diff --git a/src/fastqc/script.sh b/src/fastqc/script.sh index 3b9461b..808d300 100644 --- a/src/fastqc/script.sh +++ b/src/fastqc/script.sh @@ -30,10 +30,12 @@ fastqc -o $tmpdir ${input[*]} file1=$(basename -- "${input[0]}") read1="${file1%.fastq*}" -file2=$(basename -- "${input[1]}") -read2="${file2%.fastq*}" - [[ -e "${tmpdir}/${read1}_fastqc.html" ]] && cp "${tmpdir}/${read1}_fastqc.html" $par_fastqc_html_1 -[[ -e "${tmpdir}/${read2}_fastqc.html" ]] && cp "${tmpdir}/${read2}_fastqc.html" $par_fastqc_html_2 [[ -e "${tmpdir}/${read1}_fastqc.zip" ]] && cp "${tmpdir}/${read1}_fastqc.zip" $par_fastqc_zip_1 -[[ -e "${tmpdir}/${read2}_fastqc.zip" ]] && cp "${tmpdir}/${read2}_fastqc.zip" $par_fastqc_zip_2 + +if $par_paired; then + file2=$(basename -- "${input[1]}") + read2="${file2%.fastq*}" + [[ -e "${tmpdir}/${read2}_fastqc.html" ]] && cp "${tmpdir}/${read2}_fastqc.html" $par_fastqc_html_2 + [[ -e "${tmpdir}/${read2}_fastqc.zip" ]] && cp "${tmpdir}/${read2}_fastqc.zip" $par_fastqc_zip_2 +fi \ No newline at end of file diff --git a/src/workflows/genome_alignment_and_quant/test_run.sh b/src/workflows/genome_alignment_and_quant/test_run.sh index 550a5bd..c48d707 100755 --- a/src/workflows/genome_alignment_and_quant/test_run.sh +++ b/src/workflows/genome_alignment_and_quant/test_run.sh @@ -11,7 +11,7 @@ gunzip --keep testData/minimal_test/reference/genes.gtf.gz cat > testData/minimal_test/input_fastq/sample_sheet.csv << HERE id,fastq_1,fastq_2,strandedness WT_REP1,SRR6357070_1.fastq.gz,SRR6357070_2.fastq.gz,reverse -WT_REP2,SRR6357072_1.fastq.gz,SRR6357072_2.fastq.gz,reverse +RAP1_UNINDUCED_REP1,SRR6357073_1.fastq.gz,,reverse HERE # echo "> Test 1: STAR Salmon" diff --git a/src/workflows/pre_processing/test_run.sh b/src/workflows/pre_processing/test_run.sh index fc7651d..60fe689 100755 --- a/src/workflows/pre_processing/test_run.sh +++ b/src/workflows/pre_processing/test_run.sh @@ -11,7 +11,7 @@ tar -C testData/minimal_test/reference/salmon_index --strip-components 1 -xavf t cat > testData/minimal_test/input_fastq/sample_sheet.csv << HERE id,fastq_1,fastq_2,strandedness WT_REP2,SRR6357072_1.fastq.gz,SRR6357072_2.fastq.gz,auto -RAP1_IAA_30M_REP1,SRR6357076_1.fastq.gz,SRR6357076_2.fastq.gz,reverse +RAP1_UNINDUCED_REP1,SRR6357073_1.fastq.gz,,reverse HERE echo "> Test 1: Running workflow with trimgalore" @@ -27,7 +27,7 @@ nextflow run target/nextflow/workflows/pre_processing/main.nf \ --remove_ribo_rna false \ --ribo_database_manifest testData/minimal_test/reference/rrna-db-defaults.txt \ --skip_bbsplit false \ - --bbsplit_index test_results/output_test1/BBSplit_index \ + --bbsplit_index test_results/prepare_genome_test1/BBSplit_index \ -profile docker \ -resume diff --git a/src/workflows/pseudo_alignment_and_quant/test_run.sh b/src/workflows/pseudo_alignment_and_quant/test_run.sh index 67cae22..cdc2bd0 100755 --- a/src/workflows/pseudo_alignment_and_quant/test_run.sh +++ b/src/workflows/pseudo_alignment_and_quant/test_run.sh @@ -13,7 +13,7 @@ tar -C testData/minimal_test/reference/salmon_index --strip-components 1 -xavf t cat > testData/minimal_test/input_fastq/sample_sheet.csv << HERE id,fastq_1,fastq_2,strandedness WT_REP1,SRR6357070_1.fastq.gz,SRR6357070_2.fastq.gz,reverse -WT_REP2,SRR6357072_1.fastq.gz,SRR6357072_2.fastq.gz,reverse +RAP1_UNINDUCED_REP1,SRR6357073_1.fastq.gz,,reverse HERE echo "> Test 1: Salmon qunatification" diff --git a/src/workflows/rnaseq/main.nf b/src/workflows/rnaseq/main.nf index dbd9df8..3b416cd 100644 --- a/src/workflows/rnaseq/main.nf +++ b/src/workflows/rnaseq/main.nf @@ -22,27 +22,27 @@ workflow run_wf { | map { list -> [ "ref", - [ fasta: list[1][-1].fasta, - gtf: list[1][-1].gtf, - gff: list[1][-1].gff, - additional_fasta: list[1][-1].additional_fasta, - transcript_fasta: list[1][-1].transcript_fasta, - gene_bed: list[1][-1].gene_bed, - bbsplit_fasta_list: list[1][-1].bbsplit_fasta_list, - aligner: list[1][-1].aligner, - pseudo_aligner: list[1][-1].pseudo_aligner, - star_index: list[1][-1].star_index, - rsem_index: list[1][-1].rsem_index, - salmon_index: list[1][-1].salmon_index, - kallisto_index: list[1][-1].kallisto_index, - // splicesites: list[1][-1].splicesites, - // hisat2_index: list[1][-1].hisat2_index, - bbsplit_index: list[1][-1].bbsplit_index, - skip_bbsplit: list[1][-1].skip_bbsplit, - gencode: list[1][-1].gencode, - biotype: list[1][-1].biotype, - filter_gtf: list[1][-1].filter_gtf, - pseudo_aligner_kmer_size: list[1][-1].pseudo_aligner_kmer_size ] + [ fasta: list.collect { id, state -> state.fasta }.unique()[0], + gtf: list.collect { id, state -> state.gtf }.unique()[0], + gff: list.collect { id, state -> state.gff }.unique()[0], + additional_fasta: list.collect { id, state -> state.additional_fasta }.unique()[0], + transcript_fasta:list.collect { id, state -> state.transcript_fasta }.unique()[0], + gene_bed: list.collect { id, state -> state.gene_bed }.unique()[0], + bbsplit_fasta_list: list.collect { id, state -> state.bbsplit_fasta_list }.unique()[0], + aligner: list.collect { id, state -> state.aligner }.unique()[0], + pseudo_aligner: list.collect { id, state -> state.pseudo_aligner }.unique()[0], + star_index: list.collect { id, state -> state.star_index }.unique()[0], + rsem_index: list.collect { id, state -> state.rsem_index }.unique()[0], + salmon_index: list.collect { id, state -> state.salmon_index }.unique()[0], + kallisto_index: list.collect { id, state -> state.kallisto_index }.unique()[0], + // splicesites: list.collect { id, state -> state.splicesites }.unique()[0], + // hisat2_index: list.collect { id, state -> state.hisat2_index }.unique()[0], + bbsplit_index: list.collect { id, state -> state.bbsplit_index }.unique()[0], + skip_bbsplit: list.collect { id, state -> state.skip_bbsplit }.unique()[0], + gencode: list.collect { id, state -> state.gencode }.unique()[0], + biotype: list.collect { id, state -> state.biotype }.unique()[0], + filter_gtf: list.collect { id, state -> state.filter_gtf }.unique()[0], + pseudo_aligner_kmer_size: list.collect { id, state -> state.pseudo_aligner_kmer_size }.unique()[0] ] ] } diff --git a/target/executable/bbmap_bbsplit/.config.vsh.yaml b/target/executable/bbmap_bbsplit/.config.vsh.yaml index 20c6964..1140c62 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 d2e31b0..69edcc9 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="2024-09-19T07:23:57Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:04Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 6d8869c..5f730af 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 439700d..2910da0 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="2024-09-19T07:23:58Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:04Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 fd2a073..d3558ca 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 fa66b9b..3eb5dac 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="2024-09-19T07:24:05Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:12Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 e7b0491..29472ed 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 d2ec7f6..cef68de 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="2024-09-19T07:24:05Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:13Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 744b59c..1fb25d4 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 0c4c4d8..6641855 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="2024-09-19T07:24:15Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:22Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 70bca00..82e4e2e 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/dupradar/dupradar b/target/executable/dupradar/dupradar index 1702be6..810ab82 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="2024-09-19T07:24:06Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:14Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 6472f08..1835e7b 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/fastqc/fastqc b/target/executable/fastqc/fastqc index 2955d62..bf1fa54 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="2024-09-19T07:23:59Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:05Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" LABEL org.opencontainers.image.version="multiple_fixes" VIASHDOCKER @@ -1200,13 +1200,15 @@ fastqc -o \$tmpdir \${input[*]} file1=\$(basename -- "\${input[0]}") read1="\${file1%.fastq*}" -file2=\$(basename -- "\${input[1]}") -read2="\${file2%.fastq*}" - [[ -e "\${tmpdir}/\${read1}_fastqc.html" ]] && cp "\${tmpdir}/\${read1}_fastqc.html" \$par_fastqc_html_1 -[[ -e "\${tmpdir}/\${read2}_fastqc.html" ]] && cp "\${tmpdir}/\${read2}_fastqc.html" \$par_fastqc_html_2 [[ -e "\${tmpdir}/\${read1}_fastqc.zip" ]] && cp "\${tmpdir}/\${read1}_fastqc.zip" \$par_fastqc_zip_1 -[[ -e "\${tmpdir}/\${read2}_fastqc.zip" ]] && cp "\${tmpdir}/\${read2}_fastqc.zip" \$par_fastqc_zip_2 + +if \$par_paired; then + file2=\$(basename -- "\${input[1]}") + read2="\${file2%.fastq*}" + [[ -e "\${tmpdir}/\${read2}_fastqc.html" ]] && cp "\${tmpdir}/\${read2}_fastqc.html" \$par_fastqc_html_2 + [[ -e "\${tmpdir}/\${read2}_fastqc.zip" ]] && cp "\${tmpdir}/\${read2}_fastqc.zip" \$par_fastqc_zip_2 +fi VIASHMAIN bash "\$tempscript" & wait "\$!" diff --git a/target/executable/fq_subsample/.config.vsh.yaml b/target/executable/fq_subsample/.config.vsh.yaml index 2bf0ab7..7da70f2 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 fcccece..905c823 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="2024-09-19T07:23:59Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:05Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 33ccebe..dc74a87 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/getchromsizes/getchromsizes b/target/executable/getchromsizes/getchromsizes index 649b38c..5bac749 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="2024-09-19T07:23:59Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:05Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 68ca317..c3d4f20 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/gtf2bed/gtf2bed b/target/executable/gtf2bed/gtf2bed index a1bf66a..8cb423c 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="2024-09-19T07:24:10Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:18Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 ddaa563..33dd712 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 0bab309..7ea13f9 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="2024-09-19T07:24:13Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:21Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 0c451d0..3d5d985 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/gunzip/gunzip b/target/executable/gunzip/gunzip index 1f6dde4..b44ef24 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="2024-09-19T07:23:59Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:06Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 fe2cc76..811c4c8 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 4ad281a..aa70464 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="2024-09-19T07:24:12Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:19Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 3aa3030..42dc3c5 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 ab9c627..21cf6fc 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="2024-09-19T07:24:12Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:19Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 f3c216d..7bc9f16 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 3e23526..8e2c440 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="2024-09-19T07:24:06Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:14Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 aa7218a..0e4f3cd 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 94db532..9af6ec0 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="2024-09-19T07:24:14Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:21Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 327db15..197d101 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 2d5c2f8..20715a6 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="2024-09-19T07:24:10Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:17Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 6dc742e..4d2fd0c 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 fb21efc..e3c1c6d 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="2024-09-19T07:24:09Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:17Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 b0a34fb..8507af7 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 6e238c8..649ee8c 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="2024-09-19T07:24:00Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:06Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 3690e56..7e7e16f 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/qualimap/qualimap b/target/executable/qualimap/qualimap index 2288091..29cd9d4 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="2024-09-19T07:23:58Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:04Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 943016c..a3237c2 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 be5262c..ed623ee 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="2024-09-19T07:24:11Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:19Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 e91b07a..b9d3cdf 100644 --- a/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml +++ b/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml @@ -202,8 +202,8 @@ 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 9f6e561..47b2910 100755 --- a/target/executable/rsem/rsem_merge_counts/rsem_merge_counts +++ b/target/executable/rsem/rsem_merge_counts/rsem_merge_counts @@ -490,9 +490,9 @@ 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="2024-09-19T07:24:11Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:18Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 161e3fc..fca6c8e 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 b34e94a..854389a 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="2024-09-19T07:24:09Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:16Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 d984e69..2ad98b1 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 3ba8e02..7a0dabf 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="2024-09-19T07:24:07Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:14Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 b87d9d6..3857b59 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 a8b3efa..564f772 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="2024-09-19T07:24:08Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:16Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 5b3c7be..e75b219 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 349f58c..5ad2494 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="2024-09-19T07:24:08Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:16Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 e577b70..ef863e8 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 3410ad3..e7335d4 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="2024-09-19T07:24:08Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:15Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 1977a4e..201ea5b 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 0d5bddf..13696f8 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="2024-09-19T07:24:09Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:16Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 7f2afb5..90a3671 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 41cf180..06a2aa1 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="2024-09-19T07:24:07Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:15Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 e805e3b..2705d17 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 92a3098..e61016a 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="2024-09-19T07:24:07Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:15Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 a703eb4..1e6029d 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/sortmerna/sortmerna b/target/executable/sortmerna/sortmerna index 400392f..b960c83 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="2024-09-19T07:24:14Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:21Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 f712789..f837934 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/stringtie/stringtie b/target/executable/stringtie/stringtie index 42c5927..6ceba3c 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="2024-09-19T07:24:11Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:18Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 09b9393..52646fe 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/summarizedexperiment/summarizedexperiment b/target/executable/summarizedexperiment/summarizedexperiment index e779c4c..38f2211 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="2024-09-19T07:24:14Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:22Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 5875afb..2a253de 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/trimgalore/trimgalore b/target/executable/trimgalore/trimgalore index c1af919..9da0fbf 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="2024-09-19T07:24:13Z" +LABEL org.opencontainers.image.created="2024-09-23T10:27:20Z" LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 75030de..1fc7de7 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/tx2gene/tx2gene b/target/executable/tx2gene/tx2gene index 0897a37..70c1018 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="2024-09-19T07:24:10Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:17Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 950d1cc..4c721c2 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" package_config: version: "multiple_fixes" info: diff --git a/target/executable/tximport/tximport b/target/executable/tximport/tximport index 67a23f6..f099dea 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="2024-09-19T07:24:04Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:12Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 43fa5fa..ec69217 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 3163b1a..f0da78b 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="2024-09-19T07:24:05Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:13Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 170e157..fb8fcb9 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 c06ece2..dfc6ba2 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="2024-09-19T07:24:06Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:13Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 7a37f8c..44e3ead 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 6a30fd7..924e729 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="2024-09-19T07:24:12Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:20Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 6214def..a215d1a 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 576be6b..3df2b4e 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="2024-09-19T07:24:12Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:20Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 c8ad9d2..b46e4eb 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 c1c0c79..6311a9e 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="2024-09-19T07:24:15Z" -LABEL org.opencontainers.image.source="https://x-access-token/ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" -LABEL org.opencontainers.image.revision="e14b535c3bc7d59928d25fa3b7df1f16985b4165" +LABEL org.opencontainers.image.created="2024-09-23T10:27:22Z" +LABEL org.opencontainers.image.source="https://x-access-token/ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" +LABEL org.opencontainers.image.revision="51c8525bc52b04e4457931bcb3cfb14a9026c63b" 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 4cd8ded..4650796 100644 --- a/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml +++ b/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml @@ -596,8 +596,8 @@ 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 af81118..7d39bf3 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 3edc0f1..5416376 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 1b9dc35..309adbd 100644 --- a/target/executable/workflows/pre_processing/.config.vsh.yaml +++ b/target/executable/workflows/pre_processing/.config.vsh.yaml @@ -639,8 +639,8 @@ build_info: output: "target/executable/workflows/pre_processing" executable: "target/executable/workflows/pre_processing/pre_processing" viash_version: "0.9.0" - git_commit: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 90e631a..0657acb 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 fabd836..f3b2720 100644 --- a/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml +++ b/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml @@ -285,8 +285,8 @@ build_info: output: "target/executable/workflows/pseudo_alignment_and_quant" executable: "target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant" viash_version: "0.9.0" - git_commit: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 3cbd2ff..85fba38 100644 --- a/target/executable/workflows/quality_control/.config.vsh.yaml +++ b/target/executable/workflows/quality_control/.config.vsh.yaml @@ -1592,8 +1592,8 @@ build_info: output: "target/executable/workflows/quality_control" executable: "target/executable/workflows/quality_control/quality_control" viash_version: "0.9.0" - git_commit: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 cdefced..8125d0e 100644 --- a/target/executable/workflows/rnaseq/.config.vsh.yaml +++ b/target/executable/workflows/rnaseq/.config.vsh.yaml @@ -1954,8 +1954,8 @@ build_info: output: "target/executable/workflows/rnaseq" executable: "target/executable/workflows/rnaseq/rnaseq" viash_version: "0.9.0" - git_commit: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 ccb9e03..f284027 100755 --- a/target/executable/workflows/rnaseq/rnaseq +++ b/target/executable/workflows/rnaseq/rnaseq @@ -4179,27 +4179,27 @@ workflow run_wf { | map { list -> [ "ref", - [ fasta: list[1][-1].fasta, - gtf: list[1][-1].gtf, - gff: list[1][-1].gff, - additional_fasta: list[1][-1].additional_fasta, - transcript_fasta: list[1][-1].transcript_fasta, - gene_bed: list[1][-1].gene_bed, - bbsplit_fasta_list: list[1][-1].bbsplit_fasta_list, - aligner: list[1][-1].aligner, - pseudo_aligner: list[1][-1].pseudo_aligner, - star_index: list[1][-1].star_index, - rsem_index: list[1][-1].rsem_index, - salmon_index: list[1][-1].salmon_index, - kallisto_index: list[1][-1].kallisto_index, - // splicesites: list[1][-1].splicesites, - // hisat2_index: list[1][-1].hisat2_index, - bbsplit_index: list[1][-1].bbsplit_index, - skip_bbsplit: list[1][-1].skip_bbsplit, - gencode: list[1][-1].gencode, - biotype: list[1][-1].biotype, - filter_gtf: list[1][-1].filter_gtf, - pseudo_aligner_kmer_size: list[1][-1].pseudo_aligner_kmer_size ] + [ fasta: list.collect { id, state -> state.fasta }.unique()[0], + gtf: list.collect { id, state -> state.gtf }.unique()[0], + gff: list.collect { id, state -> state.gff }.unique()[0], + additional_fasta: list.collect { id, state -> state.additional_fasta }.unique()[0], + transcript_fasta:list.collect { id, state -> state.transcript_fasta }.unique()[0], + gene_bed: list.collect { id, state -> state.gene_bed }.unique()[0], + bbsplit_fasta_list: list.collect { id, state -> state.bbsplit_fasta_list }.unique()[0], + aligner: list.collect { id, state -> state.aligner }.unique()[0], + pseudo_aligner: list.collect { id, state -> state.pseudo_aligner }.unique()[0], + star_index: list.collect { id, state -> state.star_index }.unique()[0], + rsem_index: list.collect { id, state -> state.rsem_index }.unique()[0], + salmon_index: list.collect { id, state -> state.salmon_index }.unique()[0], + kallisto_index: list.collect { id, state -> state.kallisto_index }.unique()[0], + // splicesites: list.collect { id, state -> state.splicesites }.unique()[0], + // hisat2_index: list.collect { id, state -> state.hisat2_index }.unique()[0], + bbsplit_index: list.collect { id, state -> state.bbsplit_index }.unique()[0], + skip_bbsplit: list.collect { id, state -> state.skip_bbsplit }.unique()[0], + gencode: list.collect { id, state -> state.gencode }.unique()[0], + biotype: list.collect { id, state -> state.biotype }.unique()[0], + filter_gtf: list.collect { id, state -> state.filter_gtf }.unique()[0], + pseudo_aligner_kmer_size: list.collect { id, state -> state.pseudo_aligner_kmer_size }.unique()[0] ] ] } diff --git a/target/nextflow/bbmap_bbsplit/.config.vsh.yaml b/target/nextflow/bbmap_bbsplit/.config.vsh.yaml index 6aff57e..9860d0b 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 7ec8c4a..685dbdc 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 2095a75..223b434 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 5074883..2654169 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 70f9b11..143b36e 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 180ae7a..faea778 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 31b1236..884e2db 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 4d86cc7..1fb986a 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 2176cac..91f5d05 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 7959b60..10d8217 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 317a517..021d414 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 8a4086a..d644c22 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 ff7118f..ba1bbd3 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 af9198d..f18b551 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", @@ -3166,13 +3166,15 @@ fastqc -o \\$tmpdir \\${input[*]} file1=\\$(basename -- "\\${input[0]}") read1="\\${file1%.fastq*}" -file2=\\$(basename -- "\\${input[1]}") -read2="\\${file2%.fastq*}" - [[ -e "\\${tmpdir}/\\${read1}_fastqc.html" ]] && cp "\\${tmpdir}/\\${read1}_fastqc.html" \\$par_fastqc_html_1 -[[ -e "\\${tmpdir}/\\${read2}_fastqc.html" ]] && cp "\\${tmpdir}/\\${read2}_fastqc.html" \\$par_fastqc_html_2 [[ -e "\\${tmpdir}/\\${read1}_fastqc.zip" ]] && cp "\\${tmpdir}/\\${read1}_fastqc.zip" \\$par_fastqc_zip_1 -[[ -e "\\${tmpdir}/\\${read2}_fastqc.zip" ]] && cp "\\${tmpdir}/\\${read2}_fastqc.zip" \\$par_fastqc_zip_2 + +if \\$par_paired; then + file2=\\$(basename -- "\\${input[1]}") + read2="\\${file2%.fastq*}" + [[ -e "\\${tmpdir}/\\${read2}_fastqc.html" ]] && cp "\\${tmpdir}/\\${read2}_fastqc.html" \\$par_fastqc_html_2 + [[ -e "\\${tmpdir}/\\${read2}_fastqc.zip" ]] && cp "\\${tmpdir}/\\${read2}_fastqc.zip" \\$par_fastqc_zip_2 +fi VIASHMAIN bash "$tempscript" ''' diff --git a/target/nextflow/fq_subsample/.config.vsh.yaml b/target/nextflow/fq_subsample/.config.vsh.yaml index ae6c850..4ce156f 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 c9a0f7c..25c7632 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 d8afb33..b709b9f 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 e090dd5..497bed5 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 180d9cf..bbb9096 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 b8ec293..30849d3 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 b201e0b..2781b12 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 4cf9836..e81103b 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 c0572de..f6e4e05 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 443cb17..5df83af 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 aac68ec..e34fbac 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 d9663a8..12b1beb 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 ad6e825..cd18fa2 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 0de352e..21a3774 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 a49a69f..a3583fb 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 4d8f01e..145c950 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 6dc9bc7..cf1a1e9 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 fc20cab..a7c7b85 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 fc4eba5..5cf843f 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 6b4e9b8..8b11a9c 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 9ca1507..bfed330 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 3978604..80d0cf3 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 f22a5c8..57dced0 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 a6fd083..6d38f26 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 fc6f575..362375b 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 a4fa132..c431871 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 c90c722..f0fb4c6 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 4041cd9..9369ed7 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 6d73b87..bb7beb9 100644 --- a/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml +++ b/target/nextflow/rsem/rsem_merge_counts/.config.vsh.yaml @@ -202,8 +202,8 @@ 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 12716d7..83088b4 100644 --- a/target/nextflow/rsem/rsem_merge_counts/main.nf +++ b/target/nextflow/rsem/rsem_merge_counts/main.nf @@ -3051,8 +3051,8 @@ meta = [ "engine" : "docker|native", "output" : "/workdir/root/repo/target/nextflow/rsem/rsem_merge_counts", "viash_version" : "0.9.0", - "git_commit" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 064cab2..a64fe6a 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 4bfd22d..0d9b3a0 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 b082927..9970fd5 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 c844094..e4b2417 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 298bc9a..d3c9fa2 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 4b1fde3..6be7934 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 0b0ebbd..450b5e5 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 4cc9cf8..e9f8579 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 cf904c8..0d8ae4a 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 cc4f931..5c69d21 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 ad52b99..60b4df7 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 d97ab2b..d05e1ef 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 e26fd13..a9bdd06 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 9fa779f..73dc722 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 2014271..703bd5f 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 91e611f..3c29e32 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 4ff25a7..08d24ec 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 e8315de..4f44152 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 1cb5f26..5f48e1b 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 09db76a..5cae321 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 1d10bf5..c0eb44d 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 ec86e05..6e7a333 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 b4c16d2..b584d72 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 02f166e..b252008 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 bc7fbbd..02786d6 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 b927873..40a639e 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 0e62418..297ce82 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 e41ccef..40c3bfe 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 0f29555..02e6920 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 7fb2cec..a38427e 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 4ee9a05..6c34b26 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 6dea414..9622953 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 08fca9b..2a25145 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 14e00f2..a892679 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 74ab957..edec974 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 a1d4d6b..c9dee76 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 3068ecd..826a79e 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 3bc0804..a745c17 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 50ee682..f88f7e8 100644 --- a/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml +++ b/target/nextflow/workflows/genome_alignment_and_quant/.config.vsh.yaml @@ -596,8 +596,8 @@ 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 d2c776a..24edb7d 100644 --- a/target/nextflow/workflows/genome_alignment_and_quant/main.nf +++ b/target/nextflow/workflows/genome_alignment_and_quant/main.nf @@ -3523,8 +3523,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/genome_alignment_and_quant", "viash_version" : "0.9.0", - "git_commit" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 9cf6265..7d36b8a 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 3a23301..a3af60e 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 d3185fd..49c2658 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 1fbae23..9d5840a 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 1f3bec1..29edd00 100644 --- a/target/nextflow/workflows/pre_processing/.config.vsh.yaml +++ b/target/nextflow/workflows/pre_processing/.config.vsh.yaml @@ -639,8 +639,8 @@ build_info: output: "target/nextflow/workflows/pre_processing" executable: "target/nextflow/workflows/pre_processing/main.nf" viash_version: "0.9.0" - git_commit: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 e1ec8d8..3f1d0a3 100644 --- a/target/nextflow/workflows/pre_processing/main.nf +++ b/target/nextflow/workflows/pre_processing/main.nf @@ -3587,8 +3587,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/pre_processing", "viash_version" : "0.9.0", - "git_commit" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 882ab59..9952825 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: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 34cc090..70e37a2 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" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 8649a29..02aca11 100644 --- a/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml +++ b/target/nextflow/workflows/pseudo_alignment_and_quant/.config.vsh.yaml @@ -285,8 +285,8 @@ build_info: output: "target/nextflow/workflows/pseudo_alignment_and_quant" executable: "target/nextflow/workflows/pseudo_alignment_and_quant/main.nf" viash_version: "0.9.0" - git_commit: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 978019b..47dfcd6 100644 --- a/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf +++ b/target/nextflow/workflows/pseudo_alignment_and_quant/main.nf @@ -3146,8 +3146,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/pseudo_alignment_and_quant", "viash_version" : "0.9.0", - "git_commit" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 7f451cf..e0e62e7 100644 --- a/target/nextflow/workflows/quality_control/.config.vsh.yaml +++ b/target/nextflow/workflows/quality_control/.config.vsh.yaml @@ -1592,8 +1592,8 @@ build_info: output: "target/nextflow/workflows/quality_control" executable: "target/nextflow/workflows/quality_control/main.nf" viash_version: "0.9.0" - git_commit: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 2e430ca..2b8be5c 100644 --- a/target/nextflow/workflows/quality_control/main.nf +++ b/target/nextflow/workflows/quality_control/main.nf @@ -4669,8 +4669,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/quality_control", "viash_version" : "0.9.0", - "git_commit" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 06efaa3..7c5434a 100644 --- a/target/nextflow/workflows/rnaseq/.config.vsh.yaml +++ b/target/nextflow/workflows/rnaseq/.config.vsh.yaml @@ -1954,8 +1954,8 @@ build_info: output: "target/nextflow/workflows/rnaseq" executable: "target/nextflow/workflows/rnaseq/main.nf" viash_version: "0.9.0" - git_commit: "e14b535c3bc7d59928d25fa3b7df1f16985b4165" - git_remote: "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + git_commit: "51c8525bc52b04e4457931bcb3cfb14a9026c63b" + git_remote: "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@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 b852835..2349a37 100644 --- a/target/nextflow/workflows/rnaseq/main.nf +++ b/target/nextflow/workflows/rnaseq/main.nf @@ -5091,8 +5091,8 @@ meta = [ "engine" : "native", "output" : "/workdir/root/repo/target/nextflow/workflows/rnaseq", "viash_version" : "0.9.0", - "git_commit" : "e14b535c3bc7d59928d25fa3b7df1f16985b4165", - "git_remote" : "https://x-access-token:ghs_K1f464hsvFiMldGS1InERoQTCv5a9X2D8k30@github.com/viash-hub/rnaseq" + "git_commit" : "51c8525bc52b04e4457931bcb3cfb14a9026c63b", + "git_remote" : "https://x-access-token:ghs_WkOtw4pzfOs4Jnch0yZhz9yzmkM19C302q8U@github.com/viash-hub/rnaseq" }, "package_config" : { "version" : "multiple_fixes", @@ -5168,27 +5168,27 @@ workflow run_wf { | map { list -> [ "ref", - [ fasta: list[1][-1].fasta, - gtf: list[1][-1].gtf, - gff: list[1][-1].gff, - additional_fasta: list[1][-1].additional_fasta, - transcript_fasta: list[1][-1].transcript_fasta, - gene_bed: list[1][-1].gene_bed, - bbsplit_fasta_list: list[1][-1].bbsplit_fasta_list, - aligner: list[1][-1].aligner, - pseudo_aligner: list[1][-1].pseudo_aligner, - star_index: list[1][-1].star_index, - rsem_index: list[1][-1].rsem_index, - salmon_index: list[1][-1].salmon_index, - kallisto_index: list[1][-1].kallisto_index, - // splicesites: list[1][-1].splicesites, - // hisat2_index: list[1][-1].hisat2_index, - bbsplit_index: list[1][-1].bbsplit_index, - skip_bbsplit: list[1][-1].skip_bbsplit, - gencode: list[1][-1].gencode, - biotype: list[1][-1].biotype, - filter_gtf: list[1][-1].filter_gtf, - pseudo_aligner_kmer_size: list[1][-1].pseudo_aligner_kmer_size ] + [ fasta: list.collect { id, state -> state.fasta }.unique()[0], + gtf: list.collect { id, state -> state.gtf }.unique()[0], + gff: list.collect { id, state -> state.gff }.unique()[0], + additional_fasta: list.collect { id, state -> state.additional_fasta }.unique()[0], + transcript_fasta:list.collect { id, state -> state.transcript_fasta }.unique()[0], + gene_bed: list.collect { id, state -> state.gene_bed }.unique()[0], + bbsplit_fasta_list: list.collect { id, state -> state.bbsplit_fasta_list }.unique()[0], + aligner: list.collect { id, state -> state.aligner }.unique()[0], + pseudo_aligner: list.collect { id, state -> state.pseudo_aligner }.unique()[0], + star_index: list.collect { id, state -> state.star_index }.unique()[0], + rsem_index: list.collect { id, state -> state.rsem_index }.unique()[0], + salmon_index: list.collect { id, state -> state.salmon_index }.unique()[0], + kallisto_index: list.collect { id, state -> state.kallisto_index }.unique()[0], + // splicesites: list.collect { id, state -> state.splicesites }.unique()[0], + // hisat2_index: list.collect { id, state -> state.hisat2_index }.unique()[0], + bbsplit_index: list.collect { id, state -> state.bbsplit_index }.unique()[0], + skip_bbsplit: list.collect { id, state -> state.skip_bbsplit }.unique()[0], + gencode: list.collect { id, state -> state.gencode }.unique()[0], + biotype: list.collect { id, state -> state.biotype }.unique()[0], + filter_gtf: list.collect { id, state -> state.filter_gtf }.unique()[0], + pseudo_aligner_kmer_size: list.collect { id, state -> state.pseudo_aligner_kmer_size }.unique()[0] ] ] }