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Build branch main with version main (fd0354d)

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Build pipeline: viash-hub.rnaseq.main-kqfj7

Source commit: fd0354dae8

Source message: Point to new assets dir
This commit is contained in:
CI
2024-10-03 16:22:26 +00:00
parent c106022744
commit 2fadce912e
211 changed files with 621 additions and 532 deletions
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4
target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml
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@@ -603,8 +603,8 @@ build_info:
output: "target/executable/workflows/genome_alignment_and_quant"
executable: "target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant"
viash_version: "0.9.0"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort"

4
target/executable/workflows/merge_quant_results/.config.vsh.yaml
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@@ -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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/tx2gene"
- "target/nextflow/tximport"

4
target/executable/workflows/post_processing/.config.vsh.yaml
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@@ -486,8 +486,8 @@ build_info:
output: "target/executable/workflows/post_processing"
executable: "target/executable/workflows/post_processing/post_processing"
viash_version: "0.9.0"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/picard_markduplicates"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort"

4
target/executable/workflows/pre_processing/.config.vsh.yaml
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@@ -673,8 +673,8 @@ build_info:
output: "target/executable/workflows/pre_processing"
executable: "target/executable/workflows/pre_processing/pre_processing"
viash_version: "0.9.0"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/fastqc"
- "target/nextflow/umitools/umitools_extract"

4
target/executable/workflows/prepare_genome/.config.vsh.yaml
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@@ -496,8 +496,8 @@ build_info:
output: "target/executable/workflows/prepare_genome"
executable: "target/executable/workflows/prepare_genome/prepare_genome"
viash_version: "0.9.0"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/gunzip"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread"

4
target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml
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@@ -283,8 +283,8 @@ build_info:
output: "target/executable/workflows/pseudo_alignment_and_quant"
executable: "target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant"
viash_version: "0.9.0"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant"
- "target/nextflow/kallisto/kallisto_quant"

10
target/executable/workflows/quality_control/.config.vsh.yaml
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@@ -265,7 +265,7 @@ argument_groups:
name: "--biotypes_header"
info: null
default:
- "assets/multiqc/biotypes_header.txt"
- "src/assets/multiqc/biotypes_header.txt"
must_exist: true
create_parent: true
required: false
@@ -563,7 +563,7 @@ argument_groups:
name: "--pca_header_multiqc"
info: null
default:
- "assets/multiqc/deseq2_pca_header.txt"
- "src/assets/multiqc/deseq2_pca_header.txt"
must_exist: true
create_parent: true
required: false
@@ -574,7 +574,7 @@ argument_groups:
name: "--clustering_header_multiqc"
info: null
default:
- "assets/multiqc/deseq2_clustering_header.txt"
- "src/assets/multiqc/deseq2_clustering_header.txt"
must_exist: true
create_parent: true
required: false
@@ -1596,8 +1596,8 @@ build_info:
output: "target/executable/workflows/quality_control"
executable: "target/executable/workflows/quality_control/quality_control"
viash_version: "0.9.0"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/rseqc/rseqc_bamstat"
- "target/nextflow/rseqc/rseqc_inferexperiment"

12
target/executable/workflows/quality_control/quality_control
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@@ -296,7 +296,7 @@ function ViashHelp {
echo ""
echo " --biotypes_header"
echo " type: file, file must exist"
echo " default: assets/multiqc/biotypes_header.txt"
echo " default: src/assets/multiqc/biotypes_header.txt"
echo ""
echo " --biotype"
echo " type: string"
@@ -464,11 +464,11 @@ function ViashHelp {
echo ""
echo " --pca_header_multiqc"
echo " type: file, file must exist"
echo " default: assets/multiqc/deseq2_pca_header.txt"
echo " default: src/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 " default: src/assets/multiqc/deseq2_clustering_header.txt"
echo ""
echo " --deseq2_vst"
echo " type: boolean"
@@ -2477,7 +2477,7 @@ if [ -z ${VIASH_PAR_FEATURECOUNTS_FEATURE_TYPE+x} ]; then
VIASH_PAR_FEATURECOUNTS_FEATURE_TYPE="exon"
fi
if [ -z ${VIASH_PAR_BIOTYPES_HEADER+x} ]; then
VIASH_PAR_BIOTYPES_HEADER="assets/multiqc/biotypes_header.txt"
VIASH_PAR_BIOTYPES_HEADER="src/assets/multiqc/biotypes_header.txt"
fi
if [ -z ${VIASH_PAR_RSEQC_MODULES+x} ]; then
VIASH_PAR_RSEQC_MODULES="bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication"
@@ -2546,10 +2546,10 @@ 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="assets/multiqc/deseq2_pca_header.txt"
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="assets/multiqc/deseq2_clustering_header.txt"
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"

14
target/executable/workflows/rnaseq/.config.vsh.yaml
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@@ -295,7 +295,7 @@ argument_groups:
\ be used to create the database for SortMeRNA."
info: null
default:
- "assets/rrna-db-defaults.txt"
- "src/assets/rrna-db-defaults.txt"
must_exist: true
create_parent: true
required: false
@@ -683,7 +683,7 @@ argument_groups:
name: "--pca_header_multiqc"
info: null
default:
- "assets/multiqc/deseq2_pca_header.txt"
- "src/assets/multiqc/deseq2_pca_header.txt"
must_exist: true
create_parent: true
required: false
@@ -694,7 +694,7 @@ argument_groups:
name: "--clustering_header_multiqc"
info: null
default:
- "assets/multiqc/deseq2_clustering_header.txt"
- "src/assets/multiqc/deseq2_clustering_header.txt"
must_exist: true
create_parent: true
required: false
@@ -754,7 +754,7 @@ argument_groups:
name: "--multiqc_custom_config"
info: null
default:
- "assets/multiqc_config.yml"
- "src/assets/multiqc_config.yml"
must_exist: true
create_parent: true
required: false
@@ -772,7 +772,7 @@ argument_groups:
name: "--multiqc_methods_description"
info: null
default:
- "assets/methods_description_template.yml"
- "src/assets/methods_description_template.yml"
must_exist: true
create_parent: true
required: false
@@ -2117,8 +2117,8 @@ build_info:
output: "target/executable/workflows/rnaseq"
executable: "target/executable/workflows/rnaseq/rnaseq"
viash_version: "0.9.0"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/workflows/prepare_genome"
- "target/nextflow/cat_fastq"

20
target/executable/workflows/rnaseq/rnaseq
View File

@@ -314,7 +314,7 @@ function ViashHelp {
echo ""
echo " --ribo_database_manifest"
echo " type: file, file must exist"
echo " default: assets/rrna-db-defaults.txt"
echo " default: src/assets/rrna-db-defaults.txt"
echo " Text file containing paths to fasta files (one per line) that will be"
echo " used to create the database for SortMeRNA."
echo ""
@@ -545,11 +545,11 @@ function ViashHelp {
echo ""
echo " --pca_header_multiqc"
echo " type: file, file must exist"
echo " default: assets/multiqc/deseq2_pca_header.txt"
echo " default: src/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 " default: src/assets/multiqc/deseq2_clustering_header.txt"
echo ""
echo " --deseq2_vst"
echo " type: boolean"
@@ -576,14 +576,14 @@ function ViashHelp {
echo "Multiqc paramenters:"
echo " --multiqc_custom_config"
echo " type: file, file must exist"
echo " default: assets/multiqc_config.yml"
echo " default: src/assets/multiqc_config.yml"
echo ""
echo " --multiqc_title"
echo " type: string"
echo ""
echo " --multiqc_methods_description"
echo " type: file, file must exist"
echo " default: assets/methods_description_template.yml"
echo " default: src/assets/methods_description_template.yml"
echo ""
echo "Output:"
echo " --output_fasta"
@@ -3202,7 +3202,7 @@ if [ -z ${VIASH_PAR_REMOVE_RIBO_RNA+x} ]; then
VIASH_PAR_REMOVE_RIBO_RNA="false"
fi
if [ -z ${VIASH_PAR_RIBO_DATABASE_MANIFEST+x} ]; then
VIASH_PAR_RIBO_DATABASE_MANIFEST="assets/rrna-db-defaults.txt"
VIASH_PAR_RIBO_DATABASE_MANIFEST="src/assets/rrna-db-defaults.txt"
fi
if [ -z ${VIASH_PAR_WITH_UMI+x} ]; then
VIASH_PAR_WITH_UMI="false"
@@ -3319,10 +3319,10 @@ if [ -z ${VIASH_PAR_EXTRA_PRESEQ_ARGS+x} ]; then
VIASH_PAR_EXTRA_PRESEQ_ARGS="-verbose -seed 1 -seg_len 100000000"
fi
if [ -z ${VIASH_PAR_PCA_HEADER_MULTIQC+x} ]; then
VIASH_PAR_PCA_HEADER_MULTIQC="assets/multiqc/deseq2_pca_header.txt"
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="assets/multiqc/deseq2_clustering_header.txt"
VIASH_PAR_CLUSTERING_HEADER_MULTIQC="src/assets/multiqc/deseq2_clustering_header.txt"
fi
if [ -z ${VIASH_PAR_DESEQ2_VST+x} ]; then
VIASH_PAR_DESEQ2_VST="true"
@@ -3337,10 +3337,10 @@ if [ -z ${VIASH_PAR_RSEQC_MODULES+x} ]; then
VIASH_PAR_RSEQC_MODULES="bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication"
fi
if [ -z ${VIASH_PAR_MULTIQC_CUSTOM_CONFIG+x} ]; then
VIASH_PAR_MULTIQC_CUSTOM_CONFIG="assets/multiqc_config.yml"
VIASH_PAR_MULTIQC_CUSTOM_CONFIG="src/assets/multiqc_config.yml"
fi
if [ -z ${VIASH_PAR_MULTIQC_METHODS_DESCRIPTION+x} ]; then
VIASH_PAR_MULTIQC_METHODS_DESCRIPTION="assets/methods_description_template.yml"
VIASH_PAR_MULTIQC_METHODS_DESCRIPTION="src/assets/methods_description_template.yml"
fi
if [ -z ${VIASH_PAR_OUTPUT_FASTA+x} ]; then
VIASH_PAR_OUTPUT_FASTA="reference/genome.fasta"