diff --git a/src/workflows/rnaseq/config.vsh.yaml b/src/workflows/rnaseq/config.vsh.yaml index 4526e8c..0060fda 100644 --- a/src/workflows/rnaseq/config.vsh.yaml +++ b/src/workflows/rnaseq/config.vsh.yaml @@ -349,39 +349,39 @@ argument_groups: - name: "--output_fasta" type: file direction: output - default: genome/reference_genome.fasta + default: reference/genome.fasta - name: "--output_gtf" type: file direction: output - default: genome/gene_annotation.gtf + default: reference/gene_annotation.gtf - name: "--output_transcript_fasta" type: file direction: output - default: genome/transcriptome.fasta + default: reference/transcriptome.fasta - name: "--output_gene_bed" type: file direction: output - default: genome/gene_annotation.bed + default: reference/gene_annotation.bed - name: "--output_star_index" type: file direction: output description: Path to STAR index. - default: genome/index/STAR + default: reference/index/STAR - name: "--output_salmon_index" type: file direction: output description: Path to Salmon index. - default: genome/index/Salmon + default: reference/index/Salmon - name: "--output_bbsplit_index" type: file direction: output description: Path to BBSplit index. - default: genome/index/BBSplit + default: reference/index/BBSplit - name: "--output_kallisto_index" type: file direction: output description: Path to Kallisto index. - default: genome/index/Kallisto + default: reference/index/Kallisto # fastq - name: "--output_fastq_1" diff --git a/target/executable/bbmap_bbsplit/.config.vsh.yaml b/target/executable/bbmap_bbsplit/.config.vsh.yaml index 975a7d6..6a44ce9 100644 --- a/target/executable/bbmap_bbsplit/.config.vsh.yaml +++ b/target/executable/bbmap_bbsplit/.config.vsh.yaml @@ -238,8 +238,8 @@ build_info: output: "target/executable/bbmap_bbsplit" executable: "target/executable/bbmap_bbsplit/bbmap_bbsplit" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/bbmap_bbsplit/bbmap_bbsplit b/target/executable/bbmap_bbsplit/bbmap_bbsplit index 4084e27..bcc775d 100755 --- a/target/executable/bbmap_bbsplit/bbmap_bbsplit +++ b/target/executable/bbmap_bbsplit/bbmap_bbsplit @@ -506,9 +506,9 @@ tar xzf BBMap_39.01.tar.gz && \ cp -r bbmap/* /usr/local/bin LABEL org.opencontainers.image.description="Companion container for running component bbmap_bbsplit" -LABEL org.opencontainers.image.created="2024-09-30T12:29:41Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:05Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/bedtools_genomecov/.config.vsh.yaml b/target/executable/bedtools_genomecov/.config.vsh.yaml index 4d723e1..822095b 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/bedtools_genomecov/bedtools_genomecov b/target/executable/bedtools_genomecov/bedtools_genomecov index 7368397..217209c 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="2024-09-30T12:29:42Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:06Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/cat_additional_fasta/.config.vsh.yaml b/target/executable/cat_additional_fasta/.config.vsh.yaml index 17bbae5..5616400 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/cat_additional_fasta/cat_additional_fasta b/target/executable/cat_additional_fasta/cat_additional_fasta index c64662a..a626ff8 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="2024-09-30T12:29:50Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:13Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/cat_fastq/.config.vsh.yaml b/target/executable/cat_fastq/.config.vsh.yaml index f38b3a6..fe7fb96 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/cat_fastq/cat_fastq b/target/executable/cat_fastq/cat_fastq index 9c82bd7..f02f52b 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="2024-09-30T12:29:50Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:14Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/deseq2_qc/.config.vsh.yaml b/target/executable/deseq2_qc/.config.vsh.yaml index 5c28bc7..2664641 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/deseq2_qc/deseq2_qc b/target/executable/deseq2_qc/deseq2_qc index 16fe7a1..4d7998b 100755 --- a/target/executable/deseq2_qc/deseq2_qc +++ b/target/executable/deseq2_qc/deseq2_qc @@ -502,9 +502,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag Rscript -e 'remotes::install_url(c("https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz"), repos = "https://cran.rstudio.com")' LABEL org.opencontainers.image.description="Companion container for running component deseq2_qc" -LABEL org.opencontainers.image.created="2024-09-30T12:30:02Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:24Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/dupradar/.config.vsh.yaml b/target/executable/dupradar/.config.vsh.yaml index dc7210f..6537f30 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/dupradar/dupradar b/target/executable/dupradar/dupradar index fe1d19b..2005823 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="2024-09-30T12:29:52Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:15Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/fastqc/.config.vsh.yaml b/target/executable/fastqc/.config.vsh.yaml index de15122..265301a 100644 --- a/target/executable/fastqc/.config.vsh.yaml +++ b/target/executable/fastqc/.config.vsh.yaml @@ -198,8 +198,8 @@ build_info: output: "target/executable/fastqc" executable: "target/executable/fastqc/fastqc" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/fastqc/fastqc b/target/executable/fastqc/fastqc index dd20cf3..2f93ce3 100755 --- a/target/executable/fastqc/fastqc +++ b/target/executable/fastqc/fastqc @@ -490,9 +490,9 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component fastqc" -LABEL org.opencontainers.image.created="2024-09-30T12:29:43Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:07Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/fq_subsample/.config.vsh.yaml b/target/executable/fq_subsample/.config.vsh.yaml index d9f42d6..5c9620d 100644 --- a/target/executable/fq_subsample/.config.vsh.yaml +++ b/target/executable/fq_subsample/.config.vsh.yaml @@ -177,8 +177,8 @@ build_info: output: "target/executable/fq_subsample" executable: "target/executable/fq_subsample/fq_subsample" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/fq_subsample/fq_subsample b/target/executable/fq_subsample/fq_subsample index d3a230c..b2ab428 100755 --- a/target/executable/fq_subsample/fq_subsample +++ b/target/executable/fq_subsample/fq_subsample @@ -485,9 +485,9 @@ cargo install --locked --path . && \ mv /usr/local/fq/target/release/fq /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component fq_subsample" -LABEL org.opencontainers.image.created="2024-09-30T12:29:43Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:06Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/getchromsizes/.config.vsh.yaml b/target/executable/getchromsizes/.config.vsh.yaml index ecf280e..bbab9c2 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/getchromsizes/getchromsizes b/target/executable/getchromsizes/getchromsizes index aea837a..d18d6db 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="2024-09-30T12:29:43Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:07Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/gtf2bed/.config.vsh.yaml b/target/executable/gtf2bed/.config.vsh.yaml index 9122e3f..8ab4a59 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/gtf2bed/gtf2bed b/target/executable/gtf2bed/gtf2bed index a12b252..09b5d15 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="2024-09-30T12:29:57Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:19Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/gtf_filter/.config.vsh.yaml b/target/executable/gtf_filter/.config.vsh.yaml index 48b6483..ec87e4a 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/gtf_filter/gtf_filter b/target/executable/gtf_filter/gtf_filter index d748811..5f521df 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="2024-09-30T12:30:00Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:23Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/gunzip/.config.vsh.yaml b/target/executable/gunzip/.config.vsh.yaml index 7058b79..e733ce6 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/gunzip/gunzip b/target/executable/gunzip/gunzip index 6dd5b6b..804ba4b 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="2024-09-30T12:29:44Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:07Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/kallisto/kallisto_index/.config.vsh.yaml b/target/executable/kallisto/kallisto_index/.config.vsh.yaml index 51beef2..cd5d588 100644 --- a/target/executable/kallisto/kallisto_index/.config.vsh.yaml +++ b/target/executable/kallisto/kallisto_index/.config.vsh.yaml @@ -155,8 +155,8 @@ build_info: output: "target/executable/kallisto/kallisto_index" executable: "target/executable/kallisto/kallisto_index/kallisto_index" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/kallisto/kallisto_index/kallisto_index b/target/executable/kallisto/kallisto_index/kallisto_index index fa6fcac..113cf1a 100755 --- a/target/executable/kallisto/kallisto_index/kallisto_index +++ b/target/executable/kallisto/kallisto_index/kallisto_index @@ -471,9 +471,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \ mv kallisto/kallisto /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_index" -LABEL org.opencontainers.image.created="2024-09-30T12:29:59Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:21Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml index 1b45318..0ed06db 100644 --- a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml +++ b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml @@ -253,8 +253,8 @@ build_info: output: "target/executable/kallisto/kallisto_quant" executable: "target/executable/kallisto/kallisto_quant/kallisto_quant" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/kallisto/kallisto_quant/kallisto_quant b/target/executable/kallisto/kallisto_quant/kallisto_quant index e56181c..df1f36f 100755 --- a/target/executable/kallisto/kallisto_quant/kallisto_quant +++ b/target/executable/kallisto/kallisto_quant/kallisto_quant @@ -515,9 +515,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \ mv kallisto/kallisto /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_quant" -LABEL org.opencontainers.image.created="2024-09-30T12:29:58Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:21Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/multiqc_custom_biotype/.config.vsh.yaml b/target/executable/multiqc_custom_biotype/.config.vsh.yaml index 1f5d81a..c54e343 100644 --- a/target/executable/multiqc_custom_biotype/.config.vsh.yaml +++ b/target/executable/multiqc_custom_biotype/.config.vsh.yaml @@ -170,8 +170,8 @@ build_info: output: "target/executable/multiqc_custom_biotype" executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/multiqc_custom_biotype/multiqc_custom_biotype b/target/executable/multiqc_custom_biotype/multiqc_custom_biotype index 96627c6..4ca034c 100755 --- a/target/executable/multiqc_custom_biotype/multiqc_custom_biotype +++ b/target/executable/multiqc_custom_biotype/multiqc_custom_biotype @@ -481,9 +481,9 @@ RUN apt-get update && \ RUN pip install --upgrade pip LABEL org.opencontainers.image.description="Companion container for running component multiqc_custom_biotype" -LABEL org.opencontainers.image.created="2024-09-30T12:29:52Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:15Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/picard_markduplicates/.config.vsh.yaml b/target/executable/picard_markduplicates/.config.vsh.yaml index b74fc09..9f14e1c 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/picard_markduplicates/picard_markduplicates b/target/executable/picard_markduplicates/picard_markduplicates index 7e4175c..f3d619c 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="2024-09-30T12:30:01Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:23Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/prepare_multiqc_input/.config.vsh.yaml b/target/executable/prepare_multiqc_input/.config.vsh.yaml index cbdc3e8..cc5c085 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/prepare_multiqc_input/prepare_multiqc_input b/target/executable/prepare_multiqc_input/prepare_multiqc_input index 204e162..34a74cd 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="2024-09-30T12:29:56Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:19Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml b/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml index c696b3a..0f043f0 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta b/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta index 25f8cf9..ac03d84 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="2024-09-30T12:29:56Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:18Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/preseq_lcextrap/.config.vsh.yaml b/target/executable/preseq_lcextrap/.config.vsh.yaml index 819685d..0e25b25 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/preseq_lcextrap/preseq_lcextrap b/target/executable/preseq_lcextrap/preseq_lcextrap index 3d269e7..77687c1 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="2024-09-30T12:29:44Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:08Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/qualimap/.config.vsh.yaml b/target/executable/qualimap/.config.vsh.yaml index d9ebec3..38a2d42 100644 --- a/target/executable/qualimap/.config.vsh.yaml +++ b/target/executable/qualimap/.config.vsh.yaml @@ -271,8 +271,8 @@ build_info: output: "target/executable/qualimap" executable: "target/executable/qualimap/qualimap" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/qualimap/qualimap b/target/executable/qualimap/qualimap index 4d6e5c6..06710c1 100755 --- a/target/executable/qualimap/qualimap +++ b/target/executable/qualimap/qualimap @@ -537,9 +537,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag Rscript -e 'remotes::install_cran(c("optparse"), repos = "https://cran.rstudio.com")' LABEL org.opencontainers.image.description="Companion container for running component qualimap" -LABEL org.opencontainers.image.created="2024-09-30T12:29:42Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:06Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml index 993a190..f4bfd46 100644 --- a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml +++ b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml @@ -299,8 +299,8 @@ build_info: output: "target/executable/rsem/rsem_calculate_expression" executable: "target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression index 1711056..92cfd90 100755 --- a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression +++ b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression @@ -542,9 +542,9 @@ echo 'export PATH=$PATH:/usr/local/bin' >> ~/.bashrc && \ /bin/bash -c "source /etc/profile && source ~/.bashrc && echo $PATH && which STAR" LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_calculate_expression" -LABEL org.opencontainers.image.created="2024-09-30T12:29:58Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:20Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml b/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml index 3795cbe..06af82d 100644 --- a/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml +++ b/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml @@ -182,8 +182,8 @@ build_info: output: "target/executable/rsem/rsem_merge_counts" executable: "target/executable/rsem/rsem_merge_counts/rsem_merge_counts" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rsem/rsem_merge_counts/rsem_merge_counts b/target/executable/rsem/rsem_merge_counts/rsem_merge_counts index 26ad9df..0aab804 100755 --- a/target/executable/rsem/rsem_merge_counts/rsem_merge_counts +++ b/target/executable/rsem/rsem_merge_counts/rsem_merge_counts @@ -483,9 +483,9 @@ function ViashDockerfile { FROM ubuntu:22.04 ENTRYPOINT [] LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_merge_counts" -LABEL org.opencontainers.image.created="2024-09-30T12:29:58Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:20Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml index 95ac4b6..f93620d 100644 --- a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml @@ -163,8 +163,8 @@ build_info: output: "target/executable/rseqc/rseqc_bamstat" executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat index 035eb8d..4fd8850 100755 --- a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat +++ b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat @@ -477,9 +477,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_bamstat" -LABEL org.opencontainers.image.created="2024-09-30T12:29:55Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:18Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml index bb772ac..12a23ea 100644 --- a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml @@ -186,8 +186,8 @@ build_info: output: "target/executable/rseqc/rseqc_inferexperiment" executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment index d58115d..79b2ad6 100755 --- a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment +++ b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment @@ -487,9 +487,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_inferexperiment" -LABEL org.opencontainers.image.created="2024-09-30T12:29:53Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:16Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml b/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml index 8da9a08..590a3b3 100644 --- a/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml +++ b/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml @@ -272,8 +272,8 @@ build_info: output: "target/executable/rseqc/rseqc_innerdistance" executable: "target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance b/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance index c3856c9..918dcd4 100755 --- a/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance +++ b/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance @@ -529,9 +529,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "RSeQC" LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_innerdistance" -LABEL org.opencontainers.image.created="2024-09-30T12:29:55Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:17Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml b/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml index 37eafd5..d948d38 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation b/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation index 9e9823f..0785d89 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="2024-09-30T12:29:54Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:17Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml b/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml index 14e4043..93c3aa7 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation b/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation index 2141b09..81ac341 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="2024-09-30T12:29:54Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:17Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml b/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml index 030a4d1..244d0ce 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution b/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution index 95351df..d5803ab 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="2024-09-30T12:29:56Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:18Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml b/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml index e4c71d0..fc70fd4 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication b/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication index ecc0841..fecd51d 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="2024-09-30T12:29:53Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:16Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/rseqc/rseqc_tin/.config.vsh.yaml b/target/executable/rseqc/rseqc_tin/.config.vsh.yaml index cde5af1..23a3f2e 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/rseqc/rseqc_tin/rseqc_tin b/target/executable/rseqc/rseqc_tin/rseqc_tin index b73bcb8..b58efce 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="2024-09-30T12:29:53Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:16Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/sortmerna/.config.vsh.yaml b/target/executable/sortmerna/.config.vsh.yaml index b35f92b..99d1385 100644 --- a/target/executable/sortmerna/.config.vsh.yaml +++ b/target/executable/sortmerna/.config.vsh.yaml @@ -198,8 +198,8 @@ build_info: output: "target/executable/sortmerna" executable: "target/executable/sortmerna/sortmerna" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/sortmerna/sortmerna b/target/executable/sortmerna/sortmerna index 468d580..609e99f 100755 --- a/target/executable/sortmerna/sortmerna +++ b/target/executable/sortmerna/sortmerna @@ -492,9 +492,9 @@ wget --no-check-certificate https://github.com/sortmerna/sortmerna/releases/down bash sortmerna-4.3.6-Linux.sh --skip-license LABEL org.opencontainers.image.description="Companion container for running component sortmerna" -LABEL org.opencontainers.image.created="2024-09-30T12:30:00Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:23Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/stringtie/.config.vsh.yaml b/target/executable/stringtie/.config.vsh.yaml index 087ae22..e2bfcba 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/stringtie/stringtie b/target/executable/stringtie/stringtie index d404b8c..9ee85d8 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="2024-09-30T12:29:57Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:20Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/summarizedexperiment/.config.vsh.yaml b/target/executable/summarizedexperiment/.config.vsh.yaml index 872f666..d46fd23 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/summarizedexperiment/summarizedexperiment b/target/executable/summarizedexperiment/summarizedexperiment index f936a15..24e69fb 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="2024-09-30T12:30:01Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:23Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/trimgalore/.config.vsh.yaml b/target/executable/trimgalore/.config.vsh.yaml index e800fdc..1efa1b5 100644 --- a/target/executable/trimgalore/.config.vsh.yaml +++ b/target/executable/trimgalore/.config.vsh.yaml @@ -788,8 +788,8 @@ build_info: output: "target/executable/trimgalore" executable: "target/executable/trimgalore/trimgalore" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/trimgalore/trimgalore b/target/executable/trimgalore/trimgalore index 98c43b3..6023ad0 100755 --- a/target/executable/trimgalore/trimgalore +++ b/target/executable/trimgalore/trimgalore @@ -858,9 +858,9 @@ ENTRYPOINT [] RUN echo "TrimGalore: `trim_galore --version | sed -n 's/.*version\s\+\([0-9]\+\.[0-9]\+\.[0-9]\+\).*/\1/p'`" > /var/software_versions.txt LABEL org.opencontainers.image.description="Companion container for running component trimgalore" -LABEL org.opencontainers.image.created="2024-09-30T12:30:00Z" +LABEL org.opencontainers.image.created="2024-10-01T09:00:22Z" LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/tx2gene/.config.vsh.yaml b/target/executable/tx2gene/.config.vsh.yaml index cf0a429..5eeb417 100644 --- a/target/executable/tx2gene/.config.vsh.yaml +++ b/target/executable/tx2gene/.config.vsh.yaml @@ -192,8 +192,8 @@ build_info: output: "target/executable/tx2gene" executable: "target/executable/tx2gene/tx2gene" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/tx2gene/tx2gene b/target/executable/tx2gene/tx2gene index 864baca..518a0dc 100755 --- a/target/executable/tx2gene/tx2gene +++ b/target/executable/tx2gene/tx2gene @@ -487,9 +487,9 @@ RUN apt-get update && \ RUN pip install --upgrade pip LABEL org.opencontainers.image.description="Companion container for running component tx2gene" -LABEL org.opencontainers.image.created="2024-09-30T12:29:57Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:19Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/tximport/.config.vsh.yaml b/target/executable/tximport/.config.vsh.yaml index 8184c5c..dcdbca0 100644 --- a/target/executable/tximport/.config.vsh.yaml +++ b/target/executable/tximport/.config.vsh.yaml @@ -247,8 +247,8 @@ build_info: output: "target/executable/tximport" executable: "target/executable/tximport/tximport" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/tximport/tximport b/target/executable/tximport/tximport index 962b89b..e761b55 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="2024-09-30T12:29:49Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:13Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/ucsc/bedclip/.config.vsh.yaml b/target/executable/ucsc/bedclip/.config.vsh.yaml index e6585ca..425d5df 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/ucsc/bedclip/bedclip b/target/executable/ucsc/bedclip/bedclip index 0bf5c13..467f8c2 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="2024-09-30T12:29:51Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:14Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml b/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml index 57a6273..bc8e1ec 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig b/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig index 27acae1..ea1eb77 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="2024-09-30T12:29:51Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:15Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/umitools/umitools_dedup/.config.vsh.yaml b/target/executable/umitools/umitools_dedup/.config.vsh.yaml index ae4851b..e81ae73 100644 --- a/target/executable/umitools/umitools_dedup/.config.vsh.yaml +++ b/target/executable/umitools/umitools_dedup/.config.vsh.yaml @@ -195,8 +195,8 @@ build_info: output: "target/executable/umitools/umitools_dedup" executable: "target/executable/umitools/umitools_dedup/umitools_dedup" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/umitools/umitools_dedup/umitools_dedup b/target/executable/umitools/umitools_dedup/umitools_dedup index d9b9c0d..4365354 100755 --- a/target/executable/umitools/umitools_dedup/umitools_dedup +++ b/target/executable/umitools/umitools_dedup/umitools_dedup @@ -489,9 +489,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "umi_tools" LABEL org.opencontainers.image.description="Companion container for running component umitools umitools_dedup" -LABEL org.opencontainers.image.created="2024-09-30T12:29:59Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:21Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/umitools/umitools_extract/.config.vsh.yaml b/target/executable/umitools/umitools_extract/.config.vsh.yaml index 8f5038c..b6a7932 100644 --- a/target/executable/umitools/umitools_extract/.config.vsh.yaml +++ b/target/executable/umitools/umitools_extract/.config.vsh.yaml @@ -253,8 +253,8 @@ build_info: output: "target/executable/umitools/umitools_extract" executable: "target/executable/umitools/umitools_extract/umitools_extract" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/umitools/umitools_extract/umitools_extract b/target/executable/umitools/umitools_extract/umitools_extract index 3dda0b3..e0d6111 100755 --- a/target/executable/umitools/umitools_extract/umitools_extract +++ b/target/executable/umitools/umitools_extract/umitools_extract @@ -521,9 +521,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "umi_tools" LABEL org.opencontainers.image.description="Companion container for running component umitools umitools_extract" -LABEL org.opencontainers.image.created="2024-09-30T12:29:59Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:22Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER diff --git a/target/executable/umitools_prepareforquant/.config.vsh.yaml b/target/executable/umitools_prepareforquant/.config.vsh.yaml index 2cf378d..7d981d4 100644 --- a/target/executable/umitools_prepareforquant/.config.vsh.yaml +++ b/target/executable/umitools_prepareforquant/.config.vsh.yaml @@ -156,8 +156,8 @@ build_info: output: "target/executable/umitools_prepareforquant" executable: "target/executable/umitools_prepareforquant/umitools_prepareforquant" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/umitools_prepareforquant/umitools_prepareforquant b/target/executable/umitools_prepareforquant/umitools_prepareforquant index f4c4167..7a0e349 100755 --- a/target/executable/umitools_prepareforquant/umitools_prepareforquant +++ b/target/executable/umitools_prepareforquant/umitools_prepareforquant @@ -473,9 +473,9 @@ RUN pip install --upgrade pip && \ pip install --upgrade --no-cache-dir "umi_tools" "pysam" LABEL org.opencontainers.image.description="Companion container for running component umitools_prepareforquant" -LABEL org.opencontainers.image.created="2024-09-30T12:30:01Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="dc43230e43731e5733fffba429a1190f08dbc742" +LABEL org.opencontainers.image.created="2024-10-01T09:00:24Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" LABEL org.opencontainers.image.version="multiple_fixes" 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 c691685..c90bedd 100644 --- a/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml +++ b/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml @@ -603,8 +603,8 @@ build_info: output: "target/executable/workflows/genome_alignment_and_quant" executable: "target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort" diff --git a/target/executable/workflows/merge_quant_results/.config.vsh.yaml b/target/executable/workflows/merge_quant_results/.config.vsh.yaml index 76b53f8..b7921e8 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@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 2e15fc5..edaa842 100644 --- a/target/executable/workflows/post_processing/.config.vsh.yaml +++ b/target/executable/workflows/post_processing/.config.vsh.yaml @@ -486,8 +486,8 @@ build_info: output: "target/executable/workflows/post_processing" executable: "target/executable/workflows/post_processing/post_processing" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/picard_markduplicates" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort" diff --git a/target/executable/workflows/pre_processing/.config.vsh.yaml b/target/executable/workflows/pre_processing/.config.vsh.yaml index 2af4373..fad086d 100644 --- a/target/executable/workflows/pre_processing/.config.vsh.yaml +++ b/target/executable/workflows/pre_processing/.config.vsh.yaml @@ -673,8 +673,8 @@ build_info: output: "target/executable/workflows/pre_processing" executable: "target/executable/workflows/pre_processing/pre_processing" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/fastqc" - "target/nextflow/umitools/umitools_extract" diff --git a/target/executable/workflows/prepare_genome/.config.vsh.yaml b/target/executable/workflows/prepare_genome/.config.vsh.yaml index e9f9a94..2950db2 100644 --- a/target/executable/workflows/prepare_genome/.config.vsh.yaml +++ b/target/executable/workflows/prepare_genome/.config.vsh.yaml @@ -496,8 +496,8 @@ build_info: output: "target/executable/workflows/prepare_genome" executable: "target/executable/workflows/prepare_genome/prepare_genome" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/gunzip" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread" diff --git a/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml b/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml index b071554..129174d 100644 --- a/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml +++ b/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml @@ -283,8 +283,8 @@ build_info: output: "target/executable/workflows/pseudo_alignment_and_quant" executable: "target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant" - "target/nextflow/kallisto/kallisto_quant" diff --git a/target/executable/workflows/quality_control/.config.vsh.yaml b/target/executable/workflows/quality_control/.config.vsh.yaml index f1ffedc..f99689a 100644 --- a/target/executable/workflows/quality_control/.config.vsh.yaml +++ b/target/executable/workflows/quality_control/.config.vsh.yaml @@ -1596,8 +1596,8 @@ build_info: output: "target/executable/workflows/quality_control" executable: "target/executable/workflows/quality_control/quality_control" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/rseqc/rseqc_bamstat" - "target/nextflow/rseqc/rseqc_inferexperiment" diff --git a/target/executable/workflows/rnaseq/.config.vsh.yaml b/target/executable/workflows/rnaseq/.config.vsh.yaml index 62be148..c02fca8 100644 --- a/target/executable/workflows/rnaseq/.config.vsh.yaml +++ b/target/executable/workflows/rnaseq/.config.vsh.yaml @@ -785,7 +785,7 @@ argument_groups: name: "--output_fasta" info: null default: - - "genome/reference_genome.fasta" + - "reference/genome.fasta" must_exist: true create_parent: true required: false @@ -796,7 +796,7 @@ argument_groups: name: "--output_gtf" info: null default: - - "genome/gene_annotation.gtf" + - "reference/gene_annotation.gtf" must_exist: true create_parent: true required: false @@ -807,7 +807,7 @@ argument_groups: name: "--output_transcript_fasta" info: null default: - - "genome/transcriptome.fasta" + - "reference/transcriptome.fasta" must_exist: true create_parent: true required: false @@ -818,7 +818,7 @@ argument_groups: name: "--output_gene_bed" info: null default: - - "genome/gene_annotation.bed" + - "reference/gene_annotation.bed" must_exist: true create_parent: true required: false @@ -830,7 +830,7 @@ argument_groups: description: "Path to STAR index." info: null default: - - "genome/index/STAR" + - "reference/index/STAR" must_exist: true create_parent: true required: false @@ -842,7 +842,7 @@ argument_groups: description: "Path to Salmon index." info: null default: - - "genome/index/Salmon" + - "reference/index/Salmon" must_exist: true create_parent: true required: false @@ -854,7 +854,7 @@ argument_groups: description: "Path to BBSplit index." info: null default: - - "genome/index/BBSplit" + - "reference/index/BBSplit" must_exist: true create_parent: true required: false @@ -866,7 +866,7 @@ argument_groups: description: "Path to Kallisto index." info: null default: - - "genome/index/Kallisto" + - "reference/index/Kallisto" must_exist: true create_parent: true required: false @@ -2117,8 +2117,8 @@ build_info: output: "target/executable/workflows/rnaseq" executable: "target/executable/workflows/rnaseq/rnaseq" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/workflows/prepare_genome" - "target/nextflow/cat_fastq" diff --git a/target/executable/workflows/rnaseq/rnaseq b/target/executable/workflows/rnaseq/rnaseq index 36eeb33..87cd8ab 100755 --- a/target/executable/workflows/rnaseq/rnaseq +++ b/target/executable/workflows/rnaseq/rnaseq @@ -588,38 +588,38 @@ function ViashHelp { echo "Output:" echo " --output_fasta" echo " type: file, output, file must exist" - echo " default: genome/reference_genome.fasta" + echo " default: reference/genome.fasta" echo "" echo " --output_gtf" echo " type: file, output, file must exist" - echo " default: genome/gene_annotation.gtf" + echo " default: reference/gene_annotation.gtf" echo "" echo " --output_transcript_fasta" echo " type: file, output, file must exist" - echo " default: genome/transcriptome.fasta" + echo " default: reference/transcriptome.fasta" echo "" echo " --output_gene_bed" echo " type: file, output, file must exist" - echo " default: genome/gene_annotation.bed" + echo " default: reference/gene_annotation.bed" echo "" echo " --output_star_index" echo " type: file, output, file must exist" - echo " default: genome/index/STAR" + echo " default: reference/index/STAR" echo " Path to STAR index." echo "" echo " --output_salmon_index" echo " type: file, output, file must exist" - echo " default: genome/index/Salmon" + echo " default: reference/index/Salmon" echo " Path to Salmon index." echo "" echo " --output_bbsplit_index" echo " type: file, output, file must exist" - echo " default: genome/index/BBSplit" + echo " default: reference/index/BBSplit" echo " Path to BBSplit index." echo "" echo " --output_kallisto_index" echo " type: file, output, file must exist" - echo " default: genome/index/Kallisto" + echo " default: reference/index/Kallisto" echo " Path to Kallisto index." echo "" echo " --output_fastq_1" @@ -3343,28 +3343,28 @@ if [ -z ${VIASH_PAR_MULTIQC_METHODS_DESCRIPTION+x} ]; then VIASH_PAR_MULTIQC_METHODS_DESCRIPTION="assets/methods_description_template.yml" fi if [ -z ${VIASH_PAR_OUTPUT_FASTA+x} ]; then - VIASH_PAR_OUTPUT_FASTA="genome/reference_genome.fasta" + VIASH_PAR_OUTPUT_FASTA="reference/genome.fasta" fi if [ -z ${VIASH_PAR_OUTPUT_GTF+x} ]; then - VIASH_PAR_OUTPUT_GTF="genome/gene_annotation.gtf" + VIASH_PAR_OUTPUT_GTF="reference/gene_annotation.gtf" fi if [ -z ${VIASH_PAR_OUTPUT_TRANSCRIPT_FASTA+x} ]; then - VIASH_PAR_OUTPUT_TRANSCRIPT_FASTA="genome/transcriptome.fasta" + VIASH_PAR_OUTPUT_TRANSCRIPT_FASTA="reference/transcriptome.fasta" fi if [ -z ${VIASH_PAR_OUTPUT_GENE_BED+x} ]; then - VIASH_PAR_OUTPUT_GENE_BED="genome/gene_annotation.bed" + VIASH_PAR_OUTPUT_GENE_BED="reference/gene_annotation.bed" fi if [ -z ${VIASH_PAR_OUTPUT_STAR_INDEX+x} ]; then - VIASH_PAR_OUTPUT_STAR_INDEX="genome/index/STAR" + VIASH_PAR_OUTPUT_STAR_INDEX="reference/index/STAR" fi if [ -z ${VIASH_PAR_OUTPUT_SALMON_INDEX+x} ]; then - VIASH_PAR_OUTPUT_SALMON_INDEX="genome/index/Salmon" + VIASH_PAR_OUTPUT_SALMON_INDEX="reference/index/Salmon" fi if [ -z ${VIASH_PAR_OUTPUT_BBSPLIT_INDEX+x} ]; then - VIASH_PAR_OUTPUT_BBSPLIT_INDEX="genome/index/BBSplit" + VIASH_PAR_OUTPUT_BBSPLIT_INDEX="reference/index/BBSplit" fi if [ -z ${VIASH_PAR_OUTPUT_KALLISTO_INDEX+x} ]; then - VIASH_PAR_OUTPUT_KALLISTO_INDEX="genome/index/Kallisto" + VIASH_PAR_OUTPUT_KALLISTO_INDEX="reference/index/Kallisto" fi if [ -z ${VIASH_PAR_OUTPUT_FASTQ_1+x} ]; then VIASH_PAR_OUTPUT_FASTQ_1="fastq/\$id.read_1.fastq" diff --git a/target/nextflow/bbmap_bbsplit/.config.vsh.yaml b/target/nextflow/bbmap_bbsplit/.config.vsh.yaml index c061515..f489a88 100644 --- a/target/nextflow/bbmap_bbsplit/.config.vsh.yaml +++ b/target/nextflow/bbmap_bbsplit/.config.vsh.yaml @@ -238,8 +238,8 @@ build_info: output: "target/nextflow/bbmap_bbsplit" executable: "target/nextflow/bbmap_bbsplit/main.nf" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/bbmap_bbsplit/main.nf b/target/nextflow/bbmap_bbsplit/main.nf index 6db8d07..171888e 100644 --- a/target/nextflow/bbmap_bbsplit/main.nf +++ b/target/nextflow/bbmap_bbsplit/main.nf @@ -3104,8 +3104,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/bbmap_bbsplit", "viash_version" : "0.9.0", - "git_commit" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/bedtools_genomecov/.config.vsh.yaml b/target/nextflow/bedtools_genomecov/.config.vsh.yaml index de9576b..ebea029 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/bedtools_genomecov/main.nf b/target/nextflow/bedtools_genomecov/main.nf index ac540d1..9e9dbb4 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" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/cat_additional_fasta/.config.vsh.yaml b/target/nextflow/cat_additional_fasta/.config.vsh.yaml index 04f154d..00e27f4 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/cat_additional_fasta/main.nf b/target/nextflow/cat_additional_fasta/main.nf index 0ed3073..3b86d0e 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" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/cat_fastq/.config.vsh.yaml b/target/nextflow/cat_fastq/.config.vsh.yaml index badebbb..cab7c87 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/cat_fastq/main.nf b/target/nextflow/cat_fastq/main.nf index a901634..6b0eb15 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" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/deseq2_qc/.config.vsh.yaml b/target/nextflow/deseq2_qc/.config.vsh.yaml index cf49752..59c1a2f 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/deseq2_qc/main.nf b/target/nextflow/deseq2_qc/main.nf index eeffa90..9a3c553 100644 --- a/target/nextflow/deseq2_qc/main.nf +++ b/target/nextflow/deseq2_qc/main.nf @@ -3110,8 +3110,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/deseq2_qc", "viash_version" : "0.9.0", - "git_commit" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/dupradar/.config.vsh.yaml b/target/nextflow/dupradar/.config.vsh.yaml index f742f2f..2c6eb92 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/dupradar/main.nf b/target/nextflow/dupradar/main.nf index 9d3fda3..a45bad3 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" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/fastqc/.config.vsh.yaml b/target/nextflow/fastqc/.config.vsh.yaml index 2f8eadc..c4eaa09 100644 --- a/target/nextflow/fastqc/.config.vsh.yaml +++ b/target/nextflow/fastqc/.config.vsh.yaml @@ -198,8 +198,8 @@ build_info: output: "target/nextflow/fastqc" executable: "target/nextflow/fastqc/main.nf" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/fastqc/main.nf b/target/nextflow/fastqc/main.nf index 0822d4a..45f9d7f 100644 --- a/target/nextflow/fastqc/main.nf +++ b/target/nextflow/fastqc/main.nf @@ -3056,8 +3056,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/fastqc", "viash_version" : "0.9.0", - "git_commit" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/fq_subsample/.config.vsh.yaml b/target/nextflow/fq_subsample/.config.vsh.yaml index a37d1ee..ffab427 100644 --- a/target/nextflow/fq_subsample/.config.vsh.yaml +++ b/target/nextflow/fq_subsample/.config.vsh.yaml @@ -177,8 +177,8 @@ build_info: output: "target/nextflow/fq_subsample" executable: "target/nextflow/fq_subsample/main.nf" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/fq_subsample/main.nf b/target/nextflow/fq_subsample/main.nf index 54536ab..8152dd3 100644 --- a/target/nextflow/fq_subsample/main.nf +++ b/target/nextflow/fq_subsample/main.nf @@ -3027,8 +3027,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/fq_subsample", "viash_version" : "0.9.0", - "git_commit" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/getchromsizes/.config.vsh.yaml b/target/nextflow/getchromsizes/.config.vsh.yaml index 8f2923c..2555fb1 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/getchromsizes/main.nf b/target/nextflow/getchromsizes/main.nf index dea365c..5366564 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" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/gtf2bed/.config.vsh.yaml b/target/nextflow/gtf2bed/.config.vsh.yaml index 14dde9e..ec50f11 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/gtf2bed/main.nf b/target/nextflow/gtf2bed/main.nf index 89bd790..9589e17 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" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/gtf_filter/.config.vsh.yaml b/target/nextflow/gtf_filter/.config.vsh.yaml index 60c36ac..53a7324 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/gtf_filter/main.nf b/target/nextflow/gtf_filter/main.nf index 39c1bcc..ef21e9f 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" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/gunzip/.config.vsh.yaml b/target/nextflow/gunzip/.config.vsh.yaml index 320be04..fe3c03d 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/gunzip/main.nf b/target/nextflow/gunzip/main.nf index 1cae6bd..875d861 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" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml index 379a5a1..44085af 100644 --- a/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml +++ b/target/nextflow/kallisto/kallisto_index/.config.vsh.yaml @@ -155,8 +155,8 @@ build_info: output: "target/nextflow/kallisto/kallisto_index" executable: "target/nextflow/kallisto/kallisto_index/main.nf" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/kallisto/kallisto_index/main.nf b/target/nextflow/kallisto/kallisto_index/main.nf index ae3e3d3..681a1ab 100644 --- a/target/nextflow/kallisto/kallisto_index/main.nf +++ b/target/nextflow/kallisto/kallisto_index/main.nf @@ -3002,8 +3002,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/kallisto/kallisto_index", "viash_version" : "0.9.0", - "git_commit" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml index 8dd56b6..c50489e 100644 --- a/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml +++ b/target/nextflow/kallisto/kallisto_quant/.config.vsh.yaml @@ -253,8 +253,8 @@ build_info: output: "target/nextflow/kallisto/kallisto_quant" executable: "target/nextflow/kallisto/kallisto_quant/main.nf" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/kallisto/kallisto_quant/main.nf b/target/nextflow/kallisto/kallisto_quant/main.nf index 52473d7..b893018 100644 --- a/target/nextflow/kallisto/kallisto_quant/main.nf +++ b/target/nextflow/kallisto/kallisto_quant/main.nf @@ -3114,8 +3114,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/kallisto/kallisto_quant", "viash_version" : "0.9.0", - "git_commit" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml b/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml index 2131c40..0262e5d 100644 --- a/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml +++ b/target/nextflow/multiqc_custom_biotype/.config.vsh.yaml @@ -170,8 +170,8 @@ build_info: output: "target/nextflow/multiqc_custom_biotype" executable: "target/nextflow/multiqc_custom_biotype/main.nf" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/multiqc_custom_biotype/main.nf b/target/nextflow/multiqc_custom_biotype/main.nf index 9e0b303..689912c 100644 --- a/target/nextflow/multiqc_custom_biotype/main.nf +++ b/target/nextflow/multiqc_custom_biotype/main.nf @@ -3020,8 +3020,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/multiqc_custom_biotype", "viash_version" : "0.9.0", - "git_commit" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/picard_markduplicates/.config.vsh.yaml b/target/nextflow/picard_markduplicates/.config.vsh.yaml index 600a317..7ba0dd7 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/picard_markduplicates/main.nf b/target/nextflow/picard_markduplicates/main.nf index 8b7b6e4..00f73d6 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" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/prepare_multiqc_input/.config.vsh.yaml b/target/nextflow/prepare_multiqc_input/.config.vsh.yaml index 914caf8..1d82bde 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/prepare_multiqc_input/main.nf b/target/nextflow/prepare_multiqc_input/main.nf index bc3df1c..0f301ca 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" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml b/target/nextflow/preprocess_transcripts_fasta/.config.vsh.yaml index 2675e21..df67d04 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/preprocess_transcripts_fasta/main.nf b/target/nextflow/preprocess_transcripts_fasta/main.nf index c64448f..82b1e2a 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" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/preseq_lcextrap/.config.vsh.yaml b/target/nextflow/preseq_lcextrap/.config.vsh.yaml index aac9366..09a4e14 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/preseq_lcextrap/main.nf b/target/nextflow/preseq_lcextrap/main.nf index 1a8c55e..bf01729 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" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/qualimap/.config.vsh.yaml b/target/nextflow/qualimap/.config.vsh.yaml index f36f700..80a8f53 100644 --- a/target/nextflow/qualimap/.config.vsh.yaml +++ b/target/nextflow/qualimap/.config.vsh.yaml @@ -271,8 +271,8 @@ build_info: output: "target/nextflow/qualimap" executable: "target/nextflow/qualimap/main.nf" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/qualimap/main.nf b/target/nextflow/qualimap/main.nf index e7efe5d..89ec518 100644 --- a/target/nextflow/qualimap/main.nf +++ b/target/nextflow/qualimap/main.nf @@ -3144,8 +3144,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/qualimap", "viash_version" : "0.9.0", - "git_commit" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml index 6dfe07f..ad6e413 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_calculate_expression/.config.vsh.yaml @@ -299,8 +299,8 @@ build_info: output: "target/nextflow/rsem/rsem_calculate_expression" executable: "target/nextflow/rsem/rsem_calculate_expression/main.nf" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rsem/rsem_calculate_expression/main.nf b/target/nextflow/rsem/rsem_calculate_expression/main.nf index de6555e..e08b4a6 100644 --- a/target/nextflow/rsem/rsem_calculate_expression/main.nf +++ b/target/nextflow/rsem/rsem_calculate_expression/main.nf @@ -3163,8 +3163,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rsem/rsem_calculate_expression", "viash_version" : "0.9.0", - "git_commit" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml b/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml index 5057f05..6cdd85a 100644 --- a/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml @@ -182,8 +182,8 @@ build_info: output: "target/nextflow/rsem/rsem_merge_counts" executable: "target/nextflow/rsem/rsem_merge_counts/main.nf" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rsem/rsem_merge_counts/main.nf b/target/nextflow/rsem/rsem_merge_counts/main.nf index 21751d7..5e5f0f6 100644 --- a/target/nextflow/rsem/rsem_merge_counts/main.nf +++ b/target/nextflow/rsem/rsem_merge_counts/main.nf @@ -3028,8 +3028,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rsem/rsem_merge_counts", "viash_version" : "0.9.0", - "git_commit" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml index 51b2998..c37ff8a 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_bamstat/.config.vsh.yaml @@ -163,8 +163,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_bamstat" executable: "target/nextflow/rseqc/rseqc_bamstat/main.nf" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_bamstat/main.nf b/target/nextflow/rseqc/rseqc_bamstat/main.nf index 7f24c76..3f0c246 100644 --- a/target/nextflow/rseqc/rseqc_bamstat/main.nf +++ b/target/nextflow/rseqc/rseqc_bamstat/main.nf @@ -3016,8 +3016,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_bamstat", "viash_version" : "0.9.0", - "git_commit" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml index d493919..5cd174a 100644 --- a/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_inferexperiment/.config.vsh.yaml @@ -186,8 +186,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_inferexperiment" executable: "target/nextflow/rseqc/rseqc_inferexperiment/main.nf" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_inferexperiment/main.nf b/target/nextflow/rseqc/rseqc_inferexperiment/main.nf index 32b60c5..5bad7ca 100644 --- a/target/nextflow/rseqc/rseqc_inferexperiment/main.nf +++ b/target/nextflow/rseqc/rseqc_inferexperiment/main.nf @@ -3044,8 +3044,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_inferexperiment", "viash_version" : "0.9.0", - "git_commit" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml index ceefcf1..ae0eacc 100644 --- a/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml +++ b/target/nextflow/rseqc/rseqc_innerdistance/.config.vsh.yaml @@ -272,8 +272,8 @@ build_info: output: "target/nextflow/rseqc/rseqc_innerdistance" executable: "target/nextflow/rseqc/rseqc_innerdistance/main.nf" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_innerdistance/main.nf b/target/nextflow/rseqc/rseqc_innerdistance/main.nf index 7b60322..4c44efb 100644 --- a/target/nextflow/rseqc/rseqc_innerdistance/main.nf +++ b/target/nextflow/rseqc/rseqc_innerdistance/main.nf @@ -3137,8 +3137,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_innerdistance", "viash_version" : "0.9.0", - "git_commit" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_junctionannotation/.config.vsh.yaml index ef3fb6e..f31be92 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_junctionannotation/main.nf b/target/nextflow/rseqc/rseqc_junctionannotation/main.nf index 36f202f..3d4b4ab 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" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_junctionsaturation/.config.vsh.yaml index e8f029e..354254f 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf b/target/nextflow/rseqc/rseqc_junctionsaturation/main.nf index c56975a..99b984b 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" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_readdistribution/.config.vsh.yaml index ac37cd1..5b4297e 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_readdistribution/main.nf b/target/nextflow/rseqc/rseqc_readdistribution/main.nf index 7db0319..8b8009b 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" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_readduplication/.config.vsh.yaml index 82f273e..8dd8984 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_readduplication/main.nf b/target/nextflow/rseqc/rseqc_readduplication/main.nf index d5ce97f..ceb4df4 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" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml b/target/nextflow/rseqc/rseqc_tin/.config.vsh.yaml index 6cc86bd..bb7c080 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/rseqc/rseqc_tin/main.nf b/target/nextflow/rseqc/rseqc_tin/main.nf index 1397138..7e073a6 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" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/sortmerna/.config.vsh.yaml b/target/nextflow/sortmerna/.config.vsh.yaml index 887c903..44ada9e 100644 --- a/target/nextflow/sortmerna/.config.vsh.yaml +++ b/target/nextflow/sortmerna/.config.vsh.yaml @@ -198,8 +198,8 @@ build_info: output: "target/nextflow/sortmerna" executable: "target/nextflow/sortmerna/main.nf" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/sortmerna/main.nf b/target/nextflow/sortmerna/main.nf index 2e3d7aa..bd68e43 100644 --- a/target/nextflow/sortmerna/main.nf +++ b/target/nextflow/sortmerna/main.nf @@ -3050,8 +3050,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/sortmerna", "viash_version" : "0.9.0", - "git_commit" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/stringtie/.config.vsh.yaml b/target/nextflow/stringtie/.config.vsh.yaml index 239d441..234bfc6 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/stringtie/main.nf b/target/nextflow/stringtie/main.nf index 81057a6..1a2cea0 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" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/summarizedexperiment/.config.vsh.yaml b/target/nextflow/summarizedexperiment/.config.vsh.yaml index 5c12a37..89a62de 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/summarizedexperiment/main.nf b/target/nextflow/summarizedexperiment/main.nf index c361d6f..3d5fb3f 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" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/trimgalore/.config.vsh.yaml b/target/nextflow/trimgalore/.config.vsh.yaml index 1613f1e..20114b9 100644 --- a/target/nextflow/trimgalore/.config.vsh.yaml +++ b/target/nextflow/trimgalore/.config.vsh.yaml @@ -788,8 +788,8 @@ build_info: output: "target/nextflow/trimgalore" executable: "target/nextflow/trimgalore/main.nf" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/trimgalore/main.nf b/target/nextflow/trimgalore/main.nf index d6670f2..998b29b 100644 --- a/target/nextflow/trimgalore/main.nf +++ b/target/nextflow/trimgalore/main.nf @@ -3576,8 +3576,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/trimgalore", "viash_version" : "0.9.0", - "git_commit" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/tx2gene/.config.vsh.yaml b/target/nextflow/tx2gene/.config.vsh.yaml index edf84df..ed52bb7 100644 --- a/target/nextflow/tx2gene/.config.vsh.yaml +++ b/target/nextflow/tx2gene/.config.vsh.yaml @@ -192,8 +192,8 @@ build_info: output: "target/nextflow/tx2gene" executable: "target/nextflow/tx2gene/main.nf" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/tx2gene/main.nf b/target/nextflow/tx2gene/main.nf index 6dc8ba0..e3d151f 100644 --- a/target/nextflow/tx2gene/main.nf +++ b/target/nextflow/tx2gene/main.nf @@ -3049,8 +3049,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/tx2gene", "viash_version" : "0.9.0", - "git_commit" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/tximport/.config.vsh.yaml b/target/nextflow/tximport/.config.vsh.yaml index a0e0007..983f58a 100644 --- a/target/nextflow/tximport/.config.vsh.yaml +++ b/target/nextflow/tximport/.config.vsh.yaml @@ -247,8 +247,8 @@ build_info: output: "target/nextflow/tximport" executable: "target/nextflow/tximport/main.nf" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/tximport/main.nf b/target/nextflow/tximport/main.nf index 881029f..5af8032 100644 --- a/target/nextflow/tximport/main.nf +++ b/target/nextflow/tximport/main.nf @@ -3114,8 +3114,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/tximport", "viash_version" : "0.9.0", - "git_commit" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/ucsc/bedclip/.config.vsh.yaml b/target/nextflow/ucsc/bedclip/.config.vsh.yaml index d0cd992..cc87237 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/ucsc/bedclip/main.nf b/target/nextflow/ucsc/bedclip/main.nf index e8cfee0..41f9ca6 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" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml b/target/nextflow/ucsc/bedgraphtobigwig/.config.vsh.yaml index d3aa312..672bbd8 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/ucsc/bedgraphtobigwig/main.nf b/target/nextflow/ucsc/bedgraphtobigwig/main.nf index a1e036a..2ecb7b3 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" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml b/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml index 879d724..1e84534 100644 --- a/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml +++ b/target/nextflow/umitools/umitools_dedup/.config.vsh.yaml @@ -195,8 +195,8 @@ build_info: output: "target/nextflow/umitools/umitools_dedup" executable: "target/nextflow/umitools/umitools_dedup/main.nf" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/umitools/umitools_dedup/main.nf b/target/nextflow/umitools/umitools_dedup/main.nf index 7a61bdb..dc7a832 100644 --- a/target/nextflow/umitools/umitools_dedup/main.nf +++ b/target/nextflow/umitools/umitools_dedup/main.nf @@ -3054,8 +3054,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/umitools/umitools_dedup", "viash_version" : "0.9.0", - "git_commit" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/umitools/umitools_extract/.config.vsh.yaml b/target/nextflow/umitools/umitools_extract/.config.vsh.yaml index b5dc7b0..1bc8f19 100644 --- a/target/nextflow/umitools/umitools_extract/.config.vsh.yaml +++ b/target/nextflow/umitools/umitools_extract/.config.vsh.yaml @@ -253,8 +253,8 @@ build_info: output: "target/nextflow/umitools/umitools_extract" executable: "target/nextflow/umitools/umitools_extract/main.nf" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/umitools/umitools_extract/main.nf b/target/nextflow/umitools/umitools_extract/main.nf index 3c65a06..af6bc80 100644 --- a/target/nextflow/umitools/umitools_extract/main.nf +++ b/target/nextflow/umitools/umitools_extract/main.nf @@ -3119,8 +3119,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/umitools/umitools_extract", "viash_version" : "0.9.0", - "git_commit" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/umitools_prepareforquant/.config.vsh.yaml b/target/nextflow/umitools_prepareforquant/.config.vsh.yaml index f7d0a8b..a957dac 100644 --- a/target/nextflow/umitools_prepareforquant/.config.vsh.yaml +++ b/target/nextflow/umitools_prepareforquant/.config.vsh.yaml @@ -156,8 +156,8 @@ build_info: output: "target/nextflow/umitools_prepareforquant" executable: "target/nextflow/umitools_prepareforquant/main.nf" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/nextflow/umitools_prepareforquant/main.nf b/target/nextflow/umitools_prepareforquant/main.nf index bbe71ca..6744d6b 100644 --- a/target/nextflow/umitools_prepareforquant/main.nf +++ b/target/nextflow/umitools_prepareforquant/main.nf @@ -3007,8 +3007,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/umitools_prepareforquant", "viash_version" : "0.9.0", - "git_commit" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", 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 1bf9a7a..68694d9 100644 --- a/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml +++ b/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml @@ -603,8 +603,8 @@ build_info: output: "target/nextflow/workflows/genome_alignment_and_quant" executable: "target/nextflow/workflows/genome_alignment_and_quant/main.nf" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort" diff --git a/target/nextflow/workflows/genome_alignment_and_quant/main.nf b/target/nextflow/workflows/genome_alignment_and_quant/main.nf index 9052055..caf237b 100644 --- a/target/nextflow/workflows/genome_alignment_and_quant/main.nf +++ b/target/nextflow/workflows/genome_alignment_and_quant/main.nf @@ -3531,8 +3531,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/genome_alignment_and_quant", "viash_version" : "0.9.0", - "git_commit" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml b/target/nextflow/workflows/merge_quant_results/.config.vsh.yaml index 1bbcd3b..7444af4 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: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@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 28672a3..09bd1b4 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" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/workflows/post_processing/.config.vsh.yaml b/target/nextflow/workflows/post_processing/.config.vsh.yaml index 41b27bd..f9a1ab6 100644 --- a/target/nextflow/workflows/post_processing/.config.vsh.yaml +++ b/target/nextflow/workflows/post_processing/.config.vsh.yaml @@ -486,8 +486,8 @@ build_info: output: "target/nextflow/workflows/post_processing" executable: "target/nextflow/workflows/post_processing/main.nf" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/picard_markduplicates" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort" diff --git a/target/nextflow/workflows/post_processing/main.nf b/target/nextflow/workflows/post_processing/main.nf index b9d3a27..60db58a 100644 --- a/target/nextflow/workflows/post_processing/main.nf +++ b/target/nextflow/workflows/post_processing/main.nf @@ -3397,8 +3397,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/post_processing", "viash_version" : "0.9.0", - "git_commit" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/workflows/pre_processing/.config.vsh.yaml b/target/nextflow/workflows/pre_processing/.config.vsh.yaml index f124660..aac26b7 100644 --- a/target/nextflow/workflows/pre_processing/.config.vsh.yaml +++ b/target/nextflow/workflows/pre_processing/.config.vsh.yaml @@ -673,8 +673,8 @@ build_info: output: "target/nextflow/workflows/pre_processing" executable: "target/nextflow/workflows/pre_processing/main.nf" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/fastqc" - "target/nextflow/umitools/umitools_extract" diff --git a/target/nextflow/workflows/pre_processing/main.nf b/target/nextflow/workflows/pre_processing/main.nf index 189ab50..83ea1a3 100644 --- a/target/nextflow/workflows/pre_processing/main.nf +++ b/target/nextflow/workflows/pre_processing/main.nf @@ -3626,8 +3626,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/pre_processing", "viash_version" : "0.9.0", - "git_commit" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/workflows/prepare_genome/.config.vsh.yaml b/target/nextflow/workflows/prepare_genome/.config.vsh.yaml index f47ad1c..a08176b 100644 --- a/target/nextflow/workflows/prepare_genome/.config.vsh.yaml +++ b/target/nextflow/workflows/prepare_genome/.config.vsh.yaml @@ -496,8 +496,8 @@ build_info: output: "target/nextflow/workflows/prepare_genome" executable: "target/nextflow/workflows/prepare_genome/main.nf" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/gunzip" - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread" diff --git a/target/nextflow/workflows/prepare_genome/main.nf b/target/nextflow/workflows/prepare_genome/main.nf index 20ed238..c807afa 100644 --- a/target/nextflow/workflows/prepare_genome/main.nf +++ b/target/nextflow/workflows/prepare_genome/main.nf @@ -3407,8 +3407,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/prepare_genome", "viash_version" : "0.9.0", - "git_commit" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", 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 13b7930..7106051 100644 --- a/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml +++ b/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml @@ -283,8 +283,8 @@ build_info: output: "target/nextflow/workflows/pseudo_alignment_and_quant" executable: "target/nextflow/workflows/pseudo_alignment_and_quant/main.nf" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" dependencies: - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant" - "target/nextflow/kallisto/kallisto_quant" diff --git a/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf b/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf index 4151e28..93fa7c3 100644 --- a/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf +++ b/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf @@ -3143,8 +3143,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/pseudo_alignment_and_quant", "viash_version" : "0.9.0", - "git_commit" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/workflows/quality_control/.config.vsh.yaml b/target/nextflow/workflows/quality_control/.config.vsh.yaml index b86a624..425a7aa 100644 --- a/target/nextflow/workflows/quality_control/.config.vsh.yaml +++ b/target/nextflow/workflows/quality_control/.config.vsh.yaml @@ -1596,8 +1596,8 @@ build_info: output: "target/nextflow/workflows/quality_control" executable: "target/nextflow/workflows/quality_control/main.nf" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" dependencies: - "target/nextflow/rseqc/rseqc_bamstat" - "target/nextflow/rseqc/rseqc_inferexperiment" diff --git a/target/nextflow/workflows/quality_control/main.nf b/target/nextflow/workflows/quality_control/main.nf index dcbd5f8..8a0bd1e 100644 --- a/target/nextflow/workflows/quality_control/main.nf +++ b/target/nextflow/workflows/quality_control/main.nf @@ -4676,8 +4676,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/quality_control", "viash_version" : "0.9.0", - "git_commit" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", diff --git a/target/nextflow/workflows/rnaseq/.config.vsh.yaml b/target/nextflow/workflows/rnaseq/.config.vsh.yaml index 08981ec..a9086df 100644 --- a/target/nextflow/workflows/rnaseq/.config.vsh.yaml +++ b/target/nextflow/workflows/rnaseq/.config.vsh.yaml @@ -785,7 +785,7 @@ argument_groups: name: "--output_fasta" info: null default: - - "genome/reference_genome.fasta" + - "reference/genome.fasta" must_exist: true create_parent: true required: false @@ -796,7 +796,7 @@ argument_groups: name: "--output_gtf" info: null default: - - "genome/gene_annotation.gtf" + - "reference/gene_annotation.gtf" must_exist: true create_parent: true required: false @@ -807,7 +807,7 @@ argument_groups: name: "--output_transcript_fasta" info: null default: - - "genome/transcriptome.fasta" + - "reference/transcriptome.fasta" must_exist: true create_parent: true required: false @@ -818,7 +818,7 @@ argument_groups: name: "--output_gene_bed" info: null default: - - "genome/gene_annotation.bed" + - "reference/gene_annotation.bed" must_exist: true create_parent: true required: false @@ -830,7 +830,7 @@ argument_groups: description: "Path to STAR index." info: null default: - - "genome/index/STAR" + - "reference/index/STAR" must_exist: true create_parent: true required: false @@ -842,7 +842,7 @@ argument_groups: description: "Path to Salmon index." info: null default: - - "genome/index/Salmon" + - "reference/index/Salmon" must_exist: true create_parent: true required: false @@ -854,7 +854,7 @@ argument_groups: description: "Path to BBSplit index." info: null default: - - "genome/index/BBSplit" + - "reference/index/BBSplit" must_exist: true create_parent: true required: false @@ -866,7 +866,7 @@ argument_groups: description: "Path to Kallisto index." info: null default: - - "genome/index/Kallisto" + - "reference/index/Kallisto" must_exist: true create_parent: true required: false @@ -2117,8 +2117,8 @@ build_info: output: "target/nextflow/workflows/rnaseq" executable: "target/nextflow/workflows/rnaseq/main.nf" viash_version: "0.9.0" - git_commit: "dc43230e43731e5733fffba429a1190f08dbc742" - git_remote: "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + git_commit: "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e" + git_remote: "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@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 e004628..2a4a912 100644 --- a/target/nextflow/workflows/rnaseq/main.nf +++ b/target/nextflow/workflows/rnaseq/main.nf @@ -3703,7 +3703,7 @@ meta = [ "type" : "file", "name" : "--output_fasta", "default" : [ - "genome/reference_genome.fasta" + "reference/genome.fasta" ], "must_exist" : true, "create_parent" : true, @@ -3716,7 +3716,7 @@ meta = [ "type" : "file", "name" : "--output_gtf", "default" : [ - "genome/gene_annotation.gtf" + "reference/gene_annotation.gtf" ], "must_exist" : true, "create_parent" : true, @@ -3729,7 +3729,7 @@ meta = [ "type" : "file", "name" : "--output_transcript_fasta", "default" : [ - "genome/transcriptome.fasta" + "reference/transcriptome.fasta" ], "must_exist" : true, "create_parent" : true, @@ -3742,7 +3742,7 @@ meta = [ "type" : "file", "name" : "--output_gene_bed", "default" : [ - "genome/gene_annotation.bed" + "reference/gene_annotation.bed" ], "must_exist" : true, "create_parent" : true, @@ -3756,7 +3756,7 @@ meta = [ "name" : "--output_star_index", "description" : "Path to STAR index.", "default" : [ - "genome/index/STAR" + "reference/index/STAR" ], "must_exist" : true, "create_parent" : true, @@ -3770,7 +3770,7 @@ meta = [ "name" : "--output_salmon_index", "description" : "Path to Salmon index.", "default" : [ - "genome/index/Salmon" + "reference/index/Salmon" ], "must_exist" : true, "create_parent" : true, @@ -3784,7 +3784,7 @@ meta = [ "name" : "--output_bbsplit_index", "description" : "Path to BBSplit index.", "default" : [ - "genome/index/BBSplit" + "reference/index/BBSplit" ], "must_exist" : true, "create_parent" : true, @@ -3798,7 +3798,7 @@ meta = [ "name" : "--output_kallisto_index", "description" : "Path to Kallisto index.", "default" : [ - "genome/index/Kallisto" + "reference/index/Kallisto" ], "must_exist" : true, "create_parent" : true, @@ -4891,7 +4891,7 @@ meta = [ "name" : "--dupradar_output_duprate_exp_boxplot", "description" : "path to output file (pdf) of distribution of expression box plot", "default" : [ - "dupradar/box_''' + '''plot/$id.duprate_exp_boxplot.pdf" + ''' + '''"dupradar/box_plot/$id.duprate_exp_boxplot.pdf" ], "must_exist" : true, "create_parent" : true, @@ -5283,8 +5283,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/rnaseq", "viash_version" : "0.9.0", - "git_commit" : "dc43230e43731e5733fffba429a1190f08dbc742", - "git_remote" : "https://x-access-token:ghs_J7vR9Ei9mLzQE8wOHrqImUJTsJPYcG4YNnNe@github.com/viash-hub/rnaseq" + "git_commit" : "fbc64b5f252d0e20b11d2455964e9ed5cc66d11e", + "git_remote" : "https://x-access-token:ghs_Hah86hJ3ciptfjYIU38aG0V14xJ0t21hkn3l@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes",