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Build branch add-labels with version add-labels (c466555)

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Build pipeline: viash-hub.rnaseq.add-labels-kpss4

Source commit: c466555a20

Source message: Add annotations
This commit is contained in:
CI
2024-11-27 17:11:35 +00:00
parent 846dd87f48
commit 13477349f0
276 changed files with 2470 additions and 2447 deletions
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2
src/workflows/genome_alignment_and_quant/main.nf
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@@ -1,3 +1,5 @@
// TODO: Improve logic of this wf, e.g. by splitting up in 2 subwfs
// TODO: See if this can be aligned with the pseudo-alignment branch of the logic
workflow run_wf {
take:
input_ch

1
src/workflows/pseudo_alignment_and_quant/main.nf
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@@ -1,3 +1,4 @@
// TODO: See if the logic of this can be aligned with the STAR aligner logic
workflow run_wf {
take:
input_ch

3
src/workflows/quality_control/main.nf
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@@ -240,6 +240,7 @@ workflow run_wf {
def skip_qc = list.collect { id, state -> state.skip_qc }.unique()[0]
def skip_align = list.collect { id, state -> state.skip_align }.unique()[0]
def skip_pseudo_align = list.collect { id, state -> state.skip_pseudo_align }.unique()[0]
// TODO: Are these checks necessary?
def quant_results = list.collect { id, state ->
(state.quant_results_file instanceof java.nio.file.Path && state.quant_results_file.exists()) ?
state.quant_results_file :
@@ -538,6 +539,7 @@ workflow run_wf {
)
| niceView()
// Get list of samples that failed trimming, mapping, and strand check for MultiQC report
// TODO: Refactor this to a process/step
| map { id, state ->
def fail_trimming_header = ["Sample", "Reads after trimming"]
def fail_trimming_multiqc = ""
@@ -666,6 +668,7 @@ workflow run_wf {
| map { list -> [list[0], list[1] + list[2]] }
| map { id, state ->
// TODO: Check this, necessary for setState
def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() }
[ id, mod_state ]
}

2
src/workflows/rnaseq/config.vsh.yaml
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@@ -912,7 +912,7 @@ argument_groups:
type: file
direction: output
default: pseudo_alignment_quantification/quant_merged_summarizedexperiment
resources:
- type: nextflow_script
path: main.nf

935
src/workflows/rnaseq/main.nf
View File

@@ -5,222 +5,473 @@ workflow run_wf {
main:
reference_ch = input_ch
| map { id, state ->
def biotype = state.gencode ? "gene_type" : state.featurecounts_group_type
def filter_gtf =
(
( !state.skip_alignment && state.aligner) // Condition 1: Alignment is required and aligner is set
|| ( !state.skip_pseudo_alignment && state.pseudo_aligner ) // Condition 2: Pseudoalignment is required and pseudoaligner is set
|| ( !state.transcript_fasta ) // Condition 3: Transcript FASTA file is not provided
)
&&
( !state.skip_gtf_filter ) // Condition 4: --skip_gtf_filter is not provided
[ id, state + [ biotype: biotype, filter_gtf: filter_gtf ] ]
}
| toSortedList
| map { list ->
[ "ref",
[ fasta: list.collect { id, state -> state.fasta }.unique()[0],
gtf: list.collect { id, state -> state.gtf }.unique()[0],
gff: list.collect { id, state -> state.gff }.unique()[0],
additional_fasta: list.collect { id, state -> state.additional_fasta }.unique()[0],
transcript_fasta:list.collect { id, state -> state.transcript_fasta }.unique()[0],
gene_bed: list.collect { id, state -> state.gene_bed }.unique()[0],
bbsplit_fasta_list: list.collect { id, state -> state.bbsplit_fasta_list }.unique()[0],
aligner: list.collect { id, state -> state.aligner }.unique()[0],
pseudo_aligner: list.collect { id, state -> state.pseudo_aligner }.unique()[0],
star_index: list.collect { id, state -> state.star_index }.unique()[0],
rsem_index: list.collect { id, state -> state.rsem_index }.unique()[0],
salmon_index: list.collect { id, state -> state.salmon_index }.unique()[0],
kallisto_index: list.collect { id, state -> state.kallisto_index }.unique()[0],
// splicesites: list.collect { id, state -> state.splicesites }.unique()[0],
// hisat2_index: list.collect { id, state -> state.hisat2_index }.unique()[0],
bbsplit_index: list.collect { id, state -> state.bbsplit_index }.unique()[0],
skip_bbsplit: list.collect { id, state -> state.skip_bbsplit }.unique()[0],
gencode: list.collect { id, state -> state.gencode }.unique()[0],
biotype: list.collect { id, state -> state.biotype }.unique()[0],
filter_gtf: list.collect { id, state -> state.filter_gtf }.unique()[0],
pseudo_aligner_kmer_size: list.collect { id, state -> state.pseudo_aligner_kmer_size }.unique()[0] ]
]
}
| map { id, state ->
def biotype = state.gencode ? "gene_type" : state.featurecounts_group_type
def filter_gtf =
(
( !state.skip_alignment && state.aligner) // Condition 1: Alignment is required and aligner is set
|| ( !state.skip_pseudo_alignment && state.pseudo_aligner ) // Condition 2: Pseudoalignment is required and pseudoaligner is set
|| ( !state.transcript_fasta ) // Condition 3: Transcript FASTA file is not provided
)
&&
( !state.skip_gtf_filter ) // Condition 4: --skip_gtf_filter is not provided
[ id, state + [ biotype: biotype, filter_gtf: filter_gtf ] ]
}
| toSortedList
| map { list ->
[ "ref",
[ fasta: list.collect { id, state -> state.fasta }.unique()[0],
gtf: list.collect { id, state -> state.gtf }.unique()[0],
gff: list.collect { id, state -> state.gff }.unique()[0],
additional_fasta: list.collect { id, state -> state.additional_fasta }.unique()[0],
transcript_fasta:list.collect { id, state -> state.transcript_fasta }.unique()[0],
gene_bed: list.collect { id, state -> state.gene_bed }.unique()[0],
bbsplit_fasta_list: list.collect { id, state -> state.bbsplit_fasta_list }.unique()[0],
aligner: list.collect { id, state -> state.aligner }.unique()[0],
pseudo_aligner: list.collect { id, state -> state.pseudo_aligner }.unique()[0],
star_index: list.collect { id, state -> state.star_index }.unique()[0],
rsem_index: list.collect { id, state -> state.rsem_index }.unique()[0],
salmon_index: list.collect { id, state -> state.salmon_index }.unique()[0],
kallisto_index: list.collect { id, state -> state.kallisto_index }.unique()[0],
// splicesites: list.collect { id, state -> state.splicesites }.unique()[0],
// hisat2_index: list.collect { id, state -> state.hisat2_index }.unique()[0],
bbsplit_index: list.collect { id, state -> state.bbsplit_index }.unique()[0],
skip_bbsplit: list.collect { id, state -> state.skip_bbsplit }.unique()[0],
gencode: list.collect { id, state -> state.gencode }.unique()[0],
biotype: list.collect { id, state -> state.biotype }.unique()[0],
filter_gtf: list.collect { id, state -> state.filter_gtf }.unique()[0],
pseudo_aligner_kmer_size: list.collect { id, state -> state.pseudo_aligner_kmer_size }.unique()[0] ]
]
}
// prepare all the necessary files for reference genome
| prepare_genome.run (
fromState: [
"fasta": "fasta",
"gtf": "gtf",
"gff": "gff",
"additional_fasta": "additional_fasta",
"transcript_fasta": "transcript_fasta",
"gene_bed": "gene_bed",
"bbsplit_fasta_list": "bbsplit_fasta_list",
"star_index": "star_index",
"rsem_index": "rsem_index",
"salmon_index": "salmon_index",
"kallisto_index": "kallisto_index",
"pseudo_aligner_kmer_size": "pseudo_aligner_kmer_size",
// "splicesites": "splicesites",
// "hisat2_index": "hisat2_index",
"bbsplit_index": "bbsplit_index",
"skip_bbsplit": "skip_bbsplit",
"gencode": "gencode",
"biotype": "biotype",
"filter_gtf": "filter_gtf",
"aligner": "aligner",
"pseudo_aligner": "pseudo_aligner",
"skip_alignment": "skip_alignment"
],
toState: [
"fasta": "uncompressed_fasta",
"gtf": "gtf_uncompressed",
"transcript_fasta": "transcript_fasta_uncompressed",
"fai": "fai",
"chrom_sizes": "chrom_sizes",
"bbsplit_index": "bbsplit_index_uncompressed",
"star_index": "star_index_uncompressed",
"salmon_index": "salmon_index_uncompressed",
"kallisto_index": "kallisto_index_uncompressed",
"gene_bed": "gene_bed_uncompressed"
]
)
// prepare all the necessary files for reference genome
| prepare_genome.run (
fromState: [
"fasta": "fasta",
"gtf": "gtf",
"gff": "gff",
"additional_fasta": "additional_fasta",
"transcript_fasta": "transcript_fasta",
"gene_bed": "gene_bed",
"bbsplit_fasta_list": "bbsplit_fasta_list",
"star_index": "star_index",
"rsem_index": "rsem_index",
"salmon_index": "salmon_index",
"kallisto_index": "kallisto_index",
"pseudo_aligner_kmer_size": "pseudo_aligner_kmer_size",
// "splicesites": "splicesites",
// "hisat2_index": "hisat2_index",
"bbsplit_index": "bbsplit_index",
"skip_bbsplit": "skip_bbsplit",
"gencode": "gencode",
"biotype": "biotype",
"filter_gtf": "filter_gtf",
"aligner": "aligner",
"pseudo_aligner": "pseudo_aligner",
"skip_alignment": "skip_alignment"
],
toState: [
"fasta": "uncompressed_fasta",
"gtf": "gtf_uncompressed",
"transcript_fasta": "transcript_fasta_uncompressed",
"fai": "fai",
"chrom_sizes": "chrom_sizes",
"bbsplit_index": "bbsplit_index_uncompressed",
"star_index": "star_index_uncompressed",
"salmon_index": "salmon_index_uncompressed",
"kallisto_index": "kallisto_index_uncompressed",
"gene_bed": "gene_bed_uncompressed"
]
)
// Check if contigs in genome fasta file > 512 Mbp
| map { id, state ->
(isBelowMaxContigSize(state.fai)) ? [id, state] : [id, state + [bam_csi_index: true]]
}
// Check if contigs in genome fasta file > 512 Mbp
// TODO: check where this is required and move if necessary
| map { id, state ->
(isBelowMaxContigSize(state.fai)) ? [id, state] : [id, state + [bam_csi_index: true]]
}
| map { list -> list[1]}
// Pick out the state
| map { list -> list[1]}
analysis_ch = input_ch
| combine(reference_ch)
| combine(reference_ch)
| map { list -> [list[0], list[1] + list[2]] }
| map { list -> [list[0], list[1] + list[2]] }
// Concatenate FastQ files from same sample if required
| cat_fastq.run (
fromState: [
"read_1": "fastq_1",
"read_2": "fastq_2"
],
toState: [
"fastq_1": "fastq_1",
"fastq_2": "fastq_2"
]
)
// Concatenate FastQ files from same sample if required
| cat_fastq.run (
fromState: [
"read_1": "fastq_1",
"read_2": "fastq_2"
],
toState: [
"fastq_1": "fastq_1",
"fastq_2": "fastq_2"
]
)
// Pre-process fastq files
| pre_processing.run (
fromState: [
"id": "id",
"fastq_1": "fastq_1",
"fastq_2": "fastq_2",
"umitools_bc_pattern": "umitools_bc_pattern",
"umitools_bc_pattern2": "umitools_bc_pattern2",
"strandedness": "strandedness",
"transcript_fasta": "transcript_fasta",
"gtf": "gtf",
"with_umi": "with_umi",
"bbsplit_index": "bbsplit_index",
"bbsplit_fasta_list": "bbsplit_fasta_list",
"bc_pattern": "bc_pattern",
"ribo_database_manifest": "ribo_database_manifest",
"salmon_index": "salmon_index",
"skip_qc": "skip_qc",
"skip_fastqc": "skip_fastqc",
"skip_skip_umi_extract": "skip_umi_extract",
"umi_discard_read": "umi_discard_read",
"skip_trimming": "skip_trimming",
"trimmer": "trimmer",
"skip_bbsplit": "skip_bbsplit",
"remove_ribo_rna": "remove_ribo_rna"
],
toState: [
// Pre-process fastq files
| pre_processing.run (
fromState: [
"id": "id",
"fastq_1": "fastq_1",
"fastq_2": "fastq_2",
"umitools_bc_pattern": "umitools_bc_pattern",
"umitools_bc_pattern2": "umitools_bc_pattern2",
"strandedness": "strandedness",
"transcript_fasta": "transcript_fasta",
"gtf": "gtf",
"with_umi": "with_umi",
"bbsplit_index": "bbsplit_index",
"bbsplit_fasta_list": "bbsplit_fasta_list",
"bc_pattern": "bc_pattern",
"ribo_database_manifest": "ribo_database_manifest",
"salmon_index": "salmon_index",
"skip_qc": "skip_qc",
"skip_fastqc": "skip_fastqc",
"skip_skip_umi_extract": "skip_umi_extract",
"umi_discard_read": "umi_discard_read",
"skip_trimming": "skip_trimming",
"trimmer": "trimmer",
"skip_bbsplit": "skip_bbsplit",
"remove_ribo_rna": "remove_ribo_rna"
],
toState: [
"fastqc_html_1": "fastqc_html_1",
"fastqc_html_2": "fastqc_html_2",
"fastqc_zip_1": "fastqc_zip_1",
"fastqc_zip_2": "fastqc_zip_2",
"fastq_1": "qc_output1",
"fastq_2": "qc_output2",
"trim_log_1": "trim_log_1",
"trim_log_2": "trim_log_2",
"trim_zip_1": "trim_zip_1",
"trim_zip_2": "trim_zip_2",
"trim_html_1": "trim_html_1",
"trim_html_2": "trim_html_2",
"passed_trimmed_reads": "passed_trimmed_reads",
"num_trimmed_reads": "num_trimmed_reads",
"sortmerna_log": "sortmerna_log",
"salmon_quant_output": "salmon_quant_output",
"fastp_failed_trim": "failed_trim",
"fastp_failed_trim_unpaired1": "failed_trim_unpaired1",
"fastp_failed_trim_unpaired2": "failed_trim_unpaired2",
"fastp_trim_json": "trim_json",
"fastp_trim_html": "trim_html",
"fastp_trim_merged_out": "trim_merged_out"
]
)
// Infer strandedness from Salmon pseudo-alignment results
// TODO: Turn this into a workflow step and include as a dependency
| map { id, state ->
(state.strandedness == 'auto') ?
[ id, state + [strandedness: getSalmonInferredStrandedness(state.salmon_quant_output)] ] :
[id, state]
}
// Filter FastQ files based on minimum trimmed read count after adapter trimming
// TODO: Turn this into a workflow step and include as a dependency
| map { id, state ->
def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
def num_reads = (state.skip_trimming) ?
state.min_trimmed_reads + 1 :
(
(state.trimmer == "fastp") ?
getFastpReadsAfterFiltering(state.fastp_trim_json) :
(
(!state.skip_trimming && input.size() == 2) ?
getTrimGaloreReadsAfterFiltering(state.trim_log_2) :
getTrimGaloreReadsAfterFiltering(state.trim_log_1)
)
)
def passed_trimmed_reads =
(state.skip_trimming || (num_reads >= state.min_trimmed_reads)) ?
true :
false
[ id, state + [num_trimmed_reads: num_reads, passed_trimmed_reads: passed_trimmed_reads] ]
}
// Genome alignment and quantification
| genome_alignment_and_quant.run (
runIf: { id, state -> !state.skip_alignment && state.passed_trimmed_reads },
fromState: [
"id": "id",
"fastq_1": "fastq_1",
"fastq_2": "fastq_2",
"strandedness": "strandedness",
"gtf": "gtf",
"transcript_fasta": "transcript_fasta",
"bam_csi_index": "bam_csi_index",
"aligner": "aligner",
"rsem_index": "rsem_index",
"star_index": "star_index",
"extra_star_align_args": "extra_star_align_args",
"star_ignore_sjdbgtf": "star_ignore_sjdbgtf",
"seq_platform": "seq_platform",
"seq_center": "seq_center",
"with_umi": "with_umi",
"umi_dedup_stats": "umi_dedup_stats",
"gtf_group_features": "gtf_group_features",
"gtf_extra_attributes": "gtf_extra_attributes",
"salmon_quant_libtype": "salmon_quant_libtype",
"salmon_index": "salmon_index",
"extra_rsem_calculate_expression_args": "extra_rsem_calculate_expression_args"
],
toState: [
"star_multiqc": "star_multiqc",
"rsem_multiqc": "rsem_multiqc",
"salmon_multiqc": "salmon_multiqc",
"genome_bam_sorted": "genome_bam_sorted",
"genome_bam_index": "genome_bam_index",
"genome_bam_stats": "genome_bam_stats",
"genome_bam_flagstat": "genome_bam_flagstat",
"genome_bam_idxstats": "genome_bam_idxstats",
"transcriptome_bam": "transcriptome_bam",
"transcriptome_bam_index": "transcriptome_bam_index",
"transcriptome_bam_stats": "transcriptome_bam_stats",
"transcriptome_bam_flagstat": "transcriptome_bam_flagstat",
"transcriptome_bam_idxstats": "transcriptome_bam_idxstats",
"quant_out_dir": "quant_out_dir",
"quant_results_file": "quant_results_file",
"rsem_counts_gene": "rsem_counts_gene",
"rsem_counts_transcripts": "rsem_counts_transcripts",
"bam_genome_rsem": "bam_genome_rsem",
"bam_transcript_rsem": "bam_transcript_rsem"
]
)
// Filter channels to get samples that passed STAR minimum mapping percentage
// TODO: Move to reporting or later step
| map { id, state ->
def percent_mapped = (!state.skip_alignment) ? getStarPercentMapped(state.star_multiqc) : 0.0
def passed_mapping = (percent_mapped >= state.min_mapped_reads) ? true : false
[ id, state + [percent_mapped: percent_mapped, passed_mapping: passed_mapping] ]
}
// Pseudo-alignment and quantification
| pseudo_alignment_and_quant.run (
runIf: { id, state -> !state.skip_pseudo_alignment && state.passed_trimmed_reads },
fromState: [
"id": "id",
"fastq_1": "fastq_1",
"fastq_2": "fastq_2",
"strandedness": "strandedness",
"gtf": "gtf",
"transcript_fasta": "transcript_fasta",
"pseudo_aligner": "pseudo_aligner",
"salmon_index": "salmon_index",
"kallisto_index": "kallisto_index",
"extra_star_align_args": "extra_star_align_args",
"star_ignore_sjdbgtf": "star_ignore_sjdbgtf",
"seq_platform": "seq_platform",
"seq_center": "seq_center",
"with_umi": "with_umi",
"umi_dedup_stats": "umi_dedup_stats",
"gtf_group_features": "gtf_group_features",
"gtf_extra_attributes": "gtf_extra_attributes",
"lib_type": "salmon_quant_libtype",
"kallisto_quant_fragment_length": "kallisto_quant_fragment_length",
"kallisto_quant_fragment_length_sd": "kallisto_quant_fragment_length_sd"
],
toState: [
"pseudo_quant_out_dir": "quant_out_dir",
"pseudo_salmon_quant_results_file": "salmon_quant_results_file",
"pseudo_kallisto_quant_results_file": "kallisto_quant_results_file",
"pseudo_multiqc": "pseudo_multiqc"
]
)
| map { id, state ->
def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
def paired = input.size() == 2
[ id, state + [ paired: paired ] ]
}
// Post-processing
| post_processing.run (
runIf: { id, state -> !state.skip_alignment && state.passed_trimmed_reads && state.passed_mapping },
fromState: [
"id": "id",
"paired": "paired",
"strandedness": "strandedness",
"fasta": "fasta",
"fai": "fai",
"gtf": "gtf",
"genome_bam": "genome_bam_sorted",
"chrom_sizes": "chrom_sizes",
"star_multiqc": "star_multiqc",
"extra_picard_args": "extra_picard_args",
"extra_stringtie_args": "extra_stringtie_args",
"stringtie_ignore_gtf": "stringtie_ignore_gtf",
"extra_bedtools_args": "extra_bedtools_args",
"bam_csi_index": "bam_csi_index",
"min_mapped_reads": "min_mapped_reads",
"with_umi": "with_umi",
"skip_qc": "skip_qc",
"skip_markduplicates": "skip_markduplicates",
"skip_stringtie": "skip_stringtie",
"skip_bigwig":"gencode"
],
toState: [
"genome_bam_sorted": "processed_genome_bam",
"genome_bam_index": "genome_bam_index",
"genome_bam_stats": "genome_bam_stats",
"genome_bam_flagstat": "genome_bam_flagstat",
"genome_bam_idxstats": "genome_bam_idxstats",
"markduplicates_metrics": "markduplicates_metrics",
"stringtie_transcript_gtf": "stringtie_transcript_gtf",
"stringtie_coverage_gtf": "stringtie_coverage_gtf",
"stringtie_abundance": "stringtie_abundance",
"stringtie_ballgown": "stringtie_ballgown",
"bedgraph_forward": "bedgraph_forward",
"bedgraph_reverse": "bedgraph_reverse",
"bigwig_forward": "bigwig_forward",
"bigwig_reverse": "bigwig_reverse"
]
)
// Final QC
| quality_control.run (
fromState: [
"id": "id",
"paired": "paired",
"strandedness": "strandedness",
"skip_align": "skip_alignment",
"skip_pseudo_align": "skip_pseudo_alignment",
"skip_dupradar": "skip_dupradar",
"skip_qualimap": "skip_qualimap",
"skip_rseqc": "skip_rseqc",
"skip_multiqc": "skip_multiqc",
"skip_preseq": "skip_preseq",
"gtf": "gtf",
"num_trimmed_reads": "num_trimmed_reads",
"passed_trimmed_reads": "passed_trimmed_reads",
"passed_mapping": "passed_mapping",
"percent_mapped": "percent_mapped",
"genome_bam": "genome_bam_sorted",
"genome_bam_index": "genome_bam_index",
"salmon_multiqc": "salmon_multiqc",
"quant_results_file": "quant_results_file",
"rsem_multiqc": "rsem_multiqc",
"rsem_counts_gene": "rsem_counts_gene",
"rsem_counts_transcripts": "rsem_counts_transcripts",
"pseudo_multiqc": "pseudo_multiqc",
"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",
"aligner": "aligner",
"pseudo_aligner": "pseudo_aligner",
"gene_bed": "gene_bed",
"extra_preseq_args": "extra_preseq_args",
"biotype": "biotype",
"skip_biotype_qc": "skip_biotype_qc",
"featurecounts_group_type": "featurecounts_group_type",
"featurecounts_feature_type": "featurecounts_feature_type",
"gencode": "gencode",
"skip_deseq2_qc": "skip_deseq2_qc",
"deseq2_vst": "deseq2_vst",
"multiqc_custom_config": "multiqc_custom_config",
"multiqc_title": "multiqc_title",
"multiqc_methods_description": "multiqc_methods_description",
"fastqc_zip_1": "fastqc_zip_1",
"fastqc_zip_2": "fastqc_zip_2",
"trim_log_1": "trim_log_1",
"trim_log_2": "trim_log_2",
"trim_zip_1": "trim_zip_1",
"trim_zip_2": "trim_zip_2",
"sortmerna_multiqc": "sortmerna_log",
"star_multiqc": "star_multiqc",
"genome_bam_stats": "genome_bam_stats",
"genome_bam_flagstat": "genome_bam_flagstat",
"genome_bam_idxstats": "genome_bam_idxstats",
"markduplicates_multiqc": "markduplicates_metrics",
"rseqc_modules": "rseqc_modules"
],
toState: [
"preseq_output": "preseq_output",
"bamstat_output": "bamstat_output",
"strandedness_output": "strandedness_output",
"inner_dist_output_stats": "inner_dist_output_stats",
"inner_dist_output_dist": "inner_dist_output_dist",
"inner_dist_output_freq": "inner_dist_output_freq",
"inner_dist_output_plot": "inner_dist_output_plot",
"inner_dist_output_plot_r": "inner_dist_output_plot_r",
"junction_annotation_output_log": "junction_annotation_output_log",
"junction_annotation_output_plot_r": "junction_annotation_output_plot_r",
"junction_annotation_output_junction_bed": "junction_annotation_output_junction_bed",
"junction_annotation_output_junction_interact": "junction_annotation_output_junction_interact",
"junction_annotation_output_junction_sheet": "junction_annotation_output_junction_sheet",
"junction_annotation_output_splice_events_plot": "junction_annotation_output_splice_events_plot",
"junction_annotation_output_splice_junctions_plot": "junction_annotation_output_splice_junctions_plot",
"junction_saturation_output_plot_r": "junction_saturation_output_plot_r",
"junction_saturation_output_plot": "junction_saturation_output_plot",
"read_distribution_output": "read_distribution_output",
"read_duplication_output_duplication_rate_plot_r": "read_duplication_output_duplication_rate_plot_r",
"read_duplication_output_duplication_rate_plot": "read_duplication_output_duplication_rate_plot",
"read_duplication_output_duplication_rate_mapping": "read_duplication_output_duplication_rate_mapping",
"read_duplication_output_duplication_rate_sequence": "read_duplication_output_duplication_rate_sequence",
"tin_output_summary": "tin_output_summary",
"tin_output_metrics": "tin_output_metrics",
"dupradar_output_dupmatrix": "dupradar_output_dupmatrix",
"dupradar_output_dup_intercept_mqc": "dupradar_output_dup_intercept_mqc",
"dupradar_output_duprate_exp_boxplot": "dupradar_output_duprate_exp_boxplot",
"dupradar_output_duprate_exp_densplot": "dupradar_output_duprate_exp_densplot",
"dupradar_output_duprate_exp_denscurve_mqc": "dupradar_output_duprate_exp_denscurve_mqc",
"dupradar_output_expression_histogram": "dupradar_output_expression_histogram",
"dupradar_output_intercept_slope": "dupradar_output_intercept_slope",
"qualimap_output_dir": "qualimap_output_dir",
"qualimap_output_pdf": "qualimap_output_pdf",
"featurecounts": "featurecounts",
"featurecounts_summary": "featurecounts_summary",
"featurecounts_multiqc": "featurecounts_multiqc",
"featurecounts_rrna_multiqc": "featurecounts_rrna_multiqc",
"tpm_gene": "tpm_gene",
"counts_gene": "counts_gene",
"counts_gene_length_scaled": "counts_gene_length_scaled",
"counts_gene_scaled": "counts_gene_scaled",
"tpm_transcript": "tpm_transcript",
"counts_transcript": "counts_transcript",
"qunat_merged_summarizedexperiment": "quant_merged_summarizedexperiment",
"deseq2_output": "deseq2_output",
"multiqc_report": "multiqc_report",
"multiqc_data": "multiqc_data",
"multiqc_plots": "multiqc_plots"
]
)
| map { id, state ->
def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() }
[ id, mod_state ]
}
| setState (
[
"output_fasta": "fasta",
"output_gtf": "gtf",
"output_transcript_fasta": "transcript_fasta",
"output_gene_bed": "gene_bed",
"output_bbsplit_index": "bbsplit_index",
"output_star_index": "star_index",
"output_salmon_index": "salmon_index",
"output_kallisto_index": "kallisto_index",
"fastqc_html_1": "fastqc_html_1",
"fastqc_html_2": "fastqc_html_2",
"fastqc_zip_1": "fastqc_zip_1",
"fastqc_zip_2": "fastqc_zip_2",
"fastq_1": "qc_output1",
"fastq_2": "qc_output2",
"output_fastq_1": "fastq_1",
"output_fastq_2": "fastq_2",
"trim_log_1": "trim_log_1",
"trim_log_2": "trim_log_2",
"trim_zip_1": "trim_zip_1",
"trim_zip_2": "trim_zip_2",
"trim_html_1": "trim_html_1",
"trim_html_2": "trim_html_2",
"passed_trimmed_reads": "passed_trimmed_reads",
"num_trimmed_reads": "num_trimmed_reads",
"sortmerna_log": "sortmerna_log",
"salmon_quant_output": "salmon_quant_output",
"fastp_failed_trim": "failed_trim",
"fastp_failed_trim_unpaired1": "failed_trim_unpaired1",
"fastp_failed_trim_unpaired2": "failed_trim_unpaired2",
"fastp_trim_json": "trim_json",
"fastp_trim_html": "trim_html",
"fastp_trim_merged_out": "trim_merged_out"
]
)
// Infer strandedness from Salmon pseudo-alignment results
| map { id, state ->
(state.strandedness == 'auto') ?
[ id, state + [strandedness: getSalmonInferredStrandedness(state.salmon_quant_output)] ] :
[id, state]
}
// Filter FastQ files based on minimum trimmed read count after adapter trimming
| map { id, state ->
def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
def num_reads = (state.skip_trimming) ?
state.min_trimmed_reads + 1 :
(
(state.trimmer == "fastp") ?
getFastpReadsAfterFiltering(state.fastp_trim_json) :
(
(!state.skip_trimming && input.size() == 2) ?
getTrimGaloreReadsAfterFiltering(state.trim_log_2) :
getTrimGaloreReadsAfterFiltering(state.trim_log_1)
)
)
def passed_trimmed_reads =
(state.skip_trimming || (num_reads >= state.min_trimmed_reads)) ?
true :
false
[ id, state + [num_trimmed_reads: num_reads, passed_trimmed_reads: passed_trimmed_reads] ]
}
// Genome alignment and quantification
| genome_alignment_and_quant.run (
runIf: { id, state -> !state.skip_alignment && state.passed_trimmed_reads },
fromState: [
"id": "id",
"fastq_1": "fastq_1",
"fastq_2": "fastq_2",
"strandedness": "strandedness",
"gtf": "gtf",
"transcript_fasta": "transcript_fasta",
"bam_csi_index": "bam_csi_index",
"aligner": "aligner",
"rsem_index": "rsem_index",
"star_index": "star_index",
"extra_star_align_args": "extra_star_align_args",
"star_ignore_sjdbgtf": "star_ignore_sjdbgtf",
"seq_platform": "seq_platform",
"seq_center": "seq_center",
"with_umi": "with_umi",
"umi_dedup_stats": "umi_dedup_stats",
"gtf_group_features": "gtf_group_features",
"gtf_extra_attributes": "gtf_extra_attributes",
"salmon_quant_libtype": "salmon_quant_libtype",
"salmon_index": "salmon_index",
"extra_rsem_calculate_expression_args": "extra_rsem_calculate_expression_args"
],
toState: [
"star_multiqc": "star_multiqc",
"rsem_multiqc": "rsem_multiqc",
"salmon_multiqc": "salmon_multiqc",
"star_log": "star_multiqc",
"genome_bam_sorted": "genome_bam_sorted",
"genome_bam_index": "genome_bam_index",
"genome_bam_stats": "genome_bam_stats",
@@ -231,162 +482,21 @@ workflow run_wf {
"transcriptome_bam_stats": "transcriptome_bam_stats",
"transcriptome_bam_flagstat": "transcriptome_bam_flagstat",
"transcriptome_bam_idxstats": "transcriptome_bam_idxstats",
"quant_out_dir": "quant_out_dir",
"quant_results_file": "quant_results_file",
"rsem_counts_gene": "rsem_counts_gene",
"rsem_counts_transcripts": "rsem_counts_transcripts",
"bam_genome_rsem": "bam_genome_rsem",
"bam_transcript_rsem": "bam_transcript_rsem"
]
)
// Filter channels to get samples that passed STAR minimum mapping percentage
| map { id, state ->
def percent_mapped = (!state.skip_alignment) ? getStarPercentMapped(state.star_multiqc) : 0.0
def passed_mapping = (percent_mapped >= state.min_mapped_reads) ? true : false
[ id, state + [percent_mapped: percent_mapped, passed_mapping: passed_mapping] ]
}
// Pseudo-alignment and quantification
| pseudo_alignment_and_quant.run (
runIf: { id, state -> !state.skip_pseudo_alignment && state.passed_trimmed_reads },
fromState: [
"id": "id",
"fastq_1": "fastq_1",
"fastq_2": "fastq_2",
"strandedness": "strandedness",
"gtf": "gtf",
"transcript_fasta": "transcript_fasta",
"pseudo_aligner": "pseudo_aligner",
"salmon_index": "salmon_index",
"kallisto_index": "kallisto_index",
"extra_star_align_args": "extra_star_align_args",
"star_ignore_sjdbgtf": "star_ignore_sjdbgtf",
"seq_platform": "seq_platform",
"seq_center": "seq_center",
"with_umi": "with_umi",
"umi_dedup_stats": "umi_dedup_stats",
"gtf_group_features": "gtf_group_features",
"gtf_extra_attributes": "gtf_extra_attributes",
"lib_type": "salmon_quant_libtype",
"kallisto_quant_fragment_length": "kallisto_quant_fragment_length",
"kallisto_quant_fragment_length_sd": "kallisto_quant_fragment_length_sd"
],
toState: [
"pseudo_quant_out_dir": "quant_out_dir",
"pseudo_salmon_quant_results_file": "salmon_quant_results_file",
"pseudo_kallisto_quant_results_file": "kallisto_quant_results_file",
"pseudo_multiqc": "pseudo_multiqc"
]
)
| map { id, state ->
def input = state.fastq_2 ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
def paired = input.size() == 2
[ id, state + [ paired: paired ] ]
}
// Post-processing
| post_processing.run (
runIf: { id, state -> !state.skip_alignment && state.passed_trimmed_reads && state.passed_mapping },
fromState: [
"id": "id",
"paired": "paired",
"strandedness": "strandedness",
"fasta": "fasta",
"fai": "fai",
"gtf": "gtf",
"genome_bam": "genome_bam_sorted",
"chrom_sizes": "chrom_sizes",
"star_multiqc": "star_multiqc",
"extra_picard_args": "extra_picard_args",
"extra_stringtie_args": "extra_stringtie_args",
"stringtie_ignore_gtf": "stringtie_ignore_gtf",
"extra_bedtools_args": "extra_bedtools_args",
"bam_csi_index": "bam_csi_index",
"min_mapped_reads": "min_mapped_reads",
"with_umi": "with_umi",
"skip_qc": "skip_qc",
"skip_markduplicates": "skip_markduplicates",
"skip_stringtie": "skip_stringtie",
"skip_bigwig":"gencode"
],
toState: [
"genome_bam_sorted": "processed_genome_bam",
"genome_bam_index": "genome_bam_index",
"genome_bam_stats": "genome_bam_stats",
"genome_bam_flagstat": "genome_bam_flagstat",
"genome_bam_idxstats": "genome_bam_idxstats",
"salmon_quant_results": "quant_out_dir",
"pseudo_quant_results": "pseudo_quant_out_dir",
"markduplicates_metrics": "markduplicates_metrics",
"stringtie_transcript_gtf": "stringtie_transcript_gtf",
"stringtie_coverage_gtf": "stringtie_coverage_gtf",
"stringtie_abundance": "stringtie_abundance",
"stringtie_ballgown": "stringtie_ballgown",
"featurecounts": "featurecounts",
"featurecounts_summary": "featurecounts_summary",
"featurecounts_multiqc": "featurecounts_multiqc",
"featurecounts_rrna_multiqc": "featurecounts_rrna_multiqc",
"bedgraph_forward": "bedgraph_forward",
"bedgraph_reverse": "bedgraph_reverse",
"bigwig_forward": "bigwig_forward",
"bigwig_reverse": "bigwig_reverse"
]
)
// Final QC
| quality_control.run (
fromState: [
"id": "id",
"paired": "paired",
"strandedness": "strandedness",
"skip_align": "skip_alignment",
"skip_pseudo_align": "skip_pseudo_alignment",
"skip_dupradar": "skip_dupradar",
"skip_qualimap": "skip_qualimap",
"skip_rseqc": "skip_rseqc",
"skip_multiqc": "skip_multiqc",
"skip_preseq": "skip_preseq",
"gtf": "gtf",
"num_trimmed_reads": "num_trimmed_reads",
"passed_trimmed_reads": "passed_trimmed_reads",
"passed_mapping": "passed_mapping",
"percent_mapped": "percent_mapped",
"genome_bam": "genome_bam_sorted",
"genome_bam_index": "genome_bam_index",
"salmon_multiqc": "salmon_multiqc",
"quant_results_file": "quant_results_file",
"rsem_multiqc": "rsem_multiqc",
"rsem_counts_gene": "rsem_counts_gene",
"rsem_counts_transcripts": "rsem_counts_transcripts",
"pseudo_multiqc": "pseudo_multiqc",
"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",
"aligner": "aligner",
"pseudo_aligner": "pseudo_aligner",
"gene_bed": "gene_bed",
"extra_preseq_args": "extra_preseq_args",
"biotype": "biotype",
"skip_biotype_qc": "skip_biotype_qc",
"featurecounts_group_type": "featurecounts_group_type",
"featurecounts_feature_type": "featurecounts_feature_type",
"gencode": "gencode",
"skip_deseq2_qc": "skip_deseq2_qc",
"deseq2_vst": "deseq2_vst",
"multiqc_custom_config": "multiqc_custom_config",
"multiqc_title": "multiqc_title",
"multiqc_methods_description": "multiqc_methods_description",
"fastqc_zip_1": "fastqc_zip_1",
"fastqc_zip_2": "fastqc_zip_2",
"trim_log_1": "trim_log_1",
"trim_log_2": "trim_log_2",
"trim_zip_1": "trim_zip_1",
"trim_zip_2": "trim_zip_2",
"sortmerna_multiqc": "sortmerna_log",
"star_multiqc": "star_multiqc",
"genome_bam_stats": "genome_bam_stats",
"genome_bam_flagstat": "genome_bam_flagstat",
"genome_bam_idxstats": "genome_bam_idxstats",
"markduplicates_multiqc": "markduplicates_metrics",
"rseqc_modules": "rseqc_modules"
],
toState: [
"bigwig_reverse": "bigwig_reverse",
"preseq_output": "preseq_output",
"bamstat_output": "bamstat_output",
"strandedness_output": "strandedness_output",
@@ -419,140 +529,33 @@ workflow run_wf {
"dupradar_output_expression_histogram": "dupradar_output_expression_histogram",
"dupradar_output_intercept_slope": "dupradar_output_intercept_slope",
"qualimap_output_dir": "qualimap_output_dir",
"qualimap_output_pdf": "qualimap_output_pdf",
"featurecounts": "featurecounts",
"featurecounts_summary": "featurecounts_summary",
"featurecounts_multiqc": "featurecounts_multiqc",
"featurecounts_rrna_multiqc": "featurecounts_rrna_multiqc",
"qualimap_output_pdf": "qualimap_output_pdf",
"tpm_gene": "tpm_gene",
"counts_gene": "counts_gene",
"counts_gene_length_scaled": "counts_gene_length_scaled",
"counts_gene_scaled": "counts_gene_scaled",
"tpm_transcript": "tpm_transcript",
"counts_transcript": "counts_transcript",
"qunat_merged_summarizedexperiment": "quant_merged_summarizedexperiment",
"quant_merged_summarizedexperiment": "quant_merged_summarizedexperiment",
"deseq2_output": "deseq2_output",
"pseudo_tpm_gene": "pseudo_tpm_gene",
"pseudo_counts_gene": "pseudo_counts_gene",
"pseudo_counts_gene_length_scaled": "pseudo_counts_gene_length_scaled",
"pseudo_counts_gene_scaled": "pseudo_counts_gene_scaled",
"pseudo_tpm_transcript": "pseudo_tpm_transcript",
"pseudo_counts_transcript": "pseudo_counts_transcript",
"pseudo_lengths_gene": "pseudo_lengths_gene",
"pseudo_lengths_transcript": "pseudo_lengths_transcript",
"pseudo_quant_merged_summarizedexperiment": "pseudo_quant_merged_summarizedexperiment",
"deseq2_output_pseudo": "deseq2_output_pseudo",
"multiqc_report": "multiqc_report",
"multiqc_data": "multiqc_data",
"multiqc_plots": "multiqc_plots"
]
)
| map { id, state ->
def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() }
[ id, mod_state ]
}
| setState (
[
"output_fasta": "fasta",
"output_gtf": "gtf",
"output_transcript_fasta": "transcript_fasta",
"output_gene_bed": "gene_bed",
"output_bbsplit_index": "bbsplit_index",
"output_star_index": "star_index",
"output_salmon_index": "salmon_index",
"output_kallisto_index": "kallisto_index",
"fastqc_html_1": "fastqc_html_1",
"fastqc_html_2": "fastqc_html_2",
"fastqc_zip_1": "fastqc_zip_1",
"fastqc_zip_2": "fastqc_zip_2",
"output_fastq_1": "fastq_1",
"output_fastq_2": "fastq_2",
"trim_log_1": "trim_log_1",
"trim_log_2": "trim_log_2",
"trim_zip_1": "trim_zip_1",
"trim_zip_2": "trim_zip_2",
"trim_html_1": "trim_html_1",
"trim_html_2": "trim_html_2",
"sortmerna_log": "sortmerna_log",
"star_log": "star_multiqc",
"genome_bam_sorted": "genome_bam_sorted",
"genome_bam_index": "genome_bam_index",
"genome_bam_stats": "genome_bam_stats",
"genome_bam_flagstat": "genome_bam_flagstat",
"genome_bam_idxstats": "genome_bam_idxstats",
"transcriptome_bam": "transcriptome_bam",
"transcriptome_bam_index": "transcriptome_bam_index",
"transcriptome_bam_stats": "transcriptome_bam_stats",
"transcriptome_bam_flagstat": "transcriptome_bam_flagstat",
"transcriptome_bam_idxstats": "transcriptome_bam_idxstats",
"salmon_quant_results": "quant_out_dir",
"pseudo_quant_results": "pseudo_quant_out_dir",
"markduplicates_metrics": "markduplicates_metrics",
"stringtie_transcript_gtf": "stringtie_transcript_gtf",
"stringtie_coverage_gtf": "stringtie_coverage_gtf",
"stringtie_abundance": "stringtie_abundance",
"stringtie_ballgown": "stringtie_ballgown",
"featurecounts": "featurecounts",
"featurecounts_summary": "featurecounts_summary",
"featurecounts_multiqc": "featurecounts_multiqc",
"featurecounts_rrna_multiqc": "featurecounts_rrna_multiqc",
"bedgraph_forward": "bedgraph_forward",
"bedgraph_reverse": "bedgraph_reverse",
"bigwig_forward": "bigwig_forward",
"bigwig_reverse": "bigwig_reverse",
"preseq_output": "preseq_output",
"bamstat_output": "bamstat_output",
"strandedness_output": "strandedness_output",
"inner_dist_output_stats": "inner_dist_output_stats",
"inner_dist_output_dist": "inner_dist_output_dist",
"inner_dist_output_freq": "inner_dist_output_freq",
"inner_dist_output_plot": "inner_dist_output_plot",
"inner_dist_output_plot_r": "inner_dist_output_plot_r",
"junction_annotation_output_log": "junction_annotation_output_log",
"junction_annotation_output_plot_r": "junction_annotation_output_plot_r",
"junction_annotation_output_junction_bed": "junction_annotation_output_junction_bed",
"junction_annotation_output_junction_interact": "junction_annotation_output_junction_interact",
"junction_annotation_output_junction_sheet": "junction_annotation_output_junction_sheet",
"junction_annotation_output_splice_events_plot": "junction_annotation_output_splice_events_plot",
"junction_annotation_output_splice_junctions_plot": "junction_annotation_output_splice_junctions_plot",
"junction_saturation_output_plot_r": "junction_saturation_output_plot_r",
"junction_saturation_output_plot": "junction_saturation_output_plot",
"read_distribution_output": "read_distribution_output",
"read_duplication_output_duplication_rate_plot_r": "read_duplication_output_duplication_rate_plot_r",
"read_duplication_output_duplication_rate_plot": "read_duplication_output_duplication_rate_plot",
"read_duplication_output_duplication_rate_mapping": "read_duplication_output_duplication_rate_mapping",
"read_duplication_output_duplication_rate_sequence": "read_duplication_output_duplication_rate_sequence",
"tin_output_summary": "tin_output_summary",
"tin_output_metrics": "tin_output_metrics",
"dupradar_output_dupmatrix": "dupradar_output_dupmatrix",
"dupradar_output_dup_intercept_mqc": "dupradar_output_dup_intercept_mqc",
"dupradar_output_duprate_exp_boxplot": "dupradar_output_duprate_exp_boxplot",
"dupradar_output_duprate_exp_densplot": "dupradar_output_duprate_exp_densplot",
"dupradar_output_duprate_exp_denscurve_mqc": "dupradar_output_duprate_exp_denscurve_mqc",
"dupradar_output_expression_histogram": "dupradar_output_expression_histogram",
"dupradar_output_intercept_slope": "dupradar_output_intercept_slope",
"qualimap_output_dir": "qualimap_output_dir",
"qualimap_output_pdf": "qualimap_output_pdf",
"tpm_gene": "tpm_gene",
"counts_gene": "counts_gene",
"counts_gene_length_scaled": "counts_gene_length_scaled",
"counts_gene_scaled": "counts_gene_scaled",
"tpm_transcript": "tpm_transcript",
"counts_transcript": "counts_transcript",
"quant_merged_summarizedexperiment": "quant_merged_summarizedexperiment",
"deseq2_output": "deseq2_output",
"pseudo_tpm_gene": "pseudo_tpm_gene",
"pseudo_counts_gene": "pseudo_counts_gene",
"pseudo_counts_gene_length_scaled": "pseudo_counts_gene_length_scaled",
"pseudo_counts_gene_scaled": "pseudo_counts_gene_scaled",
"pseudo_tpm_transcript": "pseudo_tpm_transcript",
"pseudo_counts_transcript": "pseudo_counts_transcript",
"pseudo_lengths_gene": "pseudo_lengths_gene",
"pseudo_lengths_transcript": "pseudo_lengths_transcript",
"pseudo_quant_merged_summarizedexperiment": "pseudo_quant_merged_summarizedexperiment",
"deseq2_output_pseudo": "deseq2_output_pseudo",
"multiqc_report": "multiqc_report",
"multiqc_data": "multiqc_data",
"multiqc_plots": "multiqc_plots"
]
)
output_ch = analysis_ch
]
)
emit:
output_ch
analysis_ch
}
import nextflow.Nextflow

6
target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/.config.vsh.yaml
View File

@@ -1083,9 +1083,9 @@ build_info:
output: "target/nextflow/fastp"
executable: "target/nextflow/fastp/main.nf"
viash_version: "0.9.0"
git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
git_tag: "v0.2.0-25-g065297b"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d"
package_config:
name: "biobox"
version: "main"

6
target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/main.nf
View File

@@ -4023,9 +4023,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/fastp",
"viash_version" : "0.9.0",
"git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9",
"git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-25-g065297b"
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d"
},
"package_config" : {
"name" : "biobox",

6
target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/.config.vsh.yaml
View File

@@ -645,9 +645,9 @@ build_info:
output: "target/nextflow/featurecounts"
executable: "target/nextflow/featurecounts/main.nf"
viash_version: "0.9.0"
git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
git_tag: "v0.2.0-25-g065297b"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d"
package_config:
name: "biobox"
version: "main"

6
target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/main.nf
View File

@@ -3549,9 +3549,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/featurecounts",
"viash_version" : "0.9.0",
"git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9",
"git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-25-g065297b"
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d"
},
"package_config" : {
"name" : "biobox",

6
target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/.config.vsh.yaml
View File

@@ -685,9 +685,9 @@ build_info:
output: "target/nextflow/gffread"
executable: "target/nextflow/gffread/main.nf"
viash_version: "0.9.0"
git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
git_tag: "v0.2.0-25-g065297b"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d"
package_config:
name: "biobox"
version: "main"

6
target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/main.nf
View File

@@ -3606,9 +3606,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/gffread",
"viash_version" : "0.9.0",
"git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9",
"git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-25-g065297b"
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d"
},
"package_config" : {
"name" : "biobox",

6
target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/.config.vsh.yaml
View File

@@ -456,9 +456,9 @@ build_info:
output: "target/nextflow/multiqc"
executable: "target/nextflow/multiqc/main.nf"
viash_version: "0.9.0"
git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
git_tag: "v0.2.0-25-g065297b"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d"
package_config:
name: "biobox"
version: "main"

6
target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/main.nf
View File

@@ -3366,9 +3366,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/multiqc",
"viash_version" : "0.9.0",
"git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9",
"git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-25-g065297b"
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d"
},
"package_config" : {
"name" : "biobox",

6
target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml
View File

@@ -416,9 +416,9 @@ build_info:
output: "target/nextflow/rsem/rsem_prepare_reference"
executable: "target/nextflow/rsem/rsem_prepare_reference/main.nf"
viash_version: "0.9.0"
git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
git_tag: "v0.2.0-25-g065297b"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d"
package_config:
name: "biobox"
version: "main"

6
target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/main.nf
View File

@@ -3245,9 +3245,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/rsem/rsem_prepare_reference",
"viash_version" : "0.9.0",
"git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9",
"git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-25-g065297b"
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d"
},
"package_config" : {
"name" : "biobox",

6
target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/.config.vsh.yaml
View File

@@ -277,9 +277,9 @@ build_info:
output: "target/nextflow/salmon/salmon_index"
executable: "target/nextflow/salmon/salmon_index/main.nf"
viash_version: "0.9.0"
git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
git_tag: "v0.2.0-25-g065297b"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d"
package_config:
name: "biobox"
version: "main"

6
target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/main.nf
View File

@@ -3129,9 +3129,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/salmon/salmon_index",
"viash_version" : "0.9.0",
"git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9",
"git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-25-g065297b"
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d"
},
"package_config" : {
"name" : "biobox",

6
target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/.config.vsh.yaml
View File

@@ -1173,9 +1173,9 @@ build_info:
output: "target/nextflow/salmon/salmon_quant"
executable: "target/nextflow/salmon/salmon_quant/main.nf"
viash_version: "0.9.0"
git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
git_tag: "v0.2.0-25-g065297b"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d"
package_config:
name: "biobox"
version: "main"

6
target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/main.nf
View File

@@ -3964,9 +3964,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/salmon/salmon_quant",
"viash_version" : "0.9.0",
"git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9",
"git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-25-g065297b"
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d"
},
"package_config" : {
"name" : "biobox",

6
target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/.config.vsh.yaml
View File

@@ -173,9 +173,9 @@ build_info:
output: "target/nextflow/samtools/samtools_flagstat"
executable: "target/nextflow/samtools/samtools_flagstat/main.nf"
viash_version: "0.9.0"
git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
git_tag: "v0.2.0-25-g065297b"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d"
package_config:
name: "biobox"
version: "main"

6
target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/main.nf
View File

@@ -3028,9 +3028,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/samtools/samtools_flagstat",
"viash_version" : "0.9.0",
"git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9",
"git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-25-g065297b"
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d"
},
"package_config" : {
"name" : "biobox",

6
target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/.config.vsh.yaml
View File

@@ -183,9 +183,9 @@ build_info:
output: "target/nextflow/samtools/samtools_idxstats"
executable: "target/nextflow/samtools/samtools_idxstats/main.nf"
viash_version: "0.9.0"
git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
git_tag: "v0.2.0-25-g065297b"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d"
package_config:
name: "biobox"
version: "main"

6
target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/main.nf
View File

@@ -3040,9 +3040,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/samtools/samtools_idxstats",
"viash_version" : "0.9.0",
"git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9",
"git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-25-g065297b"
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d"
},
"package_config" : {
"name" : "biobox",

6
target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/.config.vsh.yaml
View File

@@ -189,9 +189,9 @@ build_info:
output: "target/nextflow/samtools/samtools_index"
executable: "target/nextflow/samtools/samtools_index/main.nf"
viash_version: "0.9.0"
git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
git_tag: "v0.2.0-25-g065297b"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d"
package_config:
name: "biobox"
version: "main"

6
target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/main.nf
View File

@@ -3053,9 +3053,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/samtools/samtools_index",
"viash_version" : "0.9.0",
"git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9",
"git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-25-g065297b"
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d"
},
"package_config" : {
"name" : "biobox",

6
target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/.config.vsh.yaml
View File

@@ -332,9 +332,9 @@ build_info:
output: "target/nextflow/samtools/samtools_sort"
executable: "target/nextflow/samtools/samtools_sort/main.nf"
viash_version: "0.9.0"
git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
git_tag: "v0.2.0-25-g065297b"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d"
package_config:
name: "biobox"
version: "main"

6
target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/main.nf
View File

@@ -3225,9 +3225,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/samtools/samtools_sort",
"viash_version" : "0.9.0",
"git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9",
"git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-25-g065297b"
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d"
},
"package_config" : {
"name" : "biobox",

6
target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/.config.vsh.yaml
View File

@@ -401,9 +401,9 @@ build_info:
output: "target/nextflow/samtools/samtools_stats"
executable: "target/nextflow/samtools/samtools_stats/main.nf"
viash_version: "0.9.0"
git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
git_tag: "v0.2.0-25-g065297b"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d"
package_config:
name: "biobox"
version: "main"

6
target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/main.nf
View File

@@ -3295,9 +3295,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/samtools/samtools_stats",
"viash_version" : "0.9.0",
"git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9",
"git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-25-g065297b"
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d"
},
"package_config" : {
"name" : "biobox",

6
target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/.config.vsh.yaml
View File

@@ -2663,9 +2663,9 @@ build_info:
output: "target/nextflow/star/star_align_reads"
executable: "target/nextflow/star/star_align_reads/main.nf"
viash_version: "0.9.0"
git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
git_tag: "v0.2.0-25-g065297b"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d"
package_config:
name: "biobox"
version: "main"

6
target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/main.nf
View File

@@ -5943,9 +5943,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/star/star_align_reads",
"viash_version" : "0.9.0",
"git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9",
"git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-25-g065297b"
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d"
},
"package_config" : {
"name" : "biobox",

6
target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/.config.vsh.yaml
View File

@@ -333,9 +333,9 @@ build_info:
output: "target/nextflow/star/star_genome_generate"
executable: "target/nextflow/star/star_genome_generate/main.nf"
viash_version: "0.9.0"
git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
git_tag: "v0.2.0-25-g065297b"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d"
package_config:
name: "biobox"
version: "main"

6
target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/main.nf
View File

@@ -3195,9 +3195,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/star/star_genome_generate",
"viash_version" : "0.9.0",
"git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9",
"git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-25-g065297b"
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d"
},
"package_config" : {
"name" : "biobox",

6
target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml
View File

@@ -434,9 +434,9 @@ build_info:
output: "target/nextflow/umi_tools/umi_tools_extract"
executable: "target/nextflow/umi_tools/umi_tools_extract/main.nf"
viash_version: "0.9.0"
git_commit: "065297be5fb2d88020fc50e042bb3f49c9254ae9"
git_remote: "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox"
git_tag: "v0.2.0-25-g065297b"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d"
package_config:
name: "biobox"
version: "main"

6
target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/main.nf
View File

@@ -3299,9 +3299,9 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/umi_tools/umi_tools_extract",
"viash_version" : "0.9.0",
"git_commit" : "065297be5fb2d88020fc50e042bb3f49c9254ae9",
"git_remote" : "https://x-access-token:ghs_bGw8YykA469ibXe1g5GsidZ6N0n23m22jhvl@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-25-g065297b"
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d"
},
"package_config" : {
"name" : "biobox",

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

@@ -246,8 +246,8 @@ build_info:
output: "target/executable/bbmap_bbsplit"
executable: "target/executable/bbmap_bbsplit/bbmap_bbsplit"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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="2024-11-18T16:13:12Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:13Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -186,8 +186,8 @@ build_info:
output: "target/executable/bedtools_genomecov"
executable: "target/executable/bedtools_genomecov/bedtools_genomecov"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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="2024-11-18T16:13:11Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:11Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -190,8 +190,8 @@ build_info:
output: "target/executable/cat_additional_fasta"
executable: "target/executable/cat_additional_fasta/cat_additional_fasta"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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="2024-11-18T16:13:10Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:10Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -177,8 +177,8 @@ build_info:
output: "target/executable/cat_fastq"
executable: "target/executable/cat_fastq/cat_fastq"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

6
target/executable/cat_fastq/cat_fastq
View File

@@ -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="2024-11-18T16:13:09Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:10Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -245,8 +245,8 @@ build_info:
output: "target/executable/deseq2_qc"
executable: "target/executable/deseq2_qc/deseq2_qc"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

6
target/executable/deseq2_qc/deseq2_qc
View File

@@ -506,9 +506,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
Rscript -e 'remotes::install_cran(c("optparse", "ggplot2", "RColorBrewer", "pheatmap", "stringr", "matrixStats"), repos = "https://cran.rstudio.com")'
LABEL org.opencontainers.image.description="Companion container for running component deseq2_qc"
LABEL org.opencontainers.image.created="2024-11-18T16:13:11Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:12Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -274,8 +274,8 @@ build_info:
output: "target/executable/dupradar"
executable: "target/executable/dupradar/dupradar"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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="2024-11-18T16:13:11Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:12Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -206,8 +206,8 @@ build_info:
output: "target/executable/fastqc"
executable: "target/executable/fastqc/fastqc"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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="2024-11-18T16:13:14Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:14Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -185,8 +185,8 @@ build_info:
output: "target/executable/fq_subsample"
executable: "target/executable/fq_subsample/fq_subsample"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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="2024-11-18T16:13:12Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:13Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -175,8 +175,8 @@ build_info:
output: "target/executable/getchromsizes"
executable: "target/executable/getchromsizes/getchromsizes"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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="2024-11-18T16:13:10Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:11Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -153,8 +153,8 @@ build_info:
output: "target/executable/gtf2bed"
executable: "target/executable/gtf2bed/gtf2bed"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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="2024-11-18T16:13:12Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:12Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -163,8 +163,8 @@ build_info:
output: "target/executable/gtf_filter"
executable: "target/executable/gtf_filter/gtf_filter"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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="2024-11-18T16:13:10Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:11Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -152,8 +152,8 @@ build_info:
output: "target/executable/gunzip"
executable: "target/executable/gunzip/gunzip"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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="2024-11-18T16:13:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:07Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -163,8 +163,8 @@ build_info:
output: "target/executable/kallisto/kallisto_index"
executable: "target/executable/kallisto/kallisto_index/kallisto_index"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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="2024-11-18T16:13:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:07Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -261,8 +261,8 @@ build_info:
output: "target/executable/kallisto/kallisto_quant"
executable: "target/executable/kallisto/kallisto_quant/kallisto_quant"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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="2024-11-18T16:13:07Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:07Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -169,8 +169,8 @@ build_info:
output: "target/executable/multiqc_custom_biotype"
executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

6
target/executable/multiqc_custom_biotype/multiqc_custom_biotype
View File

@@ -476,9 +476,9 @@ function ViashDockerfile {
FROM python:latest
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component multiqc_custom_biotype"
LABEL org.opencontainers.image.created="2024-11-18T16:13:09Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:10Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -215,8 +215,8 @@ build_info:
output: "target/executable/picard_markduplicates"
executable: "target/executable/picard_markduplicates/picard_markduplicates"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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="2024-11-18T16:13:08Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:09Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -417,8 +417,8 @@ build_info:
output: "target/executable/prepare_multiqc_input"
executable: "target/executable/prepare_multiqc_input/prepare_multiqc_input"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

6
target/executable/prepare_multiqc_input/prepare_multiqc_input
View File

@@ -557,9 +557,9 @@ function ViashDockerfile {
FROM ubuntu:22.04
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component prepare_multiqc_input"
LABEL org.opencontainers.image.created="2024-11-18T16:13:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:05Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -146,8 +146,8 @@ build_info:
output: "target/executable/preprocess_transcripts_fasta"
executable: "target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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="2024-11-18T16:13:08Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:09Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -199,8 +199,8 @@ build_info:
output: "target/executable/preseq_lcextrap"
executable: "target/executable/preseq_lcextrap/preseq_lcextrap"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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="2024-11-18T16:13:08Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:08Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -279,8 +279,8 @@ build_info:
output: "target/executable/qualimap"
executable: "target/executable/qualimap/qualimap"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

6
target/executable/qualimap/qualimap
View File

@@ -537,9 +537,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
Rscript -e 'remotes::install_cran(c("optparse"), repos = "https://cran.rstudio.com")'
LABEL org.opencontainers.image.description="Companion container for running component qualimap"
LABEL org.opencontainers.image.created="2024-11-18T16:13:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -307,8 +307,8 @@ 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: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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="2024-11-18T16:13:05Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -190,8 +190,8 @@ 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: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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

@@ -483,9 +483,9 @@ function ViashDockerfile {
FROM ubuntu:22.04
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_merge_counts"
LABEL org.opencontainers.image.created="2024-11-18T16:13:05Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -171,8 +171,8 @@ build_info:
output: "target/executable/rseqc/rseqc_bamstat"
executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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="2024-11-18T16:13:10Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:10Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -194,8 +194,8 @@ build_info:
output: "target/executable/rseqc/rseqc_inferexperiment"
executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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="2024-11-18T16:13:11Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:12Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -280,8 +280,8 @@ build_info:
output: "target/executable/rseqc/rseqc_innerdistance"
executable: "target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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="2024-11-18T16:13:09Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:10Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -268,8 +268,8 @@ build_info:
output: "target/executable/rseqc/rseqc_junctionannotation"
executable: "target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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="2024-11-18T16:13:09Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:10Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -257,8 +257,8 @@ build_info:
output: "target/executable/rseqc/rseqc_junctionsaturation"
executable: "target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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="2024-11-18T16:13:10Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:11Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -170,8 +170,8 @@ build_info:
output: "target/executable/rseqc/rseqc_readdistribution"
executable: "target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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="2024-11-18T16:13:10Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:11Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -219,8 +219,8 @@ build_info:
output: "target/executable/rseqc/rseqc_readduplication"
executable: "target/executable/rseqc/rseqc_readduplication/rseqc_readduplication"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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="2024-11-18T16:13:09Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:09Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -222,8 +222,8 @@ build_info:
output: "target/executable/rseqc/rseqc_tin"
executable: "target/executable/rseqc/rseqc_tin/rseqc_tin"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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="2024-11-18T16:13:10Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:11Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -200,8 +200,8 @@ build_info:
output: "target/executable/sortmerna"
executable: "target/executable/sortmerna/sortmerna"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

6
target/executable/sortmerna/sortmerna
View File

@@ -486,9 +486,9 @@ function ViashDockerfile {
FROM quay.io/biocontainers/sortmerna:4.3.6--h9ee0642_0
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component sortmerna"
LABEL org.opencontainers.image.created="2024-11-18T16:13:13Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:14Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -224,8 +224,8 @@ build_info:
output: "target/executable/stringtie"
executable: "target/executable/stringtie/stringtie"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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="2024-11-18T16:13:14Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="89519f6e38f772746faa936930dbda45c0b09e83"
LABEL org.opencontainers.image.created="2024-11-27T16:55:15Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="c466555a20aa6b87f2d56e1b96126a1e87dd5611"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -207,8 +207,8 @@ build_info:
output: "target/executable/summarizedexperiment"
executable: "target/executable/summarizedexperiment/summarizedexperiment"
viash_version: "0.9.0"
git_commit: "89519f6e38f772746faa936930dbda45c0b09e83"
git_remote: "https://x-access-token:ghs_kCo1ZtELVBWMBkCE1xDsZSpvrjy8f60WqjB0@github.com/viash-hub/rnaseq"
git_commit: "c466555a20aa6b87f2d56e1b96126a1e87dd5611"
git_remote: "https://x-access-token:ghs_O6clxuS40ZvoCeBqdFzm7br0dH2Yc11KcQ9x@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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