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Build branch multiple_fixes with version multiple_fixes (51c8525)

Browse Source 
Build pipeline: viash-hub.rnaseq.multiple-fixes-q7sxq

Source commit: 51c8525bc5

Source message: fix workflow
This commit is contained in:
CI
2024-09-23 11:21:52 +00:00
parent 94b5f2024b
commit 38421a767c
194 changed files with 504 additions and 498 deletions
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12
src/fastqc/script.sh
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@@ -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

2
src/workflows/genome_alignment_and_quant/test_run.sh
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@@ -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"

4
src/workflows/pre_processing/test_run.sh
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@@ -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

2
src/workflows/pseudo_alignment_and_quant/test_run.sh
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@@ -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"

42
src/workflows/rnaseq/main.nf
View File

@@ -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] ]
]
}

4
target/executable/bbmap_bbsplit/.config.vsh.yaml
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@@ -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:

6
target/executable/bbmap_bbsplit/bbmap_bbsplit
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@@ -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

4
target/executable/bedtools_genomecov/.config.vsh.yaml
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@@ -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:

6
target/executable/bedtools_genomecov/bedtools_genomecov
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@@ -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

4
target/executable/cat_additional_fasta/.config.vsh.yaml
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@@ -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:

6
target/executable/cat_additional_fasta/cat_additional_fasta
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@@ -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

4
target/executable/cat_fastq/.config.vsh.yaml
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@@ -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:

6
target/executable/cat_fastq/cat_fastq
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@@ -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

4
target/executable/deseq2_qc/.config.vsh.yaml
View File

@@ -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:

6
target/executable/deseq2_qc/deseq2_qc
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@@ -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

4
target/executable/dupradar/.config.vsh.yaml
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@@ -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:

6
target/executable/dupradar/dupradar
View File

@@ -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

4
target/executable/fastqc/.config.vsh.yaml
View File

@@ -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:

18
target/executable/fastqc/fastqc
View File

@@ -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 "\$!"

4
target/executable/fq_subsample/.config.vsh.yaml
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@@ -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:

6
target/executable/fq_subsample/fq_subsample
View File

@@ -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

4
target/executable/getchromsizes/.config.vsh.yaml
View File

@@ -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:

6
target/executable/getchromsizes/getchromsizes
View File

@@ -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

4
target/executable/gtf2bed/.config.vsh.yaml
View File

@@ -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:

6
target/executable/gtf2bed/gtf2bed
View File

@@ -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

4
target/executable/gtf_filter/.config.vsh.yaml
View File

@@ -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:

6
target/executable/gtf_filter/gtf_filter
View File

@@ -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

4
target/executable/gunzip/.config.vsh.yaml
View File

@@ -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:

6
target/executable/gunzip/gunzip
View File

@@ -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

4
target/executable/kallisto/kallisto_index/.config.vsh.yaml
View File

@@ -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:

6
target/executable/kallisto/kallisto_index/kallisto_index
View File

@@ -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

4
target/executable/kallisto/kallisto_quant/.config.vsh.yaml
View File

@@ -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:

6
target/executable/kallisto/kallisto_quant/kallisto_quant
View File

@@ -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

4
target/executable/multiqc_custom_biotype/.config.vsh.yaml
View File

@@ -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:

6
target/executable/multiqc_custom_biotype/multiqc_custom_biotype
View File

@@ -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

4
target/executable/picard_markduplicates/.config.vsh.yaml
View File

@@ -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:

6
target/executable/picard_markduplicates/picard_markduplicates
View File

@@ -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

4
target/executable/prepare_multiqc_input/.config.vsh.yaml
View File

@@ -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:

6
target/executable/prepare_multiqc_input/prepare_multiqc_input
View File

@@ -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

4
target/executable/preprocess_transcripts_fasta/.config.vsh.yaml
View File

@@ -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:

6
target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta
View File

@@ -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

4
target/executable/preseq_lcextrap/.config.vsh.yaml
View File

@@ -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:

6
target/executable/preseq_lcextrap/preseq_lcextrap
View File

@@ -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

4
target/executable/qualimap/.config.vsh.yaml
View File

@@ -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:

6
target/executable/qualimap/qualimap
View File

@@ -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

4
target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml
View File

@@ -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:

6
target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression
View File

@@ -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

4
target/executable/rsem/rsem_merge_counts/.config.vsh.yaml
View File

@@ -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:

6
target/executable/rsem/rsem_merge_counts/rsem_merge_counts
View File

@@ -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

4
target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml
View File

@@ -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:

6
target/executable/rseqc/rseqc_bamstat/rseqc_bamstat
View File

@@ -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

4
target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml
View File

@@ -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:

6
target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment
View File

@@ -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

4
target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml
View File

@@ -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:

6
target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance
View File

@@ -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

4
target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml
View File

@@ -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:

6
target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation
View File

@@ -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

4
target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml
View File

@@ -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:

6
target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation
View File

@@ -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

4
target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml
View File

@@ -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:

6
target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution
View File

@@ -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

4
target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml
View File

@@ -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:

6
target/executable/rseqc/rseqc_readduplication/rseqc_readduplication
View File

@@ -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

4
target/executable/rseqc/rseqc_tin/.config.vsh.yaml
View File

@@ -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:

6
target/executable/rseqc/rseqc_tin/rseqc_tin
View File

@@ -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

4
target/executable/sortmerna/.config.vsh.yaml
View File

@@ -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:

6
target/executable/sortmerna/sortmerna
View File

@@ -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

4
target/executable/stringtie/.config.vsh.yaml
View File

@@ -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:

6
target/executable/stringtie/stringtie
View File

@@ -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

4
target/executable/summarizedexperiment/.config.vsh.yaml
View File

@@ -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:

6
target/executable/summarizedexperiment/summarizedexperiment
View File

@@ -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

4
target/executable/trimgalore/.config.vsh.yaml
View File

@@ -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:

4
target/executable/trimgalore/trimgalore
View File

@@ -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

4
target/executable/tx2gene/.config.vsh.yaml
View File

@@ -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:

6
target/executable/tx2gene/tx2gene
View File

@@ -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

4
target/executable/tximport/.config.vsh.yaml
View File

@@ -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:

6
target/executable/tximport/tximport
View File

@@ -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

4
target/executable/ucsc/bedclip/.config.vsh.yaml
View File

@@ -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:

6
target/executable/ucsc/bedclip/bedclip
View File

@@ -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

4
target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml
View File

@@ -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:

6
target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig
View File

@@ -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

4
target/executable/umitools/umitools_dedup/.config.vsh.yaml
View File

@@ -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:

6
target/executable/umitools/umitools_dedup/umitools_dedup
View File

@@ -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

4
target/executable/umitools/umitools_extract/.config.vsh.yaml
View File

@@ -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:

6
target/executable/umitools/umitools_extract/umitools_extract
View File

@@ -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

4
target/executable/umitools_prepareforquant/.config.vsh.yaml
View File

@@ -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:

6
target/executable/umitools_prepareforquant/umitools_prepareforquant
View File

@@ -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

4
target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml
View File

@@ -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"

4
target/executable/workflows/merge_quant_results/.config.vsh.yaml
View File

@@ -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"

4
target/executable/workflows/post_processing/.config.vsh.yaml
View File

@@ -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"

4
target/executable/workflows/pre_processing/.config.vsh.yaml
View File

@@ -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"

4
target/executable/workflows/prepare_genome/.config.vsh.yaml
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@@ -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"

4
target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml
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@@ -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"

4
target/executable/workflows/quality_control/.config.vsh.yaml
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@@ -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"

4
target/executable/workflows/rnaseq/.config.vsh.yaml
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@@ -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"

42
target/executable/workflows/rnaseq/rnaseq
View File

@@ -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] ]
]
}

4
target/nextflow/bbmap_bbsplit/.config.vsh.yaml
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@@ -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:

4
target/nextflow/bbmap_bbsplit/main.nf
View File

@@ -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",

4
target/nextflow/bedtools_genomecov/.config.vsh.yaml
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@@ -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:

4
target/nextflow/bedtools_genomecov/main.nf
View File

@@ -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",

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