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Build branch multiple_fixes with version multiple_fixes (b291665)

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Build pipeline: viash-hub.rnaseq.multiple-fixes-kj62j

Source commit: b291665ddc

Source message: minor changes
This commit is contained in:
CI
2024-09-24 10:36:19 +00:00
parent 29c8cdb0a2
commit 0e55094fd4
209 changed files with 15628 additions and 2971 deletions
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36
assets/multiqc_config.yml
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@@ -1,8 +1,8 @@
report_comment: >
This report has been generated by the <a href="https://github.com/data-intuitive/rnaseq.vsh" </a>
This report has been generated by the <a href="https://github.com/viash-hub/rnaseq" </a>
analysis pipeline.
report_section_order:
"rnaseq.vsh-methods-description":
"rnaseq-methods-description":
order: -1000
software_versions:
order: -1001
@@ -10,6 +10,7 @@ report_section_order:
order: -1002
export_plots: true
disable_version_detection: true
# Run only these modules
run_modules:
@@ -19,7 +20,6 @@ run_modules:
- fastp
- sortmerna
- star
# - hisat2
- rsem
- salmon
- kallisto
@@ -64,17 +64,16 @@ table_columns_visible:
fastqc:
percent_duplicates: False
extra_fn_clean_exts:
- ".salmon_quant"
fn_clean_extn:
- ".mapping_quality"
- ".genome_sorted"
- ".MarkDuplicates"
- ".MarkDuplicates_flagstat"
- ".MarkDuplicates_stats"
- ".genome_sorted"
- ".MarkDuplicates"
- ".genome_sorted_MarkDuplicates"
- ".star_aligned"
- ".read_1"
- ".read_2"
- ".read_2"
- "_merged"
# See https://github.com/ewels/MultiQC_TestData/blob/master/data/custom_content/with_config/table_headerconfig/multiqc_config.yaml
custom_data:
@@ -113,36 +112,37 @@ custom_data:
# See https://multiqc.info/docs/#optimise-file-search-patterns for details
sp:
fastqc/zip:
fastqc:
fn: "*.fastqc.zip"
cutadapt:
fn: "*.trimming_report.txt"
fn: "*.trimming_report*.txt"
fastp:
fn: "*.fastp.json"
fn: "*.fastp_out.json"
sortmerna:
fn: "*sortmerna*.log"
star:
fn: "*.star_aligned.log.final.out"
fn: "*.star_align_reads.log.txt"
# hisat2:
# fn: "*.hisat2.summary.log"
salmon/meta:
fn: "*meta_info.json"
# TODO: Add Salmon meta info
# salmon:
# fn: "*meta_info.json"
preseq:
fn: "*.lc_extrap.txt"
samtools/stats:
fn: "*.stats"
fn: "*_stats.output.txt"
samtools/flagstat:
fn: "*.flagstat"
fn: "*_flagstat.output.flagstat"
samtools/idxstats:
fn: "*.idxstats*"
fn: "*_idxstats.output.idxstats"
rseqc/bam_stat:
fn: "*.mapping_quality.txt"

4
src/cat_fastq/config.vsh.yaml
View File

@@ -25,13 +25,13 @@ argument_groups:
- name: "--fastq_1"
type: file
direction: output
default: $id_merged.fastq
default: $id_r1_merged.fastq
description: Concatenated read 1 fastq
- name: "--fastq_2"
type: file
direction: output
must_exist: false
default: $id_merged.fastq
default: $id_r2_merged.fastq
description: Concatenated read 2 fastq
resources:

5
src/prepare_multiqc_input/script.sh
View File

@@ -22,7 +22,8 @@ IFS="," read -ra star_multiqc <<< $par_star_multiqc && for file in "${star_multi
IFS="," read -ra rsem_multiqc <<< $par_rsem_multiqc && for file in "${rsem_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done
IFS="," read -ra salmon_multiqc <<< $par_salmon_multiqc && for file in "${salmon_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done
# TODO: Fetch Salmon meta info
# IFS="," read -ra salmon_multiqc <<< $par_salmon_multiqc && for file in "${salmon_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done
IFS="," read -ra samtools_stats <<< $par_samtools_stats && for file in "${samtools_stats[@]}"; do [ -e "$file" ] && cp -r "$file" $par_output/; done
@@ -37,7 +38,7 @@ IFS="," read -ra pseudo_multiqc <<< $par_pseudo_multiqc && for file in "${pseudo
IFS="," read -ra featurecounts_multiqc <<< $par_featurecounts_multiqc && for file in "${featurecounts_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done
IFS="," read -ra featurecounts_rrna_multiqc <<< $par_featurecounts_rrna_multiqc&& for file in "${featurecounts_rrna_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done
IFS="," read -ra featurecounts_rrna_multiqc <<< $par_featurecounts_rrna_multiqc && for file in "${featurecounts_rrna_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done
[ -e "$par_aligner_pca_multiqc" ] && cp -r "$par_aligner_pca_multiqc" "$par_output/"

7
src/rsem/rsem_merge_counts/config.vsh.yaml
View File

@@ -18,9 +18,6 @@ argument_groups:
- name: "--counts_transcripts"
type: file
description: Expression counts on transcript level (isoforms)
- name: "--versions"
type: file
must_exist: false
- name: "Output"
arguments:
@@ -44,10 +41,6 @@ argument_groups:
description: File containing transcript TPM across all samples.
default: rsem.merged.transcript_tpm.tsv
direction: output
- name: "--updated_versions"
type: file
default: versions.yml
direction: output
resources:
- type: bash_script

9
src/workflows/genome_alignment_and_quant/config.vsh.yaml
View File

@@ -96,7 +96,7 @@ argument_groups:
- name: "--star_multiqc"
type: file
direction: output
default: $id.log
default: $id_star.log
- name: "--genome_bam_sorted"
type: file
direction: output
@@ -145,7 +145,7 @@ argument_groups:
type: file
direction: output
default: $id.quant.sf
- name: "--counts_gene"
- name: "--rsem_counts_gene"
type: file
description: Expression counts on gene level
default: $id.genes.results
@@ -194,8 +194,9 @@ dependencies:
repository: biobox
- name: samtools/samtools_idxstats
repository: biobox
- name: umi_tools/umi_tools_dedup
repository: biobox
- name: umitools/umitools_dedup
# - name: umi_tools/umi_tools_dedup
# repository: biobox
- name: umitools_prepareforquant
# - name: umi_tools/umi_tools_prepareforquant
# repository: biobox

2
src/workflows/post_processing/test_run.sh
View File

@@ -1,6 +1,6 @@
#!/bin/bash
viash ns build --setup cb --parallel
# viash ns build --setup cb --parallel
nextflow run target/nextflow/workflows/post_processing/main.nf \
--publish_dir "testData/paired_end_test" \

15
src/workflows/quality_control/config.vsh.yaml
View File

@@ -41,10 +41,10 @@ argument_groups:
description: By default, the pipeline uses the gene_name field to obtain additional gene identifiers from the input GTF file when running Salmon.
- name: "--quant_out_dir"
type: file
description: Directory containing quantification results.
description: Directory containing Salmon quantification results.
- name: "--quant_results_file"
type: file
description: Quantification file.
description: Salmon quantification file.
- name: "--pseudo_quant_out_dir"
type: file
description: Directory containing quantification results for pseudo alignment.
@@ -59,8 +59,14 @@ argument_groups:
description: Method used for alognment and qqunatification.
- name: "--pseudo_aligner"
type: string
description: Method used for [seudo alignment and quantification.
description: Method used for pseudo alignment and quantification.
- name: "--rsem_counts_gene"
type: file
description: Expression counts on gene level
- name: "--rsem_counts_transcripts"
type: file
description: Expression counts on transcript level
- name: "--skip_qc"
type: boolean
default: false
@@ -652,6 +658,7 @@ dependencies:
- name: prepare_multiqc_input
- name: multiqc
repository: biobox
- name: rsem/rsem_merge_counts
- name: workflows/merge_quant_results
runners:

52
src/workflows/quality_control/main.nf
View File

@@ -215,6 +215,7 @@ workflow run_wf {
| toSortedList
// TODO: Get Salmon meta info
| map { list ->
def ids = list.collect { id, state -> state.id }
def strandedness = list.collect { id, state -> state.strandedness }
@@ -254,6 +255,14 @@ workflow run_wf {
(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 :
@@ -348,9 +357,9 @@ workflow run_wf {
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 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]
@@ -388,6 +397,8 @@ workflow run_wf {
read_duplication_output_duplication_rate_mapping: read_duplication_output_duplication_rate_mapping,
tin_output_summary: tin_output_summary,
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,
@@ -415,7 +426,7 @@ workflow run_wf {
// Merge quantification results of alignment
| merge_quant_results.run (
runIf: { id, state -> !state.skip_align && state.aligner == 'star_salmon' },
runIf: { id, state -> (!state.skip_align && state.aligner == 'star_salmon') || !skip_pseudo_align },
fromState: [
"salmon_quant_results": "quant_results",
"gtf": "gtf",
@@ -437,16 +448,33 @@ workflow run_wf {
key: "merge_qunat_results"
)
| rsem_merge_counts.run (
runIf: { id, state -> state.aligner == 'star_rsem' },
fromState: [
"counts_gene": "rsem_counts_gene",
"counts_transcripts": "rsem_counts_transcripts"
],
toState: [
"tpm_gene": "merged_gene_tpm",
"counts_gene": "merged_gene_counts",
"tpm_transcript": "merged_transcript_tpm",
"counts_transcript": "merged_transcript_counts"
]
)
| deseq2_qc.run (
runIf: { id, state -> !state.skip_qc && !state.skip_deseq2_qc && !state.skip_align },
fromState: [
"counts": "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"
],
fromState: { id, state ->
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
]
},
toState: [
"deseq2_output": "deseq2_output",
"deseq2_pca_multiqc": "pca_multiqc",

138
src/workflows/rnaseq/config.vsh.yaml
View File

@@ -345,6 +345,7 @@ argument_groups:
- name: Output
arguments:
# Reference files
- name: "--output_fasta"
type: file
direction: output
@@ -381,6 +382,8 @@ argument_groups:
direction: output
description: Path to Kallisto index.
default: genome/index/Kallisto
# fastq
- name: "--output_fastq_1"
type: file
direction: output
@@ -395,6 +398,8 @@ argument_groups:
must_exist: false
description: Path to output directory
default: fastq/$id.read_2.fastq
# FastQC
- name: "--fastqc_html_1"
type: file
direction: output
@@ -423,28 +428,6 @@ argument_groups:
required: false
must_exist: false
default: fastqc_raw/$id.read_2.fastqc.zip
- name: "--trim_log_1"
type: file
direction: output
required: false
must_exist: false
default: trimgalore/$id.read_1.trimming_report.txt
- name: "--trim_log_2"
type: file
direction: output
required: false
must_exist: false
default: trimgalore/$id.read_2.trimming_report.txt
- name: --fastp_trim_json
type: file
description: The fastp json format report file name
default: fastp/$id_out.json
direction: output
- name: --fastp_trim_html
type: file
description: The fastp html format report file name
default: fastp/$id_out.html
direction: output
- name: "--trim_html_1"
type: file
direction: output
@@ -469,6 +452,34 @@ argument_groups:
required: false
must_exist: false
default: fastqc_trim/$id.read_2.trimmed_fastqc.zip
# TrimGalore
- name: "--trim_log_1"
type: file
direction: output
required: false
must_exist: false
default: trimgalore/$id.read_1.trimming_report.txt
- name: "--trim_log_2"
type: file
direction: output
required: false
must_exist: false
default: trimgalore/$id.read_2.trimming_report.txt
# fastp
- name: --fastp_trim_json
type: file
description: The fastp json format report file name
default: fastp/$id_out.json
direction: output
- name: --fastp_trim_html
type: file
description: The fastp html format report file name
default: fastp/$id_out.html
direction: output
# SortMeRNA
- name: "--sortmerna_log"
type: file
direction: output
@@ -476,6 +487,8 @@ argument_groups:
required: false
must_exist: false
description: Sortmerna log file.
# STAR
- name: "--star_alignment"
type: file
direction: output
@@ -488,6 +501,16 @@ argument_groups:
type: file
direction: output
default: STAR_alignment/genome_processed/$id.genome.bam.bai
- name: "--transcriptome_bam"
type: file
direction: output
default: STAR_alignment/transcriptome_processed/$id.transcriptome.bam
- name: "--transcriptome_bam_index"
type: file
direction: output
default: STAR_alignment/transcriptome_processed/$id.transcriptome.bam.bai
# samtools
- name: "--genome_bam_stats"
type: file
direction: output
@@ -500,14 +523,6 @@ argument_groups:
type: file
direction: output
default: samtools_stats/$id.genome.idxstats
- name: "--transcriptome_bam"
type: file
direction: output
default: STAR_alignment/transcriptome_processed/$id.transcriptome.bam
- name: "--transcriptome_bam_index"
type: file
direction: output
default: STAR_alignment/transcriptome_processed/$id.transcriptome.bam.bai
- name: "--transcriptome_bam_stats"
type: file
direction: output
@@ -520,10 +535,41 @@ argument_groups:
type: file
direction: output
default: samtools_stats/$id.transcriptome.idxstats
# Salmon
- name: "--salmon_quant_results"
type: file
direction: output
default: alignment_quantification/$id
default: Salmon/$id
# RSEM
- name: "--rsem_counts_gene"
type: file
description: Expression counts on gene level
default: RSEM/$id.genes.results
direction: output
- name: "--rsem_counts_transcripts"
type: file
description: Expression counts on transcript level
default: RSEM/$id.isoforms.results
direction: output
- name: "--bam_star_rsem"
type: file
description: BAM file generated by STAR (from RSEM)
default: RSEM/$id.STAR.genome.bam
direction: output
- name: "--bam_genome_rsem"
type: file
description: Genome BAM file (from RSEM)
default: RSEM/$id.genome.bam
direction: output
- name: "--bam_transcript_rsem"
type: file
description: Transcript BAM file (from RSEM)
default: RSEM/$id.transcript.bam
direction: output
# Quantification (alignment)
- name: "--tpm_gene"
type: file
direction: output
@@ -548,14 +594,18 @@ argument_groups:
type: file
direction: output
default: alignment_quantification/transcript_counts.tsv
- name: "--salmon_merged_summarizedexperiment"
- name: "--quant_merged_summarizedexperiment"
type: file
direction: output
default: alignment_quantification/summarizedexperiment
# MarkDuplicates
- name: "--markduplicates_metrics"
type: file
direction: output
default: picard/$id.sorted.MarkDuplicates.metrics.txt
# StringTie
- name: "--stringtie_transcript_gtf"
type: file
direction: output
@@ -572,6 +622,8 @@ argument_groups:
type: file
direction: output
default: stringtie/$id.ballgown
# featureCounts
- name: "--featurecounts"
type: file
direction: output
@@ -590,6 +642,8 @@ argument_groups:
direction: output
must_exist: false
default: featurecounts/$id.featureCounts_rrna_mqc.tsv
# bedGraph
- name: "--bedgraph_forward"
type: file
direction: output
@@ -598,6 +652,8 @@ argument_groups:
type: file
direction: output
default: bedgraph/$id.reverse.bedgraph
# bigWig
- name: "--bigwig_forward"
type: file
direction: output
@@ -606,10 +662,14 @@ argument_groups:
type: file
direction: output
default: bigwig/$id.reverse.bigwig
# preseq lc_extrap
- name: "--preseq_output"
type: file
direction: output
default: preseq/$id.lc_extrap.txt
# RSeQC
- name: "--bamstat_output"
type: file
direction: output
@@ -748,6 +808,8 @@ argument_groups:
required: false
default: RSeQC/tin/xls/$id.tin.xls
description: file with TIN metrics (xls)
# DupRadar
- name: "--dupradar_output_dupmatrix"
type: file
direction: output
@@ -789,6 +851,8 @@ argument_groups:
direction: output
required: false
default: dupradar/intercept_slope/$id.intercept_slope.txt
# Qualimap
- name: "--qualimap_output_pdf"
type: file
direction: output
@@ -800,10 +864,14 @@ argument_groups:
direction: output
required: false
default: qualimap/$id
# DESeq2
- name: "--deseq2_output"
type: file
direction: output
default: deseq2_qc
# MultiQC
- name: "--multiqc_report"
type: file
direction: output
@@ -819,10 +887,8 @@ argument_groups:
- name: "--multiqc_versions"
type: file
direction: output
- name: "--versions"
type: file
must_exist: false
direction: output
# Quantification (pseudo alignment)
- name: "--pseudo_counts_gene"
type: file
direction: output

2
src/workflows/rnaseq/main.nf
View File

@@ -340,6 +340,8 @@ workflow run_wf {
"genome_bam_index": "genome_bam_index",
"quant_out_dir": "quant_out_dir",
"quant_results_file": "quant_results_file",
"rsem_counts_gene": "rsem_counts_gene",
"rsem_counts_transcripts": "rsem_counts_transcripts",
"pseudo_quant_out_dir": "pseudo_quant_out_dir",
"pseudo_salmon_quant_results_file": "pseudo_salmon_quant_results_file",
"pseudo_kallisto_quant_results_file": "pseudo_kallisto_quant_results_file",

2
src/workflows/rnaseq/test_run.sh
View File

@@ -6,9 +6,9 @@ cat > testData/minimal_test/input_fastq/sample_sheet.csv << HERE
id,fastq_1,fastq_2,strandedness
WT_REP1,SRR6357070_1.fastq.gz;SRR6357071_1.fastq.gz,SRR6357070_2.fastq.gz;SRR6357071_2.fastq.gz,reverse
WT_REP2,SRR6357072_1.fastq.gz,SRR6357072_2.fastq.gz,reverse
RAP1_IAA_30M_REP1,SRR6357076_1.fastq.gz,SRR6357076_2.fastq.gz,reverse
RAP1_UNINDUCED_REP1,SRR6357073_1.fastq.gz,,reverse
RAP1_UNINDUCED_REP2,SRR6357074_1.fastq.gz;SRR6357075_1.fastq.gz,,reverse
RAP1_IAA_30M_REP1,SRR6357076_1.fastq.gz,SRR6357076_2.fastq.gz,reverse
HERE
echo ">> Test 1: Trimming reads with Trim galore; alignment with STAR and quantification with Salmon"

637
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/umi_tools/umi_tools_dedup/.config.vsh.yaml
View File

@@ -1,637 +0,0 @@
name: "umi_tools_dedup"
namespace: "umi_tools"
version: "v0.2.0"
authors:
- name: "Emma Rousseau"
roles:
- "author"
- "maintainer"
info:
links:
email: "emma@data-intuitive.com"
github: "emmarousseau"
linkedin: "emmarousseau1"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Bioinformatician"
argument_groups:
- name: "Inputs"
arguments:
- type: "file"
name: "--input"
alternatives:
- "--stdin"
description: "Input BAM or SAM file. Use --in_sam to specify SAM format."
info: null
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--in_sam"
description: "By default, inputs are assumed to be in BAM format. Use this options\
\ to specify the use of SAM\nformat for input.\n"
info: null
direction: "input"
- type: "file"
name: "--bai"
description: "BAM index"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--random_seed"
description: "Random seed to initialize number generator with."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Outputs"
arguments:
- type: "file"
name: "--output"
alternatives:
- "--stdout"
description: "Deduplicated BAM file."
info: null
must_exist: true
create_parent: true
required: true
direction: "output"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--out_sam"
description: "By default, outputa are written in BAM format. Use this options\
\ to specify the use of SAM format\nfor output.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--paired"
description: "BAM is paired end - output both read pairs. This will also force\
\ the use of the template length\nto determine reads with the same mapping coordinates.\n"
info: null
direction: "input"
- type: "string"
name: "--output_stats"
description: "Generate files containing UMI based deduplication statistics files\
\ with this prefix in the file names.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--extract_umi_method"
description: "Specify the method by which the barcodes were encoded in the read.\n\
The options are:\n * read_id (default) \n * tag\n * umis\n"
info: null
example:
- "read_id"
required: false
choices:
- "read_id"
- "tag"
- "umis"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--umi_tag"
description: "The tag containing the UMI sequence. This is only required if the\
\ extract_umi_method is set to tag.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--umi_separator"
description: "The separator used to separate the UMI from the read sequence. This\
\ is only required if the\nextract_umi_method is set to id_read. Default: `_`.\n"
info: null
example:
- "_"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--umi_tag_split"
description: "Separate the UMI in tag by <SPLIT> and take the first element."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--umi_tag_delimiter"
description: "Separate the UMI in by <DELIMITER> and concatenate the elements."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--cell_tag"
description: "The tag containing the cell barcode sequence. This is only required\
\ if the extract_umi_method\nis set to tag.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--cell_tag_split"
description: "Separate the cell barcode in tag by <SPLIT> and take the first element."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--cell_tag_delimiter"
description: "Separate the cell barcode in by <DELIMITER> and concatenate the\
\ elements."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Grouping Options"
arguments:
- type: "string"
name: "--method"
description: "The method to use for grouping reads. \nThe options are: \n * unique\n\
\ * percentile\n * cluster\n * adjacency\n * directional (default)\n"
info: null
example:
- "directional"
required: false
choices:
- "unique"
- "percentile"
- "cluster"
- "adjacency"
- "directional"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--edit_distance_threshold"
description: "For the adjacency and cluster methods the threshold for the edit\
\ distance to connect two\nUMIs in the network can be increased. The default\
\ value of 1 works best unless the UMI is\nvery long (>14bp). Default: `1`.\n"
info: null
example:
- 1
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--spliced_is_unique"
description: "Causes two reads that start in the same position on the same strand\
\ and having the same UMI\nto be considered unique if one is spliced and the\
\ other is not. (Uses the 'N' cigar operation\nto test for splicing).\n"
info: null
direction: "input"
- type: "integer"
name: "--soft_clip_threshold"
description: "Mappers that soft clip will sometimes do so rather than mapping\
\ a spliced read if there is only\na small overhang over the exon junction.\
\ By setting this option, you can treat reads with at\nleast this many bases\
\ soft-clipped at the 3' end as spliced. Default: `4`.\n"
info: null
example:
- 4
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--multimapping_detection_method"
description: "If the sam/bam contains tags to identify multimapping reads, you\
\ can specify for use when selecting\nthe best read at a given loci. Supported\
\ tags are `NH`, `X0` and `XT`. If not specified, the read\nwith the highest\
\ mapping quality will be selected.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--read_length"
description: "Use the read length as a criteria when deduping, for e.g. sRNA-Seq."
info: null
direction: "input"
- name: "Single-cell RNA-Seq Options"
arguments:
- type: "boolean_true"
name: "--per_gene"
description: "Reads will be grouped together if they have the same gene. This\
\ is useful if your library prep\ngenerates PCR duplicates with non identical\
\ alignment positions such as CEL-Seq. Note this option\nis hardcoded to be\
\ on with the count command. I.e. counting is always performed per-gene. Must\
\ be\ncombined with either --gene_tag or --per_contig option.\n"
info: null
direction: "input"
- type: "string"
name: "--gene_tag"
description: "Deduplicate per gene. The gene information is encoded in the bam\
\ read tag specified.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--assigned_status_tag"
description: "BAM tag which describes whether a read is assigned to a gene. Defaults\
\ to the same value as given\nfor --gene_tag.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--skip_tags_regex"
description: "Use in conjunction with the --assigned_status_tag option to skip\
\ any reads where the tag matches\nthis regex. Default (\"^[__|Unassigned]\"\
) matches anything which starts with \"__\" or \"Unassigned\".\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--per_contig"
description: "Deduplicate per contig (field 3 in BAM; RNAME). All reads with the\
\ sam contig will be considered to\nhave the same alignment position. This is\
\ useful if you have aligned to a reference transcriptome\nwith one transcript\
\ per gene. If you have aligned to a transcriptome with more than one transcript\n\
per gene, you can supply a map between transcripts and gene using the --gene_transcript_map\
\ option.\n"
info: null
direction: "input"
- type: "file"
name: "--gene_transcript_map"
description: "A file containing a mapping between gene names and transcript names.\
\ The file should be tab\nseparated with the gene name in the first column and\
\ the transcript name in the second column.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--per_cell"
description: "Reads will only be grouped together if they have the same cell barcode.\
\ Can be combined with\n--per_gene.\n"
info: null
direction: "input"
- name: "SAM/BAM Options"
arguments:
- type: "integer"
name: "--mapping_quality"
description: "Minimium mapping quality (MAPQ) for a read to be retained. Default:\
\ `0`.\n"
info: null
example:
- 0
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--unmapped_reads"
description: "How unmapped reads should be handled. \nThe options are:\n * \"\
discard\": Discard all unmapped reads. (default)\n * \"use\": If read2\
\ is unmapped, deduplicate using read1 only. Requires --paired.\n * \"output\"\
: Output unmapped reads/read pairs without UMI grouping/deduplication. Only\
\ available in umi_tools group.\n"
info: null
example:
- "discard"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--chimeric_pairs"
description: "How chimeric pairs should be handled. \nThe options are:\n * \"\
discard\": Discard all chimeric read pairs.\n * \"use\": Deduplicate using\
\ read1 only. (default)\n * \"output\": Output chimeric pairs without UMI\
\ grouping/deduplication. Only available in\n umi_tools group.\n"
info: null
example:
- "use"
required: false
choices:
- "discard"
- "use"
- "output"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--unpaired_reads"
description: "How unpaired reads should be handled. \nThe options are: \n * \"\
discard\": Discard all unmapped reads.\n * \"use\": If read2 is unmapped, deduplicate\
\ using read1 only. Requires --paired. (default)\n * \"output\": Output unmapped\
\ reads/read pairs without UMI grouping/deduplication. Only available\n \
\ in umi_tools group.\n"
info: null
example:
- "use"
required: false
choices:
- "discard"
- "use"
- "output"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--ignore_umi"
description: "Ignore the UMI and group reads using mapping coordinates only."
info: null
direction: "input"
- type: "double"
name: "--subset"
description: "Only consider a fraction of the reads, chosen at random. This is\
\ useful for doing saturation\nanalyses.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--chrom"
description: "Only consider a single chromosome. This is useful for debugging/testing\
\ purposes."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Group/Dedup Options"
arguments:
- type: "boolean_true"
name: "--no_sort_output"
description: "By default, output is sorted. This involves the use of a temporary\
\ unsorted file (saved in\n--temp_dir). Use this option to turn off sorting.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--buffer_whole_contig"
description: "Forces dedup to parse an entire contig before yielding any reads\
\ for deduplication. This is the\nonly way to absolutely guarantee that all\
\ reads with the same start position are grouped together\nfor deduplication\
\ since dedup uses the start position of the read, not the alignment coordinate\
\ on\nwhich the reads are sorted. However, by default, dedup reads for another\
\ 1000bp before outputting\nread groups which will avoid any reads being missed\
\ with short read sequencing (<1000bp).\n"
info: null
direction: "input"
- name: "Common Options"
arguments:
- type: "file"
name: "--log"
alternatives:
- "-L"
description: "File with logging information."
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--log2stderr"
description: "Send logging information to stderr."
info: null
direction: "input"
- type: "integer"
name: "--verbose"
alternatives:
- "-v"
description: "Log level. The higher, the more output. Default: `0`.\n"
info: null
example:
- 0
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--error"
alternatives:
- "-E"
description: "File with error information."
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--temp_dir"
description: "Directory for temporary files. If not set, the bash environmental\
\ variable TMPDIR is used.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--compresslevel"
description: "Level of Gzip compression to use. Default=6 matches GNU gzip rather\
\ than python gzip default.\nDefault: `6`.\n"
info: null
example:
- 6
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--timeit"
description: "Store timing information in file."
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--timeit_name"
description: "Name in timing file for this class of jobs. Default: `all`.\n"
info: null
example:
- "all"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--timeit_header"
description: "Add header for timing information."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
resources:
- type: "bash_script"
path: "script.sh"
is_executable: true
description: "Deduplicate reads based on the mapping co-ordinate and the UMI attached\
\ to the read.\n"
test_resources:
- type: "bash_script"
path: "test.sh"
is_executable: true
- type: "file"
path: "test_data"
info: null
status: "enabled"
requirements:
commands:
- "ps"
keywords:
- "umi_tools"
- "deduplication"
- "dedup"
license: "MIT"
references:
doi:
- "10.1101/gr.209601.116"
links:
repository: "https://github.com/CGATOxford/UMI-tools"
homepage: "https://umi-tools.readthedocs.io/en/latest/"
documentation: "https://umi-tools.readthedocs.io/en/latest/reference/dedup.html"
runners:
- type: "executable"
id: "executable"
docker_setup_strategy: "ifneedbepullelsecachedbuild"
- type: "nextflow"
id: "nextflow"
directives:
tag: "$id"
auto:
simplifyInput: true
simplifyOutput: false
transcript: false
publish: false
config:
labels:
mem1gb: "memory = 1000000000.B"
mem2gb: "memory = 2000000000.B"
mem5gb: "memory = 5000000000.B"
mem10gb: "memory = 10000000000.B"
mem20gb: "memory = 20000000000.B"
mem50gb: "memory = 50000000000.B"
mem100gb: "memory = 100000000000.B"
mem200gb: "memory = 200000000000.B"
mem500gb: "memory = 500000000000.B"
mem1tb: "memory = 1000000000000.B"
mem2tb: "memory = 2000000000000.B"
mem5tb: "memory = 5000000000000.B"
mem10tb: "memory = 10000000000000.B"
mem20tb: "memory = 20000000000000.B"
mem50tb: "memory = 50000000000000.B"
mem100tb: "memory = 100000000000000.B"
mem200tb: "memory = 200000000000000.B"
mem500tb: "memory = 500000000000000.B"
mem1gib: "memory = 1073741824.B"
mem2gib: "memory = 2147483648.B"
mem4gib: "memory = 4294967296.B"
mem8gib: "memory = 8589934592.B"
mem16gib: "memory = 17179869184.B"
mem32gib: "memory = 34359738368.B"
mem64gib: "memory = 68719476736.B"
mem128gib: "memory = 137438953472.B"
mem256gib: "memory = 274877906944.B"
mem512gib: "memory = 549755813888.B"
mem1tib: "memory = 1099511627776.B"
mem2tib: "memory = 2199023255552.B"
mem4tib: "memory = 4398046511104.B"
mem8tib: "memory = 8796093022208.B"
mem16tib: "memory = 17592186044416.B"
mem32tib: "memory = 35184372088832.B"
mem64tib: "memory = 70368744177664.B"
mem128tib: "memory = 140737488355328.B"
mem256tib: "memory = 281474976710656.B"
mem512tib: "memory = 562949953421312.B"
cpu1: "cpus = 1"
cpu2: "cpus = 2"
cpu5: "cpus = 5"
cpu10: "cpus = 10"
cpu20: "cpus = 20"
cpu50: "cpus = 50"
cpu100: "cpus = 100"
cpu200: "cpus = 200"
cpu500: "cpus = 500"
cpu1000: "cpus = 1000"
debug: false
container: "docker"
engines:
- type: "docker"
id: "docker"
image: "quay.io/biocontainers/umi_tools:1.1.5--py39hf95cd2a_1"
target_registry: "images.viash-hub.com"
target_tag: "v0.2.0"
namespace_separator: "/"
setup:
- type: "docker"
run:
- "umi_tools -v | sed 's/ version//g' > /var/software_versions.txt\n"
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/umi_tools/umi_tools_dedup/config.vsh.yaml"
runner: "nextflow"
engine: "docker|native"
output: "target/nextflow/umi_tools/umi_tools_dedup"
executable: "target/nextflow/umi_tools/umi_tools_dedup/main.nf"
viash_version: "0.9.0"
git_commit: "7e530218844c373048bc33de58f021b6460642e5"
git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
package_config:
name: "biobox"
version: "v0.2.0"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
keywords:
- "bioinformatics"
- "modules"
- "sequencing"
license: "MIT"
organization: "vsh"
links:
repository: "https://github.com/viash-hub/biobox"
issue_tracker: "https://github.com/viash-hub/biobox/issues"

635
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/umi_tools/umi_tools_dedup/nextflow_schema.json
View File

@@ -1,635 +0,0 @@
{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "umi_tools_dedup",
"description": "Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.\n",
"type": "object",
"definitions": {
"inputs" : {
"title": "Inputs",
"type": "object",
"description": "No description",
"properties": {
"input": {
"type":
"string",
"description": "Type: `file`, required. Input BAM or SAM file",
"help_text": "Type: `file`, required. Input BAM or SAM file. Use --in_sam to specify SAM format."
}
,
"in_sam": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. By default, inputs are assumed to be in BAM format",
"help_text": "Type: `boolean_true`, default: `false`. By default, inputs are assumed to be in BAM format. Use this options to specify the use of SAM\nformat for input.\n"
,
"default": "False"
}
,
"bai": {
"type":
"string",
"description": "Type: `file`. BAM index",
"help_text": "Type: `file`. BAM index"
}
,
"random_seed": {
"type":
"integer",
"description": "Type: `integer`. Random seed to initialize number generator with",
"help_text": "Type: `integer`. Random seed to initialize number generator with."
}
}
},
"outputs" : {
"title": "Outputs",
"type": "object",
"description": "No description",
"properties": {
"output": {
"type":
"string",
"description": "Type: `file`, required, default: `$id.$key.output.output`. Deduplicated BAM file",
"help_text": "Type: `file`, required, default: `$id.$key.output.output`. Deduplicated BAM file."
,
"default": "$id.$key.output.output"
}
,
"out_sam": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. By default, outputa are written in BAM format",
"help_text": "Type: `boolean_true`, default: `false`. By default, outputa are written in BAM format. Use this options to specify the use of SAM format\nfor output.\n"
,
"default": "False"
}
,
"paired": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. BAM is paired end - output both read pairs",
"help_text": "Type: `boolean_true`, default: `false`. BAM is paired end - output both read pairs. This will also force the use of the template length\nto determine reads with the same mapping coordinates.\n"
,
"default": "False"
}
,
"output_stats": {
"type":
"string",
"description": "Type: `string`. Generate files containing UMI based deduplication statistics files with this prefix in the file names",
"help_text": "Type: `string`. Generate files containing UMI based deduplication statistics files with this prefix in the file names.\n"
}
,
"extract_umi_method": {
"type":
"string",
"description": "Type: `string`, example: `read_id`, choices: ``read_id`, `tag`, `umis``. Specify the method by which the barcodes were encoded in the read",
"help_text": "Type: `string`, example: `read_id`, choices: ``read_id`, `tag`, `umis``. Specify the method by which the barcodes were encoded in the read.\nThe options are:\n * read_id (default) \n * tag\n * umis\n",
"enum": ["read_id", "tag", "umis"]
}
,
"umi_tag": {
"type":
"string",
"description": "Type: `string`. The tag containing the UMI sequence",
"help_text": "Type: `string`. The tag containing the UMI sequence. This is only required if the extract_umi_method is set to tag.\n"
}
,
"umi_separator": {
"type":
"string",
"description": "Type: `string`, example: `_`. The separator used to separate the UMI from the read sequence",
"help_text": "Type: `string`, example: `_`. The separator used to separate the UMI from the read sequence. This is only required if the\nextract_umi_method is set to id_read. Default: `_`.\n"
}
,
"umi_tag_split": {
"type":
"string",
"description": "Type: `string`. Separate the UMI in tag by \u003cSPLIT\u003e and take the first element",
"help_text": "Type: `string`. Separate the UMI in tag by \u003cSPLIT\u003e and take the first element."
}
,
"umi_tag_delimiter": {
"type":
"string",
"description": "Type: `string`. Separate the UMI in by \u003cDELIMITER\u003e and concatenate the elements",
"help_text": "Type: `string`. Separate the UMI in by \u003cDELIMITER\u003e and concatenate the elements."
}
,
"cell_tag": {
"type":
"string",
"description": "Type: `string`. The tag containing the cell barcode sequence",
"help_text": "Type: `string`. The tag containing the cell barcode sequence. This is only required if the extract_umi_method\nis set to tag.\n"
}
,
"cell_tag_split": {
"type":
"string",
"description": "Type: `string`. Separate the cell barcode in tag by \u003cSPLIT\u003e and take the first element",
"help_text": "Type: `string`. Separate the cell barcode in tag by \u003cSPLIT\u003e and take the first element."
}
,
"cell_tag_delimiter": {
"type":
"string",
"description": "Type: `string`. Separate the cell barcode in by \u003cDELIMITER\u003e and concatenate the elements",
"help_text": "Type: `string`. Separate the cell barcode in by \u003cDELIMITER\u003e and concatenate the elements."
}
}
},
"grouping options" : {
"title": "Grouping Options",
"type": "object",
"description": "No description",
"properties": {
"method": {
"type":
"string",
"description": "Type: `string`, example: `directional`, choices: ``unique`, `percentile`, `cluster`, `adjacency`, `directional``. The method to use for grouping reads",
"help_text": "Type: `string`, example: `directional`, choices: ``unique`, `percentile`, `cluster`, `adjacency`, `directional``. The method to use for grouping reads. \nThe options are: \n * unique\n * percentile\n * cluster\n * adjacency\n * directional (default)\n",
"enum": ["unique", "percentile", "cluster", "adjacency", "directional"]
}
,
"edit_distance_threshold": {
"type":
"integer",
"description": "Type: `integer`, example: `1`. For the adjacency and cluster methods the threshold for the edit distance to connect two\nUMIs in the network can be increased",
"help_text": "Type: `integer`, example: `1`. For the adjacency and cluster methods the threshold for the edit distance to connect two\nUMIs in the network can be increased. The default value of 1 works best unless the UMI is\nvery long (\u003e14bp). Default: `1`.\n"
}
,
"spliced_is_unique": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Causes two reads that start in the same position on the same strand and having the same UMI\nto be considered unique if one is spliced and the other is not",
"help_text": "Type: `boolean_true`, default: `false`. Causes two reads that start in the same position on the same strand and having the same UMI\nto be considered unique if one is spliced and the other is not. (Uses the \u0027N\u0027 cigar operation\nto test for splicing).\n"
,
"default": "False"
}
,
"soft_clip_threshold": {
"type":
"integer",
"description": "Type: `integer`, example: `4`. Mappers that soft clip will sometimes do so rather than mapping a spliced read if there is only\na small overhang over the exon junction",
"help_text": "Type: `integer`, example: `4`. Mappers that soft clip will sometimes do so rather than mapping a spliced read if there is only\na small overhang over the exon junction. By setting this option, you can treat reads with at\nleast this many bases soft-clipped at the 3\u0027 end as spliced. Default: `4`.\n"
}
,
"multimapping_detection_method": {
"type":
"string",
"description": "Type: `string`. If the sam/bam contains tags to identify multimapping reads, you can specify for use when selecting\nthe best read at a given loci",
"help_text": "Type: `string`. If the sam/bam contains tags to identify multimapping reads, you can specify for use when selecting\nthe best read at a given loci. Supported tags are `NH`, `X0` and `XT`. If not specified, the read\nwith the highest mapping quality will be selected.\n"
}
,
"read_length": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Use the read length as a criteria when deduping, for e",
"help_text": "Type: `boolean_true`, default: `false`. Use the read length as a criteria when deduping, for e.g. sRNA-Seq."
,
"default": "False"
}
}
},
"single-cell rna-seq options" : {
"title": "Single-cell RNA-Seq Options",
"type": "object",
"description": "No description",
"properties": {
"per_gene": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Reads will be grouped together if they have the same gene",
"help_text": "Type: `boolean_true`, default: `false`. Reads will be grouped together if they have the same gene. This is useful if your library prep\ngenerates PCR duplicates with non identical alignment positions such as CEL-Seq. Note this option\nis hardcoded to be on with the count command. I.e. counting is always performed per-gene. Must be\ncombined with either --gene_tag or --per_contig option.\n"
,
"default": "False"
}
,
"gene_tag": {
"type":
"string",
"description": "Type: `string`. Deduplicate per gene",
"help_text": "Type: `string`. Deduplicate per gene. The gene information is encoded in the bam read tag specified.\n"
}
,
"assigned_status_tag": {
"type":
"string",
"description": "Type: `string`. BAM tag which describes whether a read is assigned to a gene",
"help_text": "Type: `string`. BAM tag which describes whether a read is assigned to a gene. Defaults to the same value as given\nfor --gene_tag.\n"
}
,
"skip_tags_regex": {
"type":
"string",
"description": "Type: `string`. Use in conjunction with the --assigned_status_tag option to skip any reads where the tag matches\nthis regex",
"help_text": "Type: `string`. Use in conjunction with the --assigned_status_tag option to skip any reads where the tag matches\nthis regex. Default (\"^[__|Unassigned]\") matches anything which starts with \"__\" or \"Unassigned\".\n"
}
,
"per_contig": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Deduplicate per contig (field 3 in BAM; RNAME)",
"help_text": "Type: `boolean_true`, default: `false`. Deduplicate per contig (field 3 in BAM; RNAME). All reads with the sam contig will be considered to\nhave the same alignment position. This is useful if you have aligned to a reference transcriptome\nwith one transcript per gene. If you have aligned to a transcriptome with more than one transcript\nper gene, you can supply a map between transcripts and gene using the --gene_transcript_map option.\n"
,
"default": "False"
}
,
"gene_transcript_map": {
"type":
"string",
"description": "Type: `file`. A file containing a mapping between gene names and transcript names",
"help_text": "Type: `file`. A file containing a mapping between gene names and transcript names. The file should be tab\nseparated with the gene name in the first column and the transcript name in the second column.\n"
}
,
"per_cell": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Reads will only be grouped together if they have the same cell barcode",
"help_text": "Type: `boolean_true`, default: `false`. Reads will only be grouped together if they have the same cell barcode. Can be combined with\n--per_gene.\n"
,
"default": "False"
}
}
},
"sam/bam options" : {
"title": "SAM/BAM Options",
"type": "object",
"description": "No description",
"properties": {
"mapping_quality": {
"type":
"integer",
"description": "Type: `integer`, example: `0`. Minimium mapping quality (MAPQ) for a read to be retained",
"help_text": "Type: `integer`, example: `0`. Minimium mapping quality (MAPQ) for a read to be retained. Default: `0`.\n"
}
,
"unmapped_reads": {
"type":
"string",
"description": "Type: `string`, example: `discard`. How unmapped reads should be handled",
"help_text": "Type: `string`, example: `discard`. How unmapped reads should be handled. \nThe options are:\n * \"discard\": Discard all unmapped reads. (default)\n * \"use\": If read2 is unmapped, deduplicate using read1 only. Requires --paired.\n * \"output\": Output unmapped reads/read pairs without UMI grouping/deduplication. Only available in umi_tools group.\n"
}
,
"chimeric_pairs": {
"type":
"string",
"description": "Type: `string`, example: `use`, choices: ``discard`, `use`, `output``. How chimeric pairs should be handled",
"help_text": "Type: `string`, example: `use`, choices: ``discard`, `use`, `output``. How chimeric pairs should be handled. \nThe options are:\n * \"discard\": Discard all chimeric read pairs.\n * \"use\": Deduplicate using read1 only. (default)\n * \"output\": Output chimeric pairs without UMI grouping/deduplication. Only available in\n umi_tools group.\n",
"enum": ["discard", "use", "output"]
}
,
"unpaired_reads": {
"type":
"string",
"description": "Type: `string`, example: `use`, choices: ``discard`, `use`, `output``. How unpaired reads should be handled",
"help_text": "Type: `string`, example: `use`, choices: ``discard`, `use`, `output``. How unpaired reads should be handled. \nThe options are: \n * \"discard\": Discard all unmapped reads.\n * \"use\": If read2 is unmapped, deduplicate using read1 only. Requires --paired. (default)\n * \"output\": Output unmapped reads/read pairs without UMI grouping/deduplication. Only available\n in umi_tools group.\n",
"enum": ["discard", "use", "output"]
}
,
"ignore_umi": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Ignore the UMI and group reads using mapping coordinates only",
"help_text": "Type: `boolean_true`, default: `false`. Ignore the UMI and group reads using mapping coordinates only."
,
"default": "False"
}
,
"subset": {
"type":
"number",
"description": "Type: `double`. Only consider a fraction of the reads, chosen at random",
"help_text": "Type: `double`. Only consider a fraction of the reads, chosen at random. This is useful for doing saturation\nanalyses.\n"
}
,
"chrom": {
"type":
"string",
"description": "Type: `string`. Only consider a single chromosome",
"help_text": "Type: `string`. Only consider a single chromosome. This is useful for debugging/testing purposes."
}
}
},
"group/dedup options" : {
"title": "Group/Dedup Options",
"type": "object",
"description": "No description",
"properties": {
"no_sort_output": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. By default, output is sorted",
"help_text": "Type: `boolean_true`, default: `false`. By default, output is sorted. This involves the use of a temporary unsorted file (saved in\n--temp_dir). Use this option to turn off sorting.\n"
,
"default": "False"
}
,
"buffer_whole_contig": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Forces dedup to parse an entire contig before yielding any reads for deduplication",
"help_text": "Type: `boolean_true`, default: `false`. Forces dedup to parse an entire contig before yielding any reads for deduplication. This is the\nonly way to absolutely guarantee that all reads with the same start position are grouped together\nfor deduplication since dedup uses the start position of the read, not the alignment coordinate on\nwhich the reads are sorted. However, by default, dedup reads for another 1000bp before outputting\nread groups which will avoid any reads being missed with short read sequencing (\u003c1000bp).\n"
,
"default": "False"
}
}
},
"common options" : {
"title": "Common Options",
"type": "object",
"description": "No description",
"properties": {
"log": {
"type":
"string",
"description": "Type: `file`. File with logging information",
"help_text": "Type: `file`. File with logging information."
}
,
"log2stderr": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Send logging information to stderr",
"help_text": "Type: `boolean_true`, default: `false`. Send logging information to stderr."
,
"default": "False"
}
,
"verbose": {
"type":
"integer",
"description": "Type: `integer`, example: `0`. Log level",
"help_text": "Type: `integer`, example: `0`. Log level. The higher, the more output. Default: `0`.\n"
}
,
"error": {
"type":
"string",
"description": "Type: `file`. File with error information",
"help_text": "Type: `file`. File with error information."
}
,
"temp_dir": {
"type":
"string",
"description": "Type: `string`. Directory for temporary files",
"help_text": "Type: `string`. Directory for temporary files. If not set, the bash environmental variable TMPDIR is used.\n"
}
,
"compresslevel": {
"type":
"integer",
"description": "Type: `integer`, example: `6`. Level of Gzip compression to use",
"help_text": "Type: `integer`, example: `6`. Level of Gzip compression to use. Default=6 matches GNU gzip rather than python gzip default.\nDefault: `6`.\n"
}
,
"timeit": {
"type":
"string",
"description": "Type: `file`. Store timing information in file",
"help_text": "Type: `file`. Store timing information in file."
}
,
"timeit_name": {
"type":
"string",
"description": "Type: `string`, example: `all`. Name in timing file for this class of jobs",
"help_text": "Type: `string`, example: `all`. Name in timing file for this class of jobs. Default: `all`.\n"
}
,
"timeit_header": {
"type":
"string",
"description": "Type: `string`. Add header for timing information",
"help_text": "Type: `string`. Add header for timing information."
}
}
},
"nextflow input-output arguments" : {
"title": "Nextflow input-output arguments",
"type": "object",
"description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
"properties": {
"publish_dir": {
"type":
"string",
"description": "Type: `string`, required, example: `output/`. Path to an output directory",
"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
}
,
"param_list": {
"type":
"string",
"description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
"help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
"hidden": true
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/inputs"
},
{
"$ref": "#/definitions/outputs"
},
{
"$ref": "#/definitions/grouping options"
},
{
"$ref": "#/definitions/single-cell rna-seq options"
},
{
"$ref": "#/definitions/sam/bam options"
},
{
"$ref": "#/definitions/group/dedup options"
},
{
"$ref": "#/definitions/common options"
},
{
"$ref": "#/definitions/nextflow input-output arguments"
}
]
}

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

@@ -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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/bbmap_bbsplit/bbmap_bbsplit
View File

@@ -506,9 +506,9 @@ tar xzf BBMap_39.01.tar.gz && \
cp -r bbmap/* /usr/local/bin
LABEL org.opencontainers.image.description="Companion container for running component bbmap_bbsplit"
LABEL org.opencontainers.image.created="2024-09-23T13:49:53Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:43Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/bedtools_genomecov/bedtools_genomecov
View File

@@ -481,9 +481,9 @@ mv bedtools.static /usr/local/bin/bedtools && \
chmod a+x /usr/local/bin/bedtools
LABEL org.opencontainers.image.description="Companion container for running component bedtools_genomecov"
LABEL org.opencontainers.image.created="2024-09-23T13:49:54Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:44Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/cat_additional_fasta/cat_additional_fasta
View File

@@ -480,9 +480,9 @@ function ViashDockerfile {
FROM python:latest
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component cat_additional_fasta"
LABEL org.opencontainers.image.created="2024-09-23T13:50:00Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:50Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

8
target/executable/cat_fastq/.config.vsh.yaml
View File

@@ -30,7 +30,7 @@ argument_groups:
description: "Concatenated read 1 fastq"
info: null
default:
- "$id_merged.fastq"
- "$id_r1_merged.fastq"
must_exist: true
create_parent: true
required: false
@@ -42,7 +42,7 @@ argument_groups:
description: "Concatenated read 2 fastq"
info: null
default:
- "$id_merged.fastq"
- "$id_r2_merged.fastq"
must_exist: false
create_parent: true
required: false
@@ -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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

14
target/executable/cat_fastq/cat_fastq
View File

@@ -187,12 +187,12 @@ function ViashHelp {
echo "Output:"
echo " --fastq_1"
echo " type: file, output, file must exist"
echo " default: \$id_merged.fastq"
echo " default: \$id_r1_merged.fastq"
echo " Concatenated read 1 fastq"
echo ""
echo " --fastq_2"
echo " type: file, output"
echo " default: \$id_merged.fastq"
echo " default: \$id_r2_merged.fastq"
echo " Concatenated read 2 fastq"
}
@@ -472,9 +472,9 @@ function ViashDockerfile {
FROM ubuntu:22.04
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component cat_fastq"
LABEL org.opencontainers.image.created="2024-09-23T13:50:01Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:51Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER
@@ -869,10 +869,10 @@ fi
# filling in defaults
if [ -z ${VIASH_PAR_FASTQ_1+x} ]; then
VIASH_PAR_FASTQ_1="\$id_merged.fastq"
VIASH_PAR_FASTQ_1="\$id_r1_merged.fastq"
fi
if [ -z ${VIASH_PAR_FASTQ_2+x} ]; then
VIASH_PAR_FASTQ_2="\$id_merged.fastq"
VIASH_PAR_FASTQ_2="\$id_r2_merged.fastq"
fi
# check whether required files exist

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

@@ -237,8 +237,8 @@ build_info:
output: "target/executable/deseq2_qc"
executable: "target/executable/deseq2_qc/deseq2_qc"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/deseq2_qc/deseq2_qc
View File

@@ -502,9 +502,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
Rscript -e 'remotes::install_url(c("https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz"), repos = "https://cran.rstudio.com")'
LABEL org.opencontainers.image.description="Companion container for running component deseq2_qc"
LABEL org.opencontainers.image.created="2024-09-23T13:50:10Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:13:00Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -266,8 +266,8 @@ build_info:
output: "target/executable/dupradar"
executable: "target/executable/dupradar/dupradar"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/dupradar/dupradar
View File

@@ -520,9 +520,9 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.pa
Rscript -e 'if (!requireNamespace("dupRadar", quietly = TRUE)) BiocManager::install("dupRadar")'
LABEL org.opencontainers.image.description="Companion container for running component dupradar"
LABEL org.opencontainers.image.created="2024-09-23T13:50:02Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:52Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -198,8 +198,8 @@ build_info:
output: "target/executable/fastqc"
executable: "target/executable/fastqc/fastqc"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/fastqc/fastqc
View File

@@ -490,9 +490,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component fastqc"
LABEL org.opencontainers.image.created="2024-09-23T13:49:55Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:45Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/fq_subsample/fq_subsample
View File

@@ -485,9 +485,9 @@ cargo install --locked --path . && \
mv /usr/local/fq/target/release/fq /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component fq_subsample"
LABEL org.opencontainers.image.created="2024-09-23T13:49:55Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:44Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -167,8 +167,8 @@ build_info:
output: "target/executable/getchromsizes"
executable: "target/executable/getchromsizes/getchromsizes"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/getchromsizes/getchromsizes
View File

@@ -480,9 +480,9 @@ make && \
make install
LABEL org.opencontainers.image.description="Companion container for running component getchromsizes"
LABEL org.opencontainers.image.created="2024-09-23T13:49:56Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:45Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -145,8 +145,8 @@ build_info:
output: "target/executable/gtf2bed"
executable: "target/executable/gtf2bed/gtf2bed"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/gtf2bed/gtf2bed
View File

@@ -466,9 +466,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component gtf2bed"
LABEL org.opencontainers.image.created="2024-09-23T13:50:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:56Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -155,8 +155,8 @@ build_info:
output: "target/executable/gtf_filter"
executable: "target/executable/gtf_filter/gtf_filter"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/gtf_filter/gtf_filter
View File

@@ -470,9 +470,9 @@ function ViashDockerfile {
FROM python:latest
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component gtf_filter"
LABEL org.opencontainers.image.created="2024-09-23T13:50:09Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:59Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -144,8 +144,8 @@ build_info:
output: "target/executable/gunzip"
executable: "target/executable/gunzip/gunzip"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/gunzip/gunzip
View File

@@ -466,9 +466,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component gunzip"
LABEL org.opencontainers.image.created="2024-09-23T13:49:56Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:45Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -155,8 +155,8 @@ build_info:
output: "target/executable/kallisto/kallisto_index"
executable: "target/executable/kallisto/kallisto_index/kallisto_index"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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

@@ -471,9 +471,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \
mv kallisto/kallisto /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_index"
LABEL org.opencontainers.image.created="2024-09-23T13:50:07Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:57Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -253,8 +253,8 @@ build_info:
output: "target/executable/kallisto/kallisto_quant"
executable: "target/executable/kallisto/kallisto_quant/kallisto_quant"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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

@@ -515,9 +515,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \
mv kallisto/kallisto /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_quant"
LABEL org.opencontainers.image.created="2024-09-23T13:50:07Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:57Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -170,8 +170,8 @@ build_info:
output: "target/executable/multiqc_custom_biotype"
executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/multiqc_custom_biotype/multiqc_custom_biotype
View File

@@ -481,9 +481,9 @@ RUN apt-get update && \
RUN pip install --upgrade pip
LABEL org.opencontainers.image.description="Companion container for running component multiqc_custom_biotype"
LABEL org.opencontainers.image.created="2024-09-23T13:50:02Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:52Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -207,8 +207,8 @@ build_info:
output: "target/executable/picard_markduplicates"
executable: "target/executable/picard_markduplicates/picard_markduplicates"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/picard_markduplicates/picard_markduplicates
View File

@@ -494,9 +494,9 @@ wget --no-check-certificate https://github.com/broadinstitute/picard/releases/do
mv picard.jar /usr/local/bin
LABEL org.opencontainers.image.description="Companion container for running component picard_markduplicates"
LABEL org.opencontainers.image.created="2024-09-23T13:50:09Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:59Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -409,8 +409,8 @@ build_info:
output: "target/executable/prepare_multiqc_input"
executable: "target/executable/prepare_multiqc_input/prepare_multiqc_input"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

11
target/executable/prepare_multiqc_input/prepare_multiqc_input
View File

@@ -557,9 +557,9 @@ function ViashDockerfile {
FROM ubuntu:22.04
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component prepare_multiqc_input"
LABEL org.opencontainers.image.created="2024-09-23T13:50:05Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:55Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER
@@ -2285,7 +2285,8 @@ IFS="," read -ra star_multiqc <<< \$par_star_multiqc && for file in "\${star_mul
IFS="," read -ra rsem_multiqc <<< \$par_rsem_multiqc && for file in "\${rsem_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done
IFS="," read -ra salmon_multiqc <<< \$par_salmon_multiqc && for file in "\${salmon_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done
# TODO: Fetch Salmon meta info
# IFS="," read -ra salmon_multiqc <<< \$par_salmon_multiqc && for file in "\${salmon_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done
IFS="," read -ra samtools_stats <<< \$par_samtools_stats && for file in "\${samtools_stats[@]}"; do [ -e "\$file" ] && cp -r "\$file" \$par_output/; done
@@ -2300,7 +2301,7 @@ IFS="," read -ra pseudo_multiqc <<< \$par_pseudo_multiqc && for file in "\${pseu
IFS="," read -ra featurecounts_multiqc <<< \$par_featurecounts_multiqc && for file in "\${featurecounts_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done
IFS="," read -ra featurecounts_rrna_multiqc <<< \$par_featurecounts_rrna_multiqc&& for file in "\${featurecounts_rrna_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done
IFS="," read -ra featurecounts_rrna_multiqc <<< \$par_featurecounts_rrna_multiqc && for file in "\${featurecounts_rrna_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done
[ -e "\$par_aligner_pca_multiqc" ] && cp -r "\$par_aligner_pca_multiqc" "\$par_output/"

4
target/executable/preprocess_transcripts_fasta/.config.vsh.yaml
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@@ -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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta
View File

@@ -462,9 +462,9 @@ function ViashDockerfile {
FROM ubuntu:22.04
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component preprocess_transcripts_fasta"
LABEL org.opencontainers.image.created="2024-09-23T13:50:05Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:55Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -191,8 +191,8 @@ build_info:
output: "target/executable/preseq_lcextrap"
executable: "target/executable/preseq_lcextrap/preseq_lcextrap"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/preseq_lcextrap/preseq_lcextrap
View File

@@ -495,9 +495,9 @@ mkdir build && cd build && \
make && make install && make HAVE_HTSLIB=1 all
LABEL org.opencontainers.image.description="Companion container for running component preseq_lcextrap"
LABEL org.opencontainers.image.created="2024-09-23T13:49:56Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:46Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

4
target/executable/qualimap/.config.vsh.yaml
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@@ -271,8 +271,8 @@ build_info:
output: "target/executable/qualimap"
executable: "target/executable/qualimap/qualimap"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/qualimap/qualimap
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@@ -537,9 +537,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
Rscript -e 'remotes::install_cran(c("optparse"), repos = "https://cran.rstudio.com")'
LABEL org.opencontainers.image.description="Companion container for running component qualimap"
LABEL org.opencontainers.image.created="2024-09-23T13:49:54Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:44Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -299,8 +299,8 @@ build_info:
output: "target/executable/rsem/rsem_calculate_expression"
executable: "target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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

@@ -542,9 +542,9 @@ echo 'export PATH=$PATH:/usr/local/bin' >> ~/.bashrc && \
/bin/bash -c "source /etc/profile && source ~/.bashrc && echo $PATH && which STAR"
LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_calculate_expression"
LABEL org.opencontainers.image.created="2024-09-23T13:50:07Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:57Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

24
target/executable/rsem/rsem_merge_counts/.config.vsh.yaml
View File

@@ -24,15 +24,6 @@ argument_groups:
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--versions"
info: null
must_exist: false
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Output"
arguments:
- type: "file"
@@ -83,17 +74,6 @@ argument_groups:
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--updated_versions"
info: null
default:
- "versions.yml"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
resources:
- type: "bash_script"
path: "script.sh"
@@ -202,8 +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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

62
target/executable/rsem/rsem_merge_counts/rsem_merge_counts
View File

@@ -185,9 +185,6 @@ function ViashHelp {
echo " type: file, file must exist"
echo " Expression counts on transcript level (isoforms)"
echo ""
echo " --versions"
echo " type: file"
echo ""
echo "Output:"
echo " --merged_gene_counts"
echo " type: file, output, file must exist"
@@ -208,10 +205,6 @@ function ViashHelp {
echo " type: file, output, file must exist"
echo " default: rsem.merged.transcript_tpm.tsv"
echo " File containing transcript TPM across all samples."
echo ""
echo " --updated_versions"
echo " type: file, output, file must exist"
echo " default: versions.yml"
}
# initialise variables
@@ -490,9 +483,9 @@ function ViashDockerfile {
FROM ubuntu:22.04
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_merge_counts"
LABEL org.opencontainers.image.created="2024-09-23T13:50:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:56Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER
@@ -654,17 +647,6 @@ while [[ $# -gt 0 ]]; do
VIASH_PAR_COUNTS_TRANSCRIPTS=$(ViashRemoveFlags "$1")
shift 1
;;
--versions)
[ -n "$VIASH_PAR_VERSIONS" ] && ViashError Bad arguments for option \'--versions\': \'$VIASH_PAR_VERSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_VERSIONS="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --versions. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--versions=*)
[ -n "$VIASH_PAR_VERSIONS" ] && ViashError Bad arguments for option \'--versions=*\': \'$VIASH_PAR_VERSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_VERSIONS=$(ViashRemoveFlags "$1")
shift 1
;;
--merged_gene_counts)
[ -n "$VIASH_PAR_MERGED_GENE_COUNTS" ] && ViashError Bad arguments for option \'--merged_gene_counts\': \'$VIASH_PAR_MERGED_GENE_COUNTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MERGED_GENE_COUNTS="$2"
@@ -709,17 +691,6 @@ while [[ $# -gt 0 ]]; do
VIASH_PAR_MERGED_TRANSCRIPT_TPM=$(ViashRemoveFlags "$1")
shift 1
;;
--updated_versions)
[ -n "$VIASH_PAR_UPDATED_VERSIONS" ] && ViashError Bad arguments for option \'--updated_versions\': \'$VIASH_PAR_UPDATED_VERSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_UPDATED_VERSIONS="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --updated_versions. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--updated_versions=*)
[ -n "$VIASH_PAR_UPDATED_VERSIONS" ] && ViashError Bad arguments for option \'--updated_versions=*\': \'$VIASH_PAR_UPDATED_VERSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_UPDATED_VERSIONS=$(ViashRemoveFlags "$1")
shift 1
;;
---engine)
VIASH_ENGINE_ID="$2"
shift 2
@@ -930,9 +901,6 @@ fi
if [ -z ${VIASH_PAR_MERGED_TRANSCRIPT_TPM+x} ]; then
VIASH_PAR_MERGED_TRANSCRIPT_TPM="rsem.merged.transcript_tpm.tsv"
fi
if [ -z ${VIASH_PAR_UPDATED_VERSIONS+x} ]; then
VIASH_PAR_UPDATED_VERSIONS="versions.yml"
fi
# check whether required files exist
if [ ! -z "$VIASH_PAR_COUNTS_GENE" ] && [ ! -e "$VIASH_PAR_COUNTS_GENE" ]; then
@@ -1031,9 +999,6 @@ fi
if [ ! -z "$VIASH_PAR_MERGED_TRANSCRIPT_TPM" ] && [ ! -d "$(dirname "$VIASH_PAR_MERGED_TRANSCRIPT_TPM")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_MERGED_TRANSCRIPT_TPM")"
fi
if [ ! -z "$VIASH_PAR_UPDATED_VERSIONS" ] && [ ! -d "$(dirname "$VIASH_PAR_UPDATED_VERSIONS")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_UPDATED_VERSIONS")"
fi
if [ "$VIASH_ENGINE_ID" == "native" ] ; then
if [ "$VIASH_MODE" == "run" ]; then
@@ -1055,10 +1020,6 @@ if [ ! -z "$VIASH_PAR_COUNTS_TRANSCRIPTS" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_COUNTS_TRANSCRIPTS")" )
VIASH_PAR_COUNTS_TRANSCRIPTS=$(ViashDockerAutodetectMount "$VIASH_PAR_COUNTS_TRANSCRIPTS")
fi
if [ ! -z "$VIASH_PAR_VERSIONS" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_VERSIONS")" )
VIASH_PAR_VERSIONS=$(ViashDockerAutodetectMount "$VIASH_PAR_VERSIONS")
fi
if [ ! -z "$VIASH_PAR_MERGED_GENE_COUNTS" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_MERGED_GENE_COUNTS")" )
VIASH_PAR_MERGED_GENE_COUNTS=$(ViashDockerAutodetectMount "$VIASH_PAR_MERGED_GENE_COUNTS")
@@ -1079,11 +1040,6 @@ if [ ! -z "$VIASH_PAR_MERGED_TRANSCRIPT_TPM" ]; then
VIASH_PAR_MERGED_TRANSCRIPT_TPM=$(ViashDockerAutodetectMount "$VIASH_PAR_MERGED_TRANSCRIPT_TPM")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_MERGED_TRANSCRIPT_TPM" )
fi
if [ ! -z "$VIASH_PAR_UPDATED_VERSIONS" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_UPDATED_VERSIONS")" )
VIASH_PAR_UPDATED_VERSIONS=$(ViashDockerAutodetectMount "$VIASH_PAR_UPDATED_VERSIONS")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_UPDATED_VERSIONS" )
fi
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_RESOURCES_DIR")" )
VIASH_META_RESOURCES_DIR=$(ViashDockerAutodetectMount "$VIASH_META_RESOURCES_DIR")
@@ -1155,12 +1111,10 @@ cat > "\$tempscript" << 'VIASHMAIN'
# The following code has been auto-generated by Viash.
$( if [ ! -z ${VIASH_PAR_COUNTS_GENE+x} ]; then echo "${VIASH_PAR_COUNTS_GENE}" | sed "s#'#'\"'\"'#g;s#.*#par_counts_gene='&'#" ; else echo "# par_counts_gene="; fi )
$( if [ ! -z ${VIASH_PAR_COUNTS_TRANSCRIPTS+x} ]; then echo "${VIASH_PAR_COUNTS_TRANSCRIPTS}" | sed "s#'#'\"'\"'#g;s#.*#par_counts_transcripts='&'#" ; else echo "# par_counts_transcripts="; fi )
$( if [ ! -z ${VIASH_PAR_VERSIONS+x} ]; then echo "${VIASH_PAR_VERSIONS}" | sed "s#'#'\"'\"'#g;s#.*#par_versions='&'#" ; else echo "# par_versions="; fi )
$( if [ ! -z ${VIASH_PAR_MERGED_GENE_COUNTS+x} ]; then echo "${VIASH_PAR_MERGED_GENE_COUNTS}" | sed "s#'#'\"'\"'#g;s#.*#par_merged_gene_counts='&'#" ; else echo "# par_merged_gene_counts="; fi )
$( if [ ! -z ${VIASH_PAR_MERGED_GENE_TPM+x} ]; then echo "${VIASH_PAR_MERGED_GENE_TPM}" | sed "s#'#'\"'\"'#g;s#.*#par_merged_gene_tpm='&'#" ; else echo "# par_merged_gene_tpm="; fi )
$( if [ ! -z ${VIASH_PAR_MERGED_TRANSCRIPT_COUNTS+x} ]; then echo "${VIASH_PAR_MERGED_TRANSCRIPT_COUNTS}" | sed "s#'#'\"'\"'#g;s#.*#par_merged_transcript_counts='&'#" ; else echo "# par_merged_transcript_counts="; fi )
$( if [ ! -z ${VIASH_PAR_MERGED_TRANSCRIPT_TPM+x} ]; then echo "${VIASH_PAR_MERGED_TRANSCRIPT_TPM}" | sed "s#'#'\"'\"'#g;s#.*#par_merged_transcript_tpm='&'#" ; else echo "# par_merged_transcript_tpm="; fi )
$( if [ ! -z ${VIASH_PAR_UPDATED_VERSIONS+x} ]; then echo "${VIASH_PAR_UPDATED_VERSIONS}" | sed "s#'#'\"'\"'#g;s#.*#par_updated_versions='&'#" ; else echo "# par_updated_versions="; 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 )
@@ -1225,9 +1179,6 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
if [ ! -z "$VIASH_PAR_COUNTS_TRANSCRIPTS" ]; then
VIASH_PAR_COUNTS_TRANSCRIPTS=$(ViashDockerStripAutomount "$VIASH_PAR_COUNTS_TRANSCRIPTS")
fi
if [ ! -z "$VIASH_PAR_VERSIONS" ]; then
VIASH_PAR_VERSIONS=$(ViashDockerStripAutomount "$VIASH_PAR_VERSIONS")
fi
if [ ! -z "$VIASH_PAR_MERGED_GENE_COUNTS" ]; then
VIASH_PAR_MERGED_GENE_COUNTS=$(ViashDockerStripAutomount "$VIASH_PAR_MERGED_GENE_COUNTS")
fi
@@ -1240,9 +1191,6 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
if [ ! -z "$VIASH_PAR_MERGED_TRANSCRIPT_TPM" ]; then
VIASH_PAR_MERGED_TRANSCRIPT_TPM=$(ViashDockerStripAutomount "$VIASH_PAR_MERGED_TRANSCRIPT_TPM")
fi
if [ ! -z "$VIASH_PAR_UPDATED_VERSIONS" ]; then
VIASH_PAR_UPDATED_VERSIONS=$(ViashDockerStripAutomount "$VIASH_PAR_UPDATED_VERSIONS")
fi
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR")
fi
@@ -1275,10 +1223,6 @@ if [ ! -z "$VIASH_PAR_MERGED_TRANSCRIPT_TPM" ] && [ ! -e "$VIASH_PAR_MERGED_TRAN
ViashError "Output file '$VIASH_PAR_MERGED_TRANSCRIPT_TPM' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_UPDATED_VERSIONS" ] && [ ! -e "$VIASH_PAR_UPDATED_VERSIONS" ]; then
ViashError "Output file '$VIASH_PAR_UPDATED_VERSIONS' does not exist."
exit 1
fi
exit 0

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

@@ -163,8 +163,8 @@ build_info:
output: "target/executable/rseqc/rseqc_bamstat"
executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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

@@ -477,9 +477,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_bamstat"
LABEL org.opencontainers.image.created="2024-09-23T13:50:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:54Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -186,8 +186,8 @@ build_info:
output: "target/executable/rseqc/rseqc_inferexperiment"
executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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

@@ -487,9 +487,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_inferexperiment"
LABEL org.opencontainers.image.created="2024-09-23T13:50:02Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:52Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -272,8 +272,8 @@ build_info:
output: "target/executable/rseqc/rseqc_innerdistance"
executable: "target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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

@@ -529,9 +529,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_innerdistance"
LABEL org.opencontainers.image.created="2024-09-23T13:50:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:54Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -260,8 +260,8 @@ build_info:
output: "target/executable/rseqc/rseqc_junctionannotation"
executable: "target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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

@@ -519,9 +519,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionannotation"
LABEL org.opencontainers.image.created="2024-09-23T13:50:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:53Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -249,8 +249,8 @@ build_info:
output: "target/executable/rseqc/rseqc_junctionsaturation"
executable: "target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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

@@ -522,9 +522,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionsaturation"
LABEL org.opencontainers.image.created="2024-09-23T13:50:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:53Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -162,8 +162,8 @@ build_info:
output: "target/executable/rseqc/rseqc_readdistribution"
executable: "target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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

@@ -474,9 +474,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readdistribution"
LABEL org.opencontainers.image.created="2024-09-23T13:50:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:54Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -211,8 +211,8 @@ build_info:
output: "target/executable/rseqc/rseqc_readduplication"
executable: "target/executable/rseqc/rseqc_readduplication/rseqc_readduplication"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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

@@ -499,9 +499,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readduplication"
LABEL org.opencontainers.image.created="2024-09-23T13:50:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:52Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -214,8 +214,8 @@ build_info:
output: "target/executable/rseqc/rseqc_tin"
executable: "target/executable/rseqc/rseqc_tin/rseqc_tin"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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

@@ -501,9 +501,9 @@ RUN apt-get update && \
RUN pip3 install RSeQC
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_tin"
LABEL org.opencontainers.image.created="2024-09-23T13:50:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:53Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -198,8 +198,8 @@ build_info:
output: "target/executable/sortmerna"
executable: "target/executable/sortmerna/sortmerna"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/sortmerna/sortmerna
View File

@@ -492,9 +492,9 @@ wget --no-check-certificate https://github.com/sortmerna/sortmerna/releases/down
bash sortmerna-4.3.6-Linux.sh --skip-license
LABEL org.opencontainers.image.description="Companion container for running component sortmerna"
LABEL org.opencontainers.image.created="2024-09-23T13:50:09Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:59Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -216,8 +216,8 @@ build_info:
output: "target/executable/stringtie"
executable: "target/executable/stringtie/stringtie"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/stringtie/stringtie
View File

@@ -496,9 +496,9 @@ tar -xzf stringtie-2.2.1.Linux_x86_64.tar.gz && \
cp stringtie-2.2.1.Linux_x86_64/stringtie /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component stringtie"
LABEL org.opencontainers.image.created="2024-09-23T13:50:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:56Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -199,8 +199,8 @@ build_info:
output: "target/executable/summarizedexperiment"
executable: "target/executable/summarizedexperiment/summarizedexperiment"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/summarizedexperiment/summarizedexperiment
View File

@@ -487,9 +487,9 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.pa
Rscript -e 'if (!requireNamespace("tximeta", quietly = TRUE)) BiocManager::install("tximeta")'
LABEL org.opencontainers.image.description="Companion container for running component summarizedexperiment"
LABEL org.opencontainers.image.created="2024-09-23T13:50:10Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:13:00Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -788,8 +788,8 @@ build_info:
output: "target/executable/trimgalore"
executable: "target/executable/trimgalore/trimgalore"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

4
target/executable/trimgalore/trimgalore
View File

@@ -858,9 +858,9 @@ ENTRYPOINT []
RUN echo "TrimGalore: `trim_galore --version | sed -n 's/.*version\s\+\([0-9]\+\.[0-9]\+\.[0-9]\+\).*/\1/p'`" > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component trimgalore"
LABEL org.opencontainers.image.created="2024-09-23T13:50:08Z"
LABEL org.opencontainers.image.created="2024-09-24T10:12:58Z"
LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -192,8 +192,8 @@ build_info:
output: "target/executable/tx2gene"
executable: "target/executable/tx2gene/tx2gene"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/tx2gene/tx2gene
View File

@@ -487,9 +487,9 @@ RUN apt-get update && \
RUN pip install --upgrade pip
LABEL org.opencontainers.image.description="Companion container for running component tx2gene"
LABEL org.opencontainers.image.created="2024-09-23T13:50:05Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:55Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -247,8 +247,8 @@ build_info:
output: "target/executable/tximport"
executable: "target/executable/tximport/tximport"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/tximport/tximport
View File

@@ -508,9 +508,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
Rscript -e 'remotes::install_cran(c("jsonlite"), repos = "https://cran.rstudio.com")'
LABEL org.opencontainers.image.description="Companion container for running component tximport"
LABEL org.opencontainers.image.created="2024-09-23T13:50:00Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:50Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -164,8 +164,8 @@ build_info:
output: "target/executable/ucsc/bedclip"
executable: "target/executable/ucsc/bedclip/bedclip"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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

@@ -473,9 +473,9 @@ RUN apt-get update && \
RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedClip /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component ucsc bedclip"
LABEL org.opencontainers.image.created="2024-09-23T13:50:01Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:51Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -164,8 +164,8 @@ build_info:
output: "target/executable/ucsc/bedgraphtobigwig"
executable: "target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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

@@ -473,9 +473,9 @@ RUN apt-get update && \
RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedGraphToBigWig /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component ucsc bedgraphtobigwig"
LABEL org.opencontainers.image.created="2024-09-23T13:50:01Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:51Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -195,8 +195,8 @@ build_info:
output: "target/executable/umitools/umitools_dedup"
executable: "target/executable/umitools/umitools_dedup/umitools_dedup"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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

@@ -489,9 +489,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "umi_tools"
LABEL org.opencontainers.image.description="Companion container for running component umitools umitools_dedup"
LABEL org.opencontainers.image.created="2024-09-23T13:50:08Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:58Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -253,8 +253,8 @@ build_info:
output: "target/executable/umitools/umitools_extract"
executable: "target/executable/umitools/umitools_extract/umitools_extract"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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

@@ -521,9 +521,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "umi_tools"
LABEL org.opencontainers.image.description="Companion container for running component umitools umitools_extract"
LABEL org.opencontainers.image.created="2024-09-23T13:50:08Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:12:58Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -156,8 +156,8 @@ build_info:
output: "target/executable/umitools_prepareforquant"
executable: "target/executable/umitools_prepareforquant/umitools_prepareforquant"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/umitools_prepareforquant/umitools_prepareforquant
View File

@@ -473,9 +473,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "umi_tools" "pysam"
LABEL org.opencontainers.image.description="Companion container for running component umitools_prepareforquant"
LABEL org.opencontainers.image.created="2024-09-23T13:50:10Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="de0a35359a44844ab9f5f99a38a4d13a457b05a5"
LABEL org.opencontainers.image.created="2024-09-24T10:13:00Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

16
target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml
View File

@@ -242,7 +242,7 @@ argument_groups:
name: "--star_multiqc"
info: null
default:
- "$id.log"
- "$id_star.log"
must_exist: true
create_parent: true
required: false
@@ -382,7 +382,7 @@ argument_groups:
multiple: false
multiple_sep: ";"
- type: "file"
name: "--counts_gene"
name: "--rsem_counts_gene"
description: "Expression counts on gene level"
info: null
default:
@@ -496,11 +496,9 @@ dependencies:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.2.0"
- name: "umi_tools/umi_tools_dedup"
- name: "umitools/umitools_dedup"
repository:
type: "vsh"
repo: "vsh/biobox"
tag: "v0.2.0"
type: "local"
- name: "umitools_prepareforquant"
repository:
type: "local"
@@ -596,8 +594,8 @@ 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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@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"
@@ -605,7 +603,7 @@ build_info:
- "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/v0.2.0/nextflow/umi_tools/umi_tools_dedup"
- "target/nextflow/umitools/umitools_dedup"
- "target/nextflow/umitools_prepareforquant"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant"
- "target/nextflow/rsem/rsem_calculate_expression"

34
target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant
View File

@@ -291,7 +291,7 @@ function ViashHelp {
echo "Output:"
echo " --star_multiqc"
echo " type: file, output, file must exist"
echo " default: \$id.log"
echo " default: \$id_star.log"
echo ""
echo " --genome_bam_sorted"
echo " type: file, output, file must exist"
@@ -341,7 +341,7 @@ function ViashHelp {
echo " type: file, output, file must exist"
echo " default: \$id.quant.sf"
echo ""
echo " --counts_gene"
echo " --rsem_counts_gene"
echo " type: file, output, file must exist"
echo " default: \$id.genes.results"
echo " Expression counts on gene level"
@@ -792,15 +792,15 @@ while [[ $# -gt 0 ]]; do
VIASH_PAR_QUANT_RESULTS_FILE=$(ViashRemoveFlags "$1")
shift 1
;;
--counts_gene)
[ -n "$VIASH_PAR_COUNTS_GENE" ] && ViashError Bad arguments for option \'--counts_gene\': \'$VIASH_PAR_COUNTS_GENE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_COUNTS_GENE="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --counts_gene. Use "--help" to get more information on the parameters. && exit 1
--rsem_counts_gene)
[ -n "$VIASH_PAR_RSEM_COUNTS_GENE" ] && ViashError Bad arguments for option \'--rsem_counts_gene\': \'$VIASH_PAR_RSEM_COUNTS_GENE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_RSEM_COUNTS_GENE="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --rsem_counts_gene. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--counts_gene=*)
[ -n "$VIASH_PAR_COUNTS_GENE" ] && ViashError Bad arguments for option \'--counts_gene=*\': \'$VIASH_PAR_COUNTS_GENE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_COUNTS_GENE=$(ViashRemoveFlags "$1")
--rsem_counts_gene=*)
[ -n "$VIASH_PAR_RSEM_COUNTS_GENE" ] && ViashError Bad arguments for option \'--rsem_counts_gene=*\': \'$VIASH_PAR_RSEM_COUNTS_GENE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_RSEM_COUNTS_GENE=$(ViashRemoveFlags "$1")
shift 1
;;
--counts_transcripts)
@@ -1023,7 +1023,7 @@ if [ -z ${VIASH_PAR_ALIGNER+x} ]; then
VIASH_PAR_ALIGNER="star_salmon"
fi
if [ -z ${VIASH_PAR_STAR_MULTIQC+x} ]; then
VIASH_PAR_STAR_MULTIQC="\$id.log"
VIASH_PAR_STAR_MULTIQC="\$id_star.log"
fi
if [ -z ${VIASH_PAR_GENOME_BAM_SORTED+x} ]; then
VIASH_PAR_GENOME_BAM_SORTED="\$id.genome.bam"
@@ -1061,8 +1061,8 @@ fi
if [ -z ${VIASH_PAR_QUANT_RESULTS_FILE+x} ]; then
VIASH_PAR_QUANT_RESULTS_FILE="\$id.quant.sf"
fi
if [ -z ${VIASH_PAR_COUNTS_GENE+x} ]; then
VIASH_PAR_COUNTS_GENE="\$id.genes.results"
if [ -z ${VIASH_PAR_RSEM_COUNTS_GENE+x} ]; then
VIASH_PAR_RSEM_COUNTS_GENE="\$id.genes.results"
fi
if [ -z ${VIASH_PAR_COUNTS_TRANSCRIPTS+x} ]; then
VIASH_PAR_COUNTS_TRANSCRIPTS="\$id.isoforms.results"
@@ -1273,8 +1273,8 @@ fi
if [ ! -z "$VIASH_PAR_QUANT_RESULTS_FILE" ] && [ ! -d "$(dirname "$VIASH_PAR_QUANT_RESULTS_FILE")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_QUANT_RESULTS_FILE")"
fi
if [ ! -z "$VIASH_PAR_COUNTS_GENE" ] && [ ! -d "$(dirname "$VIASH_PAR_COUNTS_GENE")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_COUNTS_GENE")"
if [ ! -z "$VIASH_PAR_RSEM_COUNTS_GENE" ] && [ ! -d "$(dirname "$VIASH_PAR_RSEM_COUNTS_GENE")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_RSEM_COUNTS_GENE")"
fi
if [ ! -z "$VIASH_PAR_COUNTS_TRANSCRIPTS" ] && [ ! -d "$(dirname "$VIASH_PAR_COUNTS_TRANSCRIPTS")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_COUNTS_TRANSCRIPTS")"
@@ -1303,6 +1303,7 @@ fi
# set dependency paths
VIASH_DEP_UMITOOLS_UMITOOLS_DEDUP="$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="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads/main.nf"
@@ -1311,7 +1312,6 @@ VIASH_DEP_SAMTOOLS_SAMTOOLS_INDEX="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox
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="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats/main.nf"
VIASH_DEP_UMI_TOOLS_UMI_TOOLS_DEDUP="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/umi_tools/umi_tools_dedup/main.nf"
VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/main.nf"
ViashDebug "Running command: $(echo $VIASH_CMD)"
@@ -1772,8 +1772,8 @@ if [ ! -z "$VIASH_PAR_QUANT_RESULTS_FILE" ] && [ ! -e "$VIASH_PAR_QUANT_RESULTS_
ViashError "Output file '$VIASH_PAR_QUANT_RESULTS_FILE' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_COUNTS_GENE" ] && [ ! -e "$VIASH_PAR_COUNTS_GENE" ]; then
ViashError "Output file '$VIASH_PAR_COUNTS_GENE' does not exist."
if [ ! -z "$VIASH_PAR_RSEM_COUNTS_GENE" ] && [ ! -e "$VIASH_PAR_RSEM_COUNTS_GENE" ]; then
ViashError "Output file '$VIASH_PAR_RSEM_COUNTS_GENE' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_COUNTS_TRANSCRIPTS" ] && [ ! -e "$VIASH_PAR_COUNTS_TRANSCRIPTS" ]; then

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

@@ -278,8 +278,8 @@ build_info:
output: "target/executable/workflows/merge_quant_results"
executable: "target/executable/workflows/merge_quant_results/merge_quant_results"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/tx2gene"
- "target/nextflow/tximport"

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

@@ -486,8 +486,8 @@ build_info:
output: "target/executable/workflows/post_processing"
executable: "target/executable/workflows/post_processing/post_processing"
viash_version: "0.9.0"
git_commit: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/picard_markduplicates"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort"

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

@@ -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: "de0a35359a44844ab9f5f99a38a4d13a457b05a5"
git_remote: "https://x-access-token:ghs_WsTMx5jJ0pjvozwYVrQC02O3bkQSqz3BBgOJ@github.com/viash-hub/rnaseq"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/fastqc"
- "target/nextflow/umitools/umitools_extract"

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