Build branch bugfix with version bugfix (7662841)
Build pipeline: viash-hub.rnaseq.bugfix-ndc9n
Source commit: 7662841e2e
Source message: clean code, remove unused arguments
This commit is contained in:
@@ -144,7 +144,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -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: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -251,7 +251,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -506,9 +506,9 @@ tar xzf BBMap_39.01.tar.gz && \
|
||||
cp -r bbmap/* /usr/local/bin
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component bbmap_bbsplit"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:11Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:32Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -84,7 +84,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -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: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -191,7 +191,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -481,9 +481,9 @@ mv bedtools.static /usr/local/bin/bedtools && \
|
||||
chmod a+x /usr/local/bin/bedtools
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component bedtools_genomecov"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:06Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:26Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -94,7 +94,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -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: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -195,7 +195,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -480,9 +480,9 @@ function ViashDockerfile {
|
||||
FROM python:latest
|
||||
ENTRYPOINT []
|
||||
LABEL org.opencontainers.image.description="Companion container for running component cat_additional_fasta"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:02Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:21Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -81,7 +81,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -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: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -182,7 +182,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -472,9 +472,9 @@ function ViashDockerfile {
|
||||
FROM ubuntu:22.04
|
||||
ENTRYPOINT []
|
||||
LABEL org.opencontainers.image.description="Companion container for running component cat_fastq"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:07Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:27Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -5,60 +5,69 @@ argument_groups:
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--counts"
|
||||
description: "count file matrix where rows are genes and columns are samples"
|
||||
description: "Count file matrix where rows are genes and columns are samples."
|
||||
info: null
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--pca_header_multiqc"
|
||||
info: null
|
||||
default:
|
||||
- "assets/multiqc/deseq2_pca_header.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--clustering_header_multiqc"
|
||||
info: null
|
||||
default:
|
||||
- "assets/multiqc/deseq2_clustering_header.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
required: true
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--deseq2_vst"
|
||||
description: "Use vst transformation instead of rlog with DESeq2"
|
||||
name: "--vst"
|
||||
description: "Use vst transformation instead of rlog with .DESeq2"
|
||||
info: null
|
||||
default:
|
||||
- true
|
||||
- false
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--count_col"
|
||||
description: "First column containing sample count data."
|
||||
info: null
|
||||
default:
|
||||
- 3
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "integer"
|
||||
name: "--id_col"
|
||||
description: "Column containing identifiers to be used."
|
||||
info: null
|
||||
default:
|
||||
- 1
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--extra_args"
|
||||
name: "--sample_suffix"
|
||||
description: "Suffix to remove after sample name in columns e.g. '.rmDup.bam'\
|
||||
\ if 'DRUG_R1.rmDup.bam'."
|
||||
info: null
|
||||
default:
|
||||
- "--id_col 1 --sample_suffix '' --outprefix deseq2 --count_col 3"
|
||||
- ""
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--extra_args2"
|
||||
name: "--outprefix"
|
||||
description: "Output prefix"
|
||||
info: null
|
||||
default:
|
||||
- "star_salmon"
|
||||
- "deseq2"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--label"
|
||||
description: "Label to used in MultiQC report"
|
||||
info: null
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
@@ -66,7 +75,7 @@ argument_groups:
|
||||
- name: "Output"
|
||||
arguments:
|
||||
- type: "file"
|
||||
name: "--deseq2_output"
|
||||
name: "--outdir"
|
||||
info: null
|
||||
default:
|
||||
- "deseq2"
|
||||
@@ -88,7 +97,7 @@ argument_groups:
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--dists_multiqc"
|
||||
name: "--sample_dists_multiqc"
|
||||
info: null
|
||||
default:
|
||||
- "deseq2.sample.dists_mqc.tsv"
|
||||
@@ -99,17 +108,13 @@ argument_groups:
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
- type: "r_script"
|
||||
path: "script.r"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "deseq2_qc.r"
|
||||
path: "deseq2_pca_header.txt"
|
||||
- type: "file"
|
||||
path: "assets/multiqc/deseq2_pca_header.txt"
|
||||
dest: "assets/multiqc/deseq2_pca_header.txt"
|
||||
- type: "file"
|
||||
path: "assets/multiqc/deseq2_clustering_header.txt"
|
||||
dest: "assets/multiqc/deseq2_clustering_header.txt"
|
||||
path: "deseq2_clustering_header.txt"
|
||||
description: "run deseq2, perform pca, generate heatmaps and scatterplots for samples\
|
||||
\ in the counts files\n"
|
||||
test_resources:
|
||||
@@ -132,7 +137,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -205,24 +210,18 @@ runners:
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "ubuntu:22.04"
|
||||
image: "rocker/r2u:22.04"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "bugfix"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "r-base"
|
||||
- "libcurl4-openssl-dev"
|
||||
- "libssl-dev"
|
||||
- "libxml2-dev"
|
||||
interactive: false
|
||||
- type: "r"
|
||||
cran:
|
||||
- "optparse"
|
||||
- "ggplot2"
|
||||
- "RColorBrewer"
|
||||
- "pheatmap"
|
||||
- "stringr"
|
||||
bioc:
|
||||
- "DESeq2"
|
||||
url:
|
||||
@@ -239,8 +238,8 @@ build_info:
|
||||
output: "target/executable/deseq2_qc"
|
||||
executable: "target/executable/deseq2_qc/deseq2_qc"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -252,7 +251,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -178,32 +178,41 @@ function ViashHelp {
|
||||
echo ""
|
||||
echo "input:"
|
||||
echo " --counts"
|
||||
echo " type: file, file must exist"
|
||||
echo " count file matrix where rows are genes and columns are samples"
|
||||
echo " type: file, required parameter, file must exist"
|
||||
echo " Count file matrix where rows are genes and columns are samples."
|
||||
echo ""
|
||||
echo " --pca_header_multiqc"
|
||||
echo " type: file, file must exist"
|
||||
echo " default: assets/multiqc/deseq2_pca_header.txt"
|
||||
echo ""
|
||||
echo " --clustering_header_multiqc"
|
||||
echo " type: file, file must exist"
|
||||
echo " default: assets/multiqc/deseq2_clustering_header.txt"
|
||||
echo ""
|
||||
echo " --deseq2_vst"
|
||||
echo " --vst"
|
||||
echo " type: boolean"
|
||||
echo " default: true"
|
||||
echo " Use vst transformation instead of rlog with DESeq2"
|
||||
echo " default: false"
|
||||
echo " Use vst transformation instead of rlog with .DESeq2"
|
||||
echo ""
|
||||
echo " --extra_args"
|
||||
echo " type: string"
|
||||
echo " default: --id_col 1 --sample_suffix '' --outprefix deseq2 --count_col 3"
|
||||
echo " --count_col"
|
||||
echo " type: integer"
|
||||
echo " default: 3"
|
||||
echo " First column containing sample count data."
|
||||
echo ""
|
||||
echo " --extra_args2"
|
||||
echo " --id_col"
|
||||
echo " type: integer"
|
||||
echo " default: 1"
|
||||
echo " Column containing identifiers to be used."
|
||||
echo ""
|
||||
echo " --sample_suffix"
|
||||
echo " type: string"
|
||||
echo " default: star_salmon"
|
||||
echo " default:"
|
||||
echo " Suffix to remove after sample name in columns e.g. '.rmDup.bam' if"
|
||||
echo " 'DRUG_R1.rmDup.bam'."
|
||||
echo ""
|
||||
echo " --outprefix"
|
||||
echo " type: string"
|
||||
echo " default: deseq2"
|
||||
echo " Output prefix"
|
||||
echo ""
|
||||
echo " --label"
|
||||
echo " type: string"
|
||||
echo " Label to used in MultiQC report"
|
||||
echo ""
|
||||
echo "Output:"
|
||||
echo " --deseq2_output"
|
||||
echo " --outdir"
|
||||
echo " type: file, output, file must exist"
|
||||
echo " default: deseq2"
|
||||
echo ""
|
||||
@@ -211,7 +220,7 @@ function ViashHelp {
|
||||
echo " type: file, output, file must exist"
|
||||
echo " default: deseq2.pca.vals_mqc.tsv"
|
||||
echo ""
|
||||
echo " --dists_multiqc"
|
||||
echo " --sample_dists_multiqc"
|
||||
echo " type: file, output, file must exist"
|
||||
echo " default: deseq2.sample.dists_mqc.tsv"
|
||||
}
|
||||
@@ -489,22 +498,18 @@ function ViashDockerfile {
|
||||
|
||||
if [[ "$engine_id" == "docker" ]]; then
|
||||
cat << 'VIASHDOCKER'
|
||||
FROM ubuntu:22.04
|
||||
FROM rocker/r2u:22.04
|
||||
ENTRYPOINT []
|
||||
RUN apt-get update && \
|
||||
DEBIAN_FRONTEND=noninteractive apt-get install -y r-base libcurl4-openssl-dev libssl-dev libxml2-dev && \
|
||||
rm -rf /var/lib/apt/lists/*
|
||||
|
||||
RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")' && \
|
||||
Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")' && \
|
||||
Rscript -e 'if (!requireNamespace("DESeq2", quietly = TRUE)) BiocManager::install("DESeq2")' && \
|
||||
Rscript -e 'remotes::install_cran(c("optparse", "ggplot2", "RColorBrewer", "pheatmap"), repos = "https://cran.rstudio.com")' && \
|
||||
Rscript -e 'remotes::install_cran(c("optparse", "ggplot2", "RColorBrewer", "pheatmap", "stringr"), repos = "https://cran.rstudio.com")' && \
|
||||
Rscript -e 'remotes::install_url(c("https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz"), repos = "https://cran.rstudio.com")'
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component deseq2_qc"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:09Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:29Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
@@ -655,70 +660,81 @@ while [[ $# -gt 0 ]]; do
|
||||
VIASH_PAR_COUNTS=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--pca_header_multiqc)
|
||||
[ -n "$VIASH_PAR_PCA_HEADER_MULTIQC" ] && ViashError Bad arguments for option \'--pca_header_multiqc\': \'$VIASH_PAR_PCA_HEADER_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_PCA_HEADER_MULTIQC="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --pca_header_multiqc. Use "--help" to get more information on the parameters. && exit 1
|
||||
--vst)
|
||||
[ -n "$VIASH_PAR_VST" ] && ViashError Bad arguments for option \'--vst\': \'$VIASH_PAR_VST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_VST="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --vst. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--pca_header_multiqc=*)
|
||||
[ -n "$VIASH_PAR_PCA_HEADER_MULTIQC" ] && ViashError Bad arguments for option \'--pca_header_multiqc=*\': \'$VIASH_PAR_PCA_HEADER_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_PCA_HEADER_MULTIQC=$(ViashRemoveFlags "$1")
|
||||
--vst=*)
|
||||
[ -n "$VIASH_PAR_VST" ] && ViashError Bad arguments for option \'--vst=*\': \'$VIASH_PAR_VST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_VST=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--clustering_header_multiqc)
|
||||
[ -n "$VIASH_PAR_CLUSTERING_HEADER_MULTIQC" ] && ViashError Bad arguments for option \'--clustering_header_multiqc\': \'$VIASH_PAR_CLUSTERING_HEADER_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_CLUSTERING_HEADER_MULTIQC="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --clustering_header_multiqc. Use "--help" to get more information on the parameters. && exit 1
|
||||
--count_col)
|
||||
[ -n "$VIASH_PAR_COUNT_COL" ] && ViashError Bad arguments for option \'--count_col\': \'$VIASH_PAR_COUNT_COL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_COUNT_COL="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --count_col. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--clustering_header_multiqc=*)
|
||||
[ -n "$VIASH_PAR_CLUSTERING_HEADER_MULTIQC" ] && ViashError Bad arguments for option \'--clustering_header_multiqc=*\': \'$VIASH_PAR_CLUSTERING_HEADER_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_CLUSTERING_HEADER_MULTIQC=$(ViashRemoveFlags "$1")
|
||||
--count_col=*)
|
||||
[ -n "$VIASH_PAR_COUNT_COL" ] && ViashError Bad arguments for option \'--count_col=*\': \'$VIASH_PAR_COUNT_COL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_COUNT_COL=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--deseq2_vst)
|
||||
[ -n "$VIASH_PAR_DESEQ2_VST" ] && ViashError Bad arguments for option \'--deseq2_vst\': \'$VIASH_PAR_DESEQ2_VST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_DESEQ2_VST="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --deseq2_vst. Use "--help" to get more information on the parameters. && exit 1
|
||||
--id_col)
|
||||
[ -n "$VIASH_PAR_ID_COL" ] && ViashError Bad arguments for option \'--id_col\': \'$VIASH_PAR_ID_COL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_ID_COL="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --id_col. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--deseq2_vst=*)
|
||||
[ -n "$VIASH_PAR_DESEQ2_VST" ] && ViashError Bad arguments for option \'--deseq2_vst=*\': \'$VIASH_PAR_DESEQ2_VST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_DESEQ2_VST=$(ViashRemoveFlags "$1")
|
||||
--id_col=*)
|
||||
[ -n "$VIASH_PAR_ID_COL" ] && ViashError Bad arguments for option \'--id_col=*\': \'$VIASH_PAR_ID_COL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_ID_COL=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--extra_args)
|
||||
[ -n "$VIASH_PAR_EXTRA_ARGS" ] && ViashError Bad arguments for option \'--extra_args\': \'$VIASH_PAR_EXTRA_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_ARGS="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_args. Use "--help" to get more information on the parameters. && exit 1
|
||||
--sample_suffix)
|
||||
[ -n "$VIASH_PAR_SAMPLE_SUFFIX" ] && ViashError Bad arguments for option \'--sample_suffix\': \'$VIASH_PAR_SAMPLE_SUFFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_SAMPLE_SUFFIX="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --sample_suffix. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--extra_args=*)
|
||||
[ -n "$VIASH_PAR_EXTRA_ARGS" ] && ViashError Bad arguments for option \'--extra_args=*\': \'$VIASH_PAR_EXTRA_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_ARGS=$(ViashRemoveFlags "$1")
|
||||
--sample_suffix=*)
|
||||
[ -n "$VIASH_PAR_SAMPLE_SUFFIX" ] && ViashError Bad arguments for option \'--sample_suffix=*\': \'$VIASH_PAR_SAMPLE_SUFFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_SAMPLE_SUFFIX=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--extra_args2)
|
||||
[ -n "$VIASH_PAR_EXTRA_ARGS2" ] && ViashError Bad arguments for option \'--extra_args2\': \'$VIASH_PAR_EXTRA_ARGS2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_ARGS2="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_args2. Use "--help" to get more information on the parameters. && exit 1
|
||||
--outprefix)
|
||||
[ -n "$VIASH_PAR_OUTPREFIX" ] && ViashError Bad arguments for option \'--outprefix\': \'$VIASH_PAR_OUTPREFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_OUTPREFIX="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --outprefix. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--extra_args2=*)
|
||||
[ -n "$VIASH_PAR_EXTRA_ARGS2" ] && ViashError Bad arguments for option \'--extra_args2=*\': \'$VIASH_PAR_EXTRA_ARGS2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_ARGS2=$(ViashRemoveFlags "$1")
|
||||
--outprefix=*)
|
||||
[ -n "$VIASH_PAR_OUTPREFIX" ] && ViashError Bad arguments for option \'--outprefix=*\': \'$VIASH_PAR_OUTPREFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_OUTPREFIX=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--deseq2_output)
|
||||
[ -n "$VIASH_PAR_DESEQ2_OUTPUT" ] && ViashError Bad arguments for option \'--deseq2_output\': \'$VIASH_PAR_DESEQ2_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_DESEQ2_OUTPUT="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --deseq2_output. Use "--help" to get more information on the parameters. && exit 1
|
||||
--label)
|
||||
[ -n "$VIASH_PAR_LABEL" ] && ViashError Bad arguments for option \'--label\': \'$VIASH_PAR_LABEL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_LABEL="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --label. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--deseq2_output=*)
|
||||
[ -n "$VIASH_PAR_DESEQ2_OUTPUT" ] && ViashError Bad arguments for option \'--deseq2_output=*\': \'$VIASH_PAR_DESEQ2_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_DESEQ2_OUTPUT=$(ViashRemoveFlags "$1")
|
||||
--label=*)
|
||||
[ -n "$VIASH_PAR_LABEL" ] && ViashError Bad arguments for option \'--label=*\': \'$VIASH_PAR_LABEL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_LABEL=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--outdir)
|
||||
[ -n "$VIASH_PAR_OUTDIR" ] && ViashError Bad arguments for option \'--outdir\': \'$VIASH_PAR_OUTDIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_OUTDIR="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --outdir. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--outdir=*)
|
||||
[ -n "$VIASH_PAR_OUTDIR" ] && ViashError Bad arguments for option \'--outdir=*\': \'$VIASH_PAR_OUTDIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_OUTDIR=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--pca_multiqc)
|
||||
@@ -732,15 +748,15 @@ while [[ $# -gt 0 ]]; do
|
||||
VIASH_PAR_PCA_MULTIQC=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--dists_multiqc)
|
||||
[ -n "$VIASH_PAR_DISTS_MULTIQC" ] && ViashError Bad arguments for option \'--dists_multiqc\': \'$VIASH_PAR_DISTS_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_DISTS_MULTIQC="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --dists_multiqc. Use "--help" to get more information on the parameters. && exit 1
|
||||
--sample_dists_multiqc)
|
||||
[ -n "$VIASH_PAR_SAMPLE_DISTS_MULTIQC" ] && ViashError Bad arguments for option \'--sample_dists_multiqc\': \'$VIASH_PAR_SAMPLE_DISTS_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_SAMPLE_DISTS_MULTIQC="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --sample_dists_multiqc. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--dists_multiqc=*)
|
||||
[ -n "$VIASH_PAR_DISTS_MULTIQC" ] && ViashError Bad arguments for option \'--dists_multiqc=*\': \'$VIASH_PAR_DISTS_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_DISTS_MULTIQC=$(ViashRemoveFlags "$1")
|
||||
--sample_dists_multiqc=*)
|
||||
[ -n "$VIASH_PAR_SAMPLE_DISTS_MULTIQC" ] && ViashError Bad arguments for option \'--sample_dists_multiqc=*\': \'$VIASH_PAR_SAMPLE_DISTS_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_SAMPLE_DISTS_MULTIQC=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
---engine)
|
||||
@@ -915,6 +931,10 @@ fi
|
||||
|
||||
|
||||
# check whether required parameters exist
|
||||
if [ -z ${VIASH_PAR_COUNTS+x} ]; then
|
||||
ViashError '--counts' is a required argument. Use "--help" to get more information on the parameters.
|
||||
exit 1
|
||||
fi
|
||||
if [ -z ${VIASH_META_NAME+x} ]; then
|
||||
ViashError 'name' is a required argument. Use "--help" to get more information on the parameters.
|
||||
exit 1
|
||||
@@ -941,29 +961,29 @@ if [ -z ${VIASH_META_TEMP_DIR+x} ]; then
|
||||
fi
|
||||
|
||||
# filling in defaults
|
||||
if [ -z ${VIASH_PAR_PCA_HEADER_MULTIQC+x} ]; then
|
||||
VIASH_PAR_PCA_HEADER_MULTIQC="assets/multiqc/deseq2_pca_header.txt"
|
||||
if [ -z ${VIASH_PAR_VST+x} ]; then
|
||||
VIASH_PAR_VST="false"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_CLUSTERING_HEADER_MULTIQC+x} ]; then
|
||||
VIASH_PAR_CLUSTERING_HEADER_MULTIQC="assets/multiqc/deseq2_clustering_header.txt"
|
||||
if [ -z ${VIASH_PAR_COUNT_COL+x} ]; then
|
||||
VIASH_PAR_COUNT_COL="3"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_DESEQ2_VST+x} ]; then
|
||||
VIASH_PAR_DESEQ2_VST="true"
|
||||
if [ -z ${VIASH_PAR_ID_COL+x} ]; then
|
||||
VIASH_PAR_ID_COL="1"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_EXTRA_ARGS+x} ]; then
|
||||
VIASH_PAR_EXTRA_ARGS="--id_col 1 --sample_suffix '' --outprefix deseq2 --count_col 3"
|
||||
if [ -z ${VIASH_PAR_SAMPLE_SUFFIX+x} ]; then
|
||||
VIASH_PAR_SAMPLE_SUFFIX=""
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_EXTRA_ARGS2+x} ]; then
|
||||
VIASH_PAR_EXTRA_ARGS2="star_salmon"
|
||||
if [ -z ${VIASH_PAR_OUTPREFIX+x} ]; then
|
||||
VIASH_PAR_OUTPREFIX="deseq2"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_DESEQ2_OUTPUT+x} ]; then
|
||||
VIASH_PAR_DESEQ2_OUTPUT="deseq2"
|
||||
if [ -z ${VIASH_PAR_OUTDIR+x} ]; then
|
||||
VIASH_PAR_OUTDIR="deseq2"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_PCA_MULTIQC+x} ]; then
|
||||
VIASH_PAR_PCA_MULTIQC="deseq2.pca.vals_mqc.tsv"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_DISTS_MULTIQC+x} ]; then
|
||||
VIASH_PAR_DISTS_MULTIQC="deseq2.sample.dists_mqc.tsv"
|
||||
if [ -z ${VIASH_PAR_SAMPLE_DISTS_MULTIQC+x} ]; then
|
||||
VIASH_PAR_SAMPLE_DISTS_MULTIQC="deseq2.sample.dists_mqc.tsv"
|
||||
fi
|
||||
|
||||
# check whether required files exist
|
||||
@@ -971,19 +991,23 @@ if [ ! -z "$VIASH_PAR_COUNTS" ] && [ ! -e "$VIASH_PAR_COUNTS" ]; then
|
||||
ViashError "Input file '$VIASH_PAR_COUNTS' does not exist."
|
||||
exit 1
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_PCA_HEADER_MULTIQC" ] && [ ! -e "$VIASH_PAR_PCA_HEADER_MULTIQC" ]; then
|
||||
ViashError "Input file '$VIASH_PAR_PCA_HEADER_MULTIQC' does not exist."
|
||||
exit 1
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_CLUSTERING_HEADER_MULTIQC" ] && [ ! -e "$VIASH_PAR_CLUSTERING_HEADER_MULTIQC" ]; then
|
||||
ViashError "Input file '$VIASH_PAR_CLUSTERING_HEADER_MULTIQC' does not exist."
|
||||
exit 1
|
||||
fi
|
||||
|
||||
# check whether parameters values are of the right type
|
||||
if [[ -n "$VIASH_PAR_DESEQ2_VST" ]]; then
|
||||
if ! [[ "$VIASH_PAR_DESEQ2_VST" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
||||
ViashError '--deseq2_vst' has to be a boolean. Use "--help" to get more information on the parameters.
|
||||
if [[ -n "$VIASH_PAR_VST" ]]; then
|
||||
if ! [[ "$VIASH_PAR_VST" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
|
||||
ViashError '--vst' has to be a boolean. Use "--help" to get more information on the parameters.
|
||||
exit 1
|
||||
fi
|
||||
fi
|
||||
if [[ -n "$VIASH_PAR_COUNT_COL" ]]; then
|
||||
if ! [[ "$VIASH_PAR_COUNT_COL" =~ ^[-+]?[0-9]+$ ]]; then
|
||||
ViashError '--count_col' has to be an integer. Use "--help" to get more information on the parameters.
|
||||
exit 1
|
||||
fi
|
||||
fi
|
||||
if [[ -n "$VIASH_PAR_ID_COL" ]]; then
|
||||
if ! [[ "$VIASH_PAR_ID_COL" =~ ^[-+]?[0-9]+$ ]]; then
|
||||
ViashError '--id_col' has to be an integer. Use "--help" to get more information on the parameters.
|
||||
exit 1
|
||||
fi
|
||||
fi
|
||||
@@ -1061,14 +1085,14 @@ if [[ -n "$VIASH_META_MEMORY_PIB" ]]; then
|
||||
fi
|
||||
|
||||
# create parent directories of output files, if so desired
|
||||
if [ ! -z "$VIASH_PAR_DESEQ2_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_DESEQ2_OUTPUT")" ]; then
|
||||
mkdir -p "$(dirname "$VIASH_PAR_DESEQ2_OUTPUT")"
|
||||
if [ ! -z "$VIASH_PAR_OUTDIR" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTDIR")" ]; then
|
||||
mkdir -p "$(dirname "$VIASH_PAR_OUTDIR")"
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_PCA_MULTIQC" ] && [ ! -d "$(dirname "$VIASH_PAR_PCA_MULTIQC")" ]; then
|
||||
mkdir -p "$(dirname "$VIASH_PAR_PCA_MULTIQC")"
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_DISTS_MULTIQC" ] && [ ! -d "$(dirname "$VIASH_PAR_DISTS_MULTIQC")" ]; then
|
||||
mkdir -p "$(dirname "$VIASH_PAR_DISTS_MULTIQC")"
|
||||
if [ ! -z "$VIASH_PAR_SAMPLE_DISTS_MULTIQC" ] && [ ! -d "$(dirname "$VIASH_PAR_SAMPLE_DISTS_MULTIQC")" ]; then
|
||||
mkdir -p "$(dirname "$VIASH_PAR_SAMPLE_DISTS_MULTIQC")"
|
||||
fi
|
||||
|
||||
if [ "$VIASH_ENGINE_ID" == "native" ] ; then
|
||||
@@ -1087,28 +1111,20 @@ if [ ! -z "$VIASH_PAR_COUNTS" ]; then
|
||||
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_COUNTS")" )
|
||||
VIASH_PAR_COUNTS=$(ViashDockerAutodetectMount "$VIASH_PAR_COUNTS")
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_PCA_HEADER_MULTIQC" ]; then
|
||||
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_PCA_HEADER_MULTIQC")" )
|
||||
VIASH_PAR_PCA_HEADER_MULTIQC=$(ViashDockerAutodetectMount "$VIASH_PAR_PCA_HEADER_MULTIQC")
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_CLUSTERING_HEADER_MULTIQC" ]; then
|
||||
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_CLUSTERING_HEADER_MULTIQC")" )
|
||||
VIASH_PAR_CLUSTERING_HEADER_MULTIQC=$(ViashDockerAutodetectMount "$VIASH_PAR_CLUSTERING_HEADER_MULTIQC")
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_DESEQ2_OUTPUT" ]; then
|
||||
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_DESEQ2_OUTPUT")" )
|
||||
VIASH_PAR_DESEQ2_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_DESEQ2_OUTPUT")
|
||||
VIASH_CHOWN_VARS+=( "$VIASH_PAR_DESEQ2_OUTPUT" )
|
||||
if [ ! -z "$VIASH_PAR_OUTDIR" ]; then
|
||||
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTDIR")" )
|
||||
VIASH_PAR_OUTDIR=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTDIR")
|
||||
VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTDIR" )
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_PCA_MULTIQC" ]; then
|
||||
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_PCA_MULTIQC")" )
|
||||
VIASH_PAR_PCA_MULTIQC=$(ViashDockerAutodetectMount "$VIASH_PAR_PCA_MULTIQC")
|
||||
VIASH_CHOWN_VARS+=( "$VIASH_PAR_PCA_MULTIQC" )
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_DISTS_MULTIQC" ]; then
|
||||
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_DISTS_MULTIQC")" )
|
||||
VIASH_PAR_DISTS_MULTIQC=$(ViashDockerAutodetectMount "$VIASH_PAR_DISTS_MULTIQC")
|
||||
VIASH_CHOWN_VARS+=( "$VIASH_PAR_DISTS_MULTIQC" )
|
||||
if [ ! -z "$VIASH_PAR_SAMPLE_DISTS_MULTIQC" ]; then
|
||||
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_SAMPLE_DISTS_MULTIQC")" )
|
||||
VIASH_PAR_SAMPLE_DISTS_MULTIQC=$(ViashDockerAutodetectMount "$VIASH_PAR_SAMPLE_DISTS_MULTIQC")
|
||||
VIASH_CHOWN_VARS+=( "$VIASH_PAR_SAMPLE_DISTS_MULTIQC" )
|
||||
fi
|
||||
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
|
||||
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_RESOURCES_DIR")" )
|
||||
@@ -1166,7 +1182,7 @@ fi
|
||||
ViashDebug "Running command: $(echo $VIASH_CMD)"
|
||||
cat << VIASHEOF | eval $VIASH_CMD
|
||||
set -e
|
||||
tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-deseq2_qc-XXXXXX").sh
|
||||
tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-deseq2_qc-XXXXXX").R
|
||||
function clean_up {
|
||||
rm "\$tempscript"
|
||||
}
|
||||
@@ -1179,85 +1195,269 @@ trap interrupt INT SIGINT
|
||||
cat > "\$tempscript" << 'VIASHMAIN'
|
||||
## VIASH START
|
||||
# The following code has been auto-generated by Viash.
|
||||
$( if [ ! -z ${VIASH_PAR_COUNTS+x} ]; then echo "${VIASH_PAR_COUNTS}" | sed "s#'#'\"'\"'#g;s#.*#par_counts='&'#" ; else echo "# par_counts="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_PCA_HEADER_MULTIQC+x} ]; then echo "${VIASH_PAR_PCA_HEADER_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_pca_header_multiqc='&'#" ; else echo "# par_pca_header_multiqc="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_CLUSTERING_HEADER_MULTIQC+x} ]; then echo "${VIASH_PAR_CLUSTERING_HEADER_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_clustering_header_multiqc='&'#" ; else echo "# par_clustering_header_multiqc="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_DESEQ2_VST+x} ]; then echo "${VIASH_PAR_DESEQ2_VST}" | sed "s#'#'\"'\"'#g;s#.*#par_deseq2_vst='&'#" ; else echo "# par_deseq2_vst="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_EXTRA_ARGS+x} ]; then echo "${VIASH_PAR_EXTRA_ARGS}" | sed "s#'#'\"'\"'#g;s#.*#par_extra_args='&'#" ; else echo "# par_extra_args="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_EXTRA_ARGS2+x} ]; then echo "${VIASH_PAR_EXTRA_ARGS2}" | sed "s#'#'\"'\"'#g;s#.*#par_extra_args2='&'#" ; else echo "# par_extra_args2="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_DESEQ2_OUTPUT+x} ]; then echo "${VIASH_PAR_DESEQ2_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_deseq2_output='&'#" ; else echo "# par_deseq2_output="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_PCA_MULTIQC+x} ]; then echo "${VIASH_PAR_PCA_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_pca_multiqc='&'#" ; else echo "# par_pca_multiqc="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_DISTS_MULTIQC+x} ]; then echo "${VIASH_PAR_DISTS_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_dists_multiqc='&'#" ; else echo "# par_dists_multiqc="; fi )
|
||||
$( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
|
||||
$( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi )
|
||||
$( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi )
|
||||
$( if [ ! -z ${VIASH_META_EXECUTABLE+x} ]; then echo "${VIASH_META_EXECUTABLE}" | sed "s#'#'\"'\"'#g;s#.*#meta_executable='&'#" ; else echo "# meta_executable="; fi )
|
||||
$( if [ ! -z ${VIASH_META_CONFIG+x} ]; then echo "${VIASH_META_CONFIG}" | sed "s#'#'\"'\"'#g;s#.*#meta_config='&'#" ; else echo "# meta_config="; fi )
|
||||
$( if [ ! -z ${VIASH_META_TEMP_DIR+x} ]; then echo "${VIASH_META_TEMP_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_temp_dir='&'#" ; else echo "# meta_temp_dir="; fi )
|
||||
$( if [ ! -z ${VIASH_META_CPUS+x} ]; then echo "${VIASH_META_CPUS}" | sed "s#'#'\"'\"'#g;s#.*#meta_cpus='&'#" ; else echo "# meta_cpus="; fi )
|
||||
$( if [ ! -z ${VIASH_META_MEMORY_B+x} ]; then echo "${VIASH_META_MEMORY_B}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_b='&'#" ; else echo "# meta_memory_b="; fi )
|
||||
$( if [ ! -z ${VIASH_META_MEMORY_KB+x} ]; then echo "${VIASH_META_MEMORY_KB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_kb='&'#" ; else echo "# meta_memory_kb="; fi )
|
||||
$( if [ ! -z ${VIASH_META_MEMORY_MB+x} ]; then echo "${VIASH_META_MEMORY_MB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_mb='&'#" ; else echo "# meta_memory_mb="; fi )
|
||||
$( if [ ! -z ${VIASH_META_MEMORY_GB+x} ]; then echo "${VIASH_META_MEMORY_GB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_gb='&'#" ; else echo "# meta_memory_gb="; fi )
|
||||
$( if [ ! -z ${VIASH_META_MEMORY_TB+x} ]; then echo "${VIASH_META_MEMORY_TB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_tb='&'#" ; else echo "# meta_memory_tb="; fi )
|
||||
$( if [ ! -z ${VIASH_META_MEMORY_PB+x} ]; then echo "${VIASH_META_MEMORY_PB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pb='&'#" ; else echo "# meta_memory_pb="; fi )
|
||||
$( if [ ! -z ${VIASH_META_MEMORY_KIB+x} ]; then echo "${VIASH_META_MEMORY_KIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_kib='&'#" ; else echo "# meta_memory_kib="; fi )
|
||||
$( if [ ! -z ${VIASH_META_MEMORY_MIB+x} ]; then echo "${VIASH_META_MEMORY_MIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_mib='&'#" ; else echo "# meta_memory_mib="; fi )
|
||||
$( if [ ! -z ${VIASH_META_MEMORY_GIB+x} ]; then echo "${VIASH_META_MEMORY_GIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_gib='&'#" ; else echo "# meta_memory_gib="; fi )
|
||||
$( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "${VIASH_META_MEMORY_TIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_tib='&'#" ; else echo "# meta_memory_tib="; fi )
|
||||
$( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pib='&'#" ; else echo "# meta_memory_pib="; fi )
|
||||
# treat warnings as errors
|
||||
.viash_orig_warn <- options(warn = 2)
|
||||
|
||||
par <- list(
|
||||
"counts" = $( if [ ! -z ${VIASH_PAR_COUNTS+x} ]; then echo -n "'"; echo -n "$VIASH_PAR_COUNTS" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
|
||||
"vst" = $( if [ ! -z ${VIASH_PAR_VST+x} ]; then echo -n "as.logical(toupper('"; echo -n "$VIASH_PAR_VST" | sed "s#['\\]#\\\\&#g"; echo "'))"; else echo NULL; fi ),
|
||||
"count_col" = $( if [ ! -z ${VIASH_PAR_COUNT_COL+x} ]; then echo -n "as.integer('"; echo -n "$VIASH_PAR_COUNT_COL" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
|
||||
"id_col" = $( if [ ! -z ${VIASH_PAR_ID_COL+x} ]; then echo -n "as.integer('"; echo -n "$VIASH_PAR_ID_COL" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
|
||||
"sample_suffix" = $( if [ ! -z ${VIASH_PAR_SAMPLE_SUFFIX+x} ]; then echo -n "'"; echo -n "$VIASH_PAR_SAMPLE_SUFFIX" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
|
||||
"outprefix" = $( if [ ! -z ${VIASH_PAR_OUTPREFIX+x} ]; then echo -n "'"; echo -n "$VIASH_PAR_OUTPREFIX" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
|
||||
"label" = $( if [ ! -z ${VIASH_PAR_LABEL+x} ]; then echo -n "'"; echo -n "$VIASH_PAR_LABEL" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
|
||||
"outdir" = $( if [ ! -z ${VIASH_PAR_OUTDIR+x} ]; then echo -n "'"; echo -n "$VIASH_PAR_OUTDIR" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
|
||||
"pca_multiqc" = $( if [ ! -z ${VIASH_PAR_PCA_MULTIQC+x} ]; then echo -n "'"; echo -n "$VIASH_PAR_PCA_MULTIQC" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
|
||||
"sample_dists_multiqc" = $( if [ ! -z ${VIASH_PAR_SAMPLE_DISTS_MULTIQC+x} ]; then echo -n "'"; echo -n "$VIASH_PAR_SAMPLE_DISTS_MULTIQC" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi )
|
||||
)
|
||||
meta <- list(
|
||||
"name" = $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo -n "'"; echo -n "$VIASH_META_NAME" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
|
||||
"functionality_name" = $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo -n "'"; echo -n "$VIASH_META_FUNCTIONALITY_NAME" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
|
||||
"resources_dir" = $( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo -n "'"; echo -n "$VIASH_META_RESOURCES_DIR" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
|
||||
"executable" = $( if [ ! -z ${VIASH_META_EXECUTABLE+x} ]; then echo -n "'"; echo -n "$VIASH_META_EXECUTABLE" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
|
||||
"config" = $( if [ ! -z ${VIASH_META_CONFIG+x} ]; then echo -n "'"; echo -n "$VIASH_META_CONFIG" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
|
||||
"temp_dir" = $( if [ ! -z ${VIASH_META_TEMP_DIR+x} ]; then echo -n "'"; echo -n "$VIASH_META_TEMP_DIR" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
|
||||
"cpus" = $( if [ ! -z ${VIASH_META_CPUS+x} ]; then echo -n "as.integer('"; echo -n "$VIASH_META_CPUS" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
|
||||
"memory_b" = $( if [ ! -z ${VIASH_META_MEMORY_B+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_B" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
|
||||
"memory_kb" = $( if [ ! -z ${VIASH_META_MEMORY_KB+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_KB" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
|
||||
"memory_mb" = $( if [ ! -z ${VIASH_META_MEMORY_MB+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_MB" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
|
||||
"memory_gb" = $( if [ ! -z ${VIASH_META_MEMORY_GB+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_GB" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
|
||||
"memory_tb" = $( if [ ! -z ${VIASH_META_MEMORY_TB+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_TB" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
|
||||
"memory_pb" = $( if [ ! -z ${VIASH_META_MEMORY_PB+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_PB" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
|
||||
"memory_kib" = $( if [ ! -z ${VIASH_META_MEMORY_KIB+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_KIB" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
|
||||
"memory_mib" = $( if [ ! -z ${VIASH_META_MEMORY_MIB+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_MIB" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
|
||||
"memory_gib" = $( if [ ! -z ${VIASH_META_MEMORY_GIB+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_GIB" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
|
||||
"memory_tib" = $( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_TIB" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
|
||||
"memory_pib" = $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_PIB" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi )
|
||||
)
|
||||
dep <- list(
|
||||
|
||||
)
|
||||
|
||||
|
||||
# restore original warn setting
|
||||
options(.viash_orig_warn)
|
||||
rm(.viash_orig_warn)
|
||||
|
||||
## VIASH END
|
||||
#!/bin/sh
|
||||
|
||||
set -eo pipefail
|
||||
# REQUIREMENTS
|
||||
|
||||
if \$par_deseq2_vst; then
|
||||
par_extra_args+=" --vst TRUE"
|
||||
fi
|
||||
## PCA, HEATMAP AND SCATTERPLOTS FOR SAMPLES IN COUNTS FILE
|
||||
## - SAMPLE NAMES HAVE TO END IN e.g. "_R1" REPRESENTING REPLICATE ID. LAST 3 CHARACTERS OF SAMPLE NAME WILL BE TRIMMED TO OBTAIN GROUP ID FOR DESEQ2 COMPARISONS.
|
||||
|
||||
tolower() {
|
||||
case \$1 in
|
||||
*[[:upper:]]*)
|
||||
printf "%s\\n" "\$1" | tr '[:upper:]' '[:lower:]'
|
||||
;;
|
||||
*)
|
||||
printf "%s\\n" "\$1"
|
||||
;;
|
||||
esac
|
||||
# LOAD LIBRARIES
|
||||
library(DESeq2)
|
||||
library(ggplot2)
|
||||
library(RColorBrewer)
|
||||
library(pheatmap)
|
||||
library(stringr)
|
||||
|
||||
if (file.exists(par\$outdir) == FALSE) {
|
||||
dir.create(par\$outdir, recursive = TRUE)
|
||||
}
|
||||
|
||||
toupper() {
|
||||
case \$1 in
|
||||
*[[:lower:]]*)
|
||||
printf "%s\\n" "\$1" | tr '[:lower:]' '[:upper:]'
|
||||
;;
|
||||
*)
|
||||
printf "%s\\n" "\$1"
|
||||
;;
|
||||
esac
|
||||
# READ IN COUNTS FILE
|
||||
count_table <- read.delim(file = par\$counts, header = TRUE, row.names = NULL)
|
||||
rownames(count_table) <- count_table[, par\$id_col]
|
||||
count_table <- count_table[, par\$count_col:ncol(count_table), drop = FALSE]
|
||||
colnames(count_table) <- gsub(par\$sample_suffix, "", colnames(count_table))
|
||||
colnames(count_table) <- gsub(pattern = '\\\\.\$', replacement = '', colnames(count_table))
|
||||
|
||||
# RUN DESEQ2
|
||||
samples_vec <- colnames(count_table)
|
||||
name_components <- strsplit(samples_vec, "_")
|
||||
n_components <- length(name_components[[1]])
|
||||
decompose <- n_components != 1 && all(sapply(name_components, length) == n_components)
|
||||
coldata <- data.frame(samples_vec, sample = samples_vec, row.names = 1)
|
||||
if (decompose) {
|
||||
groupings <- as.data.frame(lapply(1:n_components, function(i) sapply(name_components, "[[", i)))
|
||||
n_distinct <- sapply(groupings, function(grp) length(unique(grp)))
|
||||
groupings <- groupings[n_distinct != 1 & n_distinct != length(samples_vec)]
|
||||
if (ncol(groupings) != 0) {
|
||||
names(groupings) <- paste0("Group", 1:ncol(groupings))
|
||||
coldata <- cbind(coldata, groupings)
|
||||
} else {
|
||||
decompose <- FALSE
|
||||
}
|
||||
}
|
||||
|
||||
label_lower=\$(tolower "\$par_extra_args2")
|
||||
label_upper=\$(toupper "\$par_extra_args2")
|
||||
DDSFile <- paste(par\$outdir, "/", par\$outprefix, ".dds.RData", sep = "")
|
||||
|
||||
Rscript "\$meta_resources_dir/deseq2_qc.r" \\
|
||||
--count_file \$par_counts \\
|
||||
--outdir \$par_deseq2_output \\
|
||||
--cores \${meta_cpus:-1} \\
|
||||
\$par_extra_args
|
||||
counts <- count_table[, samples_vec, drop = FALSE]
|
||||
dds <- DESeqDataSetFromMatrix(countData = round(counts), colData = coldata, design = ~1)
|
||||
dds <- estimateSizeFactors(dds)
|
||||
|
||||
if [ -f "\$par_deseq2_output/R_sessionInfo.log" ]; then
|
||||
sed "s/deseq2_pca/\${label_lower}_deseq2_pca/g" < \$par_pca_header_multiqc > tmp.txt
|
||||
sed -i -e "s/DESeq2 PCA/\${label_upper} DESeq2 PCA/g" tmp.txt
|
||||
cat tmp.txt \$par_deseq2_output/*.pca.vals.txt > \$par_pca_multiqc
|
||||
# No point if only one sample, or one gene
|
||||
if (min(dim(count_table)) <= 1) {
|
||||
save(dds, file = DDSFile)
|
||||
saveRDS(dds, file = sub("\\\\.dds\\\\.RData\$", ".rds", DDSFile))
|
||||
warning("Not enough samples or genes in counts file for PCA.", call. = FALSE)
|
||||
quit(save = "no", status = 0, runLast = FALSE)
|
||||
}
|
||||
|
||||
sed "s/deseq2_clustering/\${label_lower}_deseq2_clustering/g" < \$par_clustering_header_multiqc > tmp.txt
|
||||
sed -i -e "s/DESeq2 sample/\${label_upper} DESeq2 sample/g" tmp.txt
|
||||
cat tmp.txt \$par_deseq2_output/*.sample.dists.txt > \$par_dists_multiqc
|
||||
fi
|
||||
if (!par\$vst) {
|
||||
vst_name <- "rlog"
|
||||
rld <- rlog(dds)
|
||||
} else {
|
||||
vst_name <- "vst"
|
||||
rld <- varianceStabilizingTransformation(dds)
|
||||
}
|
||||
|
||||
assay(dds, vst_name) <- assay(rld)
|
||||
save(dds, file = DDSFile)
|
||||
saveRDS(dds, file = sub("\\\\.dds\\\\.RData\$", ".rds", DDSFile))
|
||||
|
||||
# PLOT QC
|
||||
|
||||
##' PCA pre-processeor
|
||||
##'
|
||||
##' Generate all the necessary information to plot PCA from a DESeq2 object
|
||||
##' in which an assay containing a variance-stabilised matrix of counts is
|
||||
##' stored. Copied from DESeq2::plotPCA, but with additional ability to
|
||||
##' say which assay to run the PCA on.
|
||||
##'
|
||||
##' @param object The DESeq2DataSet object.
|
||||
##' @param ntop number of top genes to use for principla components, selected by highest row variance.
|
||||
##' @param assay the name or index of the assay that stores the variance-stabilised data.
|
||||
##' @return A data.frame containing the projected data alongside the grouping columns.
|
||||
##' A 'percentVar' attribute is set which includes the percentage of variation each PC explains,
|
||||
##' and additionally how much the variation within that PC is explained by the grouping variable.
|
||||
##' @author Gavin Kelly
|
||||
|
||||
plotPCA_vst <- function(object, ntop = 500, assay = length(assays(object))) {
|
||||
rv <- rowVars(assay(object, assay))
|
||||
select <- order(rv, decreasing = TRUE)[seq_len(min(ntop, length(rv)))]
|
||||
pca <- prcomp(t(assay(object, assay)[select, ]), center = TRUE, scale = FALSE)
|
||||
percentVar <- pca\$sdev^2 / sum(pca\$sdev^2)
|
||||
df <- cbind(as.data.frame(colData(object)), pca\$x)
|
||||
# Order points so extreme samples are more likely to get label
|
||||
ord <- order(abs(rank(df\$PC1) - median(df\$PC1)), abs(rank(df\$PC2) - median(df\$PC2)))
|
||||
df <- df[ord, ]
|
||||
attr(df, "percentVar") <- data.frame(PC = seq(along = percentVar), percentVar = 100 * percentVar)
|
||||
return(df)
|
||||
}
|
||||
|
||||
PlotFile <- paste(par\$outdir, "/", par\$outprefix, ".plots.pdf", sep = "")
|
||||
|
||||
pdf(file = PlotFile, onefile = TRUE, width = 7, height = 7)
|
||||
|
||||
## PCA
|
||||
ntop <- c(500, Inf)
|
||||
for (n_top_var in ntop) {
|
||||
pca_data <- plotPCA_vst(dds, assay = vst_name, ntop = n_top_var)
|
||||
percentVar <- round(attr(pca_data, "percentVar")\$percentVar)
|
||||
plot_subtitle <- ifelse(n_top_var == Inf, "All genes", paste("Top", n_top_var, "genes"))
|
||||
pl <- ggplot(pca_data, aes(PC1, PC2, label = paste0(" ", sample, " "))) +
|
||||
geom_point() +
|
||||
geom_text(check_overlap = TRUE, vjust = 0.5, hjust="inward") +
|
||||
xlab(paste0("PC1: ", percentVar[1], "% variance")) +
|
||||
ylab(paste0("PC2: ", percentVar[2], "% variance")) +
|
||||
labs(title = paste0("First PCs on ", vst_name, "-transformed data"), subtitle = plot_subtitle) +
|
||||
theme(legend.position = "top",
|
||||
panel.grid.major = element_blank(),
|
||||
panel.grid.minor = element_blank(),
|
||||
panel.background = element_blank(),
|
||||
panel.border = element_rect(colour = "black", fill = NA, size = 1))
|
||||
print(pl)
|
||||
|
||||
if (decompose) {
|
||||
pc_names <- paste0("PC", attr(pca_data, "percentVar")\$PC)
|
||||
long_pc <- reshape(pca_data, varying=pc_names, direction="long", sep="", timevar="component", idvar="pcrow")
|
||||
long_pc <- subset(long_pc, component <= 5)
|
||||
long_pc_grp <- reshape(long_pc, varying = names(groupings), direction = "long", sep = "", timevar = "grouper")
|
||||
long_pc_grp <- subset(long_pc_grp, grouper <= 5)
|
||||
long_pc_grp\$component <- paste("PC", long_pc_grp\$component)
|
||||
long_pc_grp\$grouper <- paste0(long_pc_grp\$grouper, c("st", "nd", "rd", "th", "th")[long_pc_grp\$grouper], " prefix")
|
||||
pl <- ggplot(long_pc_grp, aes(x = Group, y = PC)) +
|
||||
geom_point() +
|
||||
stat_summary(fun = mean, geom = "line", aes(group = 1)) +
|
||||
labs(x = NULL, y = NULL, subtitle = plot_subtitle, title = "PCs split by sample-name prefixes") +
|
||||
facet_grid(component ~ grouper, scales = "free_x") +
|
||||
scale_x_discrete(guide = guide_axis(n.dodge = 3))
|
||||
print(pl)
|
||||
}
|
||||
} # at end of loop, we'll be using the user-defined ntop if any, else all genes
|
||||
|
||||
## WRITE PC1 vs PC2 VALUES TO FILE
|
||||
pca_vals <- pca_data[, c("PC1", "PC2")]
|
||||
colnames(pca_vals) <- paste0(colnames(pca_vals), ": ", percentVar[1:2], '% variance')
|
||||
pca_vals <- cbind(sample = rownames(pca_vals), pca_vals)
|
||||
pca_vals_file <- paste(par\$outdir, "/", par\$outprefix, ".pca_vals.txt", sep = "")
|
||||
write.table(pca_vals, file = pca_vals_file,
|
||||
row.names = FALSE, col.names = TRUE,
|
||||
sep = "\\t", quote = TRUE)
|
||||
|
||||
## SAMPLE CORRELATION HEATMAP
|
||||
sampleDists <- dist(t(assay(dds, vst_name)))
|
||||
sampleDistMatrix <- as.matrix(sampleDists)
|
||||
colors <- colorRampPalette(rev(brewer.pal(9, "Blues")))(255)
|
||||
pheatmap(
|
||||
sampleDistMatrix,
|
||||
clustering_distance_rows = sampleDists,
|
||||
clustering_distance_cols = sampleDists,
|
||||
col = colors,
|
||||
main = paste("Euclidean distance between", vst_name, "of samples")
|
||||
)
|
||||
|
||||
## WRITE SAMPLE DISTANCES TO FILE
|
||||
sample_dist_file <- paste(par\$outdir, "/", par\$outprefix, ".sample.dists.txt", sep = "")
|
||||
write.table(cbind(sample = rownames(sampleDistMatrix), sampleDistMatrix),
|
||||
file = sample_dist_file, row.names = FALSE,
|
||||
col.names = TRUE, sep = "\\t", quote = FALSE)
|
||||
dev.off()
|
||||
|
||||
# SAVE SIZE FACTORS
|
||||
SizeFactorsDir <- paste0(par\$outdir, "/size_factors/")
|
||||
if (file.exists(SizeFactorsDir) == FALSE) {
|
||||
dir.create(SizeFactorsDir, recursive = TRUE)
|
||||
}
|
||||
|
||||
NormFactorsFile <- paste(SizeFactorsDir, par\$outprefix, ".size_factors.RData", sep = "")
|
||||
|
||||
normFactors <- sizeFactors(dds)
|
||||
save(normFactors, file = NormFactorsFile)
|
||||
|
||||
for (name in names(sizeFactors(dds))) {
|
||||
sizeFactorFile <- paste(SizeFactorsDir, name, ".txt", sep = "")
|
||||
write(as.numeric(sizeFactors(dds)[name]), file = sizeFactorFile)
|
||||
}
|
||||
|
||||
# R SESSION INFO
|
||||
RLogFile <- "R_sessionInfo.log"
|
||||
|
||||
sink(RLogFile)
|
||||
a <- sessionInfo()
|
||||
print(a)
|
||||
sink()
|
||||
|
||||
# Prepare files for MultiQC
|
||||
|
||||
readLines(paste0(meta\$resources_dir, "/deseq2_pca_header.txt")) |>
|
||||
stringr::str_replace(pattern = "#id: 'deseq2_pca'",
|
||||
replace = paste0("#id: '", par\$label, "_deseq2_pca'")) |>
|
||||
writeLines(con = "tmp.txt")
|
||||
|
||||
readLines(paste0("tmp.txt")) |>
|
||||
stringr::str_replace(pattern = "#section_name: 'DESeq2 PCA plot'",
|
||||
replace = paste0("#section_name: 'DESeq2 PCA plot - '", par\$label)) |>
|
||||
writeLines(con = "tmp.txt")
|
||||
|
||||
system2("cat", args = paste0("tmp.txt ", pca_vals_file), stdout = par\$pca_multiqc)
|
||||
|
||||
readLines(paste0(meta\$resources_dir, "/deseq2_clustering_header.txt")) |>
|
||||
stringr::str_replace(pattern = "#id: 'deseq2_clustering'",
|
||||
replace = paste0("#id: '", par\$label, "_deseq2_clustering'")) |>
|
||||
writeLines(con = "tmp.txt")
|
||||
|
||||
readLines(paste0("tmp.txt")) |>
|
||||
stringr::str_replace(pattern = "#section_name: 'DESeq2 sample similarity'",
|
||||
replace = paste0("#section_name: 'DESeq2 sample similarity - '", par\$label)) |>
|
||||
writeLines(con = "tmp.txt")
|
||||
|
||||
system2("cat", args = paste0("tmp.txt ", sample_dist_file), stdout = par\$sample_dists_multiqc)
|
||||
VIASHMAIN
|
||||
bash "\$tempscript" &
|
||||
Rscript "\$tempscript" &
|
||||
wait "\$!"
|
||||
|
||||
VIASHEOF
|
||||
@@ -1269,20 +1469,14 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
|
||||
if [ ! -z "$VIASH_PAR_COUNTS" ]; then
|
||||
VIASH_PAR_COUNTS=$(ViashDockerStripAutomount "$VIASH_PAR_COUNTS")
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_PCA_HEADER_MULTIQC" ]; then
|
||||
VIASH_PAR_PCA_HEADER_MULTIQC=$(ViashDockerStripAutomount "$VIASH_PAR_PCA_HEADER_MULTIQC")
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_CLUSTERING_HEADER_MULTIQC" ]; then
|
||||
VIASH_PAR_CLUSTERING_HEADER_MULTIQC=$(ViashDockerStripAutomount "$VIASH_PAR_CLUSTERING_HEADER_MULTIQC")
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_DESEQ2_OUTPUT" ]; then
|
||||
VIASH_PAR_DESEQ2_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_DESEQ2_OUTPUT")
|
||||
if [ ! -z "$VIASH_PAR_OUTDIR" ]; then
|
||||
VIASH_PAR_OUTDIR=$(ViashDockerStripAutomount "$VIASH_PAR_OUTDIR")
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_PCA_MULTIQC" ]; then
|
||||
VIASH_PAR_PCA_MULTIQC=$(ViashDockerStripAutomount "$VIASH_PAR_PCA_MULTIQC")
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_DISTS_MULTIQC" ]; then
|
||||
VIASH_PAR_DISTS_MULTIQC=$(ViashDockerStripAutomount "$VIASH_PAR_DISTS_MULTIQC")
|
||||
if [ ! -z "$VIASH_PAR_SAMPLE_DISTS_MULTIQC" ]; then
|
||||
VIASH_PAR_SAMPLE_DISTS_MULTIQC=$(ViashDockerStripAutomount "$VIASH_PAR_SAMPLE_DISTS_MULTIQC")
|
||||
fi
|
||||
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
|
||||
VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR")
|
||||
@@ -1300,16 +1494,16 @@ fi
|
||||
|
||||
|
||||
# check whether required files exist
|
||||
if [ ! -z "$VIASH_PAR_DESEQ2_OUTPUT" ] && [ ! -e "$VIASH_PAR_DESEQ2_OUTPUT" ]; then
|
||||
ViashError "Output file '$VIASH_PAR_DESEQ2_OUTPUT' does not exist."
|
||||
if [ ! -z "$VIASH_PAR_OUTDIR" ] && [ ! -e "$VIASH_PAR_OUTDIR" ]; then
|
||||
ViashError "Output file '$VIASH_PAR_OUTDIR' does not exist."
|
||||
exit 1
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_PCA_MULTIQC" ] && [ ! -e "$VIASH_PAR_PCA_MULTIQC" ]; then
|
||||
ViashError "Output file '$VIASH_PAR_PCA_MULTIQC' does not exist."
|
||||
exit 1
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_DISTS_MULTIQC" ] && [ ! -e "$VIASH_PAR_DISTS_MULTIQC" ]; then
|
||||
ViashError "Output file '$VIASH_PAR_DISTS_MULTIQC' does not exist."
|
||||
if [ ! -z "$VIASH_PAR_SAMPLE_DISTS_MULTIQC" ] && [ ! -e "$VIASH_PAR_SAMPLE_DISTS_MULTIQC" ]; then
|
||||
ViashError "Output file '$VIASH_PAR_SAMPLE_DISTS_MULTIQC' does not exist."
|
||||
exit 1
|
||||
fi
|
||||
|
||||
|
||||
@@ -1,246 +0,0 @@
|
||||
#!/usr/bin/env Rscript
|
||||
|
||||
################################################
|
||||
################################################
|
||||
## REQUIREMENTS ##
|
||||
################################################
|
||||
################################################
|
||||
|
||||
## PCA, HEATMAP AND SCATTERPLOTS FOR SAMPLES IN COUNTS FILE
|
||||
## - SAMPLE NAMES HAVE TO END IN e.g. "_R1" REPRESENTING REPLICATE ID. LAST 3 CHARACTERS OF SAMPLE NAME WILL BE TRIMMED TO OBTAIN GROUP ID FOR DESEQ2 COMPARISONS.
|
||||
## - PACKAGES BELOW NEED TO BE AVAILABLE TO LOAD WHEN RUNNING R
|
||||
|
||||
################################################
|
||||
################################################
|
||||
## LOAD LIBRARIES ##
|
||||
################################################
|
||||
################################################
|
||||
|
||||
library(optparse)
|
||||
library(DESeq2)
|
||||
library(ggplot2)
|
||||
library(RColorBrewer)
|
||||
library(pheatmap)
|
||||
|
||||
################################################
|
||||
################################################
|
||||
## PARSE COMMAND-LINE PARAMETERS ##
|
||||
################################################
|
||||
################################################
|
||||
|
||||
option_list <- list(
|
||||
make_option(c("-i", "--count_file"), type="character", default=NULL, metavar="path", help="Count file matrix where rows are genes and columns are samples."),
|
||||
make_option(c("-f", "--count_col"), type="integer", default=3, metavar="integer", help="First column containing sample count data."),
|
||||
make_option(c("-d", "--id_col"), type="integer", default=1, metavar="integer", help="Column containing identifiers to be used."),
|
||||
make_option(c("-r", "--sample_suffix"), type="character", default='', metavar="string", help="Suffix to remove after sample name in columns e.g. '.rmDup.bam' if 'DRUG_R1.rmDup.bam'."),
|
||||
make_option(c("-p", "--outprefix"), type="character", default='deseq2', metavar="string" , help="Output prefix."),
|
||||
make_option(c("-v", "--vst"), type="logical", default=FALSE, metavar="boolean", help="Run vst transform instead of rlog."),
|
||||
make_option(c("-c", "--cores"), type="integer", default=1, metavar="integer", help="Number of cores."),
|
||||
make_option(c("-o", "--outdir"), type="character", default="./", metavar="path", help="Output directory.")
|
||||
)
|
||||
|
||||
opt_parser <- OptionParser(option_list=option_list)
|
||||
opt <- parse_args(opt_parser)
|
||||
if (is.null(opt$count_file)){
|
||||
print_help(opt_parser)
|
||||
stop("Please provide a counts file.", call.=FALSE)
|
||||
}
|
||||
|
||||
################################################
|
||||
################################################
|
||||
## READ IN COUNTS FILE ##
|
||||
################################################
|
||||
################################################
|
||||
|
||||
count.table <- read.delim(file=opt$count_file,header=TRUE, row.names=NULL)
|
||||
rownames(count.table) <- count.table[,opt$id_col]
|
||||
count.table <- count.table[,opt$count_col:ncol(count.table),drop=FALSE]
|
||||
colnames(count.table) <- gsub(opt$sample_suffix,"",colnames(count.table))
|
||||
colnames(count.table) <- gsub(pattern='\\.$', replacement='', colnames(count.table))
|
||||
|
||||
################################################
|
||||
################################################
|
||||
## RUN DESEQ2 ##
|
||||
################################################
|
||||
################################################
|
||||
|
||||
if (file.exists(opt$outdir) == FALSE) {
|
||||
dir.create(opt$outdir, recursive=TRUE)
|
||||
}
|
||||
setwd(opt$outdir)
|
||||
|
||||
samples.vec <- colnames(count.table)
|
||||
name_components <- strsplit(samples.vec, "_")
|
||||
n_components <- length(name_components[[1]])
|
||||
decompose <- n_components!=1 && all(sapply(name_components, length)==n_components)
|
||||
coldata <- data.frame(samples.vec, sample=samples.vec, row.names=1)
|
||||
if (decompose) {
|
||||
groupings <- as.data.frame(lapply(1:n_components, function(i) sapply(name_components, "[[", i)))
|
||||
n_distinct <- sapply(groupings, function(grp) length(unique(grp)))
|
||||
groupings <- groupings[n_distinct!=1 & n_distinct!=length(samples.vec)]
|
||||
if (ncol(groupings)!=0) {
|
||||
names(groupings) <- paste0("Group", 1:ncol(groupings))
|
||||
coldata <- cbind(coldata, groupings)
|
||||
} else {
|
||||
decompose <- FALSE
|
||||
}
|
||||
}
|
||||
|
||||
DDSFile <- paste(opt$outprefix,".dds.RData",sep="")
|
||||
|
||||
counts <- count.table[,samples.vec,drop=FALSE]
|
||||
dds <- DESeqDataSetFromMatrix(countData=round(counts), colData=coldata, design=~ 1)
|
||||
dds <- estimateSizeFactors(dds)
|
||||
if (min(dim(count.table))<=1) { # No point if only one sample, or one gene
|
||||
save(dds,file=DDSFile)
|
||||
saveRDS(dds, file=sub("\\.dds\\.RData$", ".rds", DDSFile))
|
||||
warning("Not enough samples or genes in counts file for PCA.", call.=FALSE)
|
||||
quit(save = "no", status = 0, runLast = FALSE)
|
||||
}
|
||||
if (!opt$vst) {
|
||||
vst_name <- "rlog"
|
||||
rld <- rlog(dds)
|
||||
} else {
|
||||
vst_name <- "vst"
|
||||
rld <- varianceStabilizingTransformation(dds)
|
||||
}
|
||||
|
||||
assay(dds, vst_name) <- assay(rld)
|
||||
save(dds,file=DDSFile)
|
||||
saveRDS(dds, file=sub("\\.dds\\.RData$", ".rds", DDSFile))
|
||||
|
||||
################################################
|
||||
################################################
|
||||
## PLOT QC ##
|
||||
################################################
|
||||
################################################
|
||||
|
||||
##' PCA pre-processeor
|
||||
##'
|
||||
##' Generate all the necessary information to plot PCA from a DESeq2 object
|
||||
##' in which an assay containing a variance-stabilised matrix of counts is
|
||||
##' stored. Copied from DESeq2::plotPCA, but with additional ability to
|
||||
##' say which assay to run the PCA on.
|
||||
##'
|
||||
##' @param object The DESeq2DataSet object.
|
||||
##' @param ntop number of top genes to use for principla components, selected by highest row variance.
|
||||
##' @param assay the name or index of the assay that stores the variance-stabilised data.
|
||||
##' @return A data.frame containing the projected data alongside the grouping columns.
|
||||
##' A 'percentVar' attribute is set which includes the percentage of variation each PC explains,
|
||||
##' and additionally how much the variation within that PC is explained by the grouping variable.
|
||||
##' @author Gavin Kelly
|
||||
plotPCA_vst <- function (object, ntop = 500, assay=length(assays(object))) {
|
||||
rv <- rowVars(assay(object, assay))
|
||||
select <- order(rv, decreasing = TRUE)[seq_len(min(ntop, length(rv)))]
|
||||
pca <- prcomp(t(assay(object, assay)[select, ]), center=TRUE, scale=FALSE)
|
||||
percentVar <- pca$sdev^2/sum(pca$sdev^2)
|
||||
df <- cbind( as.data.frame(colData(object)), pca$x)
|
||||
#Order points so extreme samples are more likely to get label
|
||||
ord <- order(abs(rank(df$PC1)-median(df$PC1)), abs(rank(df$PC2)-median(df$PC2)))
|
||||
df <- df[ord,]
|
||||
attr(df, "percentVar") <- data.frame(PC=seq(along=percentVar), percentVar=100*percentVar)
|
||||
return(df)
|
||||
}
|
||||
|
||||
PlotFile <- paste(opt$outprefix,".plots.pdf",sep="")
|
||||
|
||||
pdf(file=PlotFile, onefile=TRUE, width=7, height=7)
|
||||
## PCA
|
||||
ntop <- c(500, Inf)
|
||||
for (n_top_var in ntop) {
|
||||
pca.data <- plotPCA_vst(dds, assay=vst_name, ntop=n_top_var)
|
||||
percentVar <- round(attr(pca.data, "percentVar")$percentVar)
|
||||
plot_subtitle <- ifelse(n_top_var==Inf, "All genes", paste("Top", n_top_var, "genes"))
|
||||
pl <- ggplot(pca.data, aes(PC1, PC2, label=paste0(" ", sample, " "))) +
|
||||
geom_point() +
|
||||
geom_text(check_overlap=TRUE, vjust=0.5, hjust="inward") +
|
||||
xlab(paste0("PC1: ",percentVar[1],"% variance")) +
|
||||
ylab(paste0("PC2: ",percentVar[2],"% variance")) +
|
||||
labs(title = paste0("First PCs on ", vst_name, "-transformed data"), subtitle = plot_subtitle) +
|
||||
theme(legend.position="top",
|
||||
panel.grid.major = element_blank(),
|
||||
panel.grid.minor = element_blank(),
|
||||
panel.background = element_blank(),
|
||||
panel.border = element_rect(colour = "black", fill=NA, size=1))
|
||||
print(pl)
|
||||
|
||||
if (decompose) {
|
||||
pc_names <- paste0("PC", attr(pca.data, "percentVar")$PC)
|
||||
long_pc <- reshape(pca.data, varying=pc_names, direction="long", sep="", timevar="component", idvar="pcrow")
|
||||
long_pc <- subset(long_pc, component<=5)
|
||||
long_pc_grp <- reshape(long_pc, varying=names(groupings), direction="long", sep="", timevar="grouper")
|
||||
long_pc_grp <- subset(long_pc_grp, grouper<=5)
|
||||
long_pc_grp$component <- paste("PC", long_pc_grp$component)
|
||||
long_pc_grp$grouper <- paste0(long_pc_grp$grouper, c("st","nd","rd","th","th")[long_pc_grp$grouper], " prefix")
|
||||
pl <- ggplot(long_pc_grp, aes(x=Group, y=PC)) +
|
||||
geom_point() +
|
||||
stat_summary(fun=mean, geom="line", aes(group = 1)) +
|
||||
labs(x=NULL, y=NULL, subtitle = plot_subtitle, title="PCs split by sample-name prefixes") +
|
||||
facet_grid(component~grouper, scales="free_x") +
|
||||
scale_x_discrete(guide = guide_axis(n.dodge = 3))
|
||||
print(pl)
|
||||
}
|
||||
} # at end of loop, we'll be using the user-defined ntop if any, else all genes
|
||||
|
||||
## WRITE PC1 vs PC2 VALUES TO FILE
|
||||
pca.vals <- pca.data[,c("PC1","PC2")]
|
||||
colnames(pca.vals) <- paste0(colnames(pca.vals), ": ", percentVar[1:2], '% variance')
|
||||
pca.vals <- cbind(sample = rownames(pca.vals), pca.vals)
|
||||
write.table(pca.vals, file = paste(opt$outprefix, ".pca.vals.txt", sep=""),
|
||||
row.names = FALSE, col.names = TRUE, sep = "\t", quote = TRUE)
|
||||
|
||||
## SAMPLE CORRELATION HEATMAP
|
||||
sampleDists <- dist(t(assay(dds, vst_name)))
|
||||
sampleDistMatrix <- as.matrix(sampleDists)
|
||||
colors <- colorRampPalette( rev(brewer.pal(9, "Blues")) )(255)
|
||||
pheatmap(
|
||||
sampleDistMatrix,
|
||||
clustering_distance_rows=sampleDists,
|
||||
clustering_distance_cols=sampleDists,
|
||||
col=colors,
|
||||
main=paste("Euclidean distance between", vst_name, "of samples")
|
||||
)
|
||||
|
||||
## WRITE SAMPLE DISTANCES TO FILE
|
||||
write.table(cbind(sample = rownames(sampleDistMatrix), sampleDistMatrix),file=paste(opt$outprefix, ".sample.dists.txt", sep=""),
|
||||
row.names=FALSE, col.names=TRUE, sep="\t", quote=FALSE)
|
||||
dev.off()
|
||||
|
||||
################################################
|
||||
################################################
|
||||
## SAVE SIZE FACTORS ##
|
||||
################################################
|
||||
################################################
|
||||
|
||||
SizeFactorsDir <- "size_factors/"
|
||||
if (file.exists(SizeFactorsDir) == FALSE) {
|
||||
dir.create(SizeFactorsDir, recursive=TRUE)
|
||||
}
|
||||
|
||||
NormFactorsFile <- paste(SizeFactorsDir,opt$outprefix, ".size_factors.RData", sep="")
|
||||
|
||||
normFactors <- sizeFactors(dds)
|
||||
save(normFactors, file=NormFactorsFile)
|
||||
|
||||
for (name in names(sizeFactors(dds))) {
|
||||
sizeFactorFile <- paste(SizeFactorsDir,name, ".txt", sep="")
|
||||
write(as.numeric(sizeFactors(dds)[name]), file=sizeFactorFile)
|
||||
}
|
||||
|
||||
################################################
|
||||
################################################
|
||||
## R SESSION INFO ##
|
||||
################################################
|
||||
################################################
|
||||
|
||||
RLogFile <- "R_sessionInfo.log"
|
||||
|
||||
sink(RLogFile)
|
||||
a <- sessionInfo()
|
||||
print(a)
|
||||
sink()
|
||||
|
||||
################################################
|
||||
################################################
|
||||
################################################
|
||||
################################################
|
||||
@@ -169,7 +169,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -266,8 +266,8 @@ build_info:
|
||||
output: "target/executable/dupradar"
|
||||
executable: "target/executable/dupradar/dupradar"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -279,7 +279,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -520,9 +520,9 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.pa
|
||||
Rscript -e 'if (!requireNamespace("dupRadar", quietly = TRUE)) BiocManager::install("dupRadar")'
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component dupradar"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:09Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:29Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -105,7 +105,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -198,8 +198,8 @@ build_info:
|
||||
output: "target/executable/fastqc"
|
||||
executable: "target/executable/fastqc/fastqc"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -211,7 +211,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -490,9 +490,9 @@ RUN apt-get update && \
|
||||
rm -rf /var/lib/apt/lists/*
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component fastqc"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:05Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:25Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -78,7 +78,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -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: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -190,7 +190,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -485,9 +485,9 @@ cargo install --locked --path . && \
|
||||
mv /usr/local/fq/target/release/fq /usr/local/bin/
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component fq_subsample"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:07Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:27Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -71,7 +71,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -167,8 +167,8 @@ build_info:
|
||||
output: "target/executable/getchromsizes"
|
||||
executable: "target/executable/getchromsizes/getchromsizes"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -180,7 +180,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -480,9 +480,9 @@ make && \
|
||||
make install
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component getchromsizes"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:04Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:24Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -52,7 +52,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -145,8 +145,8 @@ build_info:
|
||||
output: "target/executable/gtf2bed"
|
||||
executable: "target/executable/gtf2bed/gtf2bed"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -158,7 +158,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -466,9 +466,9 @@ RUN apt-get update && \
|
||||
rm -rf /var/lib/apt/lists/*
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component gtf2bed"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:03Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:23Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -67,7 +67,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -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: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -168,7 +168,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -470,9 +470,9 @@ function ViashDockerfile {
|
||||
FROM python:latest
|
||||
ENTRYPOINT []
|
||||
LABEL org.opencontainers.image.description="Companion container for running component gtf_filter"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:09Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:29Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -51,7 +51,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -144,8 +144,8 @@ build_info:
|
||||
output: "target/executable/gunzip"
|
||||
executable: "target/executable/gunzip/gunzip"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -157,7 +157,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -466,9 +466,9 @@ RUN apt-get update && \
|
||||
rm -rf /var/lib/apt/lists/*
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component gunzip"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:07Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:27Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -60,7 +60,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -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: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -168,7 +168,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -471,9 +471,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \
|
||||
mv kallisto/kallisto /usr/local/bin/
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_index"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:10Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:30Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -158,7 +158,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -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: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -266,7 +266,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -515,9 +515,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \
|
||||
mv kallisto/kallisto /usr/local/bin/
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_quant"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:10Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:30Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -23,13 +23,12 @@ argument_groups:
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--biotypes_header"
|
||||
- type: "string"
|
||||
name: "--features"
|
||||
description: "Features to count"
|
||||
info: null
|
||||
default:
|
||||
- "assets/multiqc/biotypes_header.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
- "rRNA"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
@@ -59,14 +58,11 @@ argument_groups:
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
resources:
|
||||
- type: "bash_script"
|
||||
path: "script.sh"
|
||||
- type: "python_script"
|
||||
path: "script.py"
|
||||
is_executable: true
|
||||
- type: "file"
|
||||
path: "mqc_features_stat.py"
|
||||
- type: "file"
|
||||
path: "assets/multiqc/biotypes_header.txt"
|
||||
dest: "assets/multiqc/biotypes_header.txt"
|
||||
path: "biotypes_header.txt"
|
||||
description: "Calculate features percentage for biotype counts"
|
||||
info: null
|
||||
status: "enabled"
|
||||
@@ -77,7 +73,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -150,18 +146,10 @@ runners:
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "ubuntu:22.04"
|
||||
image: "python:latest"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "bugfix"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "apt"
|
||||
packages:
|
||||
- "pip"
|
||||
interactive: false
|
||||
- type: "python"
|
||||
user: false
|
||||
upgrade: true
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
@@ -173,8 +161,8 @@ build_info:
|
||||
output: "target/executable/multiqc_custom_biotype"
|
||||
executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -186,7 +174,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -1,89 +0,0 @@
|
||||
#!/usr/bin/env python3
|
||||
|
||||
import argparse
|
||||
import logging
|
||||
import os
|
||||
|
||||
# Create a logger
|
||||
logging.basicConfig(format="%(name)s - %(asctime)s %(levelname)s: %(message)s")
|
||||
logger = logging.getLogger(__file__)
|
||||
logger.setLevel(logging.INFO)
|
||||
|
||||
mqc_main = """#id: 'biotype-gs'
|
||||
#plot_type: 'generalstats'
|
||||
#pconfig:"""
|
||||
|
||||
mqc_pconf = """# percent_{ft}:
|
||||
# title: '% {ft}'
|
||||
# namespace: 'Biotype Counts'
|
||||
# description: '% reads overlapping {ft} features'
|
||||
# max: 100
|
||||
# min: 0
|
||||
# scale: 'RdYlGn-rev'
|
||||
# format: '{{:.2f}}%'"""
|
||||
|
||||
|
||||
def mqc_feature_stat(bfile, features, outfile, sname=None):
|
||||
# If sample name not given use file name
|
||||
if not sname:
|
||||
sname = os.path.splitext(os.path.basename(bfile))[0]
|
||||
|
||||
# Try to parse and read biocount file
|
||||
fcounts = {}
|
||||
try:
|
||||
with open(bfile, "r") as bfl:
|
||||
for ln in bfl:
|
||||
if ln.startswith("#"):
|
||||
continue
|
||||
ft, cn = ln.strip().split("\t")
|
||||
fcounts[ft] = float(cn)
|
||||
except:
|
||||
logger.error("Trouble reading the biocount file {}".format(bfile))
|
||||
return
|
||||
|
||||
total_count = sum(fcounts.values())
|
||||
if total_count == 0:
|
||||
logger.error("No biocounts found, exiting")
|
||||
return
|
||||
|
||||
# Calculate percentage for each requested feature
|
||||
fpercent = {f: (fcounts[f] / total_count) * 100 if f in fcounts else 0 for f in features}
|
||||
if len(fpercent) == 0:
|
||||
logger.error("Any of given features '{}' not found in the biocount file".format(", ".join(features), bfile))
|
||||
return
|
||||
|
||||
# Prepare the output strings
|
||||
out_head, out_value, out_mqc = ("Sample", "'{}'".format(sname), mqc_main)
|
||||
for ft, pt in fpercent.items():
|
||||
out_head = "{}\tpercent_{}".format(out_head, ft)
|
||||
out_value = "{}\t{}".format(out_value, pt)
|
||||
out_mqc = "{}\n{}".format(out_mqc, mqc_pconf.format(ft=ft))
|
||||
|
||||
# Write the output to a file
|
||||
with open(outfile, "w") as ofl:
|
||||
out_final = "\n".join([out_mqc, out_head, out_value]).strip()
|
||||
ofl.write(out_final + "\n")
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
parser = argparse.ArgumentParser(description="""Calculate features percentage for biotype counts""")
|
||||
parser.add_argument("biocount", type=str, help="File with all biocounts")
|
||||
parser.add_argument(
|
||||
"-f",
|
||||
"--features",
|
||||
dest="features",
|
||||
required=True,
|
||||
nargs="+",
|
||||
help="Features to count",
|
||||
)
|
||||
parser.add_argument("-s", "--sample", dest="sample", type=str, help="Sample Name")
|
||||
parser.add_argument(
|
||||
"-o",
|
||||
"--output",
|
||||
dest="output",
|
||||
default="biocount_percent.tsv",
|
||||
type=str,
|
||||
help="Sample Name",
|
||||
)
|
||||
args = parser.parse_args()
|
||||
mqc_feature_stat(args.biocount, args.features, args.output, args.sample)
|
||||
@@ -185,9 +185,10 @@ function ViashHelp {
|
||||
echo " default: \$id"
|
||||
echo " Sample name"
|
||||
echo ""
|
||||
echo " --biotypes_header"
|
||||
echo " type: file, file must exist"
|
||||
echo " default: assets/multiqc/biotypes_header.txt"
|
||||
echo " --features"
|
||||
echo " type: string"
|
||||
echo " default: rRNA"
|
||||
echo " Features to count"
|
||||
echo ""
|
||||
echo "Output:"
|
||||
echo " --featurecounts_multiqc"
|
||||
@@ -472,18 +473,12 @@ function ViashDockerfile {
|
||||
|
||||
if [[ "$engine_id" == "docker" ]]; then
|
||||
cat << 'VIASHDOCKER'
|
||||
FROM ubuntu:22.04
|
||||
FROM python:latest
|
||||
ENTRYPOINT []
|
||||
RUN apt-get update && \
|
||||
DEBIAN_FRONTEND=noninteractive apt-get install -y pip && \
|
||||
rm -rf /var/lib/apt/lists/*
|
||||
|
||||
RUN pip install --upgrade pip
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component multiqc_custom_biotype"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:08Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:28Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
@@ -645,15 +640,15 @@ while [[ $# -gt 0 ]]; do
|
||||
VIASH_PAR_ID=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--biotypes_header)
|
||||
[ -n "$VIASH_PAR_BIOTYPES_HEADER" ] && ViashError Bad arguments for option \'--biotypes_header\': \'$VIASH_PAR_BIOTYPES_HEADER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_BIOTYPES_HEADER="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --biotypes_header. Use "--help" to get more information on the parameters. && exit 1
|
||||
--features)
|
||||
[ -n "$VIASH_PAR_FEATURES" ] && ViashError Bad arguments for option \'--features\': \'$VIASH_PAR_FEATURES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_FEATURES="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --features. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--biotypes_header=*)
|
||||
[ -n "$VIASH_PAR_BIOTYPES_HEADER" ] && ViashError Bad arguments for option \'--biotypes_header=*\': \'$VIASH_PAR_BIOTYPES_HEADER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_BIOTYPES_HEADER=$(ViashRemoveFlags "$1")
|
||||
--features=*)
|
||||
[ -n "$VIASH_PAR_FEATURES" ] && ViashError Bad arguments for option \'--features=*\': \'$VIASH_PAR_FEATURES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_FEATURES=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--featurecounts_multiqc)
|
||||
@@ -879,8 +874,8 @@ fi
|
||||
if [ -z ${VIASH_PAR_ID+x} ]; then
|
||||
VIASH_PAR_ID="\$id"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_BIOTYPES_HEADER+x} ]; then
|
||||
VIASH_PAR_BIOTYPES_HEADER="assets/multiqc/biotypes_header.txt"
|
||||
if [ -z ${VIASH_PAR_FEATURES+x} ]; then
|
||||
VIASH_PAR_FEATURES="rRNA"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_FEATURECOUNTS_MULTIQC+x} ]; then
|
||||
VIASH_PAR_FEATURECOUNTS_MULTIQC="\$id.biotype_counts_mqc.tsv"
|
||||
@@ -894,10 +889,6 @@ if [ ! -z "$VIASH_PAR_BIOCOUNTS" ] && [ ! -e "$VIASH_PAR_BIOCOUNTS" ]; then
|
||||
ViashError "Input file '$VIASH_PAR_BIOCOUNTS' does not exist."
|
||||
exit 1
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_BIOTYPES_HEADER" ] && [ ! -e "$VIASH_PAR_BIOTYPES_HEADER" ]; then
|
||||
ViashError "Input file '$VIASH_PAR_BIOTYPES_HEADER' does not exist."
|
||||
exit 1
|
||||
fi
|
||||
|
||||
# check whether parameters values are of the right type
|
||||
if [[ -n "$VIASH_META_CPUS" ]]; then
|
||||
@@ -997,10 +988,6 @@ if [ ! -z "$VIASH_PAR_BIOCOUNTS" ]; then
|
||||
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_BIOCOUNTS")" )
|
||||
VIASH_PAR_BIOCOUNTS=$(ViashDockerAutodetectMount "$VIASH_PAR_BIOCOUNTS")
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_BIOTYPES_HEADER" ]; then
|
||||
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_BIOTYPES_HEADER")" )
|
||||
VIASH_PAR_BIOTYPES_HEADER=$(ViashDockerAutodetectMount "$VIASH_PAR_BIOTYPES_HEADER")
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_FEATURECOUNTS_MULTIQC" ]; then
|
||||
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_FEATURECOUNTS_MULTIQC")" )
|
||||
VIASH_PAR_FEATURECOUNTS_MULTIQC=$(ViashDockerAutodetectMount "$VIASH_PAR_FEATURECOUNTS_MULTIQC")
|
||||
@@ -1067,7 +1054,7 @@ fi
|
||||
ViashDebug "Running command: $(echo $VIASH_CMD)"
|
||||
cat << VIASHEOF | eval $VIASH_CMD
|
||||
set -e
|
||||
tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-multiqc_custom_biotype-XXXXXX").sh
|
||||
tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-multiqc_custom_biotype-XXXXXX").py
|
||||
function clean_up {
|
||||
rm "\$tempscript"
|
||||
}
|
||||
@@ -1080,44 +1067,131 @@ trap interrupt INT SIGINT
|
||||
cat > "\$tempscript" << 'VIASHMAIN'
|
||||
## VIASH START
|
||||
# The following code has been auto-generated by Viash.
|
||||
$( if [ ! -z ${VIASH_PAR_BIOCOUNTS+x} ]; then echo "${VIASH_PAR_BIOCOUNTS}" | sed "s#'#'\"'\"'#g;s#.*#par_biocounts='&'#" ; else echo "# par_biocounts="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_ID+x} ]; then echo "${VIASH_PAR_ID}" | sed "s#'#'\"'\"'#g;s#.*#par_id='&'#" ; else echo "# par_id="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_BIOTYPES_HEADER+x} ]; then echo "${VIASH_PAR_BIOTYPES_HEADER}" | sed "s#'#'\"'\"'#g;s#.*#par_biotypes_header='&'#" ; else echo "# par_biotypes_header="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_FEATURECOUNTS_MULTIQC+x} ]; then echo "${VIASH_PAR_FEATURECOUNTS_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_featurecounts_multiqc='&'#" ; else echo "# par_featurecounts_multiqc="; fi )
|
||||
$( if [ ! -z ${VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC+x} ]; then echo "${VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_featurecounts_rrna_multiqc='&'#" ; else echo "# par_featurecounts_rrna_multiqc="; fi )
|
||||
$( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
|
||||
$( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi )
|
||||
$( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi )
|
||||
$( if [ ! -z ${VIASH_META_EXECUTABLE+x} ]; then echo "${VIASH_META_EXECUTABLE}" | sed "s#'#'\"'\"'#g;s#.*#meta_executable='&'#" ; else echo "# meta_executable="; fi )
|
||||
$( if [ ! -z ${VIASH_META_CONFIG+x} ]; then echo "${VIASH_META_CONFIG}" | sed "s#'#'\"'\"'#g;s#.*#meta_config='&'#" ; else echo "# meta_config="; fi )
|
||||
$( if [ ! -z ${VIASH_META_TEMP_DIR+x} ]; then echo "${VIASH_META_TEMP_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_temp_dir='&'#" ; else echo "# meta_temp_dir="; fi )
|
||||
$( if [ ! -z ${VIASH_META_CPUS+x} ]; then echo "${VIASH_META_CPUS}" | sed "s#'#'\"'\"'#g;s#.*#meta_cpus='&'#" ; else echo "# meta_cpus="; fi )
|
||||
$( if [ ! -z ${VIASH_META_MEMORY_B+x} ]; then echo "${VIASH_META_MEMORY_B}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_b='&'#" ; else echo "# meta_memory_b="; fi )
|
||||
$( if [ ! -z ${VIASH_META_MEMORY_KB+x} ]; then echo "${VIASH_META_MEMORY_KB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_kb='&'#" ; else echo "# meta_memory_kb="; fi )
|
||||
$( if [ ! -z ${VIASH_META_MEMORY_MB+x} ]; then echo "${VIASH_META_MEMORY_MB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_mb='&'#" ; else echo "# meta_memory_mb="; fi )
|
||||
$( if [ ! -z ${VIASH_META_MEMORY_GB+x} ]; then echo "${VIASH_META_MEMORY_GB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_gb='&'#" ; else echo "# meta_memory_gb="; fi )
|
||||
$( if [ ! -z ${VIASH_META_MEMORY_TB+x} ]; then echo "${VIASH_META_MEMORY_TB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_tb='&'#" ; else echo "# meta_memory_tb="; fi )
|
||||
$( if [ ! -z ${VIASH_META_MEMORY_PB+x} ]; then echo "${VIASH_META_MEMORY_PB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pb='&'#" ; else echo "# meta_memory_pb="; fi )
|
||||
$( if [ ! -z ${VIASH_META_MEMORY_KIB+x} ]; then echo "${VIASH_META_MEMORY_KIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_kib='&'#" ; else echo "# meta_memory_kib="; fi )
|
||||
$( if [ ! -z ${VIASH_META_MEMORY_MIB+x} ]; then echo "${VIASH_META_MEMORY_MIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_mib='&'#" ; else echo "# meta_memory_mib="; fi )
|
||||
$( if [ ! -z ${VIASH_META_MEMORY_GIB+x} ]; then echo "${VIASH_META_MEMORY_GIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_gib='&'#" ; else echo "# meta_memory_gib="; fi )
|
||||
$( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "${VIASH_META_MEMORY_TIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_tib='&'#" ; else echo "# meta_memory_tib="; fi )
|
||||
$( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pib='&'#" ; else echo "# meta_memory_pib="; fi )
|
||||
par = {
|
||||
'biocounts': $( if [ ! -z ${VIASH_PAR_BIOCOUNTS+x} ]; then echo "r'${VIASH_PAR_BIOCOUNTS//\'/\'\"\'\"r\'}'"; else echo None; fi ),
|
||||
'id': $( if [ ! -z ${VIASH_PAR_ID+x} ]; then echo "r'${VIASH_PAR_ID//\'/\'\"\'\"r\'}'"; else echo None; fi ),
|
||||
'features': $( if [ ! -z ${VIASH_PAR_FEATURES+x} ]; then echo "r'${VIASH_PAR_FEATURES//\'/\'\"\'\"r\'}'"; else echo None; fi ),
|
||||
'featurecounts_multiqc': $( if [ ! -z ${VIASH_PAR_FEATURECOUNTS_MULTIQC+x} ]; then echo "r'${VIASH_PAR_FEATURECOUNTS_MULTIQC//\'/\'\"\'\"r\'}'"; else echo None; fi ),
|
||||
'featurecounts_rrna_multiqc': $( if [ ! -z ${VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC+x} ]; then echo "r'${VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC//\'/\'\"\'\"r\'}'"; else echo None; fi )
|
||||
}
|
||||
meta = {
|
||||
'name': $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "r'${VIASH_META_NAME//\'/\'\"\'\"r\'}'"; else echo None; fi ),
|
||||
'functionality_name': $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "r'${VIASH_META_FUNCTIONALITY_NAME//\'/\'\"\'\"r\'}'"; else echo None; fi ),
|
||||
'resources_dir': $( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "r'${VIASH_META_RESOURCES_DIR//\'/\'\"\'\"r\'}'"; else echo None; fi ),
|
||||
'executable': $( if [ ! -z ${VIASH_META_EXECUTABLE+x} ]; then echo "r'${VIASH_META_EXECUTABLE//\'/\'\"\'\"r\'}'"; else echo None; fi ),
|
||||
'config': $( if [ ! -z ${VIASH_META_CONFIG+x} ]; then echo "r'${VIASH_META_CONFIG//\'/\'\"\'\"r\'}'"; else echo None; fi ),
|
||||
'temp_dir': $( if [ ! -z ${VIASH_META_TEMP_DIR+x} ]; then echo "r'${VIASH_META_TEMP_DIR//\'/\'\"\'\"r\'}'"; else echo None; fi ),
|
||||
'cpus': $( if [ ! -z ${VIASH_META_CPUS+x} ]; then echo "int(r'${VIASH_META_CPUS//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
||||
'memory_b': $( if [ ! -z ${VIASH_META_MEMORY_B+x} ]; then echo "int(r'${VIASH_META_MEMORY_B//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
||||
'memory_kb': $( if [ ! -z ${VIASH_META_MEMORY_KB+x} ]; then echo "int(r'${VIASH_META_MEMORY_KB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
||||
'memory_mb': $( if [ ! -z ${VIASH_META_MEMORY_MB+x} ]; then echo "int(r'${VIASH_META_MEMORY_MB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
||||
'memory_gb': $( if [ ! -z ${VIASH_META_MEMORY_GB+x} ]; then echo "int(r'${VIASH_META_MEMORY_GB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
||||
'memory_tb': $( if [ ! -z ${VIASH_META_MEMORY_TB+x} ]; then echo "int(r'${VIASH_META_MEMORY_TB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
||||
'memory_pb': $( if [ ! -z ${VIASH_META_MEMORY_PB+x} ]; then echo "int(r'${VIASH_META_MEMORY_PB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
||||
'memory_kib': $( if [ ! -z ${VIASH_META_MEMORY_KIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_KIB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
||||
'memory_mib': $( if [ ! -z ${VIASH_META_MEMORY_MIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_MIB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
||||
'memory_gib': $( if [ ! -z ${VIASH_META_MEMORY_GIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_GIB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
||||
'memory_tib': $( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_TIB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
|
||||
'memory_pib': $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_PIB//\'/\'\"\'\"r\'}')"; else echo None; fi )
|
||||
}
|
||||
dep = {
|
||||
|
||||
}
|
||||
|
||||
## VIASH END
|
||||
#!/bin/bash
|
||||
#!/usr/bin/env python3
|
||||
|
||||
set -eo pipefail
|
||||
import argparse
|
||||
import logging
|
||||
import os
|
||||
|
||||
cut -f 1,7 \$par_biocounts | tail -n +3 | cat \$par_biotypes_header - >> \$par_featurecounts_multiqc
|
||||
# Create a logger
|
||||
logging.basicConfig(format="%(name)s - %(asctime)s %(levelname)s: %(message)s")
|
||||
logger = logging.getLogger(__file__)
|
||||
logger.setLevel(logging.INFO)
|
||||
|
||||
python3 "\$meta_resources_dir/mqc_features_stat.py" \\
|
||||
\$par_featurecounts_multiqc \\
|
||||
-s \$par_id \\
|
||||
-f rRNA \\
|
||||
-o \$par_featurecounts_rrna_multiqc
|
||||
mqc_main = """#id: 'biotype-gs'
|
||||
#plot_type: 'generalstats'
|
||||
#pconfig:"""
|
||||
|
||||
mqc_pconf = """# percent_{ft}:
|
||||
# title: '% {ft}'
|
||||
# namespace: 'Biotype Counts'
|
||||
# description: '% reads overlapping {ft} features'
|
||||
# max: 100
|
||||
# min: 0
|
||||
# scale: 'RdYlGn-rev'
|
||||
# format: '{{:.2f}}%'"""
|
||||
|
||||
|
||||
def mqc_feature_stat(bfile, features, outfile, sname=None):
|
||||
# If sample name not given use file name
|
||||
if not sname:
|
||||
sname = os.path.splitext(os.path.basename(bfile))[0]
|
||||
|
||||
# Try to parse and read biocount file
|
||||
fcounts = {}
|
||||
try:
|
||||
with open(bfile, "r") as bfl:
|
||||
for ln in bfl:
|
||||
if ln.startswith("#"):
|
||||
continue
|
||||
ft, cn = ln.strip().split("\\t")
|
||||
fcounts[ft] = float(cn)
|
||||
except:
|
||||
logger.error("Trouble reading the biocount file {}".format(bfile))
|
||||
return
|
||||
|
||||
total_count = sum(fcounts.values())
|
||||
if total_count == 0:
|
||||
logger.error("No biocounts found, exiting")
|
||||
return
|
||||
|
||||
# Calculate percentage for each requested feature
|
||||
fpercent = {f: (fcounts[f] / total_count) * 100 if f in fcounts else 0 for f in features}
|
||||
if len(fpercent) == 0:
|
||||
logger.error("Any of given features '{}' not found in the biocount file".format(", ".join(features), bfile))
|
||||
return
|
||||
|
||||
# Prepare the output strings
|
||||
out_head, out_value, out_mqc = ("Sample", "'{}'".format(sname), mqc_main)
|
||||
for ft, pt in fpercent.items():
|
||||
out_head = "{}\\tpercent_{}".format(out_head, ft)
|
||||
out_value = "{}\\t{}".format(out_value, pt)
|
||||
out_mqc = "{}\\n{}".format(out_mqc, mqc_pconf.format(ft=ft))
|
||||
|
||||
# Write the output to a file
|
||||
with open(outfile, "w") as ofl:
|
||||
out_final = "\\n".join([out_mqc, out_head, out_value]).strip()
|
||||
ofl.write(out_final + "\\n")
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
|
||||
# Read the biotypes_header.txt file
|
||||
biotypes_header_path = os.path.join(meta["resources_dir"], 'biotypes_header.txt')
|
||||
with open(biotypes_header_path, 'r') as header_file:
|
||||
biotypes_header = header_file.read()
|
||||
|
||||
# Extract specific columns (1 and 7) and skip the first two lines
|
||||
filtered_lines = []
|
||||
with open(par["biocounts"], 'r') as biocounts_file:
|
||||
for i, line in enumerate(biocounts_file):
|
||||
if i >= 2: # Skipping first two lines
|
||||
columns = line.strip().split('\\t')
|
||||
filtered_line = f"{columns[0]}\\t{columns[6]}" # Columns 1 and 7 (0-indexed)
|
||||
filtered_lines.append(filtered_line)
|
||||
|
||||
# Concatenate the header and the processed lines
|
||||
result = biotypes_header + '\\n' + '\\n'.join(filtered_lines) + '\\n'
|
||||
|
||||
# Write the result to par_featurecounts_multiqc
|
||||
with open(par["featurecounts_multiqc"], 'w') as output_file:
|
||||
output_file.write(result)
|
||||
|
||||
mqc_feature_stat(par["featurecounts_multiqc"], par["features"], par["featurecounts_rrna_multiqc"], par["id"])
|
||||
VIASHMAIN
|
||||
bash "\$tempscript" &
|
||||
python -B "\$tempscript" &
|
||||
wait "\$!"
|
||||
|
||||
VIASHEOF
|
||||
@@ -1129,9 +1203,6 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
|
||||
if [ ! -z "$VIASH_PAR_BIOCOUNTS" ]; then
|
||||
VIASH_PAR_BIOCOUNTS=$(ViashDockerStripAutomount "$VIASH_PAR_BIOCOUNTS")
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_BIOTYPES_HEADER" ]; then
|
||||
VIASH_PAR_BIOTYPES_HEADER=$(ViashDockerStripAutomount "$VIASH_PAR_BIOTYPES_HEADER")
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_FEATURECOUNTS_MULTIQC" ]; then
|
||||
VIASH_PAR_FEATURECOUNTS_MULTIQC=$(ViashDockerStripAutomount "$VIASH_PAR_FEATURECOUNTS_MULTIQC")
|
||||
fi
|
||||
|
||||
@@ -111,7 +111,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -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: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -220,7 +220,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -494,9 +494,9 @@ wget --no-check-certificate https://github.com/broadinstitute/picard/releases/do
|
||||
mv picard.jar /usr/local/bin
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component picard_markduplicates"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:05Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:25Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -321,7 +321,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -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: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -422,7 +422,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -557,9 +557,9 @@ function ViashDockerfile {
|
||||
FROM ubuntu:22.04
|
||||
ENTRYPOINT []
|
||||
LABEL org.opencontainers.image.description="Companion container for running component prepare_multiqc_input"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:03Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:23Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -50,7 +50,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -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: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -151,7 +151,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -462,9 +462,9 @@ function ViashDockerfile {
|
||||
FROM ubuntu:22.04
|
||||
ENTRYPOINT []
|
||||
LABEL org.opencontainers.image.description="Companion container for running component preprocess_transcripts_fasta"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:05Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:25Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -71,7 +71,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -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: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -204,7 +204,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -495,9 +495,9 @@ mkdir build && cd build && \
|
||||
make && make install && make HAVE_HTSLIB=1 all
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component preseq_lcextrap"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:06Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:26Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -162,7 +162,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -271,8 +271,8 @@ build_info:
|
||||
output: "target/executable/qualimap"
|
||||
executable: "target/executable/qualimap/qualimap"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -284,7 +284,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -537,9 +537,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
|
||||
Rscript -e 'remotes::install_cran(c("optparse"), repos = "https://cran.rstudio.com")'
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component qualimap"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:08Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:28Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -176,7 +176,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -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: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -312,7 +312,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -542,9 +542,9 @@ echo 'export PATH=$PATH:/usr/local/bin' >> ~/.bashrc && \
|
||||
/bin/bash -c "source /etc/profile && source ~/.bashrc && echo $PATH && which STAR"
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_calculate_expression"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:04Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:24Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -94,7 +94,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -182,8 +182,8 @@ build_info:
|
||||
output: "target/executable/rsem/rsem_merge_counts"
|
||||
executable: "target/executable/rsem/rsem_merge_counts/rsem_merge_counts"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -195,7 +195,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -483,9 +483,9 @@ function ViashDockerfile {
|
||||
FROM ubuntu:22.04
|
||||
ENTRYPOINT []
|
||||
LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_merge_counts"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:04Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:24Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -65,7 +65,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -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: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -176,7 +176,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -477,9 +477,9 @@ RUN pip install --upgrade pip && \
|
||||
pip install --upgrade --no-cache-dir "RSeQC"
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_bamstat"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:08Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:28Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -88,7 +88,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -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: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -199,7 +199,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -487,9 +487,9 @@ RUN pip install --upgrade pip && \
|
||||
pip install --upgrade --no-cache-dir "RSeQC"
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_inferexperiment"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:07Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:27Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -173,7 +173,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -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: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -285,7 +285,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -529,9 +529,9 @@ RUN pip install --upgrade pip && \
|
||||
pip install --upgrade --no-cache-dir "RSeQC"
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_innerdistance"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:07Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:27Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -161,7 +161,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -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: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -273,7 +273,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -519,9 +519,9 @@ RUN pip install --upgrade pip && \
|
||||
pip install --upgrade --no-cache-dir "RSeQC"
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionannotation"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:08Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:28Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -150,7 +150,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -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: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -262,7 +262,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -522,9 +522,9 @@ RUN pip install --upgrade pip && \
|
||||
pip install --upgrade --no-cache-dir "RSeQC"
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionsaturation"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:09Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:29Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -64,7 +64,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -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: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -175,7 +175,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -474,9 +474,9 @@ RUN pip install --upgrade pip && \
|
||||
pip install --upgrade --no-cache-dir "RSeQC"
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readdistribution"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:06Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:26Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -112,7 +112,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -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: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -224,7 +224,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -499,9 +499,9 @@ RUN pip install --upgrade pip && \
|
||||
pip install --upgrade --no-cache-dir "RSeQC"
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readduplication"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:08Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:28Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -118,7 +118,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -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: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -227,7 +227,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -501,9 +501,9 @@ RUN apt-get update && \
|
||||
RUN pip3 install RSeQC
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_tin"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:07Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:27Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -30,7 +30,7 @@ argument_groups:
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple: true
|
||||
multiple_sep: ";"
|
||||
- name: "Output"
|
||||
arguments:
|
||||
@@ -51,7 +51,7 @@ argument_groups:
|
||||
description: "Output file for read 1."
|
||||
info: null
|
||||
default:
|
||||
- "$id.$key.read_1.fastq"
|
||||
- "$id.$key.read_1.fastq.gz"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: true
|
||||
@@ -63,7 +63,7 @@ argument_groups:
|
||||
description: "Output file for read 2."
|
||||
info: null
|
||||
default:
|
||||
- "$id.$key.read_2.fastq"
|
||||
- "$id.$key.read_2.fastq.gz"
|
||||
must_exist: false
|
||||
create_parent: true
|
||||
required: false
|
||||
@@ -104,7 +104,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -177,16 +177,10 @@ runners:
|
||||
engines:
|
||||
- type: "docker"
|
||||
id: "docker"
|
||||
image: "ubuntu:22.04"
|
||||
image: "quay.io/biocontainers/sortmerna:4.3.6--h9ee0642_0"
|
||||
target_registry: "images.viash-hub.com"
|
||||
target_tag: "bugfix"
|
||||
namespace_separator: "/"
|
||||
setup:
|
||||
- type: "docker"
|
||||
run:
|
||||
- "apt-get update && \\\napt-get install -y --no-install-recommends cmake g++\
|
||||
\ wget && \\\napt-get clean && \\\nwget --no-check-certificate https://github.com/sortmerna/sortmerna/releases/download/v4.3.6/sortmerna-4.3.6-Linux.sh\
|
||||
\ && \\\nbash sortmerna-4.3.6-Linux.sh --skip-license\n"
|
||||
entrypoint: []
|
||||
cmd: null
|
||||
- type: "native"
|
||||
@@ -198,8 +192,8 @@ build_info:
|
||||
output: "target/executable/sortmerna"
|
||||
executable: "target/executable/sortmerna/sortmerna"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -211,7 +205,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -189,7 +189,7 @@ function ViashHelp {
|
||||
echo " Input fastq"
|
||||
echo ""
|
||||
echo " --ribo_database_manifest"
|
||||
echo " type: file, file must exist"
|
||||
echo " type: file, multiple values allowed, file must exist"
|
||||
echo " Text file containing paths to fasta files (one per line) that will be"
|
||||
echo " used to create the database for SortMeRNA."
|
||||
echo ""
|
||||
@@ -201,12 +201,12 @@ function ViashHelp {
|
||||
echo ""
|
||||
echo " --fastq_1"
|
||||
echo " type: file, required parameter, output, file must exist"
|
||||
echo " default: \$id.\$key.read_1.fastq"
|
||||
echo " default: \$id.\$key.read_1.fastq.gz"
|
||||
echo " Output file for read 1."
|
||||
echo ""
|
||||
echo " --fastq_2"
|
||||
echo " type: file, output"
|
||||
echo " default: \$id.\$key.read_2.fastq"
|
||||
echo " default: \$id.\$key.read_2.fastq.gz"
|
||||
echo " Output file for read 2."
|
||||
}
|
||||
|
||||
@@ -483,18 +483,12 @@ function ViashDockerfile {
|
||||
|
||||
if [[ "$engine_id" == "docker" ]]; then
|
||||
cat << 'VIASHDOCKER'
|
||||
FROM ubuntu:22.04
|
||||
FROM quay.io/biocontainers/sortmerna:4.3.6--h9ee0642_0
|
||||
ENTRYPOINT []
|
||||
RUN apt-get update && \
|
||||
apt-get install -y --no-install-recommends cmake g++ wget && \
|
||||
apt-get clean && \
|
||||
wget --no-check-certificate https://github.com/sortmerna/sortmerna/releases/download/v4.3.6/sortmerna-4.3.6-Linux.sh && \
|
||||
bash sortmerna-4.3.6-Linux.sh --skip-license
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component sortmerna"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:06Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:26Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
@@ -663,14 +657,20 @@ while [[ $# -gt 0 ]]; do
|
||||
shift 1
|
||||
;;
|
||||
--ribo_database_manifest)
|
||||
[ -n "$VIASH_PAR_RIBO_DATABASE_MANIFEST" ] && ViashError Bad arguments for option \'--ribo_database_manifest\': \'$VIASH_PAR_RIBO_DATABASE_MANIFEST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_RIBO_DATABASE_MANIFEST="$2"
|
||||
if [ -z "$VIASH_PAR_RIBO_DATABASE_MANIFEST" ]; then
|
||||
VIASH_PAR_RIBO_DATABASE_MANIFEST="$2"
|
||||
else
|
||||
VIASH_PAR_RIBO_DATABASE_MANIFEST="$VIASH_PAR_RIBO_DATABASE_MANIFEST;""$2"
|
||||
fi
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --ribo_database_manifest. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--ribo_database_manifest=*)
|
||||
[ -n "$VIASH_PAR_RIBO_DATABASE_MANIFEST" ] && ViashError Bad arguments for option \'--ribo_database_manifest=*\': \'$VIASH_PAR_RIBO_DATABASE_MANIFEST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_RIBO_DATABASE_MANIFEST=$(ViashRemoveFlags "$1")
|
||||
if [ -z "$VIASH_PAR_RIBO_DATABASE_MANIFEST" ]; then
|
||||
VIASH_PAR_RIBO_DATABASE_MANIFEST=$(ViashRemoveFlags "$1")
|
||||
else
|
||||
VIASH_PAR_RIBO_DATABASE_MANIFEST="$VIASH_PAR_RIBO_DATABASE_MANIFEST;"$(ViashRemoveFlags "$1")
|
||||
fi
|
||||
shift 1
|
||||
;;
|
||||
--sortmerna_log)
|
||||
@@ -912,7 +912,7 @@ if [ -z ${VIASH_PAR_SORTMERNA_LOG+x} ]; then
|
||||
VIASH_PAR_SORTMERNA_LOG="\$id.sortmerna.log"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_FASTQ_2+x} ]; then
|
||||
VIASH_PAR_FASTQ_2="\$id.\$key.read_2.fastq"
|
||||
VIASH_PAR_FASTQ_2="\$id.\$key.read_2.fastq.gz"
|
||||
fi
|
||||
|
||||
# check whether required files exist
|
||||
@@ -928,9 +928,17 @@ if [ ! -z "$VIASH_PAR_INPUT" ]; then
|
||||
done
|
||||
set +f
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_RIBO_DATABASE_MANIFEST" ] && [ ! -e "$VIASH_PAR_RIBO_DATABASE_MANIFEST" ]; then
|
||||
ViashError "Input file '$VIASH_PAR_RIBO_DATABASE_MANIFEST' does not exist."
|
||||
exit 1
|
||||
if [ ! -z "$VIASH_PAR_RIBO_DATABASE_MANIFEST" ]; then
|
||||
IFS=';'
|
||||
set -f
|
||||
for file in $VIASH_PAR_RIBO_DATABASE_MANIFEST; do
|
||||
unset IFS
|
||||
if [ ! -e "$file" ]; then
|
||||
ViashError "Input file '$file' does not exist."
|
||||
exit 1
|
||||
fi
|
||||
done
|
||||
set +f
|
||||
fi
|
||||
|
||||
# check whether parameters values are of the right type
|
||||
@@ -1048,8 +1056,15 @@ if [ ! -z "$VIASH_PAR_INPUT" ]; then
|
||||
VIASH_PAR_INPUT=$(IFS=',' ; echo "${VIASH_TEST_INPUT[*]}")
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_RIBO_DATABASE_MANIFEST" ]; then
|
||||
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_RIBO_DATABASE_MANIFEST")" )
|
||||
VIASH_PAR_RIBO_DATABASE_MANIFEST=$(ViashDockerAutodetectMount "$VIASH_PAR_RIBO_DATABASE_MANIFEST")
|
||||
VIASH_TEST_RIBO_DATABASE_MANIFEST=()
|
||||
IFS=';'
|
||||
for var in $VIASH_PAR_RIBO_DATABASE_MANIFEST; do
|
||||
unset IFS
|
||||
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$var")" )
|
||||
var=$(ViashDockerAutodetectMount "$var")
|
||||
VIASH_TEST_RIBO_DATABASE_MANIFEST+=( "$var" )
|
||||
done
|
||||
VIASH_PAR_RIBO_DATABASE_MANIFEST=$(IFS=';' ; echo "${VIASH_TEST_RIBO_DATABASE_MANIFEST[*]}")
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_SORTMERNA_LOG" ]; then
|
||||
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_SORTMERNA_LOG")" )
|
||||
@@ -1166,37 +1181,37 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}"
|
||||
set -eo pipefail
|
||||
|
||||
IFS="," read -ra input <<< "\$par_input"
|
||||
|
||||
refs=()
|
||||
while IFS="," read -r path
|
||||
IFS=";" read -ra paths <<< "\$par_ribo_database_manifest"
|
||||
refs=""
|
||||
for i in "\${paths[@]}"
|
||||
do
|
||||
refs+=("--ref \$path")
|
||||
done < \$par_ribo_database_manifest
|
||||
refs+="-ref \$i "
|
||||
done
|
||||
|
||||
if [ "\$par_paired" == "false" ]; then
|
||||
sortmerna \\
|
||||
\$refs \\
|
||||
--reads "\${input[0]}" \\
|
||||
-reads \${input[0]} \\
|
||||
--threads \${meta_cpus:-1} \\
|
||||
--workdir . \\
|
||||
--aligned rRNA_reads \\
|
||||
--fastx \\
|
||||
-num_alignments 1 \\
|
||||
--other non_rRNA_reads
|
||||
# \$args
|
||||
mv non_rRNA_reads.f*q.gz "\$par_fastq_1"
|
||||
else
|
||||
sortmerna \\
|
||||
\$refs \\
|
||||
--reads \${input[0]} \\
|
||||
-reads \${input[0]} \\
|
||||
--reads \${input[1]} \\
|
||||
--threads \${meta_cpus:-1} \\
|
||||
--workdir . \\
|
||||
--aligned rRNA_reads \\
|
||||
--fastx \\
|
||||
--num_alignments 1 \\
|
||||
--other non_rRNA_reads \\
|
||||
--paired_in \\
|
||||
--out2
|
||||
# \$args
|
||||
mv non_rRNA_reads_fwd.f*q.gz \$par_fastq_1
|
||||
mv non_rRNA_reads_rev.f*q.gz \$par_fastq_2
|
||||
fi
|
||||
@@ -1226,7 +1241,17 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
|
||||
VIASH_PAR_INPUT="$VIASH_TEST_INPUT"
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_RIBO_DATABASE_MANIFEST" ]; then
|
||||
VIASH_PAR_RIBO_DATABASE_MANIFEST=$(ViashDockerStripAutomount "$VIASH_PAR_RIBO_DATABASE_MANIFEST")
|
||||
unset VIASH_TEST_RIBO_DATABASE_MANIFEST
|
||||
IFS=';'
|
||||
for var in $VIASH_PAR_RIBO_DATABASE_MANIFEST; do
|
||||
unset IFS
|
||||
if [ -z "$VIASH_TEST_RIBO_DATABASE_MANIFEST" ]; then
|
||||
VIASH_TEST_RIBO_DATABASE_MANIFEST="$(ViashDockerStripAutomount "$var")"
|
||||
else
|
||||
VIASH_TEST_RIBO_DATABASE_MANIFEST="$VIASH_TEST_RIBO_DATABASE_MANIFEST;""$(ViashDockerStripAutomount "$var")"
|
||||
fi
|
||||
done
|
||||
VIASH_PAR_RIBO_DATABASE_MANIFEST="$VIASH_TEST_RIBO_DATABASE_MANIFEST"
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_SORTMERNA_LOG" ]; then
|
||||
VIASH_PAR_SORTMERNA_LOG=$(ViashDockerStripAutomount "$VIASH_PAR_SORTMERNA_LOG")
|
||||
|
||||
@@ -121,7 +121,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -216,8 +216,8 @@ build_info:
|
||||
output: "target/executable/stringtie"
|
||||
executable: "target/executable/stringtie/stringtie"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -229,7 +229,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -496,9 +496,9 @@ tar -xzf stringtie-2.2.1.Linux_x86_64.tar.gz && \
|
||||
cp stringtie-2.2.1.Linux_x86_64/stringtie /usr/local/bin/
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component stringtie"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:08Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:28Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -100,7 +100,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -199,8 +199,8 @@ build_info:
|
||||
output: "target/executable/summarizedexperiment"
|
||||
executable: "target/executable/summarizedexperiment/summarizedexperiment"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -212,7 +212,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -487,9 +487,9 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.pa
|
||||
Rscript -e 'if (!requireNamespace("tximeta", quietly = TRUE)) BiocManager::install("tximeta")'
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component summarizedexperiment"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:05Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:25Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -687,7 +687,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -788,8 +788,8 @@ build_info:
|
||||
output: "target/executable/trimgalore"
|
||||
executable: "target/executable/trimgalore/trimgalore"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -801,7 +801,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -858,9 +858,9 @@ ENTRYPOINT []
|
||||
RUN echo "TrimGalore: `trim_galore --version | sed -n 's/.*version\s\+\([0-9]\+\.[0-9]\+\.[0-9]\+\).*/\1/p'`" > /var/software_versions.txt
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component trimgalore"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:06Z"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:26Z"
|
||||
LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -95,7 +95,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -192,8 +192,8 @@ build_info:
|
||||
output: "target/executable/tx2gene"
|
||||
executable: "target/executable/tx2gene/tx2gene"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -205,7 +205,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -487,9 +487,9 @@ RUN apt-get update && \
|
||||
RUN pip install --upgrade pip
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component tx2gene"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:09Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:29Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -143,7 +143,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -247,8 +247,8 @@ build_info:
|
||||
output: "target/executable/tximport"
|
||||
executable: "target/executable/tximport/tximport"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -260,7 +260,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -508,9 +508,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
|
||||
Rscript -e 'remotes::install_cran(c("jsonlite"), repos = "https://cran.rstudio.com")'
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component tximport"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:02Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:22Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -66,7 +66,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -164,8 +164,8 @@ build_info:
|
||||
output: "target/executable/ucsc/bedclip"
|
||||
executable: "target/executable/ucsc/bedclip/bedclip"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -177,7 +177,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -473,9 +473,9 @@ RUN apt-get update && \
|
||||
RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedClip /usr/local/bin/
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component ucsc bedclip"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:10Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:30Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -66,7 +66,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -164,8 +164,8 @@ build_info:
|
||||
output: "target/executable/ucsc/bedgraphtobigwig"
|
||||
executable: "target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -177,7 +177,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -473,9 +473,9 @@ RUN apt-get update && \
|
||||
RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedGraphToBigWig /usr/local/bin/
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component ucsc bedgraphtobigwig"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:10Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:31Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -97,7 +97,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -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: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -208,7 +208,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -489,9 +489,9 @@ RUN pip install --upgrade pip && \
|
||||
pip install --upgrade --no-cache-dir "umi_tools"
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component umitools umitools_dedup"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:11Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:31Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -155,7 +155,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -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: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -266,7 +266,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -521,9 +521,9 @@ RUN pip install --upgrade pip && \
|
||||
pip install --upgrade --no-cache-dir "umi_tools"
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component umitools umitools_extract"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:11Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:31Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -57,7 +57,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -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: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -169,7 +169,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -473,9 +473,9 @@ RUN pip install --upgrade pip && \
|
||||
pip install --upgrade --no-cache-dir "umi_tools" "pysam"
|
||||
|
||||
LABEL org.opencontainers.image.description="Companion container for running component umitools_prepareforquant"
|
||||
LABEL org.opencontainers.image.created="2024-10-23T13:30:05Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
LABEL org.opencontainers.image.created="2024-10-25T08:40:26Z"
|
||||
LABEL org.opencontainers.image.source="https://x-access-token/ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
LABEL org.opencontainers.image.revision="7662841e2e967790170bd05b667707341d27db7b"
|
||||
LABEL org.opencontainers.image.version="bugfix"
|
||||
|
||||
VIASHDOCKER
|
||||
|
||||
@@ -479,32 +479,32 @@ dependencies:
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- name: "samtools/samtools_sort"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- name: "samtools/samtools_index"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- name: "samtools/samtools_stats"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- name: "samtools/samtools_flagstat"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- name: "samtools/samtools_idxstats"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- name: "umitools/umitools_dedup"
|
||||
repository:
|
||||
type: "local"
|
||||
@@ -515,7 +515,7 @@ dependencies:
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- name: "rsem/rsem_calculate_expression"
|
||||
repository:
|
||||
type: "local"
|
||||
@@ -523,7 +523,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -603,18 +603,18 @@ 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: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@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"
|
||||
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index"
|
||||
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats"
|
||||
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat"
|
||||
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats"
|
||||
- "target/nextflow/umitools/umitools_dedup"
|
||||
- "target/nextflow/umitools_prepareforquant"
|
||||
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant"
|
||||
- "target/nextflow/rsem/rsem_calculate_expression"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
@@ -627,7 +627,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -1323,13 +1323,13 @@ fi
|
||||
VIASH_DEP_UMITOOLS_UMITOOLS_DEDUP="$VIASH_META_RESOURCES_DIR/../../../nextflow/umitools/umitools_dedup/main.nf"
|
||||
VIASH_DEP_UMITOOLS_PREPAREFORQUANT="$VIASH_META_RESOURCES_DIR/../../../nextflow/umitools_prepareforquant/main.nf"
|
||||
VIASH_DEP_RSEM_RSEM_CALCULATE_EXPRESSION="$VIASH_META_RESOURCES_DIR/../../../nextflow/rsem/rsem_calculate_expression/main.nf"
|
||||
VIASH_DEP_STAR_STAR_ALIGN_READS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads/main.nf"
|
||||
VIASH_DEP_SAMTOOLS_SAMTOOLS_SORT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort/main.nf"
|
||||
VIASH_DEP_SAMTOOLS_SAMTOOLS_INDEX="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index/main.nf"
|
||||
VIASH_DEP_SAMTOOLS_SAMTOOLS_STATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats/main.nf"
|
||||
VIASH_DEP_SAMTOOLS_SAMTOOLS_FLAGSTAT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat/main.nf"
|
||||
VIASH_DEP_SAMTOOLS_SAMTOOLS_IDXSTATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats/main.nf"
|
||||
VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/main.nf"
|
||||
VIASH_DEP_STAR_STAR_ALIGN_READS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/main.nf"
|
||||
VIASH_DEP_SAMTOOLS_SAMTOOLS_SORT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/main.nf"
|
||||
VIASH_DEP_SAMTOOLS_SAMTOOLS_INDEX="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/main.nf"
|
||||
VIASH_DEP_SAMTOOLS_SAMTOOLS_STATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/main.nf"
|
||||
VIASH_DEP_SAMTOOLS_SAMTOOLS_FLAGSTAT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/main.nf"
|
||||
VIASH_DEP_SAMTOOLS_SAMTOOLS_IDXSTATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/main.nf"
|
||||
VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/main.nf"
|
||||
|
||||
ViashDebug "Running command: $(echo $VIASH_CMD)"
|
||||
cat << VIASHEOF | eval $VIASH_CMD
|
||||
|
||||
@@ -198,7 +198,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -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: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
dependencies:
|
||||
- "target/nextflow/tx2gene"
|
||||
- "target/nextflow/tximport"
|
||||
@@ -295,7 +295,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -369,27 +369,27 @@ dependencies:
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- name: "samtools/samtools_index"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- name: "samtools/samtools_stats"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- name: "samtools/samtools_flagstat"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- name: "samtools/samtools_idxstats"
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- name: "stringtie"
|
||||
repository:
|
||||
type: "local"
|
||||
@@ -406,7 +406,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -486,15 +486,15 @@ build_info:
|
||||
output: "target/executable/workflows/post_processing"
|
||||
executable: "target/executable/workflows/post_processing/post_processing"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
dependencies:
|
||||
- "target/nextflow/picard_markduplicates"
|
||||
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort"
|
||||
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index"
|
||||
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats"
|
||||
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat"
|
||||
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats"
|
||||
- "target/nextflow/stringtie"
|
||||
- "target/nextflow/bedtools_genomecov"
|
||||
- "target/nextflow/ucsc/bedclip"
|
||||
@@ -510,7 +510,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -1143,11 +1143,11 @@ VIASH_DEP_STRINGTIE="$VIASH_META_RESOURCES_DIR/../../../nextflow/stringtie/main.
|
||||
VIASH_DEP_BEDTOOLS_GENOMECOV="$VIASH_META_RESOURCES_DIR/../../../nextflow/bedtools_genomecov/main.nf"
|
||||
VIASH_DEP_UCSC_BEDCLIP="$VIASH_META_RESOURCES_DIR/../../../nextflow/ucsc/bedclip/main.nf"
|
||||
VIASH_DEP_UCSC_BEDGRAPHTOBIGWIG="$VIASH_META_RESOURCES_DIR/../../../nextflow/ucsc/bedgraphtobigwig/main.nf"
|
||||
VIASH_DEP_SAMTOOLS_SAMTOOLS_SORT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort/main.nf"
|
||||
VIASH_DEP_SAMTOOLS_SAMTOOLS_INDEX="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index/main.nf"
|
||||
VIASH_DEP_SAMTOOLS_SAMTOOLS_STATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats/main.nf"
|
||||
VIASH_DEP_SAMTOOLS_SAMTOOLS_FLAGSTAT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat/main.nf"
|
||||
VIASH_DEP_SAMTOOLS_SAMTOOLS_IDXSTATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats/main.nf"
|
||||
VIASH_DEP_SAMTOOLS_SAMTOOLS_SORT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/main.nf"
|
||||
VIASH_DEP_SAMTOOLS_SAMTOOLS_INDEX="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/main.nf"
|
||||
VIASH_DEP_SAMTOOLS_SAMTOOLS_STATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/main.nf"
|
||||
VIASH_DEP_SAMTOOLS_SAMTOOLS_FLAGSTAT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/main.nf"
|
||||
VIASH_DEP_SAMTOOLS_SAMTOOLS_IDXSTATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/main.nf"
|
||||
|
||||
ViashDebug "Running command: $(echo $VIASH_CMD)"
|
||||
cat << VIASHEOF | eval $VIASH_CMD
|
||||
|
||||
@@ -566,7 +566,7 @@ dependencies:
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- name: "trimgalore"
|
||||
repository:
|
||||
type: "local"
|
||||
@@ -580,7 +580,7 @@ dependencies:
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- name: "fq_subsample"
|
||||
repository:
|
||||
type: "local"
|
||||
@@ -588,12 +588,12 @@ dependencies:
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -673,18 +673,18 @@ build_info:
|
||||
output: "target/executable/workflows/pre_processing"
|
||||
executable: "target/executable/workflows/pre_processing/pre_processing"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
dependencies:
|
||||
- "target/nextflow/fastqc"
|
||||
- "target/nextflow/umitools/umitools_extract"
|
||||
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/umi_tools/umi_tools_extract"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract"
|
||||
- "target/nextflow/trimgalore"
|
||||
- "target/nextflow/bbmap_bbsplit"
|
||||
- "target/nextflow/sortmerna"
|
||||
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/fastp"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/fastp"
|
||||
- "target/nextflow/fq_subsample"
|
||||
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
version: "bugfix"
|
||||
@@ -696,7 +696,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -1510,9 +1510,9 @@ VIASH_DEP_TRIMGALORE="$VIASH_META_RESOURCES_DIR/../../../nextflow/trimgalore/mai
|
||||
VIASH_DEP_BBMAP_BBSPLIT="$VIASH_META_RESOURCES_DIR/../../../nextflow/bbmap_bbsplit/main.nf"
|
||||
VIASH_DEP_SORTMERNA="$VIASH_META_RESOURCES_DIR/../../../nextflow/sortmerna/main.nf"
|
||||
VIASH_DEP_FQ_SUBSAMPLE="$VIASH_META_RESOURCES_DIR/../../../nextflow/fq_subsample/main.nf"
|
||||
VIASH_DEP_UMI_TOOLS_UMI_TOOLS_EXTRACT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/umi_tools/umi_tools_extract/main.nf"
|
||||
VIASH_DEP_FASTP="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/fastp/main.nf"
|
||||
VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/main.nf"
|
||||
VIASH_DEP_UMI_TOOLS_UMI_TOOLS_EXTRACT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/main.nf"
|
||||
VIASH_DEP_FASTP="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/fastp/main.nf"
|
||||
VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/main.nf"
|
||||
|
||||
ViashDebug "Running command: $(echo $VIASH_CMD)"
|
||||
cat << VIASHEOF | eval $VIASH_CMD
|
||||
@@ -1673,9 +1673,11 @@ workflow run_wf {
|
||||
runIf: { id, state -> state.remove_ribo_rna },
|
||||
fromState: { id, state ->
|
||||
def input = state.paired ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
|
||||
def filePaths = state.ribo_database_manifest.readLines()
|
||||
def refs = filePaths.collect { it }
|
||||
[ paired: state.paired,
|
||||
input: input,
|
||||
ribo_database_manifest: state.ribo_database_manifest ]
|
||||
ribo_database_manifest: refs ]
|
||||
},
|
||||
toState: [
|
||||
"fastq_1": "fastq_1",
|
||||
|
||||
@@ -370,7 +370,7 @@ dependencies:
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- name: "cat_additional_fasta"
|
||||
repository:
|
||||
type: "local"
|
||||
@@ -387,7 +387,7 @@ dependencies:
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- name: "getchromsizes"
|
||||
repository:
|
||||
type: "local"
|
||||
@@ -400,7 +400,7 @@ dependencies:
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- name: "bbmap_bbsplit"
|
||||
repository:
|
||||
type: "local"
|
||||
@@ -408,7 +408,7 @@ dependencies:
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- name: "kallisto/kallisto_index"
|
||||
repository:
|
||||
type: "local"
|
||||
@@ -416,7 +416,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -496,21 +496,21 @@ build_info:
|
||||
output: "target/executable/workflows/prepare_genome"
|
||||
executable: "target/executable/workflows/prepare_genome/prepare_genome"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
dependencies:
|
||||
- "target/nextflow/gunzip"
|
||||
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/gffread"
|
||||
- "target/nextflow/cat_additional_fasta"
|
||||
- "target/nextflow/gtf2bed"
|
||||
- "target/nextflow/preprocess_transcripts_fasta"
|
||||
- "target/nextflow/gtf_filter"
|
||||
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/rsem/rsem_prepare_reference"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference"
|
||||
- "target/nextflow/getchromsizes"
|
||||
- "target/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/untar"
|
||||
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_genome_generate"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate"
|
||||
- "target/nextflow/bbmap_bbsplit"
|
||||
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index"
|
||||
- "target/nextflow/kallisto/kallisto_index"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
@@ -523,7 +523,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -1111,11 +1111,11 @@ VIASH_DEP_GTF_FILTER="$VIASH_META_RESOURCES_DIR/../../../nextflow/gtf_filter/mai
|
||||
VIASH_DEP_GETCHROMSIZES="$VIASH_META_RESOURCES_DIR/../../../nextflow/getchromsizes/main.nf"
|
||||
VIASH_DEP_BBMAP_BBSPLIT="$VIASH_META_RESOURCES_DIR/../../../nextflow/bbmap_bbsplit/main.nf"
|
||||
VIASH_DEP_KALLISTO_KALLISTO_INDEX="$VIASH_META_RESOURCES_DIR/../../../nextflow/kallisto/kallisto_index/main.nf"
|
||||
VIASH_DEP_GFFREAD="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread/main.nf"
|
||||
VIASH_DEP_RSEM_RSEM_PREPARE_REFERENCE="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/rsem/rsem_prepare_reference/main.nf"
|
||||
VIASH_DEP_GFFREAD="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/gffread/main.nf"
|
||||
VIASH_DEP_RSEM_RSEM_PREPARE_REFERENCE="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/main.nf"
|
||||
VIASH_DEP_UNTAR="$VIASH_TARGET_DIR/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/untar/main.nf"
|
||||
VIASH_DEP_STAR_STAR_GENOME_GENERATE="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_genome_generate/main.nf"
|
||||
VIASH_DEP_SALMON_SALMON_INDEX="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index/main.nf"
|
||||
VIASH_DEP_STAR_STAR_GENOME_GENERATE="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/main.nf"
|
||||
VIASH_DEP_SALMON_SALMON_INDEX="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/main.nf"
|
||||
|
||||
ViashDebug "Running command: $(echo $VIASH_CMD)"
|
||||
cat << VIASHEOF | eval $VIASH_CMD
|
||||
|
||||
@@ -195,7 +195,7 @@ dependencies:
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- name: "kallisto/kallisto_quant"
|
||||
repository:
|
||||
type: "local"
|
||||
@@ -203,7 +203,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -283,10 +283,10 @@ build_info:
|
||||
output: "target/executable/workflows/pseudo_alignment_and_quant"
|
||||
executable: "target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
dependencies:
|
||||
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant"
|
||||
- "target/nextflow/kallisto/kallisto_quant"
|
||||
package_config:
|
||||
name: "rnaseq"
|
||||
@@ -299,7 +299,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -780,7 +780,7 @@ fi
|
||||
|
||||
# set dependency paths
|
||||
VIASH_DEP_KALLISTO_KALLISTO_QUANT="$VIASH_META_RESOURCES_DIR/../../../nextflow/kallisto/kallisto_quant/main.nf"
|
||||
VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/main.nf"
|
||||
VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/main.nf"
|
||||
|
||||
ViashDebug "Running command: $(echo $VIASH_CMD)"
|
||||
cat << VIASHEOF | eval $VIASH_CMD
|
||||
|
||||
@@ -559,28 +559,6 @@ argument_groups:
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--pca_header_multiqc"
|
||||
info: null
|
||||
default:
|
||||
- "src/assets/multiqc/deseq2_pca_header.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--clustering_header_multiqc"
|
||||
info: null
|
||||
default:
|
||||
- "src/assets/multiqc/deseq2_clustering_header.txt"
|
||||
must_exist: true
|
||||
create_parent: true
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "boolean"
|
||||
name: "--deseq2_vst"
|
||||
description: "Use vst transformation instead of rlog with DESeq2"
|
||||
@@ -589,24 +567,6 @@ argument_groups:
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--extra_deseq2_args"
|
||||
info: null
|
||||
default:
|
||||
- "--id_col 1 --sample_suffix '' --outprefix deseq2 --count_col 3"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "string"
|
||||
name: "--extra_deseq2_args2"
|
||||
info: null
|
||||
default:
|
||||
- "star_salmon"
|
||||
required: false
|
||||
direction: "input"
|
||||
multiple: false
|
||||
multiple_sep: ";"
|
||||
- type: "file"
|
||||
name: "--multiqc_custom_config"
|
||||
info: null
|
||||
@@ -1491,7 +1451,7 @@ dependencies:
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- name: "multiqc_custom_biotype"
|
||||
repository:
|
||||
type: "local"
|
||||
@@ -1505,7 +1465,7 @@ dependencies:
|
||||
repository:
|
||||
type: "vsh"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- name: "rsem/rsem_merge_counts"
|
||||
repository:
|
||||
type: "local"
|
||||
@@ -1516,7 +1476,7 @@ repositories:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
@@ -1596,8 +1556,8 @@ build_info:
|
||||
output: "target/executable/workflows/quality_control"
|
||||
executable: "target/executable/workflows/quality_control/quality_control"
|
||||
viash_version: "0.9.0"
|
||||
git_commit: "7687d774f298f75ef6c50895c472ee6152f2468b"
|
||||
git_remote: "https://x-access-token:ghs_7FVxN3rBdtTLQpokIz0vNdwJM0FoaA3gNdap@github.com/viash-hub/rnaseq"
|
||||
git_commit: "7662841e2e967790170bd05b667707341d27db7b"
|
||||
git_remote: "https://x-access-token:ghs_YEOtoLGbvBtbC9HDSpu57XjDztgJHV1RyBQ7@github.com/viash-hub/rnaseq"
|
||||
dependencies:
|
||||
- "target/nextflow/rseqc/rseqc_bamstat"
|
||||
- "target/nextflow/rseqc/rseqc_inferexperiment"
|
||||
@@ -1610,11 +1570,11 @@ build_info:
|
||||
- "target/nextflow/dupradar"
|
||||
- "target/nextflow/qualimap"
|
||||
- "target/nextflow/preseq_lcextrap"
|
||||
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/featurecounts"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts"
|
||||
- "target/nextflow/multiqc_custom_biotype"
|
||||
- "target/nextflow/deseq2_qc"
|
||||
- "target/nextflow/prepare_multiqc_input"
|
||||
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc"
|
||||
- "target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc"
|
||||
- "target/nextflow/rsem/rsem_merge_counts"
|
||||
- "target/nextflow/workflows/merge_quant_results"
|
||||
package_config:
|
||||
@@ -1628,7 +1588,7 @@ package_config:
|
||||
- type: "vsh"
|
||||
name: "biobox"
|
||||
repo: "vsh/biobox"
|
||||
tag: "v0.2.0"
|
||||
tag: "main"
|
||||
- type: "vsh"
|
||||
name: "craftbox"
|
||||
repo: "craftbox"
|
||||
|
||||
@@ -462,26 +462,10 @@ function ViashHelp {
|
||||
echo " --skip_deseq2_qc"
|
||||
echo " type: boolean"
|
||||
echo ""
|
||||
echo " --pca_header_multiqc"
|
||||
echo " type: file, file must exist"
|
||||
echo " default: src/assets/multiqc/deseq2_pca_header.txt"
|
||||
echo ""
|
||||
echo " --clustering_header_multiqc"
|
||||
echo " type: file, file must exist"
|
||||
echo " default: src/assets/multiqc/deseq2_clustering_header.txt"
|
||||
echo ""
|
||||
echo " --deseq2_vst"
|
||||
echo " type: boolean"
|
||||
echo " Use vst transformation instead of rlog with DESeq2"
|
||||
echo ""
|
||||
echo " --extra_deseq2_args"
|
||||
echo " type: string"
|
||||
echo " default: --id_col 1 --sample_suffix '' --outprefix deseq2 --count_col 3"
|
||||
echo ""
|
||||
echo " --extra_deseq2_args2"
|
||||
echo " type: string"
|
||||
echo " default: star_salmon"
|
||||
echo ""
|
||||
echo " --multiqc_custom_config"
|
||||
echo " type: file, file must exist"
|
||||
echo ""
|
||||
@@ -1414,28 +1398,6 @@ while [[ $# -gt 0 ]]; do
|
||||
VIASH_PAR_SKIP_DESEQ2_QC=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--pca_header_multiqc)
|
||||
[ -n "$VIASH_PAR_PCA_HEADER_MULTIQC" ] && ViashError Bad arguments for option \'--pca_header_multiqc\': \'$VIASH_PAR_PCA_HEADER_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_PCA_HEADER_MULTIQC="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --pca_header_multiqc. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--pca_header_multiqc=*)
|
||||
[ -n "$VIASH_PAR_PCA_HEADER_MULTIQC" ] && ViashError Bad arguments for option \'--pca_header_multiqc=*\': \'$VIASH_PAR_PCA_HEADER_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_PCA_HEADER_MULTIQC=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--clustering_header_multiqc)
|
||||
[ -n "$VIASH_PAR_CLUSTERING_HEADER_MULTIQC" ] && ViashError Bad arguments for option \'--clustering_header_multiqc\': \'$VIASH_PAR_CLUSTERING_HEADER_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_CLUSTERING_HEADER_MULTIQC="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --clustering_header_multiqc. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--clustering_header_multiqc=*)
|
||||
[ -n "$VIASH_PAR_CLUSTERING_HEADER_MULTIQC" ] && ViashError Bad arguments for option \'--clustering_header_multiqc=*\': \'$VIASH_PAR_CLUSTERING_HEADER_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_CLUSTERING_HEADER_MULTIQC=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--deseq2_vst)
|
||||
[ -n "$VIASH_PAR_DESEQ2_VST" ] && ViashError Bad arguments for option \'--deseq2_vst\': \'$VIASH_PAR_DESEQ2_VST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_DESEQ2_VST="$2"
|
||||
@@ -1447,28 +1409,6 @@ while [[ $# -gt 0 ]]; do
|
||||
VIASH_PAR_DESEQ2_VST=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--extra_deseq2_args)
|
||||
[ -n "$VIASH_PAR_EXTRA_DESEQ2_ARGS" ] && ViashError Bad arguments for option \'--extra_deseq2_args\': \'$VIASH_PAR_EXTRA_DESEQ2_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_DESEQ2_ARGS="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_deseq2_args. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--extra_deseq2_args=*)
|
||||
[ -n "$VIASH_PAR_EXTRA_DESEQ2_ARGS" ] && ViashError Bad arguments for option \'--extra_deseq2_args=*\': \'$VIASH_PAR_EXTRA_DESEQ2_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_DESEQ2_ARGS=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--extra_deseq2_args2)
|
||||
[ -n "$VIASH_PAR_EXTRA_DESEQ2_ARGS2" ] && ViashError Bad arguments for option \'--extra_deseq2_args2\': \'$VIASH_PAR_EXTRA_DESEQ2_ARGS2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_DESEQ2_ARGS2="$2"
|
||||
[ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_deseq2_args2. Use "--help" to get more information on the parameters. && exit 1
|
||||
shift 2
|
||||
;;
|
||||
--extra_deseq2_args2=*)
|
||||
[ -n "$VIASH_PAR_EXTRA_DESEQ2_ARGS2" ] && ViashError Bad arguments for option \'--extra_deseq2_args2=*\': \'$VIASH_PAR_EXTRA_DESEQ2_ARGS2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_EXTRA_DESEQ2_ARGS2=$(ViashRemoveFlags "$1")
|
||||
shift 1
|
||||
;;
|
||||
--multiqc_custom_config)
|
||||
[ -n "$VIASH_PAR_MULTIQC_CUSTOM_CONFIG" ] && ViashError Bad arguments for option \'--multiqc_custom_config\': \'$VIASH_PAR_MULTIQC_CUSTOM_CONFIG\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
|
||||
VIASH_PAR_MULTIQC_CUSTOM_CONFIG="$2"
|
||||
@@ -2545,18 +2485,6 @@ fi
|
||||
if [ -z ${VIASH_PAR_JAVA_MEMORY_SIZE+x} ]; then
|
||||
VIASH_PAR_JAVA_MEMORY_SIZE="4G"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_PCA_HEADER_MULTIQC+x} ]; then
|
||||
VIASH_PAR_PCA_HEADER_MULTIQC="src/assets/multiqc/deseq2_pca_header.txt"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_CLUSTERING_HEADER_MULTIQC+x} ]; then
|
||||
VIASH_PAR_CLUSTERING_HEADER_MULTIQC="src/assets/multiqc/deseq2_clustering_header.txt"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_EXTRA_DESEQ2_ARGS+x} ]; then
|
||||
VIASH_PAR_EXTRA_DESEQ2_ARGS="--id_col 1 --sample_suffix '' --outprefix deseq2 --count_col 3"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_EXTRA_DESEQ2_ARGS2+x} ]; then
|
||||
VIASH_PAR_EXTRA_DESEQ2_ARGS2="star_salmon"
|
||||
fi
|
||||
if [ -z ${VIASH_PAR_PRESEQ_OUTPUT+x} ]; then
|
||||
VIASH_PAR_PRESEQ_OUTPUT="\$id.lc_extrap.txt"
|
||||
fi
|
||||
@@ -2775,14 +2703,6 @@ if [ ! -z "$VIASH_PAR_BIOTYPES_HEADER" ] && [ ! -e "$VIASH_PAR_BIOTYPES_HEADER"
|
||||
ViashError "Input file '$VIASH_PAR_BIOTYPES_HEADER' does not exist."
|
||||
exit 1
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_PCA_HEADER_MULTIQC" ] && [ ! -e "$VIASH_PAR_PCA_HEADER_MULTIQC" ]; then
|
||||
ViashError "Input file '$VIASH_PAR_PCA_HEADER_MULTIQC' does not exist."
|
||||
exit 1
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_CLUSTERING_HEADER_MULTIQC" ] && [ ! -e "$VIASH_PAR_CLUSTERING_HEADER_MULTIQC" ]; then
|
||||
ViashError "Input file '$VIASH_PAR_CLUSTERING_HEADER_MULTIQC' does not exist."
|
||||
exit 1
|
||||
fi
|
||||
if [ ! -z "$VIASH_PAR_MULTIQC_CUSTOM_CONFIG" ] && [ ! -e "$VIASH_PAR_MULTIQC_CUSTOM_CONFIG" ]; then
|
||||
ViashError "Input file '$VIASH_PAR_MULTIQC_CUSTOM_CONFIG' does not exist."
|
||||
exit 1
|
||||
@@ -3346,8 +3266,8 @@ VIASH_DEP_DESEQ2_QC="$VIASH_META_RESOURCES_DIR/../../../nextflow/deseq2_qc/main.
|
||||
VIASH_DEP_PREPARE_MULTIQC_INPUT="$VIASH_META_RESOURCES_DIR/../../../nextflow/prepare_multiqc_input/main.nf"
|
||||
VIASH_DEP_RSEM_RSEM_MERGE_COUNTS="$VIASH_META_RESOURCES_DIR/../../../nextflow/rsem/rsem_merge_counts/main.nf"
|
||||
VIASH_DEP_WORKFLOWS_MERGE_QUANT_RESULTS="$VIASH_META_RESOURCES_DIR/../../../nextflow/workflows/merge_quant_results/main.nf"
|
||||
VIASH_DEP_FEATURECOUNTS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/featurecounts/main.nf"
|
||||
VIASH_DEP_MULTIQC="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/main.nf"
|
||||
VIASH_DEP_FEATURECOUNTS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/main.nf"
|
||||
VIASH_DEP_MULTIQC="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/main.nf"
|
||||
|
||||
ViashDebug "Running command: $(echo $VIASH_CMD)"
|
||||
cat << VIASHEOF | eval $VIASH_CMD
|
||||
@@ -3806,110 +3726,6 @@ workflow run_wf {
|
||||
] ]
|
||||
}
|
||||
|
||||
// | map { list ->
|
||||
// def ids = list.collect { id, state -> state.id }
|
||||
// def strandedness = list.collect { id, state -> state.strandedness }
|
||||
// def num_trimmed_reads = list.collect { id, state -> state.num_trimmed_reads }
|
||||
// def passed_trimmed_reads = list.collect { id, state -> state.passed_trimmed_reads }
|
||||
// def passed_mapping = list.collect { id, state -> state.passed_mapping }
|
||||
// def percent_mapped = list.collect { id, state -> state.percent_mapped }
|
||||
// def inferred_strand = list.collect { id, state -> state.inferred_strand }
|
||||
// def passed_strand_check = list.collect { id, state -> state.passed_strand_check }
|
||||
// def gtf = list.collect { id, state -> state.gtf }.unique()[0]
|
||||
// def gtf_extra_attributes = list.collect { id, state -> state.gtf_extra_attributes }.unique()[0]
|
||||
// def gtf_group_features = list.collect { id, state -> state.gtf_group_features }.unique()[0]
|
||||
// def pca_header_multiqc = list.collect { id, state -> state.pca_header_multiqc }.unique()[0]
|
||||
// def clustering_header_multiqc = list.collect { id, state -> state.clustering_header_multiqc }.unique()[0]
|
||||
// def aligner = list.collect { id, state -> state.aligner }.unique()[0]
|
||||
// def pseudo_aligner = list.collect { id, state -> state.pseudo_aligner }.unique()[0]
|
||||
// def deseq2_vst = list.collect { id, state -> state.deseq2_vst }.unique()[0]
|
||||
// def extra_deseq2_args = list.collect { id, state -> state.extra_deseq2_args }.unique()[0]
|
||||
// def extra_deseq2_args2 = list.collect { id, state -> state.extra_deseq2_args2 }.unique()[0]
|
||||
// def skip_deseq2_qc = list.collect { id, state -> state.skip_deseq2_qc }.unique()[0]
|
||||
// def skip_qc = list.collect { id, state -> state.skip_qc }.unique()[0]
|
||||
// def skip_align = list.collect { id, state -> state.skip_align }.unique()[0]
|
||||
// def skip_pseudo_align = list.collect { id, state -> state.skip_pseudo_align }.unique()[0]
|
||||
// def quant_results = list.collect { id, state ->
|
||||
// (state.quant_results_file instanceof java.nio.file.Path && state.quant_results_file.exists()) ?
|
||||
// state.quant_results_file :
|
||||
// null }
|
||||
// def rsem_counts_gene = list.collect { id, state ->
|
||||
// (state.rsem_counts_gene instanceof java.nio.file.Path && state.rsem_counts_gene.exists()) ?
|
||||
// state.rsem_counts_gene :
|
||||
// null }
|
||||
// def rsem_counts_transcripts = list.collect { id, state ->
|
||||
// (state.rsem_counts_transcripts instanceof java.nio.file.Path && state.rsem_counts_transcripts.exists()) ?
|
||||
// state.rsem_counts_transcripts :
|
||||
// null }
|
||||
// def pseudo_salmon_quant_results = list.collect { id, state ->
|
||||
// (state.pseudo_salmon_quant_results_file instanceof java.nio.file.Path && state.pseudo_salmon_quant_results_file.exists()) ?
|
||||
// state.pseudo_salmon_quant_results_file :
|
||||
// null }
|
||||
// def pseudo_kallisto_quant_results = list.collect { id, state ->
|
||||
// (state.pseudo_kallisto_quant_results_file instanceof java.nio.file.Path && state.pseudo_kallisto_quant_results_file.exists()) ?
|
||||
// state.pseudo_kallisto_quant_results_file :
|
||||
// null }
|
||||
// def fastqc_zip_1_dirs = list.collect{it[1].fastqc_zip_1.getParent()}
|
||||
// def fastqc_zip_2_dirs = list.collect{it[1].fastqc_zip_2.getParent()}
|
||||
// def trim_zip_1_dirs = list.collect{it[1].trim_zip_1.getParent()}
|
||||
// def trim_zip_2_dirs = list.collect{it[1].trim_zip_2.getParent()}
|
||||
// def trim_log_1_dirs = list.collect{it[1].trim_log_1.getParent()}
|
||||
// def trim_log_2_dirs = list.collect{it[1].trim_log_2.getParent()}
|
||||
// def sortmerna_multiqc_dirs = list.collect{it[1].sortmerna_multiqc.getParent()}
|
||||
// def star_multiqc_dirs = list.collect{it[1].star_multiqc.getParent()}
|
||||
// def genome_bam_stats_dirs = list.collect{it[1].genome_bam_stats.getParent()}
|
||||
// def genome_bam_flagstat_dirs = list.collect{it[1].genome_bam_flagstat.getParent()}
|
||||
// def genome_bam_idxstats_dirs = list.collect{it[1].genome_bam_idxstats}
|
||||
// def markduplicates_multiqc_dirs = list.collect{it[1].markduplicates_multiqc.getParent()}
|
||||
// def salmon_multiqc_dirs = list.collect{it[1].salmon_multiqc}
|
||||
// def rsem_multiqc_dirs = list.collect{it[1].rsem_multiqc.getParent()}
|
||||
// def pseudo_multiqc_dirs = list.collect{it[1].pseudo_multiqc.getParent()}
|
||||
// def featurecounts_multiqc_dirs = list.collect{it[1].featurecounts_multiqc.getParent()}
|
||||
// def featurecounts_rrna_multiqc_dirs = list.collect{it[1].featurecounts_rrna_multiqc.getParent()}
|
||||
// def preseq_output_dirs = list.collect{it[1].preseq_output.getParent()}
|
||||
// def qualimap_output_dirs = list.collect{it[1].qualimap_output_dir}
|
||||
// def dupradar_output_dup_intercept_mqc_dirs = list.collect{it[1].dupradar_output_dup_intercept_mqc.getParent()}
|
||||
// def dupradar_output_duprate_exp_denscurve_mqc_dirs = list.collect{it[1].dupradar_output_duprate_exp_denscurve_mqc.getParent()}
|
||||
// def bamstat_output_dirs = list.collect{it[1].bamstat_output.getParent()}
|
||||
// def strandedness_output_dirs = list.collect{it[1].strandedness_output.getParent()}
|
||||
// def inner_dist_output_freq_dirs = list.collect{it[1].inner_dist_output_freq.getParent()}
|
||||
// def junction_annotation_output_log_dirs = list.collect{it[1].junction_annotation_output_log.getParent()}
|
||||
// def junction_saturation_output_plot_r_dirs = list.collect{it[1].junction_saturation_output_plot_r.getParent()}
|
||||
// def read_distribution_output_dirs = list.collect{it[1].read_distribution_output.getParent()}
|
||||
// def read_duplication_output_duplication_rate_mapping_dirs = list.collect{it[1].read_duplication_output_duplication_rate_mapping.getParent()}
|
||||
// def tin_output_summary_dirs = list.collect{it[1].tin_output_summary.getParent()}
|
||||
// def multiqc_custom_config_dirs = list.collect{it[1].multiqc_custom_config.getParent()}
|
||||
// ["merged", [
|
||||
// ids: ids,
|
||||
// strandedness: strandedness,
|
||||
// num_trimmed_reads: num_trimmed_reads,
|
||||
// passed_trimmed_reads: passed_trimmed_reads,
|
||||
// passed_mapping: passed_mapping,
|
||||
// percent_mapped: percent_mapped,
|
||||
// inferred_strand: inferred_strand,
|
||||
// passed_strand_check: passed_strand_check,
|
||||
// skip_align: skip_align,
|
||||
// skip_pseudo_align: skip_pseudo_align,
|
||||
// quant_results: quant_results,
|
||||
// rsem_counts_gene: rsem_counts_gene,
|
||||
// rsem_counts_transcripts: rsem_counts_transcripts,
|
||||
// pseudo_salmon_quant_results: pseudo_salmon_quant_results,
|
||||
// pseudo_kallisto_quant_results: pseudo_kallisto_quant_results,
|
||||
// gtf: gtf,
|
||||
// gtf_extra_attributes: gtf_extra_attributes,
|
||||
// gtf_group_features: gtf_group_features,
|
||||
// pca_header_multiqc: pca_header_multiqc,
|
||||
// clustering_header_multiqc: clustering_header_multiqc,
|
||||
// aligner: aligner,
|
||||
// pseudo_aligner: pseudo_aligner,
|
||||
// deseq2_vst: deseq2_vst,
|
||||
// extra_deseq2_args: extra_deseq2_args,
|
||||
// extra_deseq2_args2: extra_deseq2_args2,
|
||||
// skip_deseq2_qc: skip_deseq2_qc,
|
||||
// multiqc_input: fastqc_zip_1_dirs + fastqc_zip_2_dirs + trim_zip_1_dirs + trim_zip_2_dirs + trim_log_1_dirs + trim_log_2_dirs + sortmerna_multiqc_dirs + star_multiqc_dirs + genome_bam_stats_dirs + genome_bam_flagstat_dirs + genome_bam_idxstats_dirs + markduplicates_multiqc_dirs + salmon_multiqc_dirs + rsem_multiqc_dirs + pseudo_multiqc_dirs + featurecounts_multiqc_dirs + featurecounts_rrna_multiqc_dirs + preseq_output_dirs + qualimap_output_dirs + dupradar_output_dup_intercept_mqc_dirs + dupradar_output_duprate_exp_denscurve_mqc_dirs + bamstat_output_dirs + strandedness_output_dirs + inner_dist_output_freq_dirs + junction_annotation_output_log_dirs + junction_saturation_output_plot_r_dirs + read_distribution_output_dirs + read_duplication_output_duplication_rate_mapping_dirs + tin_output_summary_dirs + multiqc_custom_config_dirs
|
||||
// ] ]
|
||||
// }
|
||||
|
||||
// Merge quantification results of alignment
|
||||
| merge_quant_results.run (
|
||||
runIf: { id, state -> !state.skip_align && state.aligner == 'star_salmon' },
|
||||
@@ -3954,13 +3770,11 @@ workflow run_wf {
|
||||
def counts = (state.aligner == "star_rsem") ? state.counts_gene : state.counts_gene_length_scaled
|
||||
[
|
||||
counts: counts,
|
||||
pca_header_multiqc: state.pca_header_multiqc,
|
||||
clustering_header_multiqc: state.clustering_header_multiqc,
|
||||
deseq2_vst: state.deseq2_vst,
|
||||
extra_deseq2_args: state.extra_deseq2_args,
|
||||
extra_deseq2_args2: state.extra_deseq2_args2
|
||||
vst: state.deseq2_vst,
|
||||
label: state.aligner
|
||||
]
|
||||
},
|
||||
},
|
||||
args: [count_col: 3, id_col: 1, outprefix: "deseq2"],
|
||||
toState: [
|
||||
"deseq2_output": "deseq2_output",
|
||||
"deseq2_pca_multiqc": "pca_multiqc",
|
||||
@@ -3997,18 +3811,16 @@ workflow run_wf {
|
||||
| deseq2_qc.run (
|
||||
runIf: { id, state -> !state.skip_qc && !state.skip_deseq2_qc && !state.skip_pseudo_align },
|
||||
fromState: [
|
||||
"counts": "pseudo_counts_gene_length_scaled",
|
||||
"pca_header_multiqc": "pca_header_multiqc",
|
||||
"clustering_header_multiqc": "clustering_header_multiqc",
|
||||
"deseq2_vst": "deseq2_vst",
|
||||
"extra_deseq2_args": "extra_deseq2_args",
|
||||
"extra_deseq2_args2": "extra_deseq2_args2"
|
||||
],
|
||||
"counts": "counts",
|
||||
"vst": "deseq2_vst",
|
||||
"label": "pseudo_aligner"
|
||||
],
|
||||
args: [count_col: 3, id_col: 1, outprefix: "deseq2"],
|
||||
toState: [
|
||||
"deseq2_output_pseudo": "deseq2_output",
|
||||
"deseq2_pca_multiqc_pseudo": "pca_multiqc",
|
||||
"deseq2_dists_multiqc_pseudo": "dists_multiqc"
|
||||
],
|
||||
"deseq2_output": "deseq2_output",
|
||||
"deseq2_pca_multiqc": "pca_multiqc",
|
||||
"deseq2_dists_multiqc": "dists_multiqc"
|
||||
],
|
||||
key: "deseq2_qc_pseuso_align_quant"
|
||||
)
|
||||
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user