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Build branch multiple_fixes with version multiple_fixes (f3645db)

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

Source commit: f3645db764

Source message: update config
This commit is contained in:
CI
2024-09-30 08:25:15 +00:00
parent 0e55094fd4
commit b127f32213
212 changed files with 1377 additions and 1008 deletions
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12
assets/multiqc_config.yml
View File

@@ -64,12 +64,12 @@ table_columns_visible:
fastqc:
percent_duplicates: False
fn_clean_extn:
extra_fn_clean_extn:
- ".mapping_quality"
- ".MarkDuplicates_flagstat"
- ".MarkDuplicates_stats"
- ".genome_sorted"
- ".MarkDuplicates"
- ".MarkDuplicates_flagstat.output.flagstat"
- ".MarkDuplicates_idxstats.output.idxstats"
- ".MarkDuplicates_stats.output.txt"
- ".genome_sorted_MarkDuplicates.output.bam"
- ".genome_sorted_MarkDuplicates"
- ".read_1"
- ".read_2"
@@ -112,7 +112,7 @@ custom_data:
# See https://multiqc.info/docs/#optimise-file-search-patterns for details
sp:
fastqc:
fastqc/zip:
fn: "*.fastqc.zip"
cutadapt:

8
src/prepare_multiqc_input/script.sh
View File

@@ -22,8 +22,9 @@ IFS="," read -ra star_multiqc <<< $par_star_multiqc && for file in "${star_multi
IFS="," read -ra rsem_multiqc <<< $par_rsem_multiqc && for file in "${rsem_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done
# TODO: Fetch Salmon meta info
# IFS="," read -ra salmon_multiqc <<< $par_salmon_multiqc && for file in "${salmon_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done
IFS="," read -ra salmon_multiqc <<< $par_salmon_multiqc && for file in "${salmon_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done
IFS="," read -ra pseudo_multiqc <<< $par_pseudo_multiqc && for file in "${pseudo_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done
IFS="," read -ra samtools_stats <<< $par_samtools_stats && for file in "${samtools_stats[@]}"; do [ -e "$file" ] && cp -r "$file" $par_output/; done
@@ -33,9 +34,6 @@ IFS="," read -ra samtools_idxstats <<< $par_samtools_idxstats && for file in "${
IFS="," read -ra markduplicates_multiqc <<< $par_markduplicates_multiqc && for file in "${markduplicates_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done
IFS="," read -ra pseudo_multiqc <<< $par_pseudo_multiqc && for file in "${pseudo_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done
IFS="," read -ra featurecounts_multiqc <<< $par_featurecounts_multiqc && for file in "${featurecounts_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done
IFS="," read -ra featurecounts_rrna_multiqc <<< $par_featurecounts_rrna_multiqc && for file in "${featurecounts_rrna_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done

3
src/workflows/genome_alignment_and_quant/config.vsh.yaml
View File

@@ -145,6 +145,9 @@ argument_groups:
type: file
direction: output
default: $id.quant.sf
- name: "--salmon_multiqc"
type: file
direction: output
- name: "--rsem_counts_gene"
type: file
description: Expression counts on gene level

6
src/workflows/genome_alignment_and_quant/main.nf
View File

@@ -280,6 +280,11 @@ workflow run_wf {
]
)
| map { id, state ->
def mod_state = (state.aligner == 'star_salmon') ? state + [salmon_multiqc: state.quant_out_dir] : state
[ id, mod_state ]
}
| niceView()
| rsem_calculate_expression.run (
runIf: { id, state -> state.aligner == 'star_rsem' },
fromState: [
@@ -357,6 +362,7 @@ workflow run_wf {
[ "star_alignment": "star_alignment",
"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",

12
src/workflows/post_processing/config.vsh.yaml
View File

@@ -79,27 +79,27 @@ argument_groups:
- name: "--processed_genome_bam"
type: file
direction: output
default: $id.markdup.sorted.bam
default: $id..genome.bam
- name: "--genome_bam_index"
type: file
direction: output
default: $id.markdup.sorted.bam
default: $id.genome.bam.bai
- name: "--genome_bam_stats"
type: file
direction: output
default: $id.markdup.sorted.bam.stats
default: $id.genome.stats
- name: "--genome_bam_flagstat"
type: file
direction: output
default: $id.markdup.sorted.bam.flagstat
default: $id.genome.flagstat
- name: "--genome_bam_idxstats"
type: file
direction: output
default: $id.markdup.sorted.bam.idxstats
default: $id.genome.idxstats
- name: "--markduplicates_metrics"
type: file
direction: output
default: $id.markdup.sorted.MarkDuplicates.metrics.txt
default: $id.MarkDuplicates.metrics.txt
- name: "--stringtie_transcript_gtf"
type: file
direction: output

4
src/workflows/pre_processing/config.vsh.yaml
View File

@@ -162,14 +162,14 @@ argument_groups:
required: false
must_exist: false
description: Path to output directory
default: $id.$key.read_1.fastq
default: $id.read_1.fastq
- name: "--qc_output2"
type: file
direction: output
required: false
must_exist: false
description: Path to output directory
default: $id.$key.read_2.fastq
default: $id.read_2.fastq
- name: "--fastqc_html_1"
type: file
direction: output

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

@@ -75,7 +75,7 @@ workflow run_wf {
"trim_html_1": "trimmed_fastqc_html_1",
"trim_html_2": "trimmed_fastqc_html_2"
],
args: [gzip: true]
args: [gzip: true, fastqc: true]
)
// Trim reads using fastp

1
src/workflows/pseudo_alignment_and_quant/config.vsh.yaml
View File

@@ -59,7 +59,6 @@ argument_groups:
- name: "--pseudo_multiqc"
type: file
direction: output
default: $id.quant.log
- name: "--quant_out_dir"
type: file
direction: output

7
src/workflows/pseudo_alignment_and_quant/main.nf
View File

@@ -46,11 +46,16 @@ workflow run_wf {
lib_type: state.lib_type ]
},
toState: [
"quant_outs_dir": "output",
"quant_out_dir": "output",
"salmon_quant_results_file": "quant_results"
]
)
| map { id, state ->
def mod_state = (state.pseudo_aligner == 'salmon') ? state + [pseudo_multiqc: state.quant_out_dir] : state
[ id, mod_state ]
}
| kallisto_quant.run (
runIf: { id, state -> state.pseudo_aligner == 'kallisto'},
fromState: [

12
src/workflows/quality_control/config.vsh.yaml
View File

@@ -264,11 +264,6 @@ argument_groups:
type: string
- name: "--multiqc_methods_description"
type: file
- name: "--mqc_yml"
type: file
description: Software versions
- name: "--workflow_summary"
type: file
- name: "--passed_trimmed_reads"
type: boolean
- name: "--num_trimmed_reads"
@@ -303,8 +298,8 @@ argument_groups:
must_exist: false
# - name: "--hisat2_multiqc"
# type: file
# - name: "--rsem_multiqc"
# type: file
- name: "--rsem_multiqc"
type: file
- name: "--genome_bam_stats"
type: file
must_exist: false
@@ -548,9 +543,6 @@ argument_groups:
type: file
direction: output
default: multiqc_plots
- name: "--multiqc_versions"
type: file
direction: output
# Biotype QC
- name: "--featurecounts"

291
src/workflows/quality_control/main.nf
View File

@@ -55,7 +55,7 @@ workflow run_wf {
"input": "genome_bam",
"extra_preseq_args": "extra_preseq_args"
],
toState: [ "preseq_output": "output" ],
toState: [ "preseq_output": "output" ]
)
| rseqc_bamstat.run (
@@ -214,11 +214,49 @@ workflow run_wf {
merged_ch = qc_ch
| toSortedList
// TODO: Get Salmon meta info
| map { list ->
def ids = list.collect { id, state -> state.id }
def strandedness = list.collect { id, state -> state.strandedness }
def num_trimmed_reads = list.collect { id, state -> state.num_trimmed_reads }
def passed_trimmed_reads = list.collect { id, state -> state.passed_trimmed_reads }
def passed_mapping = list.collect { id, state -> state.passed_mapping }
def percent_mapped = list.collect { id, state -> state.percent_mapped }
def inferred_strand = list.collect { id, state -> state.inferred_strand }
def passed_strand_check = list.collect { id, state -> state.passed_strand_check }
def gtf = list.collect { id, state -> state.gtf }.unique()[0]
def gtf_extra_attributes = list.collect { id, state -> state.gtf_extra_attributes }.unique()[0]
def gtf_group_features = list.collect { id, state -> state.gtf_group_features }.unique()[0]
def pca_header_multiqc = list.collect { id, state -> state.pca_header_multiqc }.unique()[0]
def clustering_header_multiqc = list.collect { id, state -> state.clustering_header_multiqc }.unique()[0]
def aligner = list.collect { id, state -> state.aligner }.unique()[0]
def pseudo_aligner = list.collect { id, state -> state.pseudo_aligner }.unique()[0]
def deseq2_vst = list.collect { id, state -> state.deseq2_vst }.unique()[0]
def extra_deseq2_args = list.collect { id, state -> state.extra_deseq2_args }.unique()[0]
def extra_deseq2_args2 = list.collect { id, state -> state.extra_deseq2_args2 }.unique()[0]
def skip_deseq2_qc = list.collect { id, state -> state.skip_deseq2_qc }.unique()[0]
def skip_qc = list.collect { id, state -> state.skip_qc }.unique()[0]
def skip_align = list.collect { id, state -> state.skip_align }.unique()[0]
def skip_pseudo_align = list.collect { id, state -> state.skip_pseudo_align }.unique()[0]
def quant_results = list.collect { id, state ->
(state.quant_results_file instanceof java.nio.file.Path && state.quant_results_file.exists()) ?
state.quant_results_file :
null }
def rsem_counts_gene = list.collect { id, state ->
(state.rsem_counts_gene instanceof java.nio.file.Path && state.rsem_counts_gene.exists()) ?
state.rsem_counts_gene :
null }
def rsem_counts_transcripts = list.collect { id, state ->
(state.rsem_counts_transcripts instanceof java.nio.file.Path && state.rsem_counts_transcripts.exists()) ?
state.rsem_counts_transcripts :
null }
def pseudo_salmon_quant_results = list.collect { id, state ->
(state.pseudo_salmon_quant_results_file instanceof java.nio.file.Path && state.pseudo_salmon_quant_results_file.exists()) ?
state.pseudo_salmon_quant_results_file :
null }
def pseudo_kallisto_quant_results = list.collect { id, state ->
(state.pseudo_kallisto_quant_results_file instanceof java.nio.file.Path && state.pseudo_kallisto_quant_results_file.exists()) ?
state.pseudo_kallisto_quant_results_file :
null }
def fastqc_zip_1 = list.collect { id, state ->
(state.fastqc_zip_1 instanceof java.nio.file.Path && state.fastqc_zip_1.exists()) ?
state.fastqc_zip_1 :
@@ -243,34 +281,14 @@ workflow run_wf {
(state.trim_log_2 instanceof java.nio.file.Path && state.trim_log_2.exists()) ?
state.trim_log_2 :
null }
def sortmerna_log = list.collect { id, state ->
(state.sortmerna_log instanceof java.nio.file.Path && state.sortmerna_log.exists()) ?
state.sortmerna_log :
def sortmerna_multiqc = list.collect { id, state ->
(state.sortmerna_multiqc instanceof java.nio.file.Path && state.sortmerna_multiqc.exists()) ?
state.sortmerna_multiqc :
null }
def star_multiqc = list.collect { id, state ->
(state.star_multiqc instanceof java.nio.file.Path && state.star_multiqc.exists()) ?
state.star_multiqc :
null }
def quant_results = list.collect { id, state ->
(state.quant_results_file instanceof java.nio.file.Path && state.quant_results_file.exists()) ?
state.quant_results_file :
null }
def rsem_counts_gene = list.collect { id, state ->
(state.rsem_counts_gene instanceof java.nio.file.Path && state.rsem_counts_gene.exists()) ?
state.rsem_counts_gene :
null }
def rsem_counts_transcripts = list.collect { id, state ->
(state.rsem_counts_transcripts instanceof java.nio.file.Path && state.rsem_counts_transcripts.exists()) ?
state.rsem_counts_transcripts :
null }
def pseudo_salmon_quant_results = list.collect { id, state ->
(state.pseudo_salmon_quant_results_file instanceof java.nio.file.Path && state.pseudo_salmon_quant_results_file.exists()) ?
state.pseudo_salmon_quant_results_file :
null }
def pseudo_kallisto_quant_results = list.collect { id, state ->
(state.pseudo_kallisto_quant_results_file instanceof java.nio.file.Path && state.pseudo_kallisto_quant_results_file.exists()) ?
state.pseudo_kallisto_quant_results_file :
null }
def genome_bam_stats = list.collect { id, state ->
(state.genome_bam_stats instanceof java.nio.file.Path && state.genome_bam_stats.exists()) ?
state.genome_bam_stats :
@@ -287,6 +305,14 @@ workflow run_wf {
(state.markduplicates_multiqc instanceof java.nio.file.Path && state.markduplicates_multiqc.exists()) ?
state.markduplicates_multiqc :
null }
def salmon_multiqc = list.collect { id, state ->
(state.salmon_multiqc instanceof java.nio.file.Path && state.salmon_multiqc.exists()) ?
state.salmon_multiqc :
null }
def rsem_multiqc = list.collect { id, state ->
(state.rsem_multiqc instanceof java.nio.file.Path && state.rsem_multiqc.exists()) ?
state.rsem_multiqc :
null }
def pseudo_multiqc = list.collect { id, state ->
(state.pseudo_multiqc instanceof java.nio.file.Path && state.pseudo_multiqc.exists()) ?
state.pseudo_multiqc :
@@ -347,55 +373,18 @@ workflow run_wf {
(state.tin_output_summary instanceof java.nio.file.Path && state.tin_output_summary.exists()) ?
state.tin_output_summary :
null }
def num_trimmed_reads = list.collect { id, state -> state.num_trimmed_reads }
def passed_trimmed_reads = list.collect { id, state -> state.passed_trimmed_reads }
def passed_mapping = list.collect { id, state -> state.passed_mapping }
def percent_mapped = list.collect { id, state -> state.percent_mapped }
def inferred_strand = list.collect { id, state -> state.inferred_strand }
def passed_strand_check = list.collect { id, state -> state.passed_strand_check }
def gtf = list.collect { id, state -> state.gtf }.unique()[0]
def gtf_extra_attributes = list.collect { id, state -> state.gtf_extra_attributes }.unique()[0]
def gtf_group_features = list.collect { id, state -> state.gtf_group_features }.unique()[0]
def pca_header_multiqc = list.collect { id, state -> state.pca_header_multiqc }.unique()[0]
def clustering_header_multiqc = list.collect { id, state -> state.clustering_header_multiqc }.unique()[0]
def aligner = list.collect { id, state -> state.aligner }.unique()[0]
def pseudo_aligner = list.collect { id, state -> state.pseudo_aligner }.unique()[0]
def deseq2_vst = list.collect { id, state -> state.deseq2_vst }.unique()[0]
def extra_deseq2_args = list.collect { id, state -> state.extra_deseq2_args }.unique()[0]
def extra_deseq2_args2 = list.collect { id, state -> state.extra_deseq2_args2 }.unique()[0]
def skip_deseq2_qc = list.collect { id, state -> state.skip_deseq2_qc }.unique()[0]
def multiqc_custom_config = list.collect { id, state -> state.multiqc_custom_config }.unique()[0]
def skip_qc = list.collect { id, state -> state.skip_qc }.unique()[0]
def skip_align = list.collect { id, state -> state.skip_align }.unique()[0]
def skip_pseudo_align = list.collect { id, state -> state.skip_pseudo_align }.unique()[0]
["merged", [
ids: ids,
strandedness: strandedness,
fastqc_zip: fastqc_zip_1 + fastqc_zip_2,
trim_zip: trim_zip_1 + trim_zip_2,
trim_log: trim_log_1 + trim_log_2,
sortmerna_log: sortmerna_log,
star_multiqc: star_multiqc,
salmon_multiqc: quant_results,
genome_bam_stats: genome_bam_stats,
genome_bam_flagstat: genome_bam_flagstat,
genome_bam_idxstats: genome_bam_idxstats,
markduplicates_multiqc: markduplicates_multiqc,
pseudo_multiqc: pseudo_multiqc,
featurecounts_multiqc: featurecounts_multiqc,
featurecounts_rrna_multiqc: featurecounts_rrna_multiqc,
preseq_output: preseq_output,
qualimap_output_dir: qualimap_output_dir,
dupradar_output_dup_intercept_mqc: dupradar_output_dup_intercept_mqc,
dupradar_output_duprate_exp_denscurve_mqc: dupradar_output_duprate_exp_denscurve_mqc,
bamstat_output: bamstat_output,
inner_dist_output_freq: inner_dist_output_freq,
inferexperiment_multiqc: inferexperiment_multiqc,
junction_annotation_output_log: junction_annotation_output_log,
junction_saturation_output_plot_r: junction_saturation_output_plot_r,
read_distribution_output: read_distribution_output,
read_duplication_output_duplication_rate_mapping: read_duplication_output_duplication_rate_mapping,
tin_output_summary: tin_output_summary,
num_trimmed_reads: num_trimmed_reads,
passed_trimmed_reads: passed_trimmed_reads,
passed_mapping: passed_mapping,
percent_mapped: percent_mapped,
inferred_strand: inferred_strand,
passed_strand_check: passed_strand_check,
skip_align: skip_align,
skip_pseudo_align: skip_pseudo_align,
quant_results: quant_results,
rsem_counts_gene: rsem_counts_gene,
rsem_counts_transcripts: rsem_counts_transcripts,
@@ -412,21 +401,143 @@ workflow run_wf {
extra_deseq2_args: extra_deseq2_args,
extra_deseq2_args2: extra_deseq2_args2,
skip_deseq2_qc: skip_deseq2_qc,
num_trimmed_reads: num_trimmed_reads,
passed_trimmed_reads: passed_trimmed_reads,
passed_mapping: passed_mapping,
percent_mapped: percent_mapped,
inferred_strand: inferred_strand,
passed_strand_check: passed_strand_check,
multiqc_custom_config: multiqc_custom_config,
skip_align: skip_align,
skip_pseudo_align: skip_pseudo_align
fastqc_zip: fastqc_zip_1 + fastqc_zip_2,
trim_zip: trim_zip_1 + trim_zip_2,
trim_log: trim_log_1 + trim_log_2,
sortmerna_multiqc: sortmerna_multiqc,
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_multiqc,
salmon_multiqc: salmon_multiqc,
rsem_multiqc: rsem_multiqc,
pseudo_multiqc: pseudo_multiqc,
featurecounts_multiqc: featurecounts_multiqc,
featurecounts_rrna_multiqc: featurecounts_rrna_multiqc,
preseq_output: preseq_output,
qualimap_output_dir: qualimap_output_dir,
dupradar_output_dup_intercept_mqc: dupradar_output_dup_intercept_mqc,
dupradar_output_duprate_exp_denscurve_mqc: dupradar_output_duprate_exp_denscurve_mqc,
bamstat_output: bamstat_output,
inner_dist_output_freq: inner_dist_output_freq,
inferexperiment_multiqc: inferexperiment_multiqc,
junction_annotation_output_log: junction_annotation_output_log,
junction_saturation_output_plot_r: junction_saturation_output_plot_r,
read_distribution_output: read_distribution_output,
read_duplication_output_duplication_rate_mapping: read_duplication_output_duplication_rate_mapping,
tin_output_summary: tin_output_summary,
multiqc_custom_config: multiqc_custom_config
] ]
}
// | map { list ->
// def ids = list.collect { id, state -> state.id }
// def strandedness = list.collect { id, state -> state.strandedness }
// def num_trimmed_reads = list.collect { id, state -> state.num_trimmed_reads }
// def passed_trimmed_reads = list.collect { id, state -> state.passed_trimmed_reads }
// def passed_mapping = list.collect { id, state -> state.passed_mapping }
// def percent_mapped = list.collect { id, state -> state.percent_mapped }
// def inferred_strand = list.collect { id, state -> state.inferred_strand }
// def passed_strand_check = list.collect { id, state -> state.passed_strand_check }
// def gtf = list.collect { id, state -> state.gtf }.unique()[0]
// def gtf_extra_attributes = list.collect { id, state -> state.gtf_extra_attributes }.unique()[0]
// def gtf_group_features = list.collect { id, state -> state.gtf_group_features }.unique()[0]
// def pca_header_multiqc = list.collect { id, state -> state.pca_header_multiqc }.unique()[0]
// def clustering_header_multiqc = list.collect { id, state -> state.clustering_header_multiqc }.unique()[0]
// def aligner = list.collect { id, state -> state.aligner }.unique()[0]
// def pseudo_aligner = list.collect { id, state -> state.pseudo_aligner }.unique()[0]
// def deseq2_vst = list.collect { id, state -> state.deseq2_vst }.unique()[0]
// def extra_deseq2_args = list.collect { id, state -> state.extra_deseq2_args }.unique()[0]
// def extra_deseq2_args2 = list.collect { id, state -> state.extra_deseq2_args2 }.unique()[0]
// def skip_deseq2_qc = list.collect { id, state -> state.skip_deseq2_qc }.unique()[0]
// def skip_qc = list.collect { id, state -> state.skip_qc }.unique()[0]
// def skip_align = list.collect { id, state -> state.skip_align }.unique()[0]
// def skip_pseudo_align = list.collect { id, state -> state.skip_pseudo_align }.unique()[0]
// def quant_results = list.collect { id, state ->
// (state.quant_results_file instanceof java.nio.file.Path && state.quant_results_file.exists()) ?
// state.quant_results_file :
// null }
// def rsem_counts_gene = list.collect { id, state ->
// (state.rsem_counts_gene instanceof java.nio.file.Path && state.rsem_counts_gene.exists()) ?
// state.rsem_counts_gene :
// null }
// def rsem_counts_transcripts = list.collect { id, state ->
// (state.rsem_counts_transcripts instanceof java.nio.file.Path && state.rsem_counts_transcripts.exists()) ?
// state.rsem_counts_transcripts :
// null }
// def pseudo_salmon_quant_results = list.collect { id, state ->
// (state.pseudo_salmon_quant_results_file instanceof java.nio.file.Path && state.pseudo_salmon_quant_results_file.exists()) ?
// state.pseudo_salmon_quant_results_file :
// null }
// def pseudo_kallisto_quant_results = list.collect { id, state ->
// (state.pseudo_kallisto_quant_results_file instanceof java.nio.file.Path && state.pseudo_kallisto_quant_results_file.exists()) ?
// state.pseudo_kallisto_quant_results_file :
// null }
// def fastqc_zip_1_dirs = list.collect{it[1].fastqc_zip_1.getParent()}
// def fastqc_zip_2_dirs = list.collect{it[1].fastqc_zip_2.getParent()}
// def trim_zip_1_dirs = list.collect{it[1].trim_zip_1.getParent()}
// def trim_zip_2_dirs = list.collect{it[1].trim_zip_2.getParent()}
// def trim_log_1_dirs = list.collect{it[1].trim_log_1.getParent()}
// def trim_log_2_dirs = list.collect{it[1].trim_log_2.getParent()}
// def sortmerna_multiqc_dirs = list.collect{it[1].sortmerna_multiqc.getParent()}
// def star_multiqc_dirs = list.collect{it[1].star_multiqc.getParent()}
// def genome_bam_stats_dirs = list.collect{it[1].genome_bam_stats.getParent()}
// def genome_bam_flagstat_dirs = list.collect{it[1].genome_bam_flagstat.getParent()}
// def genome_bam_idxstats_dirs = list.collect{it[1].genome_bam_idxstats}
// def markduplicates_multiqc_dirs = list.collect{it[1].markduplicates_multiqc.getParent()}
// def salmon_multiqc_dirs = list.collect{it[1].salmon_multiqc}
// def rsem_multiqc_dirs = list.collect{it[1].rsem_multiqc.getParent()}
// def pseudo_multiqc_dirs = list.collect{it[1].pseudo_multiqc.getParent()}
// def featurecounts_multiqc_dirs = list.collect{it[1].featurecounts_multiqc.getParent()}
// def featurecounts_rrna_multiqc_dirs = list.collect{it[1].featurecounts_rrna_multiqc.getParent()}
// def preseq_output_dirs = list.collect{it[1].preseq_output.getParent()}
// def qualimap_output_dirs = list.collect{it[1].qualimap_output_dir}
// def dupradar_output_dup_intercept_mqc_dirs = list.collect{it[1].dupradar_output_dup_intercept_mqc.getParent()}
// def dupradar_output_duprate_exp_denscurve_mqc_dirs = list.collect{it[1].dupradar_output_duprate_exp_denscurve_mqc.getParent()}
// def bamstat_output_dirs = list.collect{it[1].bamstat_output.getParent()}
// def strandedness_output_dirs = list.collect{it[1].strandedness_output.getParent()}
// def inner_dist_output_freq_dirs = list.collect{it[1].inner_dist_output_freq.getParent()}
// def junction_annotation_output_log_dirs = list.collect{it[1].junction_annotation_output_log.getParent()}
// def junction_saturation_output_plot_r_dirs = list.collect{it[1].junction_saturation_output_plot_r.getParent()}
// def read_distribution_output_dirs = list.collect{it[1].read_distribution_output.getParent()}
// def read_duplication_output_duplication_rate_mapping_dirs = list.collect{it[1].read_duplication_output_duplication_rate_mapping.getParent()}
// def tin_output_summary_dirs = list.collect{it[1].tin_output_summary.getParent()}
// def multiqc_custom_config_dirs = list.collect{it[1].multiqc_custom_config.getParent()}
// ["merged", [
// ids: ids,
// strandedness: strandedness,
// num_trimmed_reads: num_trimmed_reads,
// passed_trimmed_reads: passed_trimmed_reads,
// passed_mapping: passed_mapping,
// percent_mapped: percent_mapped,
// inferred_strand: inferred_strand,
// passed_strand_check: passed_strand_check,
// skip_align: skip_align,
// skip_pseudo_align: skip_pseudo_align,
// quant_results: quant_results,
// rsem_counts_gene: rsem_counts_gene,
// rsem_counts_transcripts: rsem_counts_transcripts,
// pseudo_salmon_quant_results: pseudo_salmon_quant_results,
// pseudo_kallisto_quant_results: pseudo_kallisto_quant_results,
// gtf: gtf,
// gtf_extra_attributes: gtf_extra_attributes,
// gtf_group_features: gtf_group_features,
// pca_header_multiqc: pca_header_multiqc,
// clustering_header_multiqc: clustering_header_multiqc,
// aligner: aligner,
// pseudo_aligner: pseudo_aligner,
// deseq2_vst: deseq2_vst,
// extra_deseq2_args: extra_deseq2_args,
// extra_deseq2_args2: extra_deseq2_args2,
// skip_deseq2_qc: skip_deseq2_qc,
// multiqc_input: fastqc_zip_1_dirs + fastqc_zip_2_dirs + trim_zip_1_dirs + trim_zip_2_dirs + trim_log_1_dirs + trim_log_2_dirs + sortmerna_multiqc_dirs + star_multiqc_dirs + genome_bam_stats_dirs + genome_bam_flagstat_dirs + genome_bam_idxstats_dirs + markduplicates_multiqc_dirs + salmon_multiqc_dirs + rsem_multiqc_dirs + pseudo_multiqc_dirs + featurecounts_multiqc_dirs + featurecounts_rrna_multiqc_dirs + preseq_output_dirs + qualimap_output_dirs + dupradar_output_dup_intercept_mqc_dirs + dupradar_output_duprate_exp_denscurve_mqc_dirs + bamstat_output_dirs + strandedness_output_dirs + inner_dist_output_freq_dirs + junction_annotation_output_log_dirs + junction_saturation_output_plot_r_dirs + read_distribution_output_dirs + read_duplication_output_duplication_rate_mapping_dirs + tin_output_summary_dirs + multiqc_custom_config_dirs
// ] ]
// }
// Merge quantification results of alignment
| merge_quant_results.run (
runIf: { id, state -> (!state.skip_align && state.aligner == 'star_salmon') || !skip_pseudo_align },
runIf: { id, state -> !state.skip_align && state.aligner == 'star_salmon' },
fromState: [
"salmon_quant_results": "quant_results",
"gtf": "gtf",
@@ -445,7 +556,7 @@ workflow run_wf {
"lengths_transcript": "lengths_transcript",
"quant_merged_summarizedexperiment": "quant_merged_summarizedexperiment"
],
key: "merge_qunat_results"
key: "merge_quant_results"
)
| rsem_merge_counts.run (
@@ -575,14 +686,15 @@ workflow run_wf {
"fastqc_raw_multiqc": "fastqc_zip",
"fastqc_trim_multiqc": "trim_zip",
"trim_log_multiqc": "trim_log",
"sortmerna_multiqc": "sortmerna_log",
"sortmerna_multiqc": "sortmerna_multiqc",
"star_multiqc": "star_multiqc",
"salmon_multiqc": "salmon_multiqc",
"rsem_multiqc": "rsem_multiqc",
"pseudo_multiqc": "pseudo_multiqc",
"samtools_stats": "genome_bam_stats",
"samtools_flagstat": "genome_bam_flagstat",
"samtools_idxstats": "genome_bam_idxstats",
"markduplicates_multiqc": "markduplicates_multiqc",
"pseudo_multiqc": "pseudo_multiqc",
"markduplicates_multiqc": "markduplicates_multiqc",
"featurecounts_multiqc": "featurecounts_multiqc",
"featurecounts_rrna_multiqc": "featurecounts_rrna_multiqc",
"aligner_pca_multiqc": "deseq2_pca_multiqc",
@@ -614,7 +726,7 @@ workflow run_wf {
toState: [
"multiqc_report": "output_report",
"multiqc_data": "output_data",
"multiqc_plots": "output_plots",
"multiqc_plots": "output_plots"
]
)
@@ -716,8 +828,7 @@ workflow run_wf {
"deseq2_output_pseudo": "deseq2_output_pseudo",
"multiqc_report": "multiqc_report",
"multiqc_data": "multiqc_data",
"multiqc_plots": "multiqc_plots",
"multiqc_versions": "multiqc_versions"
"multiqc_plots": "multiqc_plots"
]
)
@@ -777,3 +888,5 @@ def getInferexperimentStrandedness(inferexperiment_file, cutoff=30) {
return [ strandedness, sense, antisense, undetermined ]
}

8
src/workflows/rnaseq/config.vsh.yaml
View File

@@ -536,11 +536,15 @@ argument_groups:
direction: output
default: samtools_stats/$id.transcriptome.idxstats
# Salmon
# Transcript quantification
- name: "--salmon_quant_results"
type: file
direction: output
default: Salmon/$id
default: STAR_Salmon/$id
- name: "--pseudo_quant_results"
type: file
direction: output
default: Pseudo_align_quant/$id
# RSEM
- name: "--rsem_counts_gene"

29
src/workflows/rnaseq/main.nf
View File

@@ -219,6 +219,8 @@ workflow run_wf {
toState: [
"star_alignment": "star_alignment",
"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",
@@ -244,7 +246,7 @@ workflow run_wf {
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 },
@@ -336,18 +338,23 @@ workflow run_wf {
"skip_align": "skip_alignment",
"skip_pseudo_align": "skip_pseudo_alignment",
"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",
"quant_out_dir": "quant_out_dir",
"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",
"pseudo_multiqc": "pseudo_multiqc",
"gene_bed": "gene_bed",
"extra_preseq_args": "extra_preseq_args",
"extra_featurecounts_args": "extra_featurecounts_args",
@@ -375,11 +382,7 @@ workflow run_wf {
"genome_bam_flagstat": "genome_bam_flagstat",
"genome_bam_idxstats": "genome_bam_idxstats",
"markduplicates_multiqc": "markduplicates_metrics",
"rseqc_modules": "rseqc_modules",
"num_trimmed_reads": "num_trimmed_reads",
"passed_trimmed_reads": "passed_trimmed_reads",
"passed_mapping": "passed_mapping",
"percent_mapped": "percent_mapped"
"rseqc_modules": "rseqc_modules"
],
toState: [
"preseq_output": "preseq_output",
@@ -425,7 +428,7 @@ workflow run_wf {
"counts_gene_scaled": "counts_gene_scaled",
"tpm_transcript": "tpm_transcript",
"counts_transcript": "counts_transcript",
"salmon_merged_summarizedexperiment": "salmon_merged_summarizedexperiment",
"qunat_merged_summarizedexperiment": "quant_merged_summarizedexperiment",
"deseq2_output": "deseq2_output",
"multiqc_report": "multiqc_report",
"multiqc_data": "multiqc_data",
@@ -472,7 +475,8 @@ workflow run_wf {
"transcriptome_bam_stats": "transcriptome_bam_stats",
"transcriptome_bam_flagstat": "transcriptome_bam_flagstat",
"transcriptome_bam_idxstats": "transcriptome_bam_idxstats",
"salmon_quant_results": "salmon_quant_results",
"salmon_quant_results": "quant_out_dir",
"pseudo_quant_results": "pseudo_quant_out_dir",
"stringtie_transcript_gtf": "stringtie_transcript_gtf",
"stringtie_coverage_gtf": "stringtie_coverage_gtf",
"stringtie_abundance": "stringtie_abundance",
@@ -538,8 +542,7 @@ workflow run_wf {
"deseq2_output_pseudo": "deseq2_output_pseudo",
"multiqc_report": "multiqc_report",
"multiqc_data": "multiqc_data",
"multiqc_plots": "multiqc_plots",
"multiqc_versions": "multiqc_versions"
"multiqc_plots": "multiqc_plots"
]
)
@@ -618,7 +621,7 @@ def getFastpReadsAfterFiltering(json_file) {
}
//
// Function that parses and returns the alignment rate from the STAR log output
// Function that parses and returns the alignment rate from the STAR log outputs
//
def getStarPercentMapped(align_log) {
def percent_aligned = 0

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

@@ -238,8 +238,8 @@ build_info:
output: "target/executable/bbmap_bbsplit"
executable: "target/executable/bbmap_bbsplit/bbmap_bbsplit"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/bbmap_bbsplit/bbmap_bbsplit
View File

@@ -506,9 +506,9 @@ tar xzf BBMap_39.01.tar.gz && \
cp -r bbmap/* /usr/local/bin
LABEL org.opencontainers.image.description="Companion container for running component bbmap_bbsplit"
LABEL org.opencontainers.image.created="2024-09-24T10:12:43Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:18Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -178,8 +178,8 @@ build_info:
output: "target/executable/bedtools_genomecov"
executable: "target/executable/bedtools_genomecov/bedtools_genomecov"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/bedtools_genomecov/bedtools_genomecov
View File

@@ -481,9 +481,9 @@ mv bedtools.static /usr/local/bin/bedtools && \
chmod a+x /usr/local/bin/bedtools
LABEL org.opencontainers.image.description="Companion container for running component bedtools_genomecov"
LABEL org.opencontainers.image.created="2024-09-24T10:12:44Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:18Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -182,8 +182,8 @@ build_info:
output: "target/executable/cat_additional_fasta"
executable: "target/executable/cat_additional_fasta/cat_additional_fasta"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/cat_additional_fasta/cat_additional_fasta
View File

@@ -480,9 +480,9 @@ function ViashDockerfile {
FROM python:latest
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component cat_additional_fasta"
LABEL org.opencontainers.image.created="2024-09-24T10:12:50Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:25Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -169,8 +169,8 @@ build_info:
output: "target/executable/cat_fastq"
executable: "target/executable/cat_fastq/cat_fastq"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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="2024-09-24T10:12:51Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:26Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -237,8 +237,8 @@ build_info:
output: "target/executable/deseq2_qc"
executable: "target/executable/deseq2_qc/deseq2_qc"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/deseq2_qc/deseq2_qc
View File

@@ -502,9 +502,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
Rscript -e 'remotes::install_url(c("https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz"), repos = "https://cran.rstudio.com")'
LABEL org.opencontainers.image.description="Companion container for running component deseq2_qc"
LABEL org.opencontainers.image.created="2024-09-24T10:13:00Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:35Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -266,8 +266,8 @@ build_info:
output: "target/executable/dupradar"
executable: "target/executable/dupradar/dupradar"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/dupradar/dupradar
View File

@@ -520,9 +520,9 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.pa
Rscript -e 'if (!requireNamespace("dupRadar", quietly = TRUE)) BiocManager::install("dupRadar")'
LABEL org.opencontainers.image.description="Companion container for running component dupradar"
LABEL org.opencontainers.image.created="2024-09-24T10:12:52Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:27Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -198,8 +198,8 @@ build_info:
output: "target/executable/fastqc"
executable: "target/executable/fastqc/fastqc"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/fastqc/fastqc
View File

@@ -490,9 +490,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component fastqc"
LABEL org.opencontainers.image.created="2024-09-24T10:12:45Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:19Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -177,8 +177,8 @@ build_info:
output: "target/executable/fq_subsample"
executable: "target/executable/fq_subsample/fq_subsample"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/fq_subsample/fq_subsample
View File

@@ -485,9 +485,9 @@ cargo install --locked --path . && \
mv /usr/local/fq/target/release/fq /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component fq_subsample"
LABEL org.opencontainers.image.created="2024-09-24T10:12:44Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:19Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -167,8 +167,8 @@ build_info:
output: "target/executable/getchromsizes"
executable: "target/executable/getchromsizes/getchromsizes"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/getchromsizes/getchromsizes
View File

@@ -480,9 +480,9 @@ make && \
make install
LABEL org.opencontainers.image.description="Companion container for running component getchromsizes"
LABEL org.opencontainers.image.created="2024-09-24T10:12:45Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:20Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -145,8 +145,8 @@ build_info:
output: "target/executable/gtf2bed"
executable: "target/executable/gtf2bed/gtf2bed"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/gtf2bed/gtf2bed
View File

@@ -466,9 +466,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component gtf2bed"
LABEL org.opencontainers.image.created="2024-09-24T10:12:56Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:31Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -155,8 +155,8 @@ build_info:
output: "target/executable/gtf_filter"
executable: "target/executable/gtf_filter/gtf_filter"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/gtf_filter/gtf_filter
View File

@@ -470,9 +470,9 @@ function ViashDockerfile {
FROM python:latest
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component gtf_filter"
LABEL org.opencontainers.image.created="2024-09-24T10:12:59Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:34Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -144,8 +144,8 @@ build_info:
output: "target/executable/gunzip"
executable: "target/executable/gunzip/gunzip"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/gunzip/gunzip
View File

@@ -466,9 +466,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component gunzip"
LABEL org.opencontainers.image.created="2024-09-24T10:12:45Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:20Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -155,8 +155,8 @@ build_info:
output: "target/executable/kallisto/kallisto_index"
executable: "target/executable/kallisto/kallisto_index/kallisto_index"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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

@@ -471,9 +471,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \
mv kallisto/kallisto /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_index"
LABEL org.opencontainers.image.created="2024-09-24T10:12:57Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:32Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -253,8 +253,8 @@ build_info:
output: "target/executable/kallisto/kallisto_quant"
executable: "target/executable/kallisto/kallisto_quant/kallisto_quant"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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

@@ -515,9 +515,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \
mv kallisto/kallisto /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_quant"
LABEL org.opencontainers.image.created="2024-09-24T10:12:57Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:32Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -170,8 +170,8 @@ build_info:
output: "target/executable/multiqc_custom_biotype"
executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/multiqc_custom_biotype/multiqc_custom_biotype
View File

@@ -481,9 +481,9 @@ RUN apt-get update && \
RUN pip install --upgrade pip
LABEL org.opencontainers.image.description="Companion container for running component multiqc_custom_biotype"
LABEL org.opencontainers.image.created="2024-09-24T10:12:52Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:27Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -207,8 +207,8 @@ build_info:
output: "target/executable/picard_markduplicates"
executable: "target/executable/picard_markduplicates/picard_markduplicates"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/picard_markduplicates/picard_markduplicates
View File

@@ -494,9 +494,9 @@ wget --no-check-certificate https://github.com/broadinstitute/picard/releases/do
mv picard.jar /usr/local/bin
LABEL org.opencontainers.image.description="Companion container for running component picard_markduplicates"
LABEL org.opencontainers.image.created="2024-09-24T10:12:59Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:34Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -409,8 +409,8 @@ build_info:
output: "target/executable/prepare_multiqc_input"
executable: "target/executable/prepare_multiqc_input/prepare_multiqc_input"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

14
target/executable/prepare_multiqc_input/prepare_multiqc_input
View File

@@ -557,9 +557,9 @@ function ViashDockerfile {
FROM ubuntu:22.04
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component prepare_multiqc_input"
LABEL org.opencontainers.image.created="2024-09-24T10:12:55Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:30Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER
@@ -2285,8 +2285,9 @@ IFS="," read -ra star_multiqc <<< \$par_star_multiqc && for file in "\${star_mul
IFS="," read -ra rsem_multiqc <<< \$par_rsem_multiqc && for file in "\${rsem_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done
# TODO: Fetch Salmon meta info
# IFS="," read -ra salmon_multiqc <<< \$par_salmon_multiqc && for file in "\${salmon_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done
IFS="," read -ra salmon_multiqc <<< \$par_salmon_multiqc && for file in "\${salmon_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done
IFS="," read -ra pseudo_multiqc <<< \$par_pseudo_multiqc && for file in "\${pseudo_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done
IFS="," read -ra samtools_stats <<< \$par_samtools_stats && for file in "\${samtools_stats[@]}"; do [ -e "\$file" ] && cp -r "\$file" \$par_output/; done
@@ -2296,9 +2297,6 @@ IFS="," read -ra samtools_idxstats <<< \$par_samtools_idxstats && for file in "\
IFS="," read -ra markduplicates_multiqc <<< \$par_markduplicates_multiqc && for file in "\${markduplicates_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done
IFS="," read -ra pseudo_multiqc <<< \$par_pseudo_multiqc && for file in "\${pseudo_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done
IFS="," read -ra featurecounts_multiqc <<< \$par_featurecounts_multiqc && for file in "\${featurecounts_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done
IFS="," read -ra featurecounts_rrna_multiqc <<< \$par_featurecounts_rrna_multiqc && for file in "\${featurecounts_rrna_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done

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

@@ -138,8 +138,8 @@ build_info:
output: "target/executable/preprocess_transcripts_fasta"
executable: "target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta
View File

@@ -462,9 +462,9 @@ function ViashDockerfile {
FROM ubuntu:22.04
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component preprocess_transcripts_fasta"
LABEL org.opencontainers.image.created="2024-09-24T10:12:55Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:30Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -191,8 +191,8 @@ build_info:
output: "target/executable/preseq_lcextrap"
executable: "target/executable/preseq_lcextrap/preseq_lcextrap"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/preseq_lcextrap/preseq_lcextrap
View File

@@ -495,9 +495,9 @@ mkdir build && cd build && \
make && make install && make HAVE_HTSLIB=1 all
LABEL org.opencontainers.image.description="Companion container for running component preseq_lcextrap"
LABEL org.opencontainers.image.created="2024-09-24T10:12:46Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:20Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -271,8 +271,8 @@ build_info:
output: "target/executable/qualimap"
executable: "target/executable/qualimap/qualimap"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/qualimap/qualimap
View File

@@ -537,9 +537,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
Rscript -e 'remotes::install_cran(c("optparse"), repos = "https://cran.rstudio.com")'
LABEL org.opencontainers.image.description="Companion container for running component qualimap"
LABEL org.opencontainers.image.created="2024-09-24T10:12:44Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:19Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -299,8 +299,8 @@ build_info:
output: "target/executable/rsem/rsem_calculate_expression"
executable: "target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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

@@ -542,9 +542,9 @@ echo 'export PATH=$PATH:/usr/local/bin' >> ~/.bashrc && \
/bin/bash -c "source /etc/profile && source ~/.bashrc && echo $PATH && which STAR"
LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_calculate_expression"
LABEL org.opencontainers.image.created="2024-09-24T10:12:57Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:32Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -182,8 +182,8 @@ build_info:
output: "target/executable/rsem/rsem_merge_counts"
executable: "target/executable/rsem/rsem_merge_counts/rsem_merge_counts"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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="2024-09-24T10:12:56Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:31Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -163,8 +163,8 @@ build_info:
output: "target/executable/rseqc/rseqc_bamstat"
executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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

@@ -477,9 +477,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_bamstat"
LABEL org.opencontainers.image.created="2024-09-24T10:12:54Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:29Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -186,8 +186,8 @@ build_info:
output: "target/executable/rseqc/rseqc_inferexperiment"
executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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

@@ -487,9 +487,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_inferexperiment"
LABEL org.opencontainers.image.created="2024-09-24T10:12:52Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:27Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -272,8 +272,8 @@ build_info:
output: "target/executable/rseqc/rseqc_innerdistance"
executable: "target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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

@@ -529,9 +529,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_innerdistance"
LABEL org.opencontainers.image.created="2024-09-24T10:12:54Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:29Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -260,8 +260,8 @@ build_info:
output: "target/executable/rseqc/rseqc_junctionannotation"
executable: "target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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

@@ -519,9 +519,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionannotation"
LABEL org.opencontainers.image.created="2024-09-24T10:12:53Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:29Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -249,8 +249,8 @@ build_info:
output: "target/executable/rseqc/rseqc_junctionsaturation"
executable: "target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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

@@ -522,9 +522,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionsaturation"
LABEL org.opencontainers.image.created="2024-09-24T10:12:53Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:28Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -162,8 +162,8 @@ build_info:
output: "target/executable/rseqc/rseqc_readdistribution"
executable: "target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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

@@ -474,9 +474,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readdistribution"
LABEL org.opencontainers.image.created="2024-09-24T10:12:54Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:30Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -211,8 +211,8 @@ build_info:
output: "target/executable/rseqc/rseqc_readduplication"
executable: "target/executable/rseqc/rseqc_readduplication/rseqc_readduplication"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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

@@ -499,9 +499,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readduplication"
LABEL org.opencontainers.image.created="2024-09-24T10:12:52Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:28Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -214,8 +214,8 @@ build_info:
output: "target/executable/rseqc/rseqc_tin"
executable: "target/executable/rseqc/rseqc_tin/rseqc_tin"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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

@@ -501,9 +501,9 @@ RUN apt-get update && \
RUN pip3 install RSeQC
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_tin"
LABEL org.opencontainers.image.created="2024-09-24T10:12:53Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:28Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -198,8 +198,8 @@ build_info:
output: "target/executable/sortmerna"
executable: "target/executable/sortmerna/sortmerna"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/sortmerna/sortmerna
View File

@@ -492,9 +492,9 @@ wget --no-check-certificate https://github.com/sortmerna/sortmerna/releases/down
bash sortmerna-4.3.6-Linux.sh --skip-license
LABEL org.opencontainers.image.description="Companion container for running component sortmerna"
LABEL org.opencontainers.image.created="2024-09-24T10:12:59Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:34Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -216,8 +216,8 @@ build_info:
output: "target/executable/stringtie"
executable: "target/executable/stringtie/stringtie"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/stringtie/stringtie
View File

@@ -496,9 +496,9 @@ tar -xzf stringtie-2.2.1.Linux_x86_64.tar.gz && \
cp stringtie-2.2.1.Linux_x86_64/stringtie /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component stringtie"
LABEL org.opencontainers.image.created="2024-09-24T10:12:56Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:31Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -199,8 +199,8 @@ build_info:
output: "target/executable/summarizedexperiment"
executable: "target/executable/summarizedexperiment/summarizedexperiment"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/summarizedexperiment/summarizedexperiment
View File

@@ -487,9 +487,9 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.pa
Rscript -e 'if (!requireNamespace("tximeta", quietly = TRUE)) BiocManager::install("tximeta")'
LABEL org.opencontainers.image.description="Companion container for running component summarizedexperiment"
LABEL org.opencontainers.image.created="2024-09-24T10:13:00Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:35Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -788,8 +788,8 @@ build_info:
output: "target/executable/trimgalore"
executable: "target/executable/trimgalore/trimgalore"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

4
target/executable/trimgalore/trimgalore
View File

@@ -858,9 +858,9 @@ ENTRYPOINT []
RUN echo "TrimGalore: `trim_galore --version | sed -n 's/.*version\s\+\([0-9]\+\.[0-9]\+\.[0-9]\+\).*/\1/p'`" > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component trimgalore"
LABEL org.opencontainers.image.created="2024-09-24T10:12:58Z"
LABEL org.opencontainers.image.created="2024-09-30T07:15:33Z"
LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -192,8 +192,8 @@ build_info:
output: "target/executable/tx2gene"
executable: "target/executable/tx2gene/tx2gene"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/tx2gene/tx2gene
View File

@@ -487,9 +487,9 @@ RUN apt-get update && \
RUN pip install --upgrade pip
LABEL org.opencontainers.image.description="Companion container for running component tx2gene"
LABEL org.opencontainers.image.created="2024-09-24T10:12:55Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:31Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -247,8 +247,8 @@ build_info:
output: "target/executable/tximport"
executable: "target/executable/tximport/tximport"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/tximport/tximport
View File

@@ -508,9 +508,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
Rscript -e 'remotes::install_cran(c("jsonlite"), repos = "https://cran.rstudio.com")'
LABEL org.opencontainers.image.description="Companion container for running component tximport"
LABEL org.opencontainers.image.created="2024-09-24T10:12:50Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:25Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -164,8 +164,8 @@ build_info:
output: "target/executable/ucsc/bedclip"
executable: "target/executable/ucsc/bedclip/bedclip"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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

@@ -473,9 +473,9 @@ RUN apt-get update && \
RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedClip /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component ucsc bedclip"
LABEL org.opencontainers.image.created="2024-09-24T10:12:51Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:26Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -164,8 +164,8 @@ build_info:
output: "target/executable/ucsc/bedgraphtobigwig"
executable: "target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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

@@ -473,9 +473,9 @@ RUN apt-get update && \
RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedGraphToBigWig /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component ucsc bedgraphtobigwig"
LABEL org.opencontainers.image.created="2024-09-24T10:12:51Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:26Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -195,8 +195,8 @@ build_info:
output: "target/executable/umitools/umitools_dedup"
executable: "target/executable/umitools/umitools_dedup/umitools_dedup"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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

@@ -489,9 +489,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "umi_tools"
LABEL org.opencontainers.image.description="Companion container for running component umitools umitools_dedup"
LABEL org.opencontainers.image.created="2024-09-24T10:12:58Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:33Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -253,8 +253,8 @@ build_info:
output: "target/executable/umitools/umitools_extract"
executable: "target/executable/umitools/umitools_extract/umitools_extract"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

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

@@ -521,9 +521,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "umi_tools"
LABEL org.opencontainers.image.description="Companion container for running component umitools umitools_extract"
LABEL org.opencontainers.image.created="2024-09-24T10:12:58Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:33Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

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

@@ -156,8 +156,8 @@ build_info:
output: "target/executable/umitools_prepareforquant"
executable: "target/executable/umitools_prepareforquant/umitools_prepareforquant"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
package_config:
version: "multiple_fixes"
info:

6
target/executable/umitools_prepareforquant/umitools_prepareforquant
View File

@@ -473,9 +473,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "umi_tools" "pysam"
LABEL org.opencontainers.image.description="Companion container for running component umitools_prepareforquant"
LABEL org.opencontainers.image.created="2024-09-24T10:13:00Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
LABEL org.opencontainers.image.created="2024-09-30T07:15:35Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
LABEL org.opencontainers.image.version="multiple_fixes"
VIASHDOCKER

13
target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml
View File

@@ -381,6 +381,15 @@ argument_groups:
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--salmon_multiqc"
info: null
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--rsem_counts_gene"
description: "Expression counts on gene level"
@@ -594,8 +603,8 @@ build_info:
output: "target/executable/workflows/genome_alignment_and_quant"
executable: "target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort"

27
target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant
View File

@@ -341,6 +341,9 @@ function ViashHelp {
echo " type: file, output, file must exist"
echo " default: \$id.quant.sf"
echo ""
echo " --salmon_multiqc"
echo " type: file, output, file must exist"
echo ""
echo " --rsem_counts_gene"
echo " type: file, output, file must exist"
echo " default: \$id.genes.results"
@@ -792,6 +795,17 @@ while [[ $# -gt 0 ]]; do
VIASH_PAR_QUANT_RESULTS_FILE=$(ViashRemoveFlags "$1")
shift 1
;;
--salmon_multiqc)
[ -n "$VIASH_PAR_SALMON_MULTIQC" ] && ViashError Bad arguments for option \'--salmon_multiqc\': \'$VIASH_PAR_SALMON_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SALMON_MULTIQC="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --salmon_multiqc. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--salmon_multiqc=*)
[ -n "$VIASH_PAR_SALMON_MULTIQC" ] && ViashError Bad arguments for option \'--salmon_multiqc=*\': \'$VIASH_PAR_SALMON_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SALMON_MULTIQC=$(ViashRemoveFlags "$1")
shift 1
;;
--rsem_counts_gene)
[ -n "$VIASH_PAR_RSEM_COUNTS_GENE" ] && ViashError Bad arguments for option \'--rsem_counts_gene\': \'$VIASH_PAR_RSEM_COUNTS_GENE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_RSEM_COUNTS_GENE="$2"
@@ -1273,6 +1287,9 @@ fi
if [ ! -z "$VIASH_PAR_QUANT_RESULTS_FILE" ] && [ ! -d "$(dirname "$VIASH_PAR_QUANT_RESULTS_FILE")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_QUANT_RESULTS_FILE")"
fi
if [ ! -z "$VIASH_PAR_SALMON_MULTIQC" ] && [ ! -d "$(dirname "$VIASH_PAR_SALMON_MULTIQC")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_SALMON_MULTIQC")"
fi
if [ ! -z "$VIASH_PAR_RSEM_COUNTS_GENE" ] && [ ! -d "$(dirname "$VIASH_PAR_RSEM_COUNTS_GENE")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_RSEM_COUNTS_GENE")"
fi
@@ -1614,6 +1631,11 @@ workflow run_wf {
]
)
| map { id, state ->
def mod_state = (state.aligner == 'star_salmon') ? state + [salmon_multiqc: state.quant_out_dir] : state
[ id, mod_state ]
}
| niceView()
| rsem_calculate_expression.run (
runIf: { id, state -> state.aligner == 'star_rsem' },
fromState: [
@@ -1691,6 +1713,7 @@ workflow run_wf {
[ "star_alignment": "star_alignment",
"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",
@@ -1772,6 +1795,10 @@ if [ ! -z "$VIASH_PAR_QUANT_RESULTS_FILE" ] && [ ! -e "$VIASH_PAR_QUANT_RESULTS_
ViashError "Output file '$VIASH_PAR_QUANT_RESULTS_FILE' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_SALMON_MULTIQC" ] && [ ! -e "$VIASH_PAR_SALMON_MULTIQC" ]; then
ViashError "Output file '$VIASH_PAR_SALMON_MULTIQC' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_RSEM_COUNTS_GENE" ] && [ ! -e "$VIASH_PAR_RSEM_COUNTS_GENE" ]; then
ViashError "Output file '$VIASH_PAR_RSEM_COUNTS_GENE' does not exist."
exit 1

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

@@ -278,8 +278,8 @@ build_info:
output: "target/executable/workflows/merge_quant_results"
executable: "target/executable/workflows/merge_quant_results/merge_quant_results"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/tx2gene"
- "target/nextflow/tximport"

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

@@ -199,7 +199,7 @@ argument_groups:
name: "--processed_genome_bam"
info: null
default:
- "$id.markdup.sorted.bam"
- "$id..genome.bam"
must_exist: true
create_parent: true
required: false
@@ -210,7 +210,7 @@ argument_groups:
name: "--genome_bam_index"
info: null
default:
- "$id.markdup.sorted.bam"
- "$id.genome.bam.bai"
must_exist: true
create_parent: true
required: false
@@ -221,7 +221,7 @@ argument_groups:
name: "--genome_bam_stats"
info: null
default:
- "$id.markdup.sorted.bam.stats"
- "$id.genome.stats"
must_exist: true
create_parent: true
required: false
@@ -232,7 +232,7 @@ argument_groups:
name: "--genome_bam_flagstat"
info: null
default:
- "$id.markdup.sorted.bam.flagstat"
- "$id.genome.flagstat"
must_exist: true
create_parent: true
required: false
@@ -243,7 +243,7 @@ argument_groups:
name: "--genome_bam_idxstats"
info: null
default:
- "$id.markdup.sorted.bam.idxstats"
- "$id.genome.idxstats"
must_exist: true
create_parent: true
required: false
@@ -254,7 +254,7 @@ argument_groups:
name: "--markduplicates_metrics"
info: null
default:
- "$id.markdup.sorted.MarkDuplicates.metrics.txt"
- "$id.MarkDuplicates.metrics.txt"
must_exist: true
create_parent: true
required: false
@@ -486,8 +486,8 @@ build_info:
output: "target/executable/workflows/post_processing"
executable: "target/executable/workflows/post_processing/post_processing"
viash_version: "0.9.0"
git_commit: "b291665ddc01d0f8072d9d3d7b4aa9932afb84df"
git_remote: "https://x-access-token:ghs_qzx8ub2s5n4pMItYHe6AI1j20ftDAd0MJkoX@github.com/viash-hub/rnaseq"
git_commit: "f3645db764dda85eb0fbd0439e7ca872b46a0dcb"
git_remote: "https://x-access-token:ghs_m75EeJ1B6zDP9gDmsS4xLoILESsIc60jDSa0@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/picard_markduplicates"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort"

24
target/executable/workflows/post_processing/post_processing
View File

@@ -269,27 +269,27 @@ function ViashHelp {
echo "Output:"
echo " --processed_genome_bam"
echo " type: file, output, file must exist"
echo " default: \$id.markdup.sorted.bam"
echo " default: \$id..genome.bam"
echo ""
echo " --genome_bam_index"
echo " type: file, output, file must exist"
echo " default: \$id.markdup.sorted.bam"
echo " default: \$id.genome.bam.bai"
echo ""
echo " --genome_bam_stats"
echo " type: file, output, file must exist"
echo " default: \$id.markdup.sorted.bam.stats"
echo " default: \$id.genome.stats"
echo ""
echo " --genome_bam_flagstat"
echo " type: file, output, file must exist"
echo " default: \$id.markdup.sorted.bam.flagstat"
echo " default: \$id.genome.flagstat"
echo ""
echo " --genome_bam_idxstats"
echo " type: file, output, file must exist"
echo " default: \$id.markdup.sorted.bam.idxstats"
echo " default: \$id.genome.idxstats"
echo ""
echo " --markduplicates_metrics"
echo " type: file, output, file must exist"
echo " default: \$id.markdup.sorted.MarkDuplicates.metrics.txt"
echo " default: \$id.MarkDuplicates.metrics.txt"
echo ""
echo " --stringtie_transcript_gtf"
echo " type: file, output, file must exist"
@@ -887,22 +887,22 @@ if [ -z ${VIASH_PAR_WITH_UMI+x} ]; then
VIASH_PAR_WITH_UMI="false"
fi
if [ -z ${VIASH_PAR_PROCESSED_GENOME_BAM+x} ]; then
VIASH_PAR_PROCESSED_GENOME_BAM="\$id.markdup.sorted.bam"
VIASH_PAR_PROCESSED_GENOME_BAM="\$id..genome.bam"
fi
if [ -z ${VIASH_PAR_GENOME_BAM_INDEX+x} ]; then
VIASH_PAR_GENOME_BAM_INDEX="\$id.markdup.sorted.bam"
VIASH_PAR_GENOME_BAM_INDEX="\$id.genome.bam.bai"
fi
if [ -z ${VIASH_PAR_GENOME_BAM_STATS+x} ]; then
VIASH_PAR_GENOME_BAM_STATS="\$id.markdup.sorted.bam.stats"
VIASH_PAR_GENOME_BAM_STATS="\$id.genome.stats"
fi
if [ -z ${VIASH_PAR_GENOME_BAM_FLAGSTAT+x} ]; then
VIASH_PAR_GENOME_BAM_FLAGSTAT="\$id.markdup.sorted.bam.flagstat"
VIASH_PAR_GENOME_BAM_FLAGSTAT="\$id.genome.flagstat"
fi
if [ -z ${VIASH_PAR_GENOME_BAM_IDXSTATS+x} ]; then
VIASH_PAR_GENOME_BAM_IDXSTATS="\$id.markdup.sorted.bam.idxstats"
VIASH_PAR_GENOME_BAM_IDXSTATS="\$id.genome.idxstats"
fi
if [ -z ${VIASH_PAR_MARKDUPLICATES_METRICS+x} ]; then
VIASH_PAR_MARKDUPLICATES_METRICS="\$id.markdup.sorted.MarkDuplicates.metrics.txt"
VIASH_PAR_MARKDUPLICATES_METRICS="\$id.MarkDuplicates.metrics.txt"
fi
if [ -z ${VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF+x} ]; then
VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF="\$id.stringtie.transcripts.gtf"

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