executable: "target/executable/getchromsizes/getchromsizes" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/getchromsizes/getchromsizes b/target/executable/getchromsizes/getchromsizes index f887888..fb598cc 100755 --- a/target/executable/getchromsizes/getchromsizes +++ b/target/executable/getchromsizes/getchromsizes @@ -480,9 +480,9 @@ make && \ make install LABEL org.opencontainers.image.description="Companion container for running component getchromsizes" -LABEL org.opencontainers.image.created="2024-10-01T10:01:52Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:07Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/gtf2bed/.config.vsh.yaml b/target/executable/gtf2bed/.config.vsh.yaml index 09c5b1e..795b9aa 100644 --- a/target/executable/gtf2bed/.config.vsh.yaml +++ b/target/executable/gtf2bed/.config.vsh.yaml @@ -145,8 +145,8 @@ build_info: output: "target/executable/gtf2bed" executable: "target/executable/gtf2bed/gtf2bed" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/gtf2bed/gtf2bed b/target/executable/gtf2bed/gtf2bed index 2c0857b..b476498 100755 --- a/target/executable/gtf2bed/gtf2bed +++ b/target/executable/gtf2bed/gtf2bed @@ -466,9 +466,9 @@ 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="2024-10-01T10:02:06Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:20Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/gtf_filter/.config.vsh.yaml b/target/executable/gtf_filter/.config.vsh.yaml index 68f1590..d804c87 100644 --- a/target/executable/gtf_filter/.config.vsh.yaml +++ b/target/executable/gtf_filter/.config.vsh.yaml @@ -155,8 +155,8 @@ build_info: output: "target/executable/gtf_filter" executable: "target/executable/gtf_filter/gtf_filter" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/gtf_filter/gtf_filter b/target/executable/gtf_filter/gtf_filter index 466459d..b3abd27 100755 --- a/target/executable/gtf_filter/gtf_filter +++ b/target/executable/gtf_filter/gtf_filter @@ -470,9 +470,9 @@ function ViashDockerfile { FROM python:latest ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component gtf_filter" -LABEL org.opencontainers.image.created="2024-10-01T10:02:09Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:23Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/gunzip/.config.vsh.yaml b/target/executable/gunzip/.config.vsh.yaml index 6e78e95..a6260eb 100644 --- a/target/executable/gunzip/.config.vsh.yaml +++ b/target/executable/gunzip/.config.vsh.yaml @@ -144,8 +144,8 @@ build_info: output: "target/executable/gunzip" executable: "target/executable/gunzip/gunzip" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/gunzip/gunzip b/target/executable/gunzip/gunzip index dbd2b3a..3c6bfee 100755 --- a/target/executable/gunzip/gunzip +++ b/target/executable/gunzip/gunzip @@ -466,9 +466,9 @@ 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="2024-10-01T10:01:52Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:07Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/kallisto/kallisto_index/.config.vsh.yaml b/target/executable/kallisto/kallisto_index/.config.vsh.yaml index 612c0e2..21b8187 100644 --- a/target/executable/kallisto/kallisto_index/.config.vsh.yaml +++ b/target/executable/kallisto/kallisto_index/.config.vsh.yaml @@ -155,8 +155,8 @@ build_info: output: "target/executable/kallisto/kallisto_index" executable: "target/executable/kallisto/kallisto_index/kallisto_index" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/kallisto/kallisto_index/kallisto_index b/target/executable/kallisto/kallisto_index/kallisto_index index dd1713e..b171b5c 100755 --- a/target/executable/kallisto/kallisto_index/kallisto_index +++ b/target/executable/kallisto/kallisto_index/kallisto_index @@ -471,9 +471,9 @@ 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="2024-10-01T10:02:07Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:22Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml index cb55b44..75eb5ed 100644 --- a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml +++ b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml @@ -253,8 +253,8 @@ build_info: output: "target/executable/kallisto/kallisto_quant" executable: "target/executable/kallisto/kallisto_quant/kallisto_quant" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/kallisto/kallisto_quant/kallisto_quant b/target/executable/kallisto/kallisto_quant/kallisto_quant index 495cd67..3337927 100755 --- a/target/executable/kallisto/kallisto_quant/kallisto_quant +++ b/target/executable/kallisto/kallisto_quant/kallisto_quant @@ -515,9 +515,9 @@ 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="2024-10-01T10:02:07Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:21Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/multiqc_custom_biotype/.config.vsh.yaml b/target/executable/multiqc_custom_biotype/.config.vsh.yaml index 9f747c2..2041898 100644 --- a/target/executable/multiqc_custom_biotype/.config.vsh.yaml +++ b/target/executable/multiqc_custom_biotype/.config.vsh.yaml @@ -64,6 +64,9 @@ resources: is_executable: true - type: "file" path: "mqc_features_stat.py" +- type: "file" + path: "assets/multiqc/biotypes_header.txt" + dest: "assets/multiqc/biotypes_header.txt" description: "Calculate features percentage for biotype counts" info: null status: "enabled" @@ -170,8 +173,8 @@ build_info: output: "target/executable/multiqc_custom_biotype" executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/multiqc_custom_biotype/assets/multiqc/biotypes_header.txt b/target/executable/multiqc_custom_biotype/assets/multiqc/biotypes_header.txt new file mode 100644 index 0000000..dff52c0 --- /dev/null +++ b/target/executable/multiqc_custom_biotype/assets/multiqc/biotypes_header.txt @@ -0,0 +1,11 @@ +# id: 'biotype_counts' +# section_name: 'Biotype Counts' +# description: "shows reads overlapping genomic features of different biotypes, +# counted by featureCounts." +# plot_type: 'bargraph' +# anchor: 'featurecounts_biotype' +# pconfig: +# id: "featurecounts_biotype_plot" +# title: "featureCounts: Biotypes" +# xlab: "# Reads" +# cpswitch_counts_label: "Number of Reads" diff --git a/target/executable/multiqc_custom_biotype/multiqc_custom_biotype b/target/executable/multiqc_custom_biotype/multiqc_custom_biotype index 6e1a081..5e2690f 100755 --- a/target/executable/multiqc_custom_biotype/multiqc_custom_biotype +++ b/target/executable/multiqc_custom_biotype/multiqc_custom_biotype @@ -481,9 +481,9 @@ 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="2024-10-01T10:02:01Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:15Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/picard_markduplicates/.config.vsh.yaml b/target/executable/picard_markduplicates/.config.vsh.yaml index 0f191d8..b45feca 100644 --- a/target/executable/picard_markduplicates/.config.vsh.yaml +++ b/target/executable/picard_markduplicates/.config.vsh.yaml @@ -207,8 +207,8 @@ build_info: output: "target/executable/picard_markduplicates" executable: "target/executable/picard_markduplicates/picard_markduplicates" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/picard_markduplicates/picard_markduplicates b/target/executable/picard_markduplicates/picard_markduplicates index af2b158..7941c01 100755 --- a/target/executable/picard_markduplicates/picard_markduplicates +++ b/target/executable/picard_markduplicates/picard_markduplicates @@ -494,9 +494,9 @@ 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="2024-10-01T10:02:09Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:24Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/prepare_multiqc_input/.config.vsh.yaml b/target/executable/prepare_multiqc_input/.config.vsh.yaml index f22363a..87a4f13 100644 --- a/target/executable/prepare_multiqc_input/.config.vsh.yaml +++ b/target/executable/prepare_multiqc_input/.config.vsh.yaml @@ -409,8 +409,8 @@ build_info: output: "target/executable/prepare_multiqc_input" executable: "target/executable/prepare_multiqc_input/prepare_multiqc_input" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/prepare_multiqc_input/prepare_multiqc_input b/target/executable/prepare_multiqc_input/prepare_multiqc_input index a05e600..9361704 100755 --- a/target/executable/prepare_multiqc_input/prepare_multiqc_input +++ b/target/executable/prepare_multiqc_input/prepare_multiqc_input @@ -557,9 +557,9 @@ 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="2024-10-01T10:02:05Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:19Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml b/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml index 0b84374..4b5ac07 100644 --- a/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml +++ b/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml @@ -138,8 +138,8 @@ build_info: output: "target/executable/preprocess_transcripts_fasta" executable: "target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta b/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta index 946dd70..70726be 100755 --- a/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta +++ b/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta @@ -462,9 +462,9 @@ 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="2024-10-01T10:02:04Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:19Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/preseq_lcextrap/.config.vsh.yaml b/target/executable/preseq_lcextrap/.config.vsh.yaml index f445fb1..1d457bd 100644 --- a/target/executable/preseq_lcextrap/.config.vsh.yaml +++ b/target/executable/preseq_lcextrap/.config.vsh.yaml @@ -191,8 +191,8 @@ build_info: output: "target/executable/preseq_lcextrap" executable: "target/executable/preseq_lcextrap/preseq_lcextrap" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/preseq_lcextrap/preseq_lcextrap b/target/executable/preseq_lcextrap/preseq_lcextrap index 2995f4d..4aadeb3 100755 --- a/target/executable/preseq_lcextrap/preseq_lcextrap +++ b/target/executable/preseq_lcextrap/preseq_lcextrap @@ -495,9 +495,9 @@ 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="2024-10-01T10:01:53Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:07Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/qualimap/.config.vsh.yaml b/target/executable/qualimap/.config.vsh.yaml index 11eab9e..b39318a 100644 --- a/target/executable/qualimap/.config.vsh.yaml +++ b/target/executable/qualimap/.config.vsh.yaml @@ -271,8 +271,8 @@ build_info: output: "target/executable/qualimap" executable: "target/executable/qualimap/qualimap" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/qualimap/qualimap b/target/executable/qualimap/qualimap index aabe489..704c420 100755 --- a/target/executable/qualimap/qualimap +++ b/target/executable/qualimap/qualimap @@ -537,9 +537,9 @@ 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="2024-10-01T10:01:51Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:06Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml index 1bde55d..e8b3fed 100644 --- a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml +++ b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml @@ -299,8 +299,8 @@ 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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression index 303f288..36377e5 100755 --- a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression +++ b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression @@ -542,9 +542,9 @@ 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="2024-10-01T10:02:06Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:21Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml b/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml index a48fbc6..cd07cbb 100644 --- a/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml +++ b/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml @@ -182,8 +182,8 @@ 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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/rsem/rsem_merge_counts/rsem_merge_counts b/target/executable/rsem/rsem_merge_counts/rsem_merge_counts index 681b32b..0058384 100755 --- a/target/executable/rsem/rsem_merge_counts/rsem_merge_counts +++ b/target/executable/rsem/rsem_merge_counts/rsem_merge_counts @@ -483,9 +483,9 @@ 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="2024-10-01T10:02:06Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:21Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml index e890a9c..1b9050f 100644 --- a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml @@ -163,8 +163,8 @@ build_info: output: "target/executable/rseqc/rseqc_bamstat" executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat index b625355..20524c9 100755 --- a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat +++ b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat @@ -477,9 +477,9 @@ 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="2024-10-01T10:02:04Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:18Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml index f15c898..c200ffd 100644 --- a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml @@ -186,8 +186,8 @@ build_info: output: "target/executable/rseqc/rseqc_inferexperiment" executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment index 7e29155..0523622 100755 --- a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment +++ b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment @@ -487,9 +487,9 @@ 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="2024-10-01T10:02:01Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:15Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml b/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml index 6ae2048..9d85c77 100644 --- a/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml @@ -272,8 +272,8 @@ build_info: output: "target/executable/rseqc/rseqc_innerdistance" executable: "target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance b/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance index c5c2860..e184ad5 100755 --- a/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance +++ b/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance @@ -529,9 +529,9 @@ 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="2024-10-01T10:02:03Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:18Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml b/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml index ba46fe4..020cf11 100644 --- a/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml @@ -260,8 +260,8 @@ build_info: output: "target/executable/rseqc/rseqc_junctionannotation" executable: "target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation b/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation index ef3702e..41bfa0d 100755 --- a/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation +++ b/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation @@ -519,9 +519,9 @@ 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="2024-10-01T10:02:03Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:17Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml b/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml index 0efcad0..7cb41ee 100644 --- a/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml @@ -249,8 +249,8 @@ build_info: output: "target/executable/rseqc/rseqc_junctionsaturation" executable: "target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation b/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation index f627e12..9b2d8c0 100755 --- a/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation +++ b/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation @@ -522,9 +522,9 @@ 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="2024-10-01T10:02:03Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:17Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml b/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml index 8595052..57e07e0 100644 --- a/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml @@ -162,8 +162,8 @@ build_info: output: "target/executable/rseqc/rseqc_readdistribution" executable: "target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution b/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution index 6b21425..c9c62dd 100755 --- a/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution +++ b/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution @@ -474,9 +474,9 @@ 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="2024-10-01T10:02:04Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:18Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml b/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml index ef92d93..ce77862 100644 --- a/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml @@ -211,8 +211,8 @@ build_info: output: "target/executable/rseqc/rseqc_readduplication" executable: "target/executable/rseqc/rseqc_readduplication/rseqc_readduplication" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication b/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication index e33f314..0173e33 100755 --- a/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication +++ b/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication @@ -499,9 +499,9 @@ 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="2024-10-01T10:02:02Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:16Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_tin/.config.vsh.yaml b/target/executable/rseqc/rseqc_tin/.config.vsh.yaml index bfa909d..cf084a4 100644 --- a/target/executable/rseqc/rseqc_tin/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_tin/.config.vsh.yaml @@ -214,8 +214,8 @@ build_info: output: "target/executable/rseqc/rseqc_tin" executable: "target/executable/rseqc/rseqc_tin/rseqc_tin" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/rseqc/rseqc_tin/rseqc_tin b/target/executable/rseqc/rseqc_tin/rseqc_tin index 8d19d29..618ce71 100755 --- a/target/executable/rseqc/rseqc_tin/rseqc_tin +++ b/target/executable/rseqc/rseqc_tin/rseqc_tin @@ -501,9 +501,9 @@ 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="2024-10-01T10:02:02Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:16Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/sortmerna/.config.vsh.yaml b/target/executable/sortmerna/.config.vsh.yaml index 6da1def..ed4e253 100644 --- a/target/executable/sortmerna/.config.vsh.yaml +++ b/target/executable/sortmerna/.config.vsh.yaml @@ -198,8 +198,8 @@ build_info: output: "target/executable/sortmerna" executable: "target/executable/sortmerna/sortmerna" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/sortmerna/sortmerna b/target/executable/sortmerna/sortmerna index 6f26b8d..74c61d9 100755 --- a/target/executable/sortmerna/sortmerna +++ b/target/executable/sortmerna/sortmerna @@ -492,9 +492,9 @@ 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="2024-10-01T10:02:09Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:23Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/stringtie/.config.vsh.yaml b/target/executable/stringtie/.config.vsh.yaml index 09cba5d..ebb60c7 100644 --- a/target/executable/stringtie/.config.vsh.yaml +++ b/target/executable/stringtie/.config.vsh.yaml @@ -216,8 +216,8 @@ build_info: output: "target/executable/stringtie" executable: "target/executable/stringtie/stringtie" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/stringtie/stringtie b/target/executable/stringtie/stringtie index bd3b787..efec08d 100755 --- a/target/executable/stringtie/stringtie +++ b/target/executable/stringtie/stringtie @@ -496,9 +496,9 @@ 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="2024-10-01T10:02:06Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:20Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/summarizedexperiment/.config.vsh.yaml b/target/executable/summarizedexperiment/.config.vsh.yaml index df2c8e6..632c7af 100644 --- a/target/executable/summarizedexperiment/.config.vsh.yaml +++ b/target/executable/summarizedexperiment/.config.vsh.yaml @@ -199,8 +199,8 @@ build_info: output: "target/executable/summarizedexperiment" executable: "target/executable/summarizedexperiment/summarizedexperiment" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/summarizedexperiment/summarizedexperiment b/target/executable/summarizedexperiment/summarizedexperiment index ef7910f..bb8ff1f 100755 --- a/target/executable/summarizedexperiment/summarizedexperiment +++ b/target/executable/summarizedexperiment/summarizedexperiment @@ -487,9 +487,9 @@ 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="2024-10-01T10:02:10Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:24Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/trimgalore/.config.vsh.yaml b/target/executable/trimgalore/.config.vsh.yaml index 4caa820..e4f1210 100644 --- a/target/executable/trimgalore/.config.vsh.yaml +++ b/target/executable/trimgalore/.config.vsh.yaml @@ -788,8 +788,8 @@ build_info: output: "target/executable/trimgalore" executable: "target/executable/trimgalore/trimgalore" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/trimgalore/trimgalore b/target/executable/trimgalore/trimgalore index 34b9926..86ceaa8 100755 --- a/target/executable/trimgalore/trimgalore +++ b/target/executable/trimgalore/trimgalore @@ -858,9 +858,9 @@ 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="2024-10-01T10:02:08Z" +LABEL org.opencontainers.image.created="2024-10-03T15:52:23Z" LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/tx2gene/.config.vsh.yaml b/target/executable/tx2gene/.config.vsh.yaml index 37617a0..4f56e04 100644 --- a/target/executable/tx2gene/.config.vsh.yaml +++ b/target/executable/tx2gene/.config.vsh.yaml @@ -192,8 +192,8 @@ build_info: output: "target/executable/tx2gene" executable: "target/executable/tx2gene/tx2gene" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/tx2gene/tx2gene b/target/executable/tx2gene/tx2gene index d8191bc..a1d958c 100755 --- a/target/executable/tx2gene/tx2gene +++ b/target/executable/tx2gene/tx2gene @@ -487,9 +487,9 @@ 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="2024-10-01T10:02:05Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:20Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/tximport/.config.vsh.yaml b/target/executable/tximport/.config.vsh.yaml index 6989b7b..976fb94 100644 --- a/target/executable/tximport/.config.vsh.yaml +++ b/target/executable/tximport/.config.vsh.yaml @@ -247,8 +247,8 @@ build_info: output: "target/executable/tximport" executable: "target/executable/tximport/tximport" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/tximport/tximport b/target/executable/tximport/tximport index d320a10..47bfd87 100755 --- a/target/executable/tximport/tximport +++ b/target/executable/tximport/tximport @@ -508,9 +508,9 @@ 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="2024-10-01T10:01:59Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:12Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/ucsc/bedclip/.config.vsh.yaml b/target/executable/ucsc/bedclip/.config.vsh.yaml index 73b11d9..82dea84 100644 --- a/target/executable/ucsc/bedclip/.config.vsh.yaml +++ b/target/executable/ucsc/bedclip/.config.vsh.yaml @@ -164,8 +164,8 @@ build_info: output: "target/executable/ucsc/bedclip" executable: "target/executable/ucsc/bedclip/bedclip" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/ucsc/bedclip/bedclip b/target/executable/ucsc/bedclip/bedclip index d948639..29f69ca 100755 --- a/target/executable/ucsc/bedclip/bedclip +++ b/target/executable/ucsc/bedclip/bedclip @@ -473,9 +473,9 @@ 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="2024-10-01T10:02:00Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:13Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml b/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml index 9a62b13..4b6b5ef 100644 --- a/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml +++ b/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml @@ -164,8 +164,8 @@ build_info: output: "target/executable/ucsc/bedgraphtobigwig" executable: "target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig b/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig index 0fa813c..8aff2d0 100755 --- a/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig +++ b/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig @@ -473,9 +473,9 @@ 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="2024-10-01T10:02:00Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:14Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/umitools/umitools_dedup/.config.vsh.yaml b/target/executable/umitools/umitools_dedup/.config.vsh.yaml index 193e1b2..c1db8bf 100644 --- a/target/executable/umitools/umitools_dedup/.config.vsh.yaml +++ b/target/executable/umitools/umitools_dedup/.config.vsh.yaml @@ -195,8 +195,8 @@ build_info: output: "target/executable/umitools/umitools_dedup" executable: "target/executable/umitools/umitools_dedup/umitools_dedup" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/umitools/umitools_dedup/umitools_dedup b/target/executable/umitools/umitools_dedup/umitools_dedup index 20b20d4..7b51c77 100755 --- a/target/executable/umitools/umitools_dedup/umitools_dedup +++ b/target/executable/umitools/umitools_dedup/umitools_dedup @@ -489,9 +489,9 @@ 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="2024-10-01T10:02:07Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:22Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/umitools/umitools_extract/.config.vsh.yaml b/target/executable/umitools/umitools_extract/.config.vsh.yaml index 973bc93..9930eb0 100644 --- a/target/executable/umitools/umitools_extract/.config.vsh.yaml +++ b/target/executable/umitools/umitools_extract/.config.vsh.yaml @@ -253,8 +253,8 @@ build_info: output: "target/executable/umitools/umitools_extract" executable: "target/executable/umitools/umitools_extract/umitools_extract" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/umitools/umitools_extract/umitools_extract b/target/executable/umitools/umitools_extract/umitools_extract index 8192e96..a150ab1 100755 --- a/target/executable/umitools/umitools_extract/umitools_extract +++ b/target/executable/umitools/umitools_extract/umitools_extract @@ -521,9 +521,9 @@ 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="2024-10-01T10:02:08Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:22Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/umitools_prepareforquant/.config.vsh.yaml b/target/executable/umitools_prepareforquant/.config.vsh.yaml index ecfb6cf..095a423 100644 --- a/target/executable/umitools_prepareforquant/.config.vsh.yaml +++ b/target/executable/umitools_prepareforquant/.config.vsh.yaml @@ -156,8 +156,8 @@ build_info: output: "target/executable/umitools_prepareforquant" executable: "target/executable/umitools_prepareforquant/umitools_prepareforquant" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/executable/umitools_prepareforquant/umitools_prepareforquant b/target/executable/umitools_prepareforquant/umitools_prepareforquant index d028ca0..36b2a04 100755 --- a/target/executable/umitools_prepareforquant/umitools_prepareforquant +++ b/target/executable/umitools_prepareforquant/umitools_prepareforquant @@ -473,9 +473,9 @@ 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="2024-10-01T10:02:10Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8" +LABEL org.opencontainers.image.created="2024-10-03T15:52:24Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b" LABEL org.opencontainers.image.version="main" VIASHDOCKER 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 cd04238..7c3dea0 100644 --- a/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml +++ b/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml @@ -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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@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" diff --git a/target/executable/workflows/merge_quant_results/.config.vsh.yaml b/target/executable/workflows/merge_quant_results/.config.vsh.yaml index a5b08c0..1f73b4d 100644 --- a/target/executable/workflows/merge_quant_results/.config.vsh.yaml +++ b/target/executable/workflows/merge_quant_results/.config.vsh.yaml @@ -278,8 +278,8 @@ 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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/tx2gene" - "target/nextflow/tximport" diff --git a/target/executable/workflows/post_processing/.config.vsh.yaml b/target/executable/workflows/post_processing/.config.vsh.yaml index b4dbadc..5620a7d 100644 --- a/target/executable/workflows/post_processing/.config.vsh.yaml +++ b/target/executable/workflows/post_processing/.config.vsh.yaml @@ -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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/picard_markduplicates" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort" diff --git a/target/executable/workflows/pre_processing/.config.vsh.yaml b/target/executable/workflows/pre_processing/.config.vsh.yaml index 1ccf1f1..9ce3e85 100644 --- a/target/executable/workflows/pre_processing/.config.vsh.yaml +++ b/target/executable/workflows/pre_processing/.config.vsh.yaml @@ -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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/fastqc" - "target/nextflow/umitools/umitools_extract" diff --git a/target/executable/workflows/prepare_genome/.config.vsh.yaml b/target/executable/workflows/prepare_genome/.config.vsh.yaml index 0a1142a..85743e7 100644 --- a/target/executable/workflows/prepare_genome/.config.vsh.yaml +++ b/target/executable/workflows/prepare_genome/.config.vsh.yaml @@ -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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/gunzip" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread" 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 33edd15..8c0079d 100644 --- a/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml +++ b/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml @@ -283,8 +283,8 @@ 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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant" - "target/nextflow/kallisto/kallisto_quant" diff --git a/target/executable/workflows/quality_control/.config.vsh.yaml b/target/executable/workflows/quality_control/.config.vsh.yaml index b0a6067..793b073 100644 --- a/target/executable/workflows/quality_control/.config.vsh.yaml +++ b/target/executable/workflows/quality_control/.config.vsh.yaml @@ -265,7 +265,7 @@ argument_groups: name: "--biotypes_header" info: null default: - - "assets/multiqc/biotypes_header.txt" + - "src/assets/multiqc/biotypes_header.txt" must_exist: true create_parent: true required: false @@ -563,7 +563,7 @@ argument_groups: name: "--pca_header_multiqc" info: null default: - - "assets/multiqc/deseq2_pca_header.txt" + - "src/assets/multiqc/deseq2_pca_header.txt" must_exist: true create_parent: true required: false @@ -574,7 +574,7 @@ argument_groups: name: "--clustering_header_multiqc" info: null default: - - "assets/multiqc/deseq2_clustering_header.txt" + - "src/assets/multiqc/deseq2_clustering_header.txt" must_exist: true create_parent: true required: false @@ -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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/rseqc/rseqc_bamstat" - "target/nextflow/rseqc/rseqc_inferexperiment" diff --git a/target/executable/workflows/quality_control/quality_control b/target/executable/workflows/quality_control/quality_control index c98b849..b56550f 100755 --- a/target/executable/workflows/quality_control/quality_control +++ b/target/executable/workflows/quality_control/quality_control @@ -296,7 +296,7 @@ function ViashHelp { echo "" echo " --biotypes_header" echo " type: file, file must exist" - echo " default: assets/multiqc/biotypes_header.txt" + echo " default: src/assets/multiqc/biotypes_header.txt" echo "" echo " --biotype" echo " type: string" @@ -464,11 +464,11 @@ function ViashHelp { echo "" echo " --pca_header_multiqc" echo " type: file, file must exist" - echo " default: assets/multiqc/deseq2_pca_header.txt" + echo " default: src/assets/multiqc/deseq2_pca_header.txt" echo "" echo " --clustering_header_multiqc" echo " type: file, file must exist" - echo " default: assets/multiqc/deseq2_clustering_header.txt" + echo " default: src/assets/multiqc/deseq2_clustering_header.txt" echo "" echo " --deseq2_vst" echo " type: boolean" @@ -2477,7 +2477,7 @@ if [ -z ${VIASH_PAR_FEATURECOUNTS_FEATURE_TYPE+x} ]; then VIASH_PAR_FEATURECOUNTS_FEATURE_TYPE="exon" fi if [ -z ${VIASH_PAR_BIOTYPES_HEADER+x} ]; then - VIASH_PAR_BIOTYPES_HEADER="assets/multiqc/biotypes_header.txt" + VIASH_PAR_BIOTYPES_HEADER="src/assets/multiqc/biotypes_header.txt" fi if [ -z ${VIASH_PAR_RSEQC_MODULES+x} ]; then VIASH_PAR_RSEQC_MODULES="bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication" @@ -2546,10 +2546,10 @@ if [ -z ${VIASH_PAR_JAVA_MEMORY_SIZE+x} ]; then VIASH_PAR_JAVA_MEMORY_SIZE="4G" fi if [ -z ${VIASH_PAR_PCA_HEADER_MULTIQC+x} ]; then - VIASH_PAR_PCA_HEADER_MULTIQC="assets/multiqc/deseq2_pca_header.txt" + VIASH_PAR_PCA_HEADER_MULTIQC="src/assets/multiqc/deseq2_pca_header.txt" fi if [ -z ${VIASH_PAR_CLUSTERING_HEADER_MULTIQC+x} ]; then - VIASH_PAR_CLUSTERING_HEADER_MULTIQC="assets/multiqc/deseq2_clustering_header.txt" + VIASH_PAR_CLUSTERING_HEADER_MULTIQC="src/assets/multiqc/deseq2_clustering_header.txt" fi if [ -z ${VIASH_PAR_EXTRA_DESEQ2_ARGS+x} ]; then VIASH_PAR_EXTRA_DESEQ2_ARGS="--id_col 1 --sample_suffix '' --outprefix deseq2 --count_col 3" diff --git a/target/executable/workflows/rnaseq/.config.vsh.yaml b/target/executable/workflows/rnaseq/.config.vsh.yaml index 8c4eb86..cc12ab8 100644 --- a/target/executable/workflows/rnaseq/.config.vsh.yaml +++ b/target/executable/workflows/rnaseq/.config.vsh.yaml @@ -295,7 +295,7 @@ argument_groups: \ be used to create the database for SortMeRNA." info: null default: - - "assets/rrna-db-defaults.txt" + - "src/assets/rrna-db-defaults.txt" must_exist: true create_parent: true required: false @@ -683,7 +683,7 @@ argument_groups: name: "--pca_header_multiqc" info: null default: - - "assets/multiqc/deseq2_pca_header.txt" + - "src/assets/multiqc/deseq2_pca_header.txt" must_exist: true create_parent: true required: false @@ -694,7 +694,7 @@ argument_groups: name: "--clustering_header_multiqc" info: null default: - - "assets/multiqc/deseq2_clustering_header.txt" + - "src/assets/multiqc/deseq2_clustering_header.txt" must_exist: true create_parent: true required: false @@ -754,7 +754,7 @@ argument_groups: name: "--multiqc_custom_config" info: null default: - - "assets/multiqc_config.yml" + - "src/assets/multiqc_config.yml" must_exist: true create_parent: true required: false @@ -772,7 +772,7 @@ argument_groups: name: "--multiqc_methods_description" info: null default: - - "assets/methods_description_template.yml" + - "src/assets/methods_description_template.yml" must_exist: true create_parent: true required: false @@ -2117,8 +2117,8 @@ build_info: output: "target/executable/workflows/rnaseq" executable: "target/executable/workflows/rnaseq/rnaseq" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/workflows/prepare_genome" - "target/nextflow/cat_fastq" diff --git a/target/executable/workflows/rnaseq/rnaseq b/target/executable/workflows/rnaseq/rnaseq index e50bfb9..f038f38 100755 --- a/target/executable/workflows/rnaseq/rnaseq +++ b/target/executable/workflows/rnaseq/rnaseq @@ -314,7 +314,7 @@ function ViashHelp { echo "" echo " --ribo_database_manifest" echo " type: file, file must exist" - echo " default: assets/rrna-db-defaults.txt" + echo " default: src/assets/rrna-db-defaults.txt" echo " Text file containing paths to fasta files (one per line) that will be" echo " used to create the database for SortMeRNA." echo "" @@ -545,11 +545,11 @@ function ViashHelp { echo "" echo " --pca_header_multiqc" echo " type: file, file must exist" - echo " default: assets/multiqc/deseq2_pca_header.txt" + echo " default: src/assets/multiqc/deseq2_pca_header.txt" echo "" echo " --clustering_header_multiqc" echo " type: file, file must exist" - echo " default: assets/multiqc/deseq2_clustering_header.txt" + echo " default: src/assets/multiqc/deseq2_clustering_header.txt" echo "" echo " --deseq2_vst" echo " type: boolean" @@ -576,14 +576,14 @@ function ViashHelp { echo "Multiqc paramenters:" echo " --multiqc_custom_config" echo " type: file, file must exist" - echo " default: assets/multiqc_config.yml" + echo " default: src/assets/multiqc_config.yml" echo "" echo " --multiqc_title" echo " type: string" echo "" echo " --multiqc_methods_description" echo " type: file, file must exist" - echo " default: assets/methods_description_template.yml" + echo " default: src/assets/methods_description_template.yml" echo "" echo "Output:" echo " --output_fasta" @@ -3202,7 +3202,7 @@ if [ -z ${VIASH_PAR_REMOVE_RIBO_RNA+x} ]; then VIASH_PAR_REMOVE_RIBO_RNA="false" fi if [ -z ${VIASH_PAR_RIBO_DATABASE_MANIFEST+x} ]; then - VIASH_PAR_RIBO_DATABASE_MANIFEST="assets/rrna-db-defaults.txt" + VIASH_PAR_RIBO_DATABASE_MANIFEST="src/assets/rrna-db-defaults.txt" fi if [ -z ${VIASH_PAR_WITH_UMI+x} ]; then VIASH_PAR_WITH_UMI="false" @@ -3319,10 +3319,10 @@ if [ -z ${VIASH_PAR_EXTRA_PRESEQ_ARGS+x} ]; then VIASH_PAR_EXTRA_PRESEQ_ARGS="-verbose -seed 1 -seg_len 100000000" fi if [ -z ${VIASH_PAR_PCA_HEADER_MULTIQC+x} ]; then - VIASH_PAR_PCA_HEADER_MULTIQC="assets/multiqc/deseq2_pca_header.txt" + VIASH_PAR_PCA_HEADER_MULTIQC="src/assets/multiqc/deseq2_pca_header.txt" fi if [ -z ${VIASH_PAR_CLUSTERING_HEADER_MULTIQC+x} ]; then - VIASH_PAR_CLUSTERING_HEADER_MULTIQC="assets/multiqc/deseq2_clustering_header.txt" + VIASH_PAR_CLUSTERING_HEADER_MULTIQC="src/assets/multiqc/deseq2_clustering_header.txt" fi if [ -z ${VIASH_PAR_DESEQ2_VST+x} ]; then VIASH_PAR_DESEQ2_VST="true" @@ -3337,10 +3337,10 @@ if [ -z ${VIASH_PAR_RSEQC_MODULES+x} ]; then VIASH_PAR_RSEQC_MODULES="bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication" fi if [ -z ${VIASH_PAR_MULTIQC_CUSTOM_CONFIG+x} ]; then - VIASH_PAR_MULTIQC_CUSTOM_CONFIG="assets/multiqc_config.yml" + VIASH_PAR_MULTIQC_CUSTOM_CONFIG="src/assets/multiqc_config.yml" fi if [ -z ${VIASH_PAR_MULTIQC_METHODS_DESCRIPTION+x} ]; then - VIASH_PAR_MULTIQC_METHODS_DESCRIPTION="assets/methods_description_template.yml" + VIASH_PAR_MULTIQC_METHODS_DESCRIPTION="src/assets/methods_description_template.yml" fi if [ -z ${VIASH_PAR_OUTPUT_FASTA+x} ]; then VIASH_PAR_OUTPUT_FASTA="reference/genome.fasta" diff --git a/target/nextflow/bbmap_bbsplit/.config.vsh.yaml b/target/nextflow/bbmap_bbsplit/.config.vsh.yaml index 58336eb..478c585 100644 --- a/target/nextflow/bbmap_bbsplit/.config.vsh.yaml +++ b/target/nextflow/bbmap_bbsplit/.config.vsh.yaml @@ -238,8 +238,8 @@ build_info: output: "target/nextflow/bbmap_bbsplit" executable: "target/nextflow/bbmap_bbsplit/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/bbmap_bbsplit/main.nf b/target/nextflow/bbmap_bbsplit/main.nf index 5a8b993..a4684b5 100644 --- a/target/nextflow/bbmap_bbsplit/main.nf +++ b/target/nextflow/bbmap_bbsplit/main.nf @@ -3104,8 +3104,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/bbmap_bbsplit", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/bedtools_genomecov/.config.vsh.yaml b/target/nextflow/bedtools_genomecov/.config.vsh.yaml index a8ba404..44f30a2 100644 --- a/target/nextflow/bedtools_genomecov/.config.vsh.yaml +++ b/target/nextflow/bedtools_genomecov/.config.vsh.yaml @@ -178,8 +178,8 @@ build_info: output: "target/nextflow/bedtools_genomecov" executable: "target/nextflow/bedtools_genomecov/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/bedtools_genomecov/main.nf b/target/nextflow/bedtools_genomecov/main.nf index baacec5..5c71b81 100644 --- a/target/nextflow/bedtools_genomecov/main.nf +++ b/target/nextflow/bedtools_genomecov/main.nf @@ -3031,8 +3031,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/bedtools_genomecov", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/cat_additional_fasta/.config.vsh.yaml b/target/nextflow/cat_additional_fasta/.config.vsh.yaml index 7996df6..4b2cca6 100644 --- a/target/nextflow/cat_additional_fasta/.config.vsh.yaml +++ b/target/nextflow/cat_additional_fasta/.config.vsh.yaml @@ -182,8 +182,8 @@ build_info: output: "target/nextflow/cat_additional_fasta" executable: "target/nextflow/cat_additional_fasta/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/cat_additional_fasta/main.nf b/target/nextflow/cat_additional_fasta/main.nf index 6d16023..0163e94 100644 --- a/target/nextflow/cat_additional_fasta/main.nf +++ b/target/nextflow/cat_additional_fasta/main.nf @@ -3032,8 +3032,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/cat_additional_fasta", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/cat_fastq/.config.vsh.yaml b/target/nextflow/cat_fastq/.config.vsh.yaml index c53e9f7..a972b8d 100644 --- a/target/nextflow/cat_fastq/.config.vsh.yaml +++ b/target/nextflow/cat_fastq/.config.vsh.yaml @@ -169,8 +169,8 @@ build_info: output: "target/nextflow/cat_fastq" executable: "target/nextflow/cat_fastq/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/cat_fastq/main.nf b/target/nextflow/cat_fastq/main.nf index f88157f..375ed6d 100644 --- a/target/nextflow/cat_fastq/main.nf +++ b/target/nextflow/cat_fastq/main.nf @@ -3023,8 +3023,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/cat_fastq", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/deseq2_qc/.config.vsh.yaml b/target/nextflow/deseq2_qc/.config.vsh.yaml index af85432..86b77b5 100644 --- a/target/nextflow/deseq2_qc/.config.vsh.yaml +++ b/target/nextflow/deseq2_qc/.config.vsh.yaml @@ -1,11 +1,11 @@ name: "deseq2_qc" version: "main" argument_groups: -- name: "Input" +- name: "input" arguments: - type: "file" name: "--counts" - description: "Count file matrix where rows are genes and columns are samples" + description: "count file matrix where rows are genes and columns are samples" info: null must_exist: true create_parent: true @@ -104,7 +104,13 @@ resources: is_executable: true - type: "file" path: "deseq2_qc.r" -description: "Run DESeq2, perform PCA, generate heatmaps and scatterplots for samples\ +- type: "file" + path: "assets/multiqc/deseq2_pca_header.txt" + dest: "assets/multiqc/deseq2_pca_header.txt" +- type: "file" + path: "assets/multiqc/deseq2_clustering_header.txt" + dest: "assets/multiqc/deseq2_clustering_header.txt" +description: "run deseq2, perform pca, generate heatmaps and scatterplots for samples\ \ in the counts files\n" test_resources: - type: "bash_script" @@ -112,10 +118,6 @@ test_resources: is_executable: true - type: "file" path: "counts.tsv" -- type: "file" - path: "deseq2_pca_header.txt" -- type: "file" - path: "deseq2_clustering_header.txt" info: migration_info: git_repo: "https://github.com/nf-core/rnaseq.git" @@ -237,8 +239,8 @@ build_info: output: "target/nextflow/deseq2_qc" executable: "target/nextflow/deseq2_qc/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/deseq2_qc/assets/multiqc/deseq2_clustering_header.txt b/target/nextflow/deseq2_qc/assets/multiqc/deseq2_clustering_header.txt new file mode 100644 index 0000000..04e10ef --- /dev/null +++ b/target/nextflow/deseq2_qc/assets/multiqc/deseq2_clustering_header.txt @@ -0,0 +1,12 @@ +#id: 'deseq2_clustering' +#section_name: 'DESeq2 sample similarity' +#description: "is generated from clustering by Euclidean distances between +# DESeq2 +# rlog values for each sample +# in the deseq2_qc.r script." +#plot_type: 'heatmap' +#anchor: 'deseq2_clustering' +#pconfig: +# title: 'DESeq2: Heatmap of the sample-to-sample distances' +# xlab: True +# reverseColors: True diff --git a/target/nextflow/deseq2_qc/assets/multiqc/deseq2_pca_header.txt b/target/nextflow/deseq2_qc/assets/multiqc/deseq2_pca_header.txt new file mode 100644 index 0000000..2599732 --- /dev/null +++ b/target/nextflow/deseq2_qc/assets/multiqc/deseq2_pca_header.txt @@ -0,0 +1,11 @@ +#id: 'deseq2_pca' +#section_name: 'DESeq2 PCA plot' +#description: "PCA plot between samples in the experiment. +# These values are calculated using DESeq2 +# in the deseq2_qc.r script." +#plot_type: 'scatter' +#anchor: 'deseq2_pca' +#pconfig: +# title: 'DESeq2: Principal component plot' +# xlab: PC1 +# ylab: PC2 diff --git a/target/nextflow/deseq2_qc/main.nf b/target/nextflow/deseq2_qc/main.nf index eaef2ff..4acf679 100644 --- a/target/nextflow/deseq2_qc/main.nf +++ b/target/nextflow/deseq2_qc/main.nf @@ -2808,12 +2808,12 @@ meta = [ "version" : "main", "argument_groups" : [ { - "name" : "Input", + "name" : "input", "arguments" : [ { "type" : "file", "name" : "--counts", - "description" : "Count file matrix where rows are genes and columns are samples", + "description" : "count file matrix where rows are genes and columns are samples", "must_exist" : true, "create_parent" : true, "required" : false, @@ -2937,9 +2937,19 @@ meta = [ { "type" : "file", "path" : "deseq2_qc.r" + }, + { + "type" : "file", + "path" : "/src/assets/multiqc/deseq2_pca_header.txt", + "dest" : "assets/multiqc/deseq2_pca_header.txt" + }, + { + "type" : "file", + "path" : "/src/assets/multiqc/deseq2_clustering_header.txt", + "dest" : "assets/multiqc/deseq2_clustering_header.txt" } ], - "description" : "Run DESeq2, perform PCA, generate heatmaps and scatterplots for samples in the counts files\n", + "description" : "run deseq2, perform pca, generate heatmaps and scatterplots for samples in the counts files\n", "test_resources" : [ { "type" : "bash_script", @@ -2949,14 +2959,6 @@ meta = [ { "type" : "file", "path" : "/testData/unit_test_resources/counts.tsv" - }, - { - "type" : "file", - "path" : "/assets/multiqc/deseq2_pca_header.txt" - }, - { - "type" : "file", - "path" : "/assets/multiqc/deseq2_clustering_header.txt" } ], "info" : { @@ -3110,8 +3112,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/deseq2_qc", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/deseq2_qc/nextflow.config b/target/nextflow/deseq2_qc/nextflow.config index 47b4a82..2275751 100644 --- a/target/nextflow/deseq2_qc/nextflow.config +++ b/target/nextflow/deseq2_qc/nextflow.config @@ -3,7 +3,7 @@ manifest { mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' version = 'main' - description = 'Run DESeq2, perform PCA, generate heatmaps and scatterplots for samples in the counts files\n' + description = 'run deseq2, perform pca, generate heatmaps and scatterplots for samples in the counts files\n' } process.container = 'nextflow/bash:latest' diff --git a/target/nextflow/deseq2_qc/nextflow_schema.json b/target/nextflow/deseq2_qc/nextflow_schema.json index 94e8ce8..b723a87 100644 --- a/target/nextflow/deseq2_qc/nextflow_schema.json +++ b/target/nextflow/deseq2_qc/nextflow_schema.json @@ -1,14 +1,14 @@ { "$schema": "http://json-schema.org/draft-07/schema", "title": "deseq2_qc", -"description": "Run DESeq2, perform PCA, generate heatmaps and scatterplots for samples in the counts files\n", +"description": "run deseq2, perform pca, generate heatmaps and scatterplots for samples in the counts files\n", "type": "object", "definitions": { "input" : { - "title": "Input", + "title": "input", "type": "object", "description": "No description", "properties": { @@ -17,8 +17,8 @@ "counts": { "type": "string", - "description": "Type: `file`. Count file matrix where rows are genes and columns are samples", - "help_text": "Type: `file`. Count file matrix where rows are genes and columns are samples" + "description": "Type: `file`. count file matrix where rows are genes and columns are samples", + "help_text": "Type: `file`. count file matrix where rows are genes and columns are samples" } diff --git a/target/nextflow/dupradar/.config.vsh.yaml b/target/nextflow/dupradar/.config.vsh.yaml index fb73433..dce3852 100644 --- a/target/nextflow/dupradar/.config.vsh.yaml +++ b/target/nextflow/dupradar/.config.vsh.yaml @@ -266,8 +266,8 @@ build_info: output: "target/nextflow/dupradar" executable: "target/nextflow/dupradar/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/dupradar/main.nf b/target/nextflow/dupradar/main.nf index 1c22cd0..5bdf25b 100644 --- a/target/nextflow/dupradar/main.nf +++ b/target/nextflow/dupradar/main.nf @@ -3136,8 +3136,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/dupradar", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/fastqc/.config.vsh.yaml b/target/nextflow/fastqc/.config.vsh.yaml index e896689..d598f0c 100644 --- a/target/nextflow/fastqc/.config.vsh.yaml +++ b/target/nextflow/fastqc/.config.vsh.yaml @@ -198,8 +198,8 @@ build_info: output: "target/nextflow/fastqc" executable: "target/nextflow/fastqc/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/fastqc/main.nf b/target/nextflow/fastqc/main.nf index 82e14ba..12f121f 100644 --- a/target/nextflow/fastqc/main.nf +++ b/target/nextflow/fastqc/main.nf @@ -3056,8 +3056,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/fastqc", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/fq_subsample/.config.vsh.yaml b/target/nextflow/fq_subsample/.config.vsh.yaml index b58b9ea..057f195 100644 --- a/target/nextflow/fq_subsample/.config.vsh.yaml +++ b/target/nextflow/fq_subsample/.config.vsh.yaml @@ -177,8 +177,8 @@ build_info: output: "target/nextflow/fq_subsample" executable: "target/nextflow/fq_subsample/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/fq_subsample/main.nf b/target/nextflow/fq_subsample/main.nf index c88f9c3..4240756 100644 --- a/target/nextflow/fq_subsample/main.nf +++ b/target/nextflow/fq_subsample/main.nf @@ -3027,8 +3027,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/fq_subsample", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/getchromsizes/.config.vsh.yaml b/target/nextflow/getchromsizes/.config.vsh.yaml index 9abe4e5..46c64e4 100644 --- a/target/nextflow/getchromsizes/.config.vsh.yaml +++ b/target/nextflow/getchromsizes/.config.vsh.yaml @@ -167,8 +167,8 @@ build_info: output: "target/nextflow/getchromsizes" executable: "target/nextflow/getchromsizes/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/getchromsizes/main.nf b/target/nextflow/getchromsizes/main.nf index dc90cd8..502f0dd 100644 --- a/target/nextflow/getchromsizes/main.nf +++ b/target/nextflow/getchromsizes/main.nf @@ -3013,8 +3013,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/getchromsizes", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/gtf2bed/.config.vsh.yaml b/target/nextflow/gtf2bed/.config.vsh.yaml index d4ba96a..c9b5101 100644 --- a/target/nextflow/gtf2bed/.config.vsh.yaml +++ b/target/nextflow/gtf2bed/.config.vsh.yaml @@ -145,8 +145,8 @@ build_info: output: "target/nextflow/gtf2bed" executable: "target/nextflow/gtf2bed/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/gtf2bed/main.nf b/target/nextflow/gtf2bed/main.nf index 3ef4070..84ed9ff 100644 --- a/target/nextflow/gtf2bed/main.nf +++ b/target/nextflow/gtf2bed/main.nf @@ -2995,8 +2995,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/gtf2bed", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/gtf_filter/.config.vsh.yaml b/target/nextflow/gtf_filter/.config.vsh.yaml index 46b22c6..4999d8b 100644 --- a/target/nextflow/gtf_filter/.config.vsh.yaml +++ b/target/nextflow/gtf_filter/.config.vsh.yaml @@ -155,8 +155,8 @@ build_info: output: "target/nextflow/gtf_filter" executable: "target/nextflow/gtf_filter/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/gtf_filter/main.nf b/target/nextflow/gtf_filter/main.nf index b876cef..6937862 100644 --- a/target/nextflow/gtf_filter/main.nf +++ b/target/nextflow/gtf_filter/main.nf @@ -3003,8 +3003,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/gtf_filter", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/gunzip/.config.vsh.yaml b/target/nextflow/gunzip/.config.vsh.yaml index df04e35..912a8e4 100644 --- a/target/nextflow/gunzip/.config.vsh.yaml +++ b/target/nextflow/gunzip/.config.vsh.yaml @@ -144,8 +144,8 @@ build_info: output: "target/nextflow/gunzip" executable: "target/nextflow/gunzip/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/gunzip/main.nf b/target/nextflow/gunzip/main.nf index 398f951..42b380b 100644 --- a/target/nextflow/gunzip/main.nf +++ b/target/nextflow/gunzip/main.nf @@ -2992,8 +2992,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/gunzip", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml index eec3a34..e92769a 100644 --- a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml +++ b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml @@ -155,8 +155,8 @@ build_info: output: "target/nextflow/kallisto/kallisto_index" executable: "target/nextflow/kallisto/kallisto_index/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/kallisto/kallisto_index/main.nf b/target/nextflow/kallisto/kallisto_index/main.nf index d30b9ca..f3734fc 100644 --- a/target/nextflow/kallisto/kallisto_index/main.nf +++ b/target/nextflow/kallisto/kallisto_index/main.nf @@ -3002,8 +3002,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/kallisto/kallisto_index", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml index f0ff052..1881cd8 100644 --- a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml +++ b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml @@ -253,8 +253,8 @@ build_info: output: "target/nextflow/kallisto/kallisto_quant" executable: "target/nextflow/kallisto/kallisto_quant/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/kallisto/kallisto_quant/main.nf b/target/nextflow/kallisto/kallisto_quant/main.nf index 87f5106..3643f51 100644 --- a/target/nextflow/kallisto/kallisto_quant/main.nf +++ b/target/nextflow/kallisto/kallisto_quant/main.nf @@ -3114,8 +3114,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/kallisto/kallisto_quant", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml b/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml index 6e4312b..e66352d 100644 --- a/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml +++ b/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml @@ -64,6 +64,9 @@ resources: is_executable: true - type: "file" path: "mqc_features_stat.py" +- type: "file" + path: "assets/multiqc/biotypes_header.txt" + dest: "assets/multiqc/biotypes_header.txt" description: "Calculate features percentage for biotype counts" info: null status: "enabled" @@ -170,8 +173,8 @@ build_info: output: "target/nextflow/multiqc_custom_biotype" executable: "target/nextflow/multiqc_custom_biotype/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/multiqc_custom_biotype/assets/multiqc/biotypes_header.txt b/target/nextflow/multiqc_custom_biotype/assets/multiqc/biotypes_header.txt new file mode 100644 index 0000000..dff52c0 --- /dev/null +++ b/target/nextflow/multiqc_custom_biotype/assets/multiqc/biotypes_header.txt @@ -0,0 +1,11 @@ +# id: 'biotype_counts' +# section_name: 'Biotype Counts' +# description: "shows reads overlapping genomic features of different biotypes, +# counted by featureCounts." +# plot_type: 'bargraph' +# anchor: 'featurecounts_biotype' +# pconfig: +# id: "featurecounts_biotype_plot" +# title: "featureCounts: Biotypes" +# xlab: "# Reads" +# cpswitch_counts_label: "Number of Reads" diff --git a/target/nextflow/multiqc_custom_biotype/main.nf b/target/nextflow/multiqc_custom_biotype/main.nf index e1dc491..24be1d7 100644 --- a/target/nextflow/multiqc_custom_biotype/main.nf +++ b/target/nextflow/multiqc_custom_biotype/main.nf @@ -2889,6 +2889,11 @@ meta = [ { "type" : "file", "path" : "mqc_features_stat.py" + }, + { + "type" : "file", + "path" : "/src/assets/multiqc/biotypes_header.txt", + "dest" : "assets/multiqc/biotypes_header.txt" } ], "description" : "Calculate features percentage for biotype counts", @@ -3020,8 +3025,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/multiqc_custom_biotype", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/picard_markduplicates/.config.vsh.yaml b/target/nextflow/picard_markduplicates/.config.vsh.yaml index 2aa1a86..7494fb1 100644 --- a/target/nextflow/picard_markduplicates/.config.vsh.yaml +++ b/target/nextflow/picard_markduplicates/.config.vsh.yaml @@ -207,8 +207,8 @@ build_info: output: "target/nextflow/picard_markduplicates" executable: "target/nextflow/picard_markduplicates/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/picard_markduplicates/main.nf b/target/nextflow/picard_markduplicates/main.nf index e9ab878..5412bcf 100644 --- a/target/nextflow/picard_markduplicates/main.nf +++ b/target/nextflow/picard_markduplicates/main.nf @@ -3063,8 +3063,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/picard_markduplicates", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/prepare_multiqc_input/.config.vsh.yaml b/target/nextflow/prepare_multiqc_input/.config.vsh.yaml index aab0543..59c4dd5 100644 --- a/target/nextflow/prepare_multiqc_input/.config.vsh.yaml +++ b/target/nextflow/prepare_multiqc_input/.config.vsh.yaml @@ -409,8 +409,8 @@ build_info: output: "target/nextflow/prepare_multiqc_input" executable: "target/nextflow/prepare_multiqc_input/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/prepare_multiqc_input/main.nf b/target/nextflow/prepare_multiqc_input/main.nf index 2db2b7b..bb2efb4 100644 --- a/target/nextflow/prepare_multiqc_input/main.nf +++ b/target/nextflow/prepare_multiqc_input/main.nf @@ -3277,8 +3277,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/prepare_multiqc_input", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml b/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml index 7e6958d..5cea1da 100644 --- a/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml +++ b/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml @@ -138,8 +138,8 @@ build_info: output: "target/nextflow/preprocess_transcripts_fasta" executable: "target/nextflow/preprocess_transcripts_fasta/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/preprocess_transcripts_fasta/main.nf b/target/nextflow/preprocess_transcripts_fasta/main.nf index c235488..370dd9b 100644 --- a/target/nextflow/preprocess_transcripts_fasta/main.nf +++ b/target/nextflow/preprocess_transcripts_fasta/main.nf @@ -2982,8 +2982,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/preprocess_transcripts_fasta", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/preseq_lcextrap/.config.vsh.yaml b/target/nextflow/preseq_lcextrap/.config.vsh.yaml index 8310108..aece042 100644 --- a/target/nextflow/preseq_lcextrap/.config.vsh.yaml +++ b/target/nextflow/preseq_lcextrap/.config.vsh.yaml @@ -191,8 +191,8 @@ build_info: output: "target/nextflow/preseq_lcextrap" executable: "target/nextflow/preseq_lcextrap/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/preseq_lcextrap/main.nf b/target/nextflow/preseq_lcextrap/main.nf index 155c0f9..cb7f322 100644 --- a/target/nextflow/preseq_lcextrap/main.nf +++ b/target/nextflow/preseq_lcextrap/main.nf @@ -3035,8 +3035,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/preseq_lcextrap", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/qualimap/.config.vsh.yaml b/target/nextflow/qualimap/.config.vsh.yaml index 006f995..34924b5 100644 --- a/target/nextflow/qualimap/.config.vsh.yaml +++ b/target/nextflow/qualimap/.config.vsh.yaml @@ -271,8 +271,8 @@ build_info: output: "target/nextflow/qualimap" executable: "target/nextflow/qualimap/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/qualimap/main.nf b/target/nextflow/qualimap/main.nf index 5bd600c..eb9abfb 100644 --- a/target/nextflow/qualimap/main.nf +++ b/target/nextflow/qualimap/main.nf @@ -3144,8 +3144,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/qualimap", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml index 0df5912..4211cea 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml @@ -299,8 +299,8 @@ 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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/rsem/rsem_calculate_expression/main.nf b/target/nextflow/rsem/rsem_calculate_expression/main.nf index 69faf78..cd154a0 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/main.nf +++ b/target/nextflow/rsem/rsem_calculate_expression/main.nf @@ -3163,8 +3163,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rsem/rsem_calculate_expression", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml b/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml index 1260b81..2c67d9e 100644 --- a/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml @@ -182,8 +182,8 @@ 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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/rsem/rsem_merge_counts/main.nf b/target/nextflow/rsem/rsem_merge_counts/main.nf index ae04731..e3add00 100644 --- a/target/nextflow/rsem/rsem_merge_counts/main.nf +++ b/target/nextflow/rsem/rsem_merge_counts/main.nf @@ -3028,8 +3028,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rsem/rsem_merge_counts", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml index edb53fb..0d77de6 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml @@ -163,8 +163,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_bamstat" executable: "target/nextflow/rseqc/rseqc_bamstat/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/rseqc/rseqc_bamstat/main.nf b/target/nextflow/rseqc/rseqc_bamstat/main.nf index acc6d08..02ad4b2 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/main.nf +++ b/target/nextflow/rseqc/rseqc_bamstat/main.nf @@ -3016,8 +3016,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_bamstat", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml index 56c160a..4311bf7 100644 --- a/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml @@ -186,8 +186,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_inferexperiment" executable: "target/nextflow/rseqc/rseqc_inferexperiment/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/main.nf b/target/nextflow/rseqc/rseqc_inferexperiment/main.nf index 0aac828..c800683 100644 --- a/target/nextflow/rseqc/rseqc_inferexperiment/main.nf +++ b/target/nextflow/rseqc/rseqc_inferexperiment/main.nf @@ -3044,8 +3044,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_inferexperiment", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml index 30677e3..6ffc40b 100644 --- a/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml @@ -272,8 +272,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_innerdistance" executable: "target/nextflow/rseqc/rseqc_innerdistance/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/rseqc/rseqc_innerdistance/main.nf b/target/nextflow/rseqc/rseqc_innerdistance/main.nf index e8bfe39..3b6a9ee 100644 --- a/target/nextflow/rseqc/rseqc_innerdistance/main.nf +++ b/target/nextflow/rseqc/rseqc_innerdistance/main.nf @@ -3137,8 +3137,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_innerdistance", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml index 80122c1..2d306b7 100644 --- a/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml @@ -260,8 +260,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_junctionannotation" executable: "target/nextflow/rseqc/rseqc_junctionannotation/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/rseqc/rseqc_junctionannotation/main.nf b/target/nextflow/rseqc/rseqc_junctionannotation/main.nf index 75b41b1..c68150a 100644 --- a/target/nextflow/rseqc/rseqc_junctionannotation/main.nf +++ b/target/nextflow/rseqc/rseqc_junctionannotation/main.nf @@ -3128,8 +3128,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_junctionannotation", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml index 6b3f5fe..4e5639e 100644 --- a/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml @@ -249,8 +249,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_junctionsaturation" executable: "target/nextflow/rseqc/rseqc_junctionsaturation/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf b/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf index d226b6e..127b422 100644 --- a/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf +++ b/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf @@ -3113,8 +3113,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_junctionsaturation", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml index ef65802..1383126 100644 --- a/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml @@ -162,8 +162,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_readdistribution" executable: "target/nextflow/rseqc/rseqc_readdistribution/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/rseqc/rseqc_readdistribution/main.nf b/target/nextflow/rseqc/rseqc_readdistribution/main.nf index 70813d2..1eb495d 100644 --- a/target/nextflow/rseqc/rseqc_readdistribution/main.nf +++ b/target/nextflow/rseqc/rseqc_readdistribution/main.nf @@ -3017,8 +3017,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_readdistribution", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml index dbc5476..630fd97 100644 --- a/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml @@ -211,8 +211,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_readduplication" executable: "target/nextflow/rseqc/rseqc_readduplication/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/rseqc/rseqc_readduplication/main.nf b/target/nextflow/rseqc/rseqc_readduplication/main.nf index d98b685..a7b5d59 100644 --- a/target/nextflow/rseqc/rseqc_readduplication/main.nf +++ b/target/nextflow/rseqc/rseqc_readduplication/main.nf @@ -3071,8 +3071,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_readduplication", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml index c32fafb..9bac47c 100644 --- a/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml @@ -214,8 +214,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_tin" executable: "target/nextflow/rseqc/rseqc_tin/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/rseqc/rseqc_tin/main.nf b/target/nextflow/rseqc/rseqc_tin/main.nf index e43dd8a..52f38d7 100644 --- a/target/nextflow/rseqc/rseqc_tin/main.nf +++ b/target/nextflow/rseqc/rseqc_tin/main.nf @@ -3076,8 +3076,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_tin", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/sortmerna/.config.vsh.yaml b/target/nextflow/sortmerna/.config.vsh.yaml index 2cb796f..0ec38f6 100644 --- a/target/nextflow/sortmerna/.config.vsh.yaml +++ b/target/nextflow/sortmerna/.config.vsh.yaml @@ -198,8 +198,8 @@ build_info: output: "target/nextflow/sortmerna" executable: "target/nextflow/sortmerna/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/sortmerna/main.nf b/target/nextflow/sortmerna/main.nf index 70beeca..f618574 100644 --- a/target/nextflow/sortmerna/main.nf +++ b/target/nextflow/sortmerna/main.nf @@ -3050,8 +3050,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/sortmerna", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/stringtie/.config.vsh.yaml b/target/nextflow/stringtie/.config.vsh.yaml index 34765d3..f398114 100644 --- a/target/nextflow/stringtie/.config.vsh.yaml +++ b/target/nextflow/stringtie/.config.vsh.yaml @@ -216,8 +216,8 @@ build_info: output: "target/nextflow/stringtie" executable: "target/nextflow/stringtie/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/stringtie/main.nf b/target/nextflow/stringtie/main.nf index 41e0ba2..6f0471b 100644 --- a/target/nextflow/stringtie/main.nf +++ b/target/nextflow/stringtie/main.nf @@ -3073,8 +3073,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/stringtie", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/summarizedexperiment/.config.vsh.yaml b/target/nextflow/summarizedexperiment/.config.vsh.yaml index 7e10d25..e5a55dd 100644 --- a/target/nextflow/summarizedexperiment/.config.vsh.yaml +++ b/target/nextflow/summarizedexperiment/.config.vsh.yaml @@ -199,8 +199,8 @@ build_info: output: "target/nextflow/summarizedexperiment" executable: "target/nextflow/summarizedexperiment/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/summarizedexperiment/main.nf b/target/nextflow/summarizedexperiment/main.nf index f7f38e3..2695768 100644 --- a/target/nextflow/summarizedexperiment/main.nf +++ b/target/nextflow/summarizedexperiment/main.nf @@ -3054,8 +3054,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/summarizedexperiment", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/trimgalore/.config.vsh.yaml b/target/nextflow/trimgalore/.config.vsh.yaml index 2d98568..ec87af2 100644 --- a/target/nextflow/trimgalore/.config.vsh.yaml +++ b/target/nextflow/trimgalore/.config.vsh.yaml @@ -788,8 +788,8 @@ build_info: output: "target/nextflow/trimgalore" executable: "target/nextflow/trimgalore/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/trimgalore/main.nf b/target/nextflow/trimgalore/main.nf index 7050ae6..631b9d7 100644 --- a/target/nextflow/trimgalore/main.nf +++ b/target/nextflow/trimgalore/main.nf @@ -3576,8 +3576,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/trimgalore", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/tx2gene/.config.vsh.yaml b/target/nextflow/tx2gene/.config.vsh.yaml index ab6ff2b..0a695fc 100644 --- a/target/nextflow/tx2gene/.config.vsh.yaml +++ b/target/nextflow/tx2gene/.config.vsh.yaml @@ -192,8 +192,8 @@ build_info: output: "target/nextflow/tx2gene" executable: "target/nextflow/tx2gene/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/tx2gene/main.nf b/target/nextflow/tx2gene/main.nf index de6ae4b..c299c04 100644 --- a/target/nextflow/tx2gene/main.nf +++ b/target/nextflow/tx2gene/main.nf @@ -3049,8 +3049,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/tx2gene", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/tximport/.config.vsh.yaml b/target/nextflow/tximport/.config.vsh.yaml index 889ee89..bdf3c56 100644 --- a/target/nextflow/tximport/.config.vsh.yaml +++ b/target/nextflow/tximport/.config.vsh.yaml @@ -247,8 +247,8 @@ build_info: output: "target/nextflow/tximport" executable: "target/nextflow/tximport/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/tximport/main.nf b/target/nextflow/tximport/main.nf index d6f7922..d73747a 100644 --- a/target/nextflow/tximport/main.nf +++ b/target/nextflow/tximport/main.nf @@ -3114,8 +3114,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/tximport", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/ucsc/bedclip/.config.vsh.yaml b/target/nextflow/ucsc/bedclip/.config.vsh.yaml index f13cb3e..6e4b4ea 100644 --- a/target/nextflow/ucsc/bedclip/.config.vsh.yaml +++ b/target/nextflow/ucsc/bedclip/.config.vsh.yaml @@ -164,8 +164,8 @@ build_info: output: "target/nextflow/ucsc/bedclip" executable: "target/nextflow/ucsc/bedclip/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/ucsc/bedclip/main.nf b/target/nextflow/ucsc/bedclip/main.nf index 8471274..36a9264 100644 --- a/target/nextflow/ucsc/bedclip/main.nf +++ b/target/nextflow/ucsc/bedclip/main.nf @@ -3018,8 +3018,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/ucsc/bedclip", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml b/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml index e4ef8b3..dc374e0 100644 --- a/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml +++ b/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml @@ -164,8 +164,8 @@ build_info: output: "target/nextflow/ucsc/bedgraphtobigwig" executable: "target/nextflow/ucsc/bedgraphtobigwig/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/ucsc/bedgraphtobigwig/main.nf b/target/nextflow/ucsc/bedgraphtobigwig/main.nf index 035a399..fdf96b1 100644 --- a/target/nextflow/ucsc/bedgraphtobigwig/main.nf +++ b/target/nextflow/ucsc/bedgraphtobigwig/main.nf @@ -3018,8 +3018,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/ucsc/bedgraphtobigwig", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml b/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml index e1ddfd5..edbfe41 100644 --- a/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml +++ b/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml @@ -195,8 +195,8 @@ build_info: output: "target/nextflow/umitools/umitools_dedup" executable: "target/nextflow/umitools/umitools_dedup/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/umitools/umitools_dedup/main.nf b/target/nextflow/umitools/umitools_dedup/main.nf index d892c73..ae11e4b 100644 --- a/target/nextflow/umitools/umitools_dedup/main.nf +++ b/target/nextflow/umitools/umitools_dedup/main.nf @@ -3054,8 +3054,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/umitools/umitools_dedup", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/umitools/umitools_extract/.config.vsh.yaml b/target/nextflow/umitools/umitools_extract/.config.vsh.yaml index 46f28eb..9037875 100644 --- a/target/nextflow/umitools/umitools_extract/.config.vsh.yaml +++ b/target/nextflow/umitools/umitools_extract/.config.vsh.yaml @@ -253,8 +253,8 @@ build_info: output: "target/nextflow/umitools/umitools_extract" executable: "target/nextflow/umitools/umitools_extract/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/umitools/umitools_extract/main.nf b/target/nextflow/umitools/umitools_extract/main.nf index 4173fba..94f7ea8 100644 --- a/target/nextflow/umitools/umitools_extract/main.nf +++ b/target/nextflow/umitools/umitools_extract/main.nf @@ -3119,8 +3119,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/umitools/umitools_extract", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/umitools_prepareforquant/.config.vsh.yaml b/target/nextflow/umitools_prepareforquant/.config.vsh.yaml index 18bc501..3ec0802 100644 --- a/target/nextflow/umitools_prepareforquant/.config.vsh.yaml +++ b/target/nextflow/umitools_prepareforquant/.config.vsh.yaml @@ -156,8 +156,8 @@ build_info: output: "target/nextflow/umitools_prepareforquant" executable: "target/nextflow/umitools_prepareforquant/main.nf" viash_version: "0.9.0" - git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" package_config: version: "main" info: diff --git a/target/nextflow/umitools_prepareforquant/main.nf b/target/nextflow/umitools_prepareforquant/main.nf index 06a3f3b..aaf357e 100644 --- a/target/nextflow/umitools_prepareforquant/main.nf +++ b/target/nextflow/umitools_prepareforquant/main.nf @@ -3007,8 +3007,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/umitools_prepareforquant", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", 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 b2a4d5e..81ed609 100644 --- a/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml +++ b/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml @@ -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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@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" diff --git a/target/nextflow/workflows/genome_alignment_and_quant/main.nf b/target/nextflow/workflows/genome_alignment_and_quant/main.nf index 4cf00f5..95cf552 100644 --- a/target/nextflow/workflows/genome_alignment_and_quant/main.nf +++ b/target/nextflow/workflows/genome_alignment_and_quant/main.nf @@ -3531,8 +3531,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/genome_alignment_and_quant", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml b/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml index 693e16a..ac2fc02 100644 --- a/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml +++ b/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml @@ -278,8 +278,8 @@ 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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/tx2gene" - "target/nextflow/tximport" diff --git a/target/nextflow/workflows/merge_quant_results/main.nf b/target/nextflow/workflows/merge_quant_results/main.nf index b106e33..2878c95 100644 --- a/target/nextflow/workflows/merge_quant_results/main.nf +++ b/target/nextflow/workflows/merge_quant_results/main.nf @@ -3149,8 +3149,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/merge_quant_results", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/workflows/post_processing/.config.vsh.yaml b/target/nextflow/workflows/post_processing/.config.vsh.yaml index 74b5e5e..4bffb6d 100644 --- a/target/nextflow/workflows/post_processing/.config.vsh.yaml +++ b/target/nextflow/workflows/post_processing/.config.vsh.yaml @@ -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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/picard_markduplicates" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort" diff --git a/target/nextflow/workflows/post_processing/main.nf b/target/nextflow/workflows/post_processing/main.nf index 59147dd..fdbaa43 100644 --- a/target/nextflow/workflows/post_processing/main.nf +++ b/target/nextflow/workflows/post_processing/main.nf @@ -3397,8 +3397,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/post_processing", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/workflows/pre_processing/.config.vsh.yaml b/target/nextflow/workflows/pre_processing/.config.vsh.yaml index 7107944..f5ac8f9 100644 --- a/target/nextflow/workflows/pre_processing/.config.vsh.yaml +++ b/target/nextflow/workflows/pre_processing/.config.vsh.yaml @@ -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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/fastqc" - "target/nextflow/umitools/umitools_extract" diff --git a/target/nextflow/workflows/pre_processing/main.nf b/target/nextflow/workflows/pre_processing/main.nf index 3f94236..ff25c35 100644 --- a/target/nextflow/workflows/pre_processing/main.nf +++ b/target/nextflow/workflows/pre_processing/main.nf @@ -3626,8 +3626,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/pre_processing", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/workflows/prepare_genome/.config.vsh.yaml b/target/nextflow/workflows/prepare_genome/.config.vsh.yaml index 5dc4666..e2afcdc 100644 --- a/target/nextflow/workflows/prepare_genome/.config.vsh.yaml +++ b/target/nextflow/workflows/prepare_genome/.config.vsh.yaml @@ -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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/gunzip" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread" diff --git a/target/nextflow/workflows/prepare_genome/main.nf b/target/nextflow/workflows/prepare_genome/main.nf index 96a50b0..59f34a9 100644 --- a/target/nextflow/workflows/prepare_genome/main.nf +++ b/target/nextflow/workflows/prepare_genome/main.nf @@ -3407,8 +3407,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/prepare_genome", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", 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 460673c..1a23a18 100644 --- a/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml +++ b/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml @@ -283,8 +283,8 @@ 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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant" - "target/nextflow/kallisto/kallisto_quant" diff --git a/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf b/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf index a20b161..e394756 100644 --- a/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf +++ b/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf @@ -3143,8 +3143,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/pseudo_alignment_and_quant", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/workflows/quality_control/.config.vsh.yaml b/target/nextflow/workflows/quality_control/.config.vsh.yaml index ccb0e4e..fe9ee36 100644 --- a/target/nextflow/workflows/quality_control/.config.vsh.yaml +++ b/target/nextflow/workflows/quality_control/.config.vsh.yaml @@ -265,7 +265,7 @@ argument_groups: name: "--biotypes_header" info: null default: - - "assets/multiqc/biotypes_header.txt" + - "src/assets/multiqc/biotypes_header.txt" must_exist: true create_parent: true required: false @@ -563,7 +563,7 @@ argument_groups: name: "--pca_header_multiqc" info: null default: - - "assets/multiqc/deseq2_pca_header.txt" + - "src/assets/multiqc/deseq2_pca_header.txt" must_exist: true create_parent: true required: false @@ -574,7 +574,7 @@ argument_groups: name: "--clustering_header_multiqc" info: null default: - - "assets/multiqc/deseq2_clustering_header.txt" + - "src/assets/multiqc/deseq2_clustering_header.txt" must_exist: true create_parent: true required: false @@ -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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/rseqc/rseqc_bamstat" - "target/nextflow/rseqc/rseqc_inferexperiment" diff --git a/target/nextflow/workflows/quality_control/main.nf b/target/nextflow/workflows/quality_control/main.nf index e304852..0f2b8e4 100644 --- a/target/nextflow/workflows/quality_control/main.nf +++ b/target/nextflow/workflows/quality_control/main.nf @@ -3104,7 +3104,7 @@ meta = [ "type" : "file", "name" : "--biotypes_header", "default" : [ - "assets/multiqc/biotypes_header.txt" + "src/assets/multiqc/biotypes_header.txt" ], "must_exist" : true, "create_parent" : true, @@ -3429,7 +3429,7 @@ meta = [ "type" : "file", "name" : "--pca_header_multiqc", "default" : [ - "assets/multiqc/deseq2_pca_header.txt" + "src/assets/multiqc/deseq2_pca_header.txt" ], "must_exist" : true, "create_parent" : true, @@ -3442,7 +3442,7 @@ meta = [ "type" : "file", "name" : "--clustering_header_multiqc", "default" : [ - "assets/multiqc/deseq2_clustering_header.txt" + "src/assets/multiqc/deseq2_clustering_header.txt" ], "must_exist" : true, "create_parent" : true, @@ -4676,8 +4676,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/quality_control", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/workflows/quality_control/nextflow_schema.json b/target/nextflow/workflows/quality_control/nextflow_schema.json index 41438af..42d520e 100644 --- a/target/nextflow/workflows/quality_control/nextflow_schema.json +++ b/target/nextflow/workflows/quality_control/nextflow_schema.json @@ -296,10 +296,10 @@ "biotypes_header": { "type": "string", - "description": "Type: `file`, default: `assets/multiqc/biotypes_header.txt`. ", - "help_text": "Type: `file`, default: `assets/multiqc/biotypes_header.txt`. " + "description": "Type: `file`, default: `src/assets/multiqc/biotypes_header.txt`. ", + "help_text": "Type: `file`, default: `src/assets/multiqc/biotypes_header.txt`. " , - "default": "assets/multiqc/biotypes_header.txt" + "default": "src/assets/multiqc/biotypes_header.txt" } @@ -585,10 +585,10 @@ "pca_header_multiqc": { "type": "string", - "description": "Type: `file`, default: `assets/multiqc/deseq2_pca_header.txt`. ", - "help_text": "Type: `file`, default: `assets/multiqc/deseq2_pca_header.txt`. " + "description": "Type: `file`, default: `src/assets/multiqc/deseq2_pca_header.txt`. ", + "help_text": "Type: `file`, default: `src/assets/multiqc/deseq2_pca_header.txt`. " , - "default": "assets/multiqc/deseq2_pca_header.txt" + "default": "src/assets/multiqc/deseq2_pca_header.txt" } @@ -596,10 +596,10 @@ "clustering_header_multiqc": { "type": "string", - "description": "Type: `file`, default: `assets/multiqc/deseq2_clustering_header.txt`. ", - "help_text": "Type: `file`, default: `assets/multiqc/deseq2_clustering_header.txt`. " + "description": "Type: `file`, default: `src/assets/multiqc/deseq2_clustering_header.txt`. ", + "help_text": "Type: `file`, default: `src/assets/multiqc/deseq2_clustering_header.txt`. " , - "default": "assets/multiqc/deseq2_clustering_header.txt" + "default": "src/assets/multiqc/deseq2_clustering_header.txt" } diff --git a/target/nextflow/workflows/rnaseq/.config.vsh.yaml b/target/nextflow/workflows/rnaseq/.config.vsh.yaml index c5a7f34..3120f2c 100644 --- a/target/nextflow/workflows/rnaseq/.config.vsh.yaml +++ b/target/nextflow/workflows/rnaseq/.config.vsh.yaml @@ -295,7 +295,7 @@ argument_groups: \ be used to create the database for SortMeRNA." info: null default: - - "assets/rrna-db-defaults.txt" + - "src/assets/rrna-db-defaults.txt" must_exist: true create_parent: true required: false @@ -683,7 +683,7 @@ argument_groups: name: "--pca_header_multiqc" info: null default: - - "assets/multiqc/deseq2_pca_header.txt" + - "src/assets/multiqc/deseq2_pca_header.txt" must_exist: true create_parent: true required: false @@ -694,7 +694,7 @@ argument_groups: name: "--clustering_header_multiqc" info: null default: - - "assets/multiqc/deseq2_clustering_header.txt" + - "src/assets/multiqc/deseq2_clustering_header.txt" must_exist: true create_parent: true required: false @@ -754,7 +754,7 @@ argument_groups: name: "--multiqc_custom_config" info: null default: - - "assets/multiqc_config.yml" + - "src/assets/multiqc_config.yml" must_exist: true create_parent: true required: false @@ -772,7 +772,7 @@ argument_groups: name: "--multiqc_methods_description" info: null default: - - "assets/methods_description_template.yml" + - "src/assets/methods_description_template.yml" must_exist: true create_parent: true required: false @@ -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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8" - git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b" + git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/workflows/prepare_genome" - "target/nextflow/cat_fastq" diff --git a/target/nextflow/workflows/rnaseq/main.nf b/target/nextflow/workflows/rnaseq/main.nf index 7741f4d..5ec8f12 100644 --- a/target/nextflow/workflows/rnaseq/main.nf +++ b/target/nextflow/workflows/rnaseq/main.nf @@ -3132,7 +3132,7 @@ meta = [ "name" : "--ribo_database_manifest", "description" : "Text file containing paths to fasta files (one per line) that will be used to create the database for SortMeRNA.", "default" : [ - "assets/rrna-db-defaults.txt" + "src/assets/rrna-db-defaults.txt" ], "must_exist" : true, "create_parent" : true, @@ -3577,7 +3577,7 @@ meta = [ "type" : "file", "name" : "--pca_header_multiqc", "default" : [ - "assets/multiqc/deseq2_pca_header.txt" + "src/assets/multiqc/deseq2_pca_header.txt" ], "must_exist" : true, "create_parent" : true, @@ -3590,7 +3590,7 @@ meta = [ "type" : "file", "name" : "--clustering_header_multiqc", "default" : [ - "assets/multiqc/deseq2_clustering_header.txt" + "src/assets/multiqc/deseq2_clustering_header.txt" ], "must_exist" : true, "create_parent" : true, @@ -3664,7 +3664,7 @@ meta = [ "type" : "file", "name" : "--multiqc_custom_config", "default" : [ - "assets/multiqc_config.yml" + "src/assets/multiqc_config.yml" ], "must_exist" : true, "create_parent" : true, @@ -3685,7 +3685,7 @@ meta = [ "type" : "file", "name" : "--multiqc_methods_description", "default" : [ - "assets/methods_description_template.yml" + "src/assets/methods_description_template.yml" ], "must_exist" : true, "create_parent" : true, @@ -4891,7 +4891,7 @@ meta = [ "name" : "--dupradar_output_duprate_exp_boxplot", "description" : "path to output file (pdf) of distribution of expression box plot", "default" : [ - "dupradar/''' + '''box_plot/$id.duprate_exp_boxplot.pdf" + ''' + ''' "dupradar/box_plot/$id.duprate_exp_boxplot.pdf" ], "must_exist" : true, "create_parent" : true, @@ -5283,8 +5283,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/rnaseq", "viash_version" : "0.9.0", - "git_commit" : "1d87dc7c24f540c96460e69322f06d4be0bb7be8", - "git_remote" : "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq" + "git_commit" : "fd0354dae813d953b107e8fa856f3cd4e7939f2b", + "git_remote" : "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "main", diff --git a/target/nextflow/workflows/rnaseq/nextflow_schema.json b/target/nextflow/workflows/rnaseq/nextflow_schema.json index cb85c7f..ae21368 100644 --- a/target/nextflow/workflows/rnaseq/nextflow_schema.json +++ b/target/nextflow/workflows/rnaseq/nextflow_schema.json @@ -330,10 +330,10 @@ "ribo_database_manifest": { "type": "string", - "description": "Type: `file`, default: `assets/rrna-db-defaults.txt`. Text file containing paths to fasta files (one per line) that will be used to create the database for SortMeRNA", - "help_text": "Type: `file`, default: `assets/rrna-db-defaults.txt`. Text file containing paths to fasta files (one per line) that will be used to create the database for SortMeRNA." + "description": "Type: `file`, default: `src/assets/rrna-db-defaults.txt`. Text file containing paths to fasta files (one per line) that will be used to create the database for SortMeRNA", + "help_text": "Type: `file`, default: `src/assets/rrna-db-defaults.txt`. Text file containing paths to fasta files (one per line) that will be used to create the database for SortMeRNA." , - "default": "assets/rrna-db-defaults.txt" + "default": "src/assets/rrna-db-defaults.txt" } @@ -859,10 +859,10 @@ "pca_header_multiqc": { "type": "string", - "description": "Type: `file`, default: `assets/multiqc/deseq2_pca_header.txt`. ", - "help_text": "Type: `file`, default: `assets/multiqc/deseq2_pca_header.txt`. " + "description": "Type: `file`, default: `src/assets/multiqc/deseq2_pca_header.txt`. ", + "help_text": "Type: `file`, default: `src/assets/multiqc/deseq2_pca_header.txt`. " , - "default": "assets/multiqc/deseq2_pca_header.txt" + "default": "src/assets/multiqc/deseq2_pca_header.txt" } @@ -870,10 +870,10 @@ "clustering_header_multiqc": { "type": "string", - "description": "Type: `file`, default: `assets/multiqc/deseq2_clustering_header.txt`. ", - "help_text": "Type: `file`, default: `assets/multiqc/deseq2_clustering_header.txt`. " + "description": "Type: `file`, default: `src/assets/multiqc/deseq2_clustering_header.txt`. ", + "help_text": "Type: `file`, default: `src/assets/multiqc/deseq2_clustering_header.txt`. " , - "default": "assets/multiqc/deseq2_clustering_header.txt" + "default": "src/assets/multiqc/deseq2_clustering_header.txt" } @@ -937,10 +937,10 @@ "multiqc_custom_config": { "type": "string", - "description": "Type: `file`, default: `assets/multiqc_config.yml`. ", - "help_text": "Type: `file`, default: `assets/multiqc_config.yml`. " + "description": "Type: `file`, default: `src/assets/multiqc_config.yml`. ", + "help_text": "Type: `file`, default: `src/assets/multiqc_config.yml`. " , - "default": "assets/multiqc_config.yml" + "default": "src/assets/multiqc_config.yml" } @@ -958,10 +958,10 @@ "multiqc_methods_description": { "type": "string", - "description": "Type: `file`, default: `assets/methods_description_template.yml`. ", - "help_text": "Type: `file`, default: `assets/methods_description_template.yml`. " + "description": "Type: `file`, default: `src/assets/methods_description_template.yml`. ", + "help_text": "Type: `file`, default: `src/assets/methods_description_template.yml`. " , - "default": "assets/methods_description_template.yml" + "default": "src/assets/methods_description_template.yml" }