diff --git a/src/workflows/quality_control/main.nf b/src/workflows/quality_control/main.nf index d90cc07..180a690 100644 --- a/src/workflows/quality_control/main.nf +++ b/src/workflows/quality_control/main.nf @@ -202,6 +202,7 @@ workflow run_wf { // TODO: Add outdir as an output argument to the qualimap module on biobox. // Qualimap ouputs a few more raw data files to outdir but since the module is using a temporary directory as output dir these files are lost. | qualimap_rnaseq.run( + runIf: { id, state -> !state.skip_qc && !state.skip_qualimap && !state.skip_align }, fromState: [ "bam": "genome_bam", "gtf": "gtf", diff --git a/target/executable/bedtools_genomecov/.config.vsh.yaml b/target/executable/bedtools_genomecov/.config.vsh.yaml index ef4c58c..a19cad4 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/bedtools_genomecov/bedtools_genomecov b/target/executable/bedtools_genomecov/bedtools_genomecov index 822fdfc..37de61f 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="2024-11-27T11:43:51Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b" +LABEL org.opencontainers.image.created="2024-11-27T17:11:16Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e" 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 634b402..bf77ebc 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/cat_additional_fasta/cat_additional_fasta b/target/executable/cat_additional_fasta/cat_additional_fasta index 11b0fb6..95efbcf 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="2024-11-27T11:43:50Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b" +LABEL org.opencontainers.image.created="2024-11-27T17:11:15Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e" 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 2beaa6b..dd675aa 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/cat_fastq/cat_fastq b/target/executable/cat_fastq/cat_fastq index b401291..a16e790 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="2024-11-27T11:43:49Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b" +LABEL org.opencontainers.image.created="2024-11-27T17:11:14Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e" 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 e994690..40636dd 100644 --- a/target/executable/deseq2_qc/.config.vsh.yaml +++ b/target/executable/deseq2_qc/.config.vsh.yaml @@ -237,8 +237,8 @@ build_info: output: "target/executable/deseq2_qc" executable: "target/executable/deseq2_qc/deseq2_qc" viash_version: "0.9.0" - git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/deseq2_qc/deseq2_qc b/target/executable/deseq2_qc/deseq2_qc index c868da1..f08a26f 100755 --- a/target/executable/deseq2_qc/deseq2_qc +++ b/target/executable/deseq2_qc/deseq2_qc @@ -506,9 +506,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag Rscript -e 'remotes::install_cran(c("optparse", "ggplot2", "RColorBrewer", "pheatmap", "stringr", "matrixStats"), repos = "https://cran.rstudio.com")' LABEL org.opencontainers.image.description="Companion container for running component deseq2_qc" -LABEL org.opencontainers.image.created="2024-11-27T11:43:49Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b" +LABEL org.opencontainers.image.created="2024-11-27T17:11:15Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/dupradar/.config.vsh.yaml b/target/executable/dupradar/.config.vsh.yaml index 203f594..33f7209 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/dupradar/dupradar b/target/executable/dupradar/dupradar index 39a8f1b..7775c6d 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="2024-11-27T11:43:51Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b" +LABEL org.opencontainers.image.created="2024-11-27T17:11:16Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/getchromsizes/.config.vsh.yaml b/target/executable/getchromsizes/.config.vsh.yaml index 61d12e7..9b61a13 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/getchromsizes/getchromsizes b/target/executable/getchromsizes/getchromsizes index c4dd3c7..6651d62 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="2024-11-27T11:43:50Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b" +LABEL org.opencontainers.image.created="2024-11-27T17:11:15Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/gtf2bed/.config.vsh.yaml b/target/executable/gtf2bed/.config.vsh.yaml index 70e8fd1..e69798e 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/gtf2bed/gtf2bed b/target/executable/gtf2bed/gtf2bed index bd66c54..5f5d060 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="2024-11-27T11:43:51Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b" +LABEL org.opencontainers.image.created="2024-11-27T17:11:17Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e" 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 baf51cc..d117761 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/gtf_filter/gtf_filter b/target/executable/gtf_filter/gtf_filter index bba566c..ca8565e 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="2024-11-27T11:43:50Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b" +LABEL org.opencontainers.image.created="2024-11-27T17:11:15Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/gunzip/.config.vsh.yaml b/target/executable/gunzip/.config.vsh.yaml index b82306b..9bff6d9 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/gunzip/gunzip b/target/executable/gunzip/gunzip index df2feb3..1796f8f 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="2024-11-27T11:43:46Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b" +LABEL org.opencontainers.image.created="2024-11-27T17:11:12Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e" 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 d80b412..c365ce3 100644 --- a/target/executable/multiqc_custom_biotype/.config.vsh.yaml +++ b/target/executable/multiqc_custom_biotype/.config.vsh.yaml @@ -165,8 +165,8 @@ build_info: output: "target/executable/multiqc_custom_biotype" executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype" viash_version: "0.9.0" - git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/multiqc_custom_biotype/multiqc_custom_biotype b/target/executable/multiqc_custom_biotype/multiqc_custom_biotype index a42c93b..086a5ab 100755 --- a/target/executable/multiqc_custom_biotype/multiqc_custom_biotype +++ b/target/executable/multiqc_custom_biotype/multiqc_custom_biotype @@ -476,9 +476,9 @@ function ViashDockerfile { FROM python:latest ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component multiqc_custom_biotype" -LABEL org.opencontainers.image.created="2024-11-27T11:43:49Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b" +LABEL org.opencontainers.image.created="2024-11-27T17:11:14Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e" 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 b319d14..87eb75b 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/picard_markduplicates/picard_markduplicates b/target/executable/picard_markduplicates/picard_markduplicates index 5ae0608..272f127 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="2024-11-27T11:43:47Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b" +LABEL org.opencontainers.image.created="2024-11-27T17:11:12Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e" 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 f61a51d..444b4f2 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/prepare_multiqc_input/prepare_multiqc_input b/target/executable/prepare_multiqc_input/prepare_multiqc_input index c6b9758..e364a0d 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="2024-11-27T11:43:46Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b" +LABEL org.opencontainers.image.created="2024-11-27T17:11:11Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e" 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 a49940b..f376fc8 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta b/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta index d39c310..327bb88 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="2024-11-27T11:43:47Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b" +LABEL org.opencontainers.image.created="2024-11-27T17:11:13Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e" 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 ac3c34e..2fbf733 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/preseq_lcextrap/preseq_lcextrap b/target/executable/preseq_lcextrap/preseq_lcextrap index 92106a8..e48d52e 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="2024-11-27T11:43:47Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b" +LABEL org.opencontainers.image.created="2024-11-27T17:11:12Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/rsem_merge_counts/.config.vsh.yaml b/target/executable/rsem_merge_counts/.config.vsh.yaml index 99e062a..5a1dad7 100644 --- a/target/executable/rsem_merge_counts/.config.vsh.yaml +++ b/target/executable/rsem_merge_counts/.config.vsh.yaml @@ -181,8 +181,8 @@ build_info: output: "target/executable/rsem_merge_counts" executable: "target/executable/rsem_merge_counts/rsem_merge_counts" viash_version: "0.9.0" - git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/rsem_merge_counts/rsem_merge_counts b/target/executable/rsem_merge_counts/rsem_merge_counts index fd2adf4..a2b8a93 100755 --- a/target/executable/rsem_merge_counts/rsem_merge_counts +++ b/target/executable/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_merge_counts" -LABEL org.opencontainers.image.created="2024-11-27T11:43:49Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b" +LABEL org.opencontainers.image.created="2024-11-27T17:11:14Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e" 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 f6cd9f2..d0fe49d 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation b/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation index db27d98..1bec1f0 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="2024-11-27T11:43:48Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b" +LABEL org.opencontainers.image.created="2024-11-27T17:11:13Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e" 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 ecb6bcc..b79aded 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation b/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation index 667c23a..9db18e1 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="2024-11-27T11:43:49Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b" +LABEL org.opencontainers.image.created="2024-11-27T17:11:14Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e" 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 2ee314e..5829326 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution b/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution index 65f1367..06907de 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="2024-11-27T11:43:49Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b" +LABEL org.opencontainers.image.created="2024-11-27T17:11:14Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e" 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 fdbd065..889ce32 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication b/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication index 684c4c5..0079298 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="2024-11-27T11:43:48Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b" +LABEL org.opencontainers.image.created="2024-11-27T17:11:13Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e" 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 f1b785f..0342b97 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/rseqc/rseqc_tin/rseqc_tin b/target/executable/rseqc/rseqc_tin/rseqc_tin index bd7ceea..84318bd 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="2024-11-27T11:43:48Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b" +LABEL org.opencontainers.image.created="2024-11-27T17:11:14Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/sortmerna/.config.vsh.yaml b/target/executable/sortmerna/.config.vsh.yaml index 6b2530c..726b535 100644 --- a/target/executable/sortmerna/.config.vsh.yaml +++ b/target/executable/sortmerna/.config.vsh.yaml @@ -192,8 +192,8 @@ build_info: output: "target/executable/sortmerna" executable: "target/executable/sortmerna/sortmerna" viash_version: "0.9.0" - git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/sortmerna/sortmerna b/target/executable/sortmerna/sortmerna index 169a650..51ad0c7 100755 --- a/target/executable/sortmerna/sortmerna +++ b/target/executable/sortmerna/sortmerna @@ -486,9 +486,9 @@ function ViashDockerfile { FROM quay.io/biocontainers/sortmerna:4.3.6--h9ee0642_0 ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component sortmerna" -LABEL org.opencontainers.image.created="2024-11-27T11:43:52Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b" +LABEL org.opencontainers.image.created="2024-11-27T17:11:17Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/stringtie/.config.vsh.yaml b/target/executable/stringtie/.config.vsh.yaml index 1813449..5148024 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/stringtie/stringtie b/target/executable/stringtie/stringtie index 855a0aa..dc165bb 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="2024-11-27T11:43:52Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b" +LABEL org.opencontainers.image.created="2024-11-27T17:11:18Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/summarizedexperiment/.config.vsh.yaml b/target/executable/summarizedexperiment/.config.vsh.yaml index 5bd5d6b..9e078e1 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/summarizedexperiment/summarizedexperiment b/target/executable/summarizedexperiment/summarizedexperiment index af420dd..137df93 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="2024-11-27T11:43:52Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b" +LABEL org.opencontainers.image.created="2024-11-27T17:11:17Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/tx2gene/.config.vsh.yaml b/target/executable/tx2gene/.config.vsh.yaml index 8045397..2a8a9d9 100644 --- a/target/executable/tx2gene/.config.vsh.yaml +++ b/target/executable/tx2gene/.config.vsh.yaml @@ -185,8 +185,8 @@ build_info: output: "target/executable/tx2gene" executable: "target/executable/tx2gene/tx2gene" viash_version: "0.9.0" - git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/tx2gene/tx2gene b/target/executable/tx2gene/tx2gene index 6daaaac..34a912f 100755 --- a/target/executable/tx2gene/tx2gene +++ b/target/executable/tx2gene/tx2gene @@ -483,9 +483,9 @@ 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="2024-11-27T11:43:50Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b" +LABEL org.opencontainers.image.created="2024-11-27T17:11:16Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e" LABEL org.opencontainers.image.version="main" VIASHDOCKER diff --git a/target/executable/tximport/.config.vsh.yaml b/target/executable/tximport/.config.vsh.yaml index dbb1495..1a70ba9 100644 --- a/target/executable/tximport/.config.vsh.yaml +++ b/target/executable/tximport/.config.vsh.yaml @@ -251,8 +251,8 @@ build_info: output: "target/executable/tximport" executable: "target/executable/tximport/tximport" viash_version: "0.9.0" - git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/tximport/tximport b/target/executable/tximport/tximport index 9c3c5bb..3d17192 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="2024-11-27T11:43:51Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b" +LABEL org.opencontainers.image.created="2024-11-27T17:11:16Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e" 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 f3a6b86..d9e3300 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/ucsc/bedclip/bedclip b/target/executable/ucsc/bedclip/bedclip index 79bb529..24d779d 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="2024-11-27T11:43:50Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b" +LABEL org.opencontainers.image.created="2024-11-27T17:11:15Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e" 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 13ad804..c8c93a6 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig b/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig index 6f22812..79ee642 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="2024-11-27T11:43:50Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="0c8a7eb648edb0567b7860756b79dfbccbbac27b" +LABEL org.opencontainers.image.created="2024-11-27T17:11:15Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="d63250ae704b6bd9a11792c4f979be2309999a2e" 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 cde74af..f63f3f1 100644 --- a/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml +++ b/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml @@ -590,8 +590,8 @@ 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads" - "target/dependencies/vsh/vsh/biobox/main/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 74ed758..b1a654b 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@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 4fbcc02..ca49fc0 100644 --- a/target/executable/workflows/post_processing/.config.vsh.yaml +++ b/target/executable/workflows/post_processing/.config.vsh.yaml @@ -477,8 +477,8 @@ build_info: output: "target/executable/workflows/post_processing" executable: "target/executable/workflows/post_processing/post_processing" viash_version: "0.9.0" - git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/picard_markduplicates" - "target/dependencies/vsh/vsh/biobox/main/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 7f29af8..2afe8eb 100644 --- a/target/executable/workflows/pre_processing/.config.vsh.yaml +++ b/target/executable/workflows/pre_processing/.config.vsh.yaml @@ -632,8 +632,8 @@ build_info: output: "target/executable/workflows/pre_processing" executable: "target/executable/workflows/pre_processing/pre_processing" viash_version: "0.9.0" - git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/main/nextflow/fastqc" - "target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract" diff --git a/target/executable/workflows/prepare_genome/.config.vsh.yaml b/target/executable/workflows/prepare_genome/.config.vsh.yaml index f80f17f..ddaf468 100644 --- a/target/executable/workflows/prepare_genome/.config.vsh.yaml +++ b/target/executable/workflows/prepare_genome/.config.vsh.yaml @@ -502,8 +502,8 @@ build_info: output: "target/executable/workflows/prepare_genome" executable: "target/executable/workflows/prepare_genome/prepare_genome" viash_version: "0.9.0" - git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/gunzip" - "target/dependencies/vsh/vsh/biobox/main/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 f2ad543..def0876 100644 --- a/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml +++ b/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml @@ -285,8 +285,8 @@ 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant" - "target/dependencies/vsh/vsh/biobox/main/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 2271736..607e24b 100644 --- a/target/executable/workflows/quality_control/.config.vsh.yaml +++ b/target/executable/workflows/quality_control/.config.vsh.yaml @@ -1554,8 +1554,8 @@ build_info: output: "target/executable/workflows/quality_control" executable: "target/executable/workflows/quality_control/quality_control" viash_version: "0.9.0" - git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_bamstat" - "target/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_inferexperiment" diff --git a/target/executable/workflows/quality_control/quality_control b/target/executable/workflows/quality_control/quality_control index c1cd030..7bc4d83 100755 --- a/target/executable/workflows/quality_control/quality_control +++ b/target/executable/workflows/quality_control/quality_control @@ -3505,6 +3505,7 @@ workflow run_wf { // TODO: Add outdir as an output argument to the qualimap module on biobox. // Qualimap ouputs a few more raw data files to outdir but since the module is using a temporary directory as output dir these files are lost. | qualimap_rnaseq.run( + runIf: { id, state -> !state.skip_qc && !state.skip_qualimap && !state.skip_align }, fromState: [ "bam": "genome_bam", "gtf": "gtf", diff --git a/target/executable/workflows/rnaseq/.config.vsh.yaml b/target/executable/workflows/rnaseq/.config.vsh.yaml index 4fc424a..7959698 100644 --- a/target/executable/workflows/rnaseq/.config.vsh.yaml +++ b/target/executable/workflows/rnaseq/.config.vsh.yaml @@ -2061,8 +2061,8 @@ build_info: output: "target/executable/workflows/rnaseq" executable: "target/executable/workflows/rnaseq/rnaseq" viash_version: "0.9.0" - git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/workflows/prepare_genome" - "target/nextflow/cat_fastq" diff --git a/target/nextflow/bedtools_genomecov/.config.vsh.yaml b/target/nextflow/bedtools_genomecov/.config.vsh.yaml index 8cd391c..345ecf3 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/bedtools_genomecov/main.nf b/target/nextflow/bedtools_genomecov/main.nf index ab3bf7f..53888df 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" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/cat_additional_fasta/.config.vsh.yaml b/target/nextflow/cat_additional_fasta/.config.vsh.yaml index 3f1b884..a88ab90 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/cat_additional_fasta/main.nf b/target/nextflow/cat_additional_fasta/main.nf index c1c615b..0e2627e 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" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/cat_fastq/.config.vsh.yaml b/target/nextflow/cat_fastq/.config.vsh.yaml index 9bfbc3e..86269e6 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/cat_fastq/main.nf b/target/nextflow/cat_fastq/main.nf index f1d8e66..3d0fe6f 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" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/deseq2_qc/.config.vsh.yaml b/target/nextflow/deseq2_qc/.config.vsh.yaml index 92c91ee..96fa759 100644 --- a/target/nextflow/deseq2_qc/.config.vsh.yaml +++ b/target/nextflow/deseq2_qc/.config.vsh.yaml @@ -237,8 +237,8 @@ build_info: output: "target/nextflow/deseq2_qc" executable: "target/nextflow/deseq2_qc/main.nf" viash_version: "0.9.0" - git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/deseq2_qc/main.nf b/target/nextflow/deseq2_qc/main.nf index 53ea4ea..f8a0f2d 100644 --- a/target/nextflow/deseq2_qc/main.nf +++ b/target/nextflow/deseq2_qc/main.nf @@ -3104,8 +3104,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/deseq2_qc", "viash_version" : "0.9.0", - "git_commit" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/dupradar/.config.vsh.yaml b/target/nextflow/dupradar/.config.vsh.yaml index 90ff245..0168541 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/dupradar/main.nf b/target/nextflow/dupradar/main.nf index 1471604..8a34405 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" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/getchromsizes/.config.vsh.yaml b/target/nextflow/getchromsizes/.config.vsh.yaml index 516c4f9..7ae934e 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/getchromsizes/main.nf b/target/nextflow/getchromsizes/main.nf index eaee980..eb0f9d1 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" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/gtf2bed/.config.vsh.yaml b/target/nextflow/gtf2bed/.config.vsh.yaml index e37b0e6..7721d0f 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/gtf2bed/main.nf b/target/nextflow/gtf2bed/main.nf index 4f90219..24241c6 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" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/gtf_filter/.config.vsh.yaml b/target/nextflow/gtf_filter/.config.vsh.yaml index 71979d1..4b07550 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/gtf_filter/main.nf b/target/nextflow/gtf_filter/main.nf index 35532f0..b220d1b 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" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/gunzip/.config.vsh.yaml b/target/nextflow/gunzip/.config.vsh.yaml index 8f283c6..09bd2a0 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/gunzip/main.nf b/target/nextflow/gunzip/main.nf index 95c0a81..90e5029 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" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml b/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml index 0591afb..d615642 100644 --- a/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml +++ b/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml @@ -165,8 +165,8 @@ build_info: output: "target/nextflow/multiqc_custom_biotype" executable: "target/nextflow/multiqc_custom_biotype/main.nf" viash_version: "0.9.0" - git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/multiqc_custom_biotype/main.nf b/target/nextflow/multiqc_custom_biotype/main.nf index bdbd248..b6dd723 100644 --- a/target/nextflow/multiqc_custom_biotype/main.nf +++ b/target/nextflow/multiqc_custom_biotype/main.nf @@ -3012,8 +3012,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/multiqc_custom_biotype", "viash_version" : "0.9.0", - "git_commit" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/picard_markduplicates/.config.vsh.yaml b/target/nextflow/picard_markduplicates/.config.vsh.yaml index e3d3e65..2565c14 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/picard_markduplicates/main.nf b/target/nextflow/picard_markduplicates/main.nf index 0cda539..8269ec1 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" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/prepare_multiqc_input/.config.vsh.yaml b/target/nextflow/prepare_multiqc_input/.config.vsh.yaml index a990214..2d44ef4 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/prepare_multiqc_input/main.nf b/target/nextflow/prepare_multiqc_input/main.nf index aa0feaa..e1e38ca 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" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml b/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml index 701953f..93ca217 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/preprocess_transcripts_fasta/main.nf b/target/nextflow/preprocess_transcripts_fasta/main.nf index e879dee..1b5377b 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" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/preseq_lcextrap/.config.vsh.yaml b/target/nextflow/preseq_lcextrap/.config.vsh.yaml index 64b1d10..5551486 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/preseq_lcextrap/main.nf b/target/nextflow/preseq_lcextrap/main.nf index 20a8630..1243e12 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" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/rsem_merge_counts/.config.vsh.yaml b/target/nextflow/rsem_merge_counts/.config.vsh.yaml index 4a8231f..f289265 100644 --- a/target/nextflow/rsem_merge_counts/.config.vsh.yaml +++ b/target/nextflow/rsem_merge_counts/.config.vsh.yaml @@ -181,8 +181,8 @@ build_info: output: "target/nextflow/rsem_merge_counts" executable: "target/nextflow/rsem_merge_counts/main.nf" viash_version: "0.9.0" - git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/rsem_merge_counts/main.nf b/target/nextflow/rsem_merge_counts/main.nf index ae2fc39..6c5675b 100644 --- a/target/nextflow/rsem_merge_counts/main.nf +++ b/target/nextflow/rsem_merge_counts/main.nf @@ -3027,8 +3027,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rsem_merge_counts", "viash_version" : "0.9.0", - "git_commit" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml index 100f49c..0e7f343 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/rseqc/rseqc_junctionannotation/main.nf b/target/nextflow/rseqc/rseqc_junctionannotation/main.nf index e568727..44465a6 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" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml index 315a79d..36de4a9 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf b/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf index 2187a7a..05ce0f2 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" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml index b771239..d9bb816 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/rseqc/rseqc_readdistribution/main.nf b/target/nextflow/rseqc/rseqc_readdistribution/main.nf index 95e3513..ac0c69d 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" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml index 12aabcf..a41dfcb 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/rseqc/rseqc_readduplication/main.nf b/target/nextflow/rseqc/rseqc_readduplication/main.nf index 4651d50..ca12d30 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" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml index 4e2dbcd..5ed13ce 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/rseqc/rseqc_tin/main.nf b/target/nextflow/rseqc/rseqc_tin/main.nf index ff2bc66..ba14fd6 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" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/sortmerna/.config.vsh.yaml b/target/nextflow/sortmerna/.config.vsh.yaml index 8ece88b..a3dc2ea 100644 --- a/target/nextflow/sortmerna/.config.vsh.yaml +++ b/target/nextflow/sortmerna/.config.vsh.yaml @@ -192,8 +192,8 @@ build_info: output: "target/nextflow/sortmerna" executable: "target/nextflow/sortmerna/main.nf" viash_version: "0.9.0" - git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/sortmerna/main.nf b/target/nextflow/sortmerna/main.nf index 5e2d5c9..9309953 100644 --- a/target/nextflow/sortmerna/main.nf +++ b/target/nextflow/sortmerna/main.nf @@ -3042,8 +3042,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/sortmerna", "viash_version" : "0.9.0", - "git_commit" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/stringtie/.config.vsh.yaml b/target/nextflow/stringtie/.config.vsh.yaml index 0fd7807..960e3e0 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/stringtie/main.nf b/target/nextflow/stringtie/main.nf index 90d35f8..e0ec024 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" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/summarizedexperiment/.config.vsh.yaml b/target/nextflow/summarizedexperiment/.config.vsh.yaml index 9be19e8..217e15f 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/summarizedexperiment/main.nf b/target/nextflow/summarizedexperiment/main.nf index d563ea2..ec285d6 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" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/tx2gene/.config.vsh.yaml b/target/nextflow/tx2gene/.config.vsh.yaml index 4c1c4ad..60cbe93 100644 --- a/target/nextflow/tx2gene/.config.vsh.yaml +++ b/target/nextflow/tx2gene/.config.vsh.yaml @@ -185,8 +185,8 @@ build_info: output: "target/nextflow/tx2gene" executable: "target/nextflow/tx2gene/main.nf" viash_version: "0.9.0" - git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/tx2gene/main.nf b/target/nextflow/tx2gene/main.nf index abf7cb0..befe030 100644 --- a/target/nextflow/tx2gene/main.nf +++ b/target/nextflow/tx2gene/main.nf @@ -3043,8 +3043,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/tx2gene", "viash_version" : "0.9.0", - "git_commit" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/tximport/.config.vsh.yaml b/target/nextflow/tximport/.config.vsh.yaml index 089999f..d8ba713 100644 --- a/target/nextflow/tximport/.config.vsh.yaml +++ b/target/nextflow/tximport/.config.vsh.yaml @@ -251,8 +251,8 @@ build_info: output: "target/nextflow/tximport" executable: "target/nextflow/tximport/main.nf" viash_version: "0.9.0" - git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/tximport/main.nf b/target/nextflow/tximport/main.nf index 2eea968..0e8b382 100644 --- a/target/nextflow/tximport/main.nf +++ b/target/nextflow/tximport/main.nf @@ -3121,8 +3121,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/tximport", "viash_version" : "0.9.0", - "git_commit" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/ucsc/bedclip/.config.vsh.yaml b/target/nextflow/ucsc/bedclip/.config.vsh.yaml index 7d9e875..1f800be 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/ucsc/bedclip/main.nf b/target/nextflow/ucsc/bedclip/main.nf index aeda798..cd6e5ee 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" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml b/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml index 5fe8812..ad805dd 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" package_config: name: "rnaseq" version: "main" diff --git a/target/nextflow/ucsc/bedgraphtobigwig/main.nf b/target/nextflow/ucsc/bedgraphtobigwig/main.nf index 9538074..f2eff2a 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" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", 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 84080e1..3957eb1 100644 --- a/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml +++ b/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml @@ -590,8 +590,8 @@ 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads" - "target/dependencies/vsh/vsh/biobox/main/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 93868ab..3b8f37a 100644 --- a/target/nextflow/workflows/genome_alignment_and_quant/main.nf +++ b/target/nextflow/workflows/genome_alignment_and_quant/main.nf @@ -3516,8 +3516,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/genome_alignment_and_quant", "viash_version" : "0.9.0", - "git_commit" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml b/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml index 40c44cd..3b37a73 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@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 e5f5c71..1ea5e5a 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" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/workflows/post_processing/.config.vsh.yaml b/target/nextflow/workflows/post_processing/.config.vsh.yaml index a7623bb..c952924 100644 --- a/target/nextflow/workflows/post_processing/.config.vsh.yaml +++ b/target/nextflow/workflows/post_processing/.config.vsh.yaml @@ -477,8 +477,8 @@ build_info: output: "target/nextflow/workflows/post_processing" executable: "target/nextflow/workflows/post_processing/main.nf" viash_version: "0.9.0" - git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/picard_markduplicates" - "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort" diff --git a/target/nextflow/workflows/post_processing/main.nf b/target/nextflow/workflows/post_processing/main.nf index b91c759..f1cccf0 100644 --- a/target/nextflow/workflows/post_processing/main.nf +++ b/target/nextflow/workflows/post_processing/main.nf @@ -3387,8 +3387,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/post_processing", "viash_version" : "0.9.0", - "git_commit" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/workflows/pre_processing/.config.vsh.yaml b/target/nextflow/workflows/pre_processing/.config.vsh.yaml index f6888d8..2a31588 100644 --- a/target/nextflow/workflows/pre_processing/.config.vsh.yaml +++ b/target/nextflow/workflows/pre_processing/.config.vsh.yaml @@ -632,8 +632,8 @@ build_info: output: "target/nextflow/workflows/pre_processing" executable: "target/nextflow/workflows/pre_processing/main.nf" viash_version: "0.9.0" - git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/main/nextflow/fastqc" - "target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract" diff --git a/target/nextflow/workflows/pre_processing/main.nf b/target/nextflow/workflows/pre_processing/main.nf index 1b8ca78..22a2b0b 100644 --- a/target/nextflow/workflows/pre_processing/main.nf +++ b/target/nextflow/workflows/pre_processing/main.nf @@ -3576,8 +3576,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/pre_processing", "viash_version" : "0.9.0", - "git_commit" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/workflows/prepare_genome/.config.vsh.yaml b/target/nextflow/workflows/prepare_genome/.config.vsh.yaml index 6aa1ec1..ca6f706 100644 --- a/target/nextflow/workflows/prepare_genome/.config.vsh.yaml +++ b/target/nextflow/workflows/prepare_genome/.config.vsh.yaml @@ -502,8 +502,8 @@ build_info: output: "target/nextflow/workflows/prepare_genome" executable: "target/nextflow/workflows/prepare_genome/main.nf" viash_version: "0.9.0" - git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/gunzip" - "target/dependencies/vsh/vsh/biobox/main/nextflow/gffread" diff --git a/target/nextflow/workflows/prepare_genome/main.nf b/target/nextflow/workflows/prepare_genome/main.nf index d85f1f4..ce7cce9 100644 --- a/target/nextflow/workflows/prepare_genome/main.nf +++ b/target/nextflow/workflows/prepare_genome/main.nf @@ -3417,8 +3417,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/prepare_genome", "viash_version" : "0.9.0", - "git_commit" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", 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 d31b3a3..da7fdb9 100644 --- a/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml +++ b/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml @@ -285,8 +285,8 @@ 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: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant" - "target/dependencies/vsh/vsh/biobox/main/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 e4844d4..ba004f4 100644 --- a/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf +++ b/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf @@ -3145,8 +3145,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/pseudo_alignment_and_quant", "viash_version" : "0.9.0", - "git_commit" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", diff --git a/target/nextflow/workflows/quality_control/.config.vsh.yaml b/target/nextflow/workflows/quality_control/.config.vsh.yaml index 1d4be06..3c251f3 100644 --- a/target/nextflow/workflows/quality_control/.config.vsh.yaml +++ b/target/nextflow/workflows/quality_control/.config.vsh.yaml @@ -1554,8 +1554,8 @@ build_info: output: "target/nextflow/workflows/quality_control" executable: "target/nextflow/workflows/quality_control/main.nf" viash_version: "0.9.0" - git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_bamstat" - "target/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_inferexperiment" diff --git a/target/nextflow/workflows/quality_control/main.nf b/target/nextflow/workflows/quality_control/main.nf index e2f92a4..49638ef 100644 --- a/target/nextflow/workflows/quality_control/main.nf +++ b/target/nextflow/workflows/quality_control/main.nf @@ -4626,8 +4626,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/quality_control", "viash_version" : "0.9.0", - "git_commit" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq", @@ -4895,6 +4895,7 @@ workflow run_wf { // TODO: Add outdir as an output argument to the qualimap module on biobox. // Qualimap ouputs a few more raw data files to outdir but since the module is using a temporary directory as output dir these files are lost. | qualimap_rnaseq.run( + runIf: { id, state -> !state.skip_qc && !state.skip_qualimap && !state.skip_align }, fromState: [ "bam": "genome_bam", "gtf": "gtf", diff --git a/target/nextflow/workflows/rnaseq/.config.vsh.yaml b/target/nextflow/workflows/rnaseq/.config.vsh.yaml index 03dcdbe..01d9cb8 100644 --- a/target/nextflow/workflows/rnaseq/.config.vsh.yaml +++ b/target/nextflow/workflows/rnaseq/.config.vsh.yaml @@ -2061,8 +2061,8 @@ build_info: output: "target/nextflow/workflows/rnaseq" executable: "target/nextflow/workflows/rnaseq/main.nf" viash_version: "0.9.0" - git_commit: "0c8a7eb648edb0567b7860756b79dfbccbbac27b" - git_remote: "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + git_commit: "d63250ae704b6bd9a11792c4f979be2309999a2e" + git_remote: "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@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 a82ba0e..55ec510 100644 --- a/target/nextflow/workflows/rnaseq/main.nf +++ b/target/nextflow/workflows/rnaseq/main.nf @@ -5227,8 +5227,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/rnaseq", "viash_version" : "0.9.0", - "git_commit" : "0c8a7eb648edb0567b7860756b79dfbccbbac27b", - "git_remote" : "https://x-access-token:ghs_7sVTZt0nXOOC3HSd5RqHBhwAcGDp1W3pcOby@github.com/viash-hub/rnaseq" + "git_commit" : "d63250ae704b6bd9a11792c4f979be2309999a2e", + "git_remote" : "https://x-access-token:ghs_ri9q8QB7jMaviilgc8bYrtSqMrabrg3q8JZY@github.com/viash-hub/rnaseq" }, "package_config" : { "name" : "rnaseq",