vsh/rnaseq
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Build branch main with version main (1d87dc7)

Browse Source 
Build pipeline: viash-hub.rnaseq.main-g2rlq

Source commit: 1d87dc7c24

Source message: Multiple fixes (#23)

* multiple fixes

* update arguments and add test

* fix biobox module calls

* fix dependency

* add rsem merge counts

* exclude general stats in multiqc report

* output markduplicates metrics

* rename output reference files
This commit is contained in:
CI
2024-10-01 10:12:28 +00:00
parent 9b29e37466
commit c106022744
237 changed files with 9490 additions and 2187 deletions
Download Patch File Download Diff File Expand all files Collapse all files

39
assets/multiqc_config.yml
View File

@@ -1,8 +1,8 @@
report_comment: >
This report has been generated by the <a href="https://github.com/data-intuitive/rnaseq.vsh" </a>
This report has been generated by the <a href="https://github.com/viash-hub/rnaseq" </a>
analysis pipeline.
report_section_order:
"rnaseq.vsh-methods-description":
"rnaseq-methods-description":
order: -1000
software_versions:
order: -1001
@@ -10,6 +10,7 @@ report_section_order:
order: -1002
export_plots: true
disable_version_detection: true
# Run only these modules
run_modules:
@@ -19,7 +20,6 @@ run_modules:
- fastp
- sortmerna
- star
# - hisat2
- rsem
- salmon
- kallisto
@@ -64,15 +64,13 @@ table_columns_visible:
fastqc:
percent_duplicates: False
extra_fn_clean_exts:
- ".salmon_quant"
- ".mapping_quality"
- ".genome_sorted"
- ".MarkDuplicates"
- ".MarkDuplicates_flagstat"
- ".MarkDuplicates_stats"
- ".genome_sorted_MarkDuplicates"
- ".star_aligned"
extra_fn_clean_extn:
# - ".mapping_quality"
# - ".MarkDuplicates_flagstat.output.flagstat"
# - ".MarkDuplicates_idxstats.output.idxstats"
# - ".MarkDuplicates_stats.output.txt"
# - ".genome_sorted_MarkDuplicates.output.bam"
# - ".genome_sorted_MarkDuplicates"
- ".read_1"
- ".read_2"
@@ -117,32 +115,31 @@ sp:
fn: "*.fastqc.zip"
cutadapt:
fn: "*.trimming_report.txt"
fn: "*.trimming_report*.txt"
fastp:
fn: "*.fastp.json"
fn: "*.fastp_out.json"
sortmerna:
fn: "*sortmerna*.log"
star:
fn: "*.star_aligned.log.final.out"
fn: "*.star_align_reads.log.txt"
# hisat2:
# fn: "*.hisat2.summary.log"
salmon/meta:
fn: "*meta_info.json"
# salmon:
# fn: "*meta_info.json"
preseq:
fn: "*.lc_extrap.txt"
samtools/stats:
fn: "*.stats"
fn: "*_stats.output.txt"
samtools/flagstat:
fn: "*.flagstat"
fn: "*_flagstat.output.flagstat"
samtools/idxstats:
fn: "*.idxstats*"
fn: "*_idxstats.output.idxstats"
rseqc/bam_stat:
fn: "*.mapping_quality.txt"

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

@@ -25,13 +25,13 @@ argument_groups:
- name: "--fastq_1"
type: file
direction: output
default: $id.read_1.merged.fastq
default: $id_r1.fastq
description: Concatenated read 1 fastq
- name: "--fastq_2"
type: file
direction: output
must_exist: false
default: $id.read_2.merged.fastq
default: $id_r2.fastq
description: Concatenated read 2 fastq
resources:

12
src/fastqc/script.sh
View File

@@ -30,10 +30,12 @@ fastqc -o $tmpdir ${input[*]}
file1=$(basename -- "${input[0]}")
read1="${file1%.fastq*}"
file2=$(basename -- "${input[1]}")
read2="${file2%.fastq*}"
[[ -e "${tmpdir}/${read1}_fastqc.html" ]] && cp "${tmpdir}/${read1}_fastqc.html" $par_fastqc_html_1
[[ -e "${tmpdir}/${read2}_fastqc.html" ]] && cp "${tmpdir}/${read2}_fastqc.html" $par_fastqc_html_2
[[ -e "${tmpdir}/${read1}_fastqc.zip" ]] && cp "${tmpdir}/${read1}_fastqc.zip" $par_fastqc_zip_1
[[ -e "${tmpdir}/${read2}_fastqc.zip" ]] && cp "${tmpdir}/${read2}_fastqc.zip" $par_fastqc_zip_2
if $par_paired; then
file2=$(basename -- "${input[1]}")
read2="${file2%.fastq*}"
[[ -e "${tmpdir}/${read2}_fastqc.html" ]] && cp "${tmpdir}/${read2}_fastqc.html" $par_fastqc_html_2
[[ -e "${tmpdir}/${read2}_fastqc.zip" ]] && cp "${tmpdir}/${read2}_fastqc.zip" $par_fastqc_zip_2
fi

11
src/kallisto/kallisto_quant/script.sh
View File

@@ -23,16 +23,7 @@ if [[ "$par_extra_args" != *"--fr-stranded"* ]] && [[ "$par_extra_args" != *"--r
fi
mkdir -p $par_output
echo "kallisto quant \
${meta_cpus:+--threads $meta_cpus} \
--index $par_index \
${par_gtf:+--gtf $par_gtf} \
${par_chromosomes:+--chromosomes $par_chromosomes} \
$single_end_params \
$strandedness \
$par_extra_args \
-o $par_output \
${input[*]} 2> >(tee -a ${par_output}/kallisto_quant.log >&2)"
kallisto quant \
${meta_cpus:+--threads $meta_cpus} \
--index $par_index \

7
src/prepare_multiqc_input/script.sh
View File

@@ -24,6 +24,8 @@ IFS="," read -ra rsem_multiqc <<< $par_rsem_multiqc && for file in "${rsem_multi
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
IFS="," read -ra samtools_flagstat <<< $par_samtools_flagstat && for file in "${samtools_flagstat[@]}"; do [ -e "$file" ] && cp -r "$file" $par_output/; done
@@ -32,12 +34,9 @@ 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
IFS="," read -ra featurecounts_rrna_multiqc <<< $par_featurecounts_rrna_multiqc && for file in "${featurecounts_rrna_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done
[ -e "$par_aligner_pca_multiqc" ] && cp -r "$par_aligner_pca_multiqc" "$par_output/"

3
src/rsem/rsem_calculate_expression/config.vsh.yaml
View File

@@ -33,9 +33,6 @@ argument_groups:
- name: "--extra_args"
type: string
description: Extra rsem-calculate-expression arguments in addition to the defaults.
- name: "--versions"
type: file
must_exist: false
- name: "Output"
arguments:

11
src/rsem/rsem_calculate_expression/script.sh
View File

@@ -19,10 +19,10 @@ fi
IFS="," read -ra input <<< $par_input
INDEX=`find -L $meta_resources_dir/ -name "*.grp" | sed 's/\.grp$//'`
INDEX=`find -L $par_index/ -name "*.grp" | sed 's/\.grp$//'`
rsem-calculate-expression \
${meta_cpus:+--num-theads $meta_cpus} \
${meta_cpus:+--num-threads $meta_cpus} \
$strandedness \
${par_paired:+--paired-end} \
$par_extra_args \
@@ -30,3 +30,10 @@ rsem-calculate-expression \
$INDEX \
$par_id
[[ -e "${par_id}.genes.results" ]] && mv "${par_id}.genes.results" $par_counts_gene
[[ -e "${par_id}id.isoforms.results" ]] && mv "${par_id}id.isoforms.results" $par_counts_transcripts
[[ -e "${par_id}.stat" ]] && mv -r "${par_id}.stat" $par_stat
# [[ -e "${par_id}.log" ]] && mv "${par_id}.log" $par_logs
[[ -e "${par_id}.STAR.genome.bam" ]] && mv "${par_id}.STAR.genome.bam" $par_bam_star
[[ -e "${par_id}.genome.bam" ]] && mv "${par_id}.genome.bam" $par_bam_genome
[[ -e "${par_id}.transcript.bam" ]] && mv "${par_id}.transcript.bam" $par_bam_transcript

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

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

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

@@ -232,13 +232,13 @@ argument_groups:
required: false
description: Output file for read 1. Only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists.
direction: output
example: read_1.fastq
example: read_1.fastq.gz
- name: --trimmed_r2
type: file
required: false
description: Output file for read 2. Only works when 1 file (single-end) or 2 files (paired-end) are specified, but not for longer lists.
direction: output
example: read_2.fastq
example: read_2.fastq.gz
- name: --trimming_report_r1
type: file
required: false

41
src/workflows/genome_alignment_and_quant/config.vsh.yaml
View File

@@ -76,7 +76,7 @@ argument_groups:
type: string
default: 'gene_name'
description: By default, the pipeline uses the gene_name field to obtain additional gene identifiers from the input GTF file when running Salmon.
- name: extra_rsem_calculate_expression_args
- name: --extra_rsem_calculate_expression_args
type: string
description: Extra arguments to pass to rsem-calculate-expression command in addition to defaults defined by the pipeline.
- name: "--aligner"
@@ -96,7 +96,7 @@ argument_groups:
- name: "--star_multiqc"
type: file
direction: output
default: $id.star_align.log
default: $id_star.log
- name: "--genome_bam_sorted"
type: file
direction: output
@@ -145,6 +145,39 @@ 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
default: $id.genes.results
direction: output
- name: "--counts_transcripts"
type: file
description: Expression counts on transcript level
default: $id.isoforms.results
direction: output
- name: "--rsem_multiqc"
type: file
description: RSEM statistics
default: $id.stat
direction: output
- name: "--bam_star_rsem"
type: file
description: BAM file generated by STAR (optional)
default: $id.STAR.genome.bam
direction: output
- name: "--bam_genome_rsem"
type: file
description: Genome BAM file (optional)
default: $id.genome.bam
direction: output
- name: "--bam_transcript_rsem"
type: file
description: Transcript BAM file (optional)
default: $id.transcript.bam
direction: output
resources:
- type: nextflow_script
@@ -165,9 +198,11 @@ dependencies:
- name: samtools/samtools_idxstats
repository: biobox
- name: umitools/umitools_dedup
# - name: umi_tools/umi_tools_dedup
# repository: biobox
- name: umitools_prepareforquant
# repository: biobox
# - name: umi_tools/umi_tools_prepareforquant
# repository: biobox
- name: salmon/salmon_quant
repository: biobox
- name: rsem/rsem_calculate_expression

12
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 ]
}
| 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",
@@ -368,7 +374,11 @@ workflow run_wf {
"transcriptome_bam_flagstat": "transcriptome_bam_flagstat",
"transcriptome_bam_idxstats": "transcriptome_bam_idxstats",
"quant_out_dir": "quant_out_dir",
"quant_results_file": "quant_results_file" ]
"quant_results_file": "quant_results_file",
"rsem_counts_gene": "rsem_counts_gene",
"rsem_counts_transcripts": "rsem_counts_transcripts",
"bam_genome_rsem": "bam_genome_rsem",
"bam_transcript_rsem": "bam_transcript_rsem" ]
)
emit:

34
src/workflows/genome_alignment_and_quant/test_run.sh
View File

@@ -1,25 +1,43 @@
#!/bin/bash
viash ns build --setup cb --parallel
# v;iash ns build --setup cb --parallel
# Split error message from standard output
# viash ns list > /dev/null
CURR=`pwd`
echo "> Preparing reference data files"
gunzip --keep testData/minimal_test/reference/genes.gtf.gz
cat > testData/minimal_test/input_fastq/sample_sheet.csv << HERE
id,fastq_1,fastq_2,strandedness
WT_REP1,SRR6357070_1.fastq.gz,SRR6357070_2.fastq.gz,reverse
WT_REP2,SRR6357072_1.fastq.gz,SRR6357072_2.fastq.gz,reverse
RAP1_UNINDUCED_REP1,SRR6357073_1.fastq.gz,,reverse
HERE
# echo "> Test 1: STAR Salmon"
# nextflow run target/nextflow/workflows/genome_alignment_and_quant/main.nf \
# --param_list testData/minimal_test/input_fastq/sample_sheet.csv \
# --publish_dir test_results/genome_alignment_test1 \
# --fasta testData/minimal_test/reference/genome.fasta \
# --gtf testData/minimal_test/reference/genes.gtf \
# --transcript_fasta testData/minimal_test/reference/transcriptome.fasta \
# --star_index test_results/output_test1/STAR_index \
# --aligner star_salmon \
# -profile docker \
# -resume
echo "> Test 2: STAR RSEM"
nextflow run target/nextflow/workflows/genome_alignment_and_quant/main.nf \
--param_list testData/minimal_test/input_fastq/sample_sheet.csv \
--publish_dir "test_results/genome_alignment_test" \
--publish_dir test_results/genome_alignment_test2 \
--fasta testData/minimal_test/reference/genome.fasta \
--gtf testData/minimal_test/reference/genes.gtf.gz \
--gtf testData/minimal_test/reference/genes.gtf \
--transcript_fasta testData/minimal_test/reference/transcriptome.fasta \
--star_index testData/test_output/star_index \
--aligner "star_rsem" \
--rsem_index test_results/output_test1/RSEM_index \
--aligner star_rsem \
--extra_rsem_calculate_expression_args "--star --star-output-genome-bam --star-gzipped-read-file --estimate-rspd --seed 1" \
-profile docker \
# -resume
-resume
echo "Removing reference data files"
rm testData/minimal_test/reference/genes.gtf

14
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
@@ -151,6 +151,8 @@ dependencies:
- name: samtools/samtools_idxstats
repository: biobox
- name: stringtie
# - name: bedtools/bedtools_genomecov
# repository: biobox
- name: bedtools_genomecov
- name: ucsc/bedclip
- name: ucsc/bedgraphtobigwig

20
src/workflows/post_processing/main.nf
View File

@@ -16,20 +16,20 @@ workflow run_wf {
"extra_picard_args": "extra_picard_args"
],
toState: [
"genome_bam": "output_bam",
"processed_genome_bam": "output_bam",
"markduplicates_metrics": "metrics"
]
)
| samtools_sort.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [ "input": "genome_bam" ],
toState: [ "genome_bam": "output" ],
fromState: [ "input": "processed_genome_bam" ],
toState: [ "processed_genome_bam": "output" ],
key: "genome_sorted_MarkDuplicates"
)
| samtools_index.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"input": "genome_bam",
"input": "processed_genome_bam",
"csi": "bam_csi_index"
],
toState: [ "genome_bam_index": "output" ],
@@ -38,7 +38,7 @@ workflow run_wf {
| samtools_stats.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"input": "genome_bam",
"input": "processed_genome_bam",
"bai": "genome_bam_index"
],
toState: [ "genome_bam_stats": "output" ],
@@ -47,7 +47,7 @@ workflow run_wf {
| samtools_flagstat.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"bam": "genome_bam",
"bam": "processed_genome_bam",
"bai": "genome_bam_index"
],
toState: [ "genome_bam_flagstat": "output" ],
@@ -56,7 +56,7 @@ workflow run_wf {
| samtools_idxstats.run(
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"bam": "genome_bam",
"bam": "processed_genome_bam",
"bai": "genome_bam_index"
],
toState: [ "genome_bam_idxstats": "output" ],
@@ -67,7 +67,7 @@ workflow run_wf {
runIf: { id, state -> !state.skip_stringtie },
fromState: [
"strandedness": "strandedness",
"bam": "genome_bam",
"bam": "processed_genome_bam",
"annotation_gtf": "gtf",
"extra_stringtie_args": "extra_stringtie_args"
],
@@ -85,7 +85,7 @@ workflow run_wf {
runIf: { id, state -> !state.skip_bigwig },
fromState: [
"strandedness": "strandedness",
"bam": "genome_bam",
"bam": "processed_genome_bam",
"extra_bedtools_args": "extra_bedtools_args"
],
toState: [
@@ -140,7 +140,7 @@ workflow run_wf {
}
| setState (
"processed_genome_bam": "genome_bam",
"processed_genome_bam": "processed_genome_bam",
"genome_bam_index": "genome_bam_index",
"genome_bam_stats": "genome_bam_stats",
"genome_bam_flagstat": "genome_bam_flagstat",

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

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

33
src/workflows/pre_processing/config.vsh.yaml
View File

@@ -139,13 +139,13 @@ argument_groups:
- name: "Read filtering options"
arguments:
- name: "--skip_bbsplit"
type: boolean
type: boolean_true
description: Skip BBSplit for removal of non-reference genome reads.
default: true
# default: true
- name: "--remove_ribo_rna"
type: boolean
type: boolean_true
description: Enable the removal of reads derived from ribosomal RNA using SortMeRNA.
default: false
# default: false
- name: "Other options"
arguments:
@@ -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
@@ -246,7 +246,20 @@ argument_groups:
direction: output
description: Results from Salmon quant
default: $id.salmon_quant_output
- name: --trim_json
type: file
description: The fastp json format report file name
default: $id.fastp_out.json
direction: output
- name: --trim_html
type: file
description: The fastp html format report file name
default: $id.fastp_out.html
direction: output
- name: --merged_out
type: file
description: File name to store merged fastp output.
direction: output
resources:
- type: nextflow_script
path: main.nf
@@ -256,14 +269,18 @@ dependencies:
- name: fastqc
# repository: biobox
- name: umitools/umitools_extract
# repository: biobox
- name: umi_tools/umi_tools_extract
repository: biobox
- name: trimgalore
# repository: biobox
- name: bbmap_bbsplit
# repository: biobox
- name: sortmerna
# repository: biobox
- name: fastp
repository: biobox
- name: fq_subsample
# repository: biobox
- name: salmon/salmon_quant
repository: biobox

16
src/workflows/pre_processing/main.nf
View File

@@ -74,7 +74,8 @@ workflow run_wf {
"trim_zip_2": "trimmed_fastqc_zip_2",
"trim_html_1": "trimmed_fastqc_html_1",
"trim_html_2": "trimmed_fastqc_html_2"
]
],
args: [gzip: true, fastqc: true]
)
// Trim reads using fastp
@@ -90,7 +91,7 @@ workflow run_wf {
],
toState: [
"fastq_1": "out1",
// "fastq_2": "out2",
"fastq_2": "out2",
"failed_trim": "failed_out",
"failed_trim_unpaired1": "unpaired1",
"failed_trim_unpaired2": "unpaired2",
@@ -154,8 +155,10 @@ workflow run_wf {
runIf: { id, state -> state.strandedness == 'auto' },
fromState: { id, state ->
def input = state.paired ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
[ input: input,
extra_args: state.extra_fq_subsample_args ]
[
input: input,
extra_args: state.extra_fq_subsample_args
]
},
toState: [
"subsampled_fastq_1": "output_1",
@@ -189,9 +192,8 @@ workflow run_wf {
def mates1 = state.paired ? state.subsampled_fastq_1 : null
def mates2 = state.paired ? state.subsampled_fastq_2 : null
[ unmated_reads: unmated_reads,
mates1: state.fastq1,
mates2: state.fastq2,
targets: state.transcript_fasta,
mates1: mates1,
mates2: mates2,
gene_map: state.gtf,
index: state.salmon_index,
lib_type: state.lib_type ]

49
src/workflows/pre_processing/test_run.sh
View File

@@ -2,30 +2,55 @@
# viash ns build --parallel --setup cb
# nextflow run target/nextflow/workflows/pre_processing/main.nf \
# --id RAP1_UNINDUCED_REP1 \
# --input 'testData/minimal_test/input_fastq/SRR6357073_1.fastq.gz' \
# --publish_dir "test_results/preprocessing_no_samplesheet" \
# --umitools_bc_pattern "NNNN" \
# -profile docker \
# -resume
echo "> Preparing reference data files"
gunzip --keep testData/minimal_test/reference/genes.gtf.gz
mkdir -p testData/minimal_test/reference/salmon_index
tar -C testData/minimal_test/reference/salmon_index --strip-components 1 -xavf testData/minimal_test/reference/salmon.tar.gz --no-same-owner
# Test paired-end data
cat > testData/minimal_test/input_fastq/sample_sheet.csv << HERE
id,fastq_1,fastq_2,strandedness
WT_REP2,SRR6357072_1.fastq.gz,SRR6357072_2.fastq.gz,reverse
RAP1_IAA_30M_REP1,SRR6357076_1.fastq.gz,SRR6357076_2.fastq.gz,reverse
WT_REP2,SRR6357072_1.fastq.gz,SRR6357072_2.fastq.gz,auto
RAP1_UNINDUCED_REP1,SRR6357073_1.fastq.gz,,reverse
HERE
echo "> Test 1: Running workflow with trimgalore"
nextflow run target/nextflow/workflows/pre_processing/main.nf \
--param_list testData/minimal_test/input_fastq/sample_sheet.csv \
--publish_dir "testData/paired_end_test" \
--publish_dir "test_results/pre_processing_test1" \
--bbsplit_fasta_list testData/minimal_test/reference/bbsplit_fasta_list.txt \
--transcript_fasta testData/minimal_test/reference/transcriptome.fasta \
--gtf testData/minimal_test/reference/gene_annotation.gtf \
--salmon_index testData/minimal_test/reference/salmon.tar.gz \
--gtf testData/minimal_test/reference/genes.gtf \
--salmon_index testData/minimal_test/reference/salmon_index \
--skip_trimming false \
--trimmer trimgalore \
--remove_ribo_rna false \
--ribo_database_manifest testData/minimal_test/reference/rrna-db-defaults.txt \
--skip_bbsplit false \
--bbsplit_index test_results/prepare_genome_test1/BBSplit_index \
-profile docker \
-resume
# echo "> Test 2: Running workflow with fastp"
# nextflow run target/nextflow/workflows/pre_processing/main.nf \
# --param_list testData/minimal_test/input_fastq/sample_sheet.csv \
# --publish_dir "test_results/pre_processing_test2" \
# --bbsplit_fasta_list testData/minimal_test/reference/bbsplit_fasta_list.txt \
# --transcript_fasta testData/minimal_test/reference/transcriptome.fasta \
# --gtf testData/minimal_test/reference/genes.gtf \
# --salmon_index testData/minimal_test/reference/salmon_index \
# --skip_trimming false \
# --trimmer fastp \
# --remove_ribo_rna false \
# --ribo_database_manifest testData/minimal_test/reference/rrna-db-defaults.txt \
# --skip_bbsplit false \
# --bbsplit_index test_results/output_test1/BBSplit_index \
# -profile docker \
# -resume
echo "Removing reference data files"
rm testData/minimal_test/reference/genes.gtf
rm -r testData/minimal_test/reference/salmon_index
# TODO: Fix error while running sortmerna component
# docker: Error response from daemon: failed to create task for container: failed to create shim task: OCI runtime create failed: runc create failed: unable to start container process: exec: "/bin/bash": stat /bin/bash: no such file or directory: unknown.

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

@@ -163,6 +163,7 @@ dependencies:
- name: salmon/salmon_index
repository: biobox
- name: kallisto/kallisto_index
# repository: biobox
runners:
- type: executable

34
src/workflows/prepare_genome/main.nf
View File

@@ -35,9 +35,15 @@ workflow run_wf {
// gff to gtf
| gffread.run (
runIf: {id, state -> !state.gtf && state.gff},
fromState: [ "input": "annotation" ],
fromState: [
"input": "gff",
"genome": "fasta"
],
toState: [ "gtf": "outfile" ],
args: [output: "gene_annotation.gtf"]
args: [
outfile: "gene_annotation.gtf",
gtf_output: true
]
)
| gtf_filter.run(
@@ -116,13 +122,19 @@ workflow run_wf {
| rsem_prepare_reference.run (
runIf: {id, state -> !state.transcript_fasta},
fromState: [
"fasta": "fasta",
"reference_fasta_files": "fasta",
"gtf": "gtf"
],
toState: [ "transcript_fasta": "transcript_fasta" ],
key: "make_transcript_fasta",
args: [transcript_fasta: "transcriptome.fasta"]
toState: [ "make_transcript_fasta_output": "output" ],
key: "make_transcript_fasta",\
args: [reference_name: "genome"]
)
| map { id, state ->
def transcript_fasta = (!state.transcript_fasta) ?
state.make_transcript_fasta_output.listFiles().find{it.name == "genome.transcripts.fa"} :
state.transcript_fasta
[ id, state + [transcript_fasta: transcript_fasta] ]
}
// chromosome size and fai index
| getchromsizes.run (
@@ -195,11 +207,12 @@ workflow run_wf {
| rsem_prepare_reference.run (
runIf: {id, state -> !state.rsem_index && state.aligner == 'star_rsem'},
fromState: [
"fasta": "fasta",
"reference_fasta_files": "fasta",
"gtf": "gtf"
],
toState: [ "rsem_index": "rsem" ],
toState: [ "rsem_index": "output" ],
key: "generate_rsem_index",
args: [reference_name: "genome"]
)
// TODO: Uncompress HISAT2 index or generate from scratch if required
@@ -229,10 +242,7 @@ workflow run_wf {
// Uncompress Kallisto index or generate from scratch if required
| untar.run (
runIf: {id, state -> state.kallisto_index},
fromState: [
"input": "kallisto_index",
"pseudo_aligner_kmer_size": "pseudo_aligner_kmer_size"
],
fromState: [ "input": "kallisto_index" ],
toState: [ "kallisto_index": "output" ],
key: "untar_kallisto_index",
args: [output: "Kallisto_index"]

64
src/workflows/prepare_genome/test_run.sh
View File

@@ -1,26 +1,50 @@
#!/bin/bash
viash ns build --setup cb --parallel
# viash ns build --setup cb --parallel -q prepare_genome
# echo "Test 1: Annotation file format - GTF"
# nextflow run target/nextflow/workflows/prepare_genome/main.nf \
# --id test1 \
# --publish_dir "test_results/prepare_genome_test1" \
# --fasta testData/minimal_test/reference/genome.fasta \
# --gtf testData/minimal_test/reference/genes.gtf.gz \
# --additional_fasta testData/minimal_test/reference/gfp.fa.gz \
# --transcript_fasta testData/minimal_test/reference/transcriptome.fasta \
# --genotype false \
# --biotype gene_biotype \
# --bbsplit_fasta_list testData/minimal_test/reference/bbsplit_fasta_list.txt \
# --salmon_index testData/minimal_test/reference/salmon.tar.gz \
# --rsem_index testData/minimal_test/reference/rsem.tar.gz \
# -profile docker \
# -resume
# echo "Test 2: Annotation file format - GFF"
# nextflow run target/nextflow/workflows/prepare_genome/main.nf \
# --id test2 \
# --publish_dir "test_results/prepare_genome_test2" \
# --fasta testData/minimal_test/reference/genome.fasta \
# --gff testData/minimal_test/reference/genes.gff.gz \
# --additional_fasta testData/minimal_test/reference/gfp.fa.gz \
# --transcript_fasta testData/minimal_test/reference/transcriptome.fasta \
# --genotype false \
# --biotype gene_biotype \
# --bbsplit_fasta_list testData/minimal_test/reference/bbsplit_fasta_list.txt \
# --salmon_index testData/minimal_test/reference/salmon.tar.gz \
# --rsem_index testData/minimal_test/reference/rsem.tar.gz \
# -profile docker \
# -resume
echo "Test 3: Annotation file format - GTF; Generate indices; Generate transcripts fasta"
nextflow run target/nextflow/workflows/prepare_genome/main.nf \
--id ref \
--publish_dir "testData/test_output" \
--fasta testData/reference/genome.fasta \
--gtf testData/reference/genes.gtf.gz \
--additional_fasta testData/reference/gfp.fa.gz \
--transcript_fasta testData/reference/transcriptome.fasta \
--id test3 \
--publish_dir "test_results/prepare_genome_test3" \
--fasta testData/minimal_test/reference/genome.fasta \
--gtf testData/minimal_test/reference/genes.gtf.gz \
--additional_fasta testData/minimal_test/reference/gfp.fa.gz \
--genotype false \
--biotype gene_biotype \
--bbsplit_fasta_list testData/reference/bbsplit_fasta_list.txt \
--salmon_index testData/reference/salmon.tar.gz \
# -profile docker \
# -resume
# --gff testData/reference/genes.gff.gz \
# --prepare_tools_indices a,b,c \
# --gene_bed "" \
# --splicesites "" \
# --star_index "" \
# --bbsplit_index "" \
# --rsem_index testData/reference/rsem.tar.gz \
# --salmon_index testData/reference/salmon.tar.gz \
# --hisat2_index testData/reference/hisat2.tar.gz \
--bbsplit_fasta_list testData/minimal_test/reference/bbsplit_fasta_list.txt \
--pseudo_aligner kallisto \
--aligner star_rsem \
-profile docker \
-resume

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

@@ -59,11 +59,10 @@ argument_groups:
- name: "--pseudo_multiqc"
type: file
direction: output
default: $id.quant.log
- name: "--quant_out_dir"
type: file
direction: output
default: $id.salmon_quant
default: $id.quant
- name: "--salmon_quant_results_file"
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_results_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: [

33
src/workflows/pseudo_alignment_and_quant/test_run.sh
View File

@@ -1,26 +1,45 @@
#!/bin/bash
viash ns build --setup cb -q pseudo_alignment_and_quant
# viash ns build --setup cb -q pseudo_alignment_and_quant
# Split error message from standard output
# viash ns list > /dev/null
CURR=`pwd`
echo "> Preparing reference data files"
gunzip --keep testData/minimal_test/reference/genes.gtf.gz
mkdir -p testData/minimal_test/reference/salmon_index
tar -C testData/minimal_test/reference/salmon_index --strip-components 1 -xavf testData/minimal_test/reference/salmon.tar.gz
# Test paired-end data
cat > testData/minimal_test/input_fastq/sample_sheet.csv << HERE
id,fastq_1,fastq_2,strandedness
WT_REP1,SRR6357070_1.fastq.gz,SRR6357070_2.fastq.gz,reverse
WT_REP2,SRR6357072_1.fastq.gz,SRR6357072_2.fastq.gz,reverse
RAP1_UNINDUCED_REP1,SRR6357073_1.fastq.gz,,reverse
HERE
echo "> Test 1: Salmon qunatification"
nextflow run target/nextflow/workflows/pseudo_alignment_and_quant/main.nf \
--param_list testData/minimal_test/input_fastq/sample_sheet.csv \
--publish_dir "test_results/psudo_alignment_test" \
--publish_dir "test_results/pseudo_alignment_test1" \
--fasta testData/minimal_test/reference/genome.fasta \
--gtf testData/minimal_test/reference/genes.gtf.gz \
--transcript_fasta testData/minimal_test/reference/transcriptome.fasta \
--salmon_index testData/minimal_test/reference/salmon.tar.gz \
--salmon_index testData/minimal_test/reference/salmon_index \
--pseudo_aligner salmon \
-profile docker \
# -resume
-resume
# echo "> Test 2: Kallisto qunatification"
# nextflow run target/nextflow/workflows/pseudo_alignment_and_quant/main.nf \
# --param_list testData/minimal_test/input_fastq/sample_sheet.csv \
# --publish_dir "test_results/pseudo_alignment_test2" \
# --fasta testData/minimal_test/reference/genome.fasta \
# --gtf testData/minimal_test/reference/genes.gtf.gz \
# --transcript_fasta testData/minimal_test/reference/transcriptome.fasta \
# --kallisto_index test_results/prepare_genome_test3/Kallisto_index \
# --pseudo_aligner kallisto \
# -profile docker \
# -resume
echo "Removing reference data files"
rm testData/minimal_test/reference/genes.gtf
rm -r testData/minimal_test/reference/salmon_index

39
src/workflows/quality_control/config.vsh.yaml
View File

@@ -41,10 +41,10 @@ argument_groups:
description: By default, the pipeline uses the gene_name field to obtain additional gene identifiers from the input GTF file when running Salmon.
- name: "--quant_out_dir"
type: file
description: Directory containing quantification results.
description: Directory containing Salmon quantification results.
- name: "--quant_results_file"
type: file
description: Quantification file.
description: Salmon quantification file.
- name: "--pseudo_quant_out_dir"
type: file
description: Directory containing quantification results for pseudo alignment.
@@ -59,7 +59,13 @@ argument_groups:
description: Method used for alognment and qqunatification.
- name: "--pseudo_aligner"
type: string
description: Method used for [seudo alignment and quantification.
description: Method used for pseudo alignment and quantification.
- name: "--rsem_counts_gene"
type: file
description: Expression counts on gene level
- name: "--rsem_counts_transcripts"
type: file
description: Expression counts on transcript level
- name: "--skip_qc"
type: boolean
@@ -258,11 +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"
@@ -297,8 +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
@@ -542,9 +543,6 @@ argument_groups:
type: file
direction: output
default: multiqc_plots
- name: "--multiqc_versions"
type: file
direction: output
# Biotype QC
- name: "--featurecounts"
@@ -600,27 +598,27 @@ argument_groups:
- name: "--pseudo_tpm_gene"
type: file
direction: output
default: salmon.merged.pseudo_gene_tpm.tsv
default: pseudo_gene_tpm.tsv
- name: "--pseudo_counts_gene"
type: file
direction: output
default: salmon.merged.pseudo_gene_counts.tsv
default: pseudo_gene_counts.tsv
- name: "--pseudo_counts_gene_length_scaled"
type: file
direction: output
default: salmon.merged.pseudo_gene_counts_length_scaled.tsv
default: pseudo_gene_counts_length_scaled.tsv
- name: "--pseudo_counts_gene_scaled"
type: file
direction: output
default: salmon.merged.pseudo_gene_counts_scaled.tsv
default: pseudo_gene_counts_scaled.tsv
- name: "--pseudo_tpm_transcript"
type: file
direction: output
default: salmon.merged.pseudo_transcript_tpm.tsv
default: pseudo_transcript_tpm.tsv
- name: "--pseudo_counts_transcript"
type: file
direction: output
default: salmon.merged.pseudo_transcript_counts.tsv
default: pseudo_transcript_counts.tsv
- name: "--pseudo_quant_merged_summarizedexperiment"
type: file
direction: output
@@ -642,6 +640,8 @@ dependencies:
- name: rseqc/rseqc_tin
- name: dupradar
- name: qualimap
# - name: qualimap/qualimap_rnaseq
# repository: biobox
- name: preseq_lcextrap
- name: featurecounts
repository: biobox
@@ -650,6 +650,7 @@ dependencies:
- name: prepare_multiqc_input
- name: multiqc
repository: biobox
- name: rsem/rsem_merge_counts
- name: workflows/merge_quant_results
runners:

294
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 (
@@ -214,10 +214,49 @@ workflow run_wf {
merged_ch = qc_ch
| toSortedList
| 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 :
@@ -242,26 +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 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 :
@@ -278,6 +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 :
@@ -338,40 +373,45 @@ 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,
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,
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,
sortmerna_multiqc: sortmerna_multiqc,
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,
salmon_multiqc: salmon_multiqc,
rsem_multiqc: rsem_multiqc,
pseudo_multiqc: pseudo_multiqc,
featurecounts_multiqc: featurecounts_multiqc,
featurecounts_rrna_multiqc: featurecounts_rrna_multiqc,
@@ -387,32 +427,114 @@ workflow run_wf {
read_distribution_output: read_distribution_output,
read_duplication_output_duplication_rate_mapping: read_duplication_output_duplication_rate_mapping,
tin_output_summary: tin_output_summary,
quant_results: quant_results,
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,
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
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' },
@@ -434,19 +556,36 @@ 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 (
runIf: { id, state -> state.aligner == 'star_rsem' },
fromState: [
"counts_gene": "rsem_counts_gene",
"counts_transcripts": "rsem_counts_transcripts"
],
toState: [
"tpm_gene": "merged_gene_tpm",
"counts_gene": "merged_gene_counts",
"tpm_transcript": "merged_transcript_tpm",
"counts_transcript": "merged_transcript_counts"
]
)
| deseq2_qc.run (
runIf: { id, state -> !state.skip_qc && !state.skip_deseq2_qc && !state.skip_align },
fromState: [
"counts": "counts_gene_length_scaled",
"pca_header_multiqc": "pca_header_multiqc",
"clustering_header_multiqc": "clustering_header_multiqc",
"deseq2_vst": "deseq2_vst",
"extra_deseq2_args": "extra_deseq2_args",
"extra_deseq2_args2": "extra_deseq2_args2"
],
fromState: { id, state ->
def counts = (state.aligner == "star_rsem") ? state.counts_gene : state.counts_gene_length_scaled
[
counts: counts,
pca_header_multiqc: state.pca_header_multiqc,
clustering_header_multiqc: state.clustering_header_multiqc,
deseq2_vst: state.deseq2_vst,
extra_deseq2_args: state.extra_deseq2_args,
extra_deseq2_args2: state.extra_deseq2_args2
]
},
toState: [
"deseq2_output": "deseq2_output",
"deseq2_pca_multiqc": "pca_multiqc",
@@ -547,14 +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",
"featurecounts_multiqc": "featurecounts_multiqc",
"featurecounts_rrna_multiqc": "featurecounts_rrna_multiqc",
"aligner_pca_multiqc": "deseq2_pca_multiqc",
@@ -583,10 +723,11 @@ workflow run_wf {
"title": "multiqc_title",
"input": "multiqc_input",
],
args: [exclude_modules: "general_stats"],
toState: [
"multiqc_report": "output_report",
"multiqc_data": "output_data",
"multiqc_plots": "output_plots",
"multiqc_plots": "output_plots"
]
)
@@ -688,8 +829,7 @@ 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"
]
)
@@ -749,3 +889,5 @@ def getInferexperimentStrandedness(inferexperiment_file, cutoff=30) {
return [ strandedness, sense, antisense, undetermined ]
}

200
src/workflows/rnaseq/config.vsh.yaml
View File

@@ -233,11 +233,7 @@ argument_groups:
- name: "--skip_pseudo_alignment"
type: boolean_true
description: Skip all of the pseudo-alignment-based processes within the pipeline.
- name: extra_rsem_prepare_reference_args
type: string
description: Extra arguments to pass to rsem-prepare-reference command in addition to defaults defined by the pipeline.
default: '--star'
- name: extra_rsem_calculate_expression_args
- name: --extra_rsem_calculate_expression_args
type: string
description: Extra arguments to pass to rsem-calculate-expression command in addition to defaults defined by the pipeline.
default: '--star --star-output-genome-bam --star-gzipped-read-file --estimate-rspd --seed 1'
@@ -349,42 +345,45 @@ argument_groups:
- name: Output
arguments:
# Reference files
- name: "--output_fasta"
type: file
direction: output
default: genome/reference_genome.fasta
default: reference/genome.fasta
- name: "--output_gtf"
type: file
direction: output
default: genome/gene_annotation.gtf
default: reference/gene_annotation.gtf
- name: "--output_transcript_fasta"
type: file
direction: output
default: genome/transcriptome.fasta
default: reference/transcriptome.fasta
- name: "--output_gene_bed"
type: file
direction: output
default: genome/gene_annotation.bed
default: reference/gene_annotation.bed
- name: "--output_star_index"
type: file
direction: output
description: Path to STAR index.
default: genome/index/STAR
default: reference/index/STAR
- name: "--output_salmon_index"
type: file
direction: output
description: Path to Salmon index.
default: genome/index/Salmon
default: reference/index/Salmon
- name: "--output_bbsplit_index"
type: file
direction: output
description: Path to BBSplit index.
default: genome/index/BBSplit
default: reference/index/BBSplit
- name: "--output_kallisto_index"
type: file
direction: output
description: Path to Kallisto index.
default: genome/index/Kallisto
default: reference/index/Kallisto
# fastq
- name: "--output_fastq_1"
type: file
direction: output
@@ -399,6 +398,8 @@ argument_groups:
must_exist: false
description: Path to output directory
default: fastq/$id.read_2.fastq
# FastQC
- name: "--fastqc_html_1"
type: file
direction: output
@@ -427,18 +428,6 @@ argument_groups:
required: false
must_exist: false
default: fastqc_raw/$id.read_2.fastqc.zip
- name: "--trim_log_1"
type: file
direction: output
required: false
must_exist: false
default: trimgalore/$id.read_1.trimming_report.txt
- name: "--trim_log_2"
type: file
direction: output
required: false
must_exist: false
default: trimgalore/$id.read_2.trimming_report.txt
- name: "--trim_html_1"
type: file
direction: output
@@ -463,6 +452,34 @@ argument_groups:
required: false
must_exist: false
default: fastqc_trim/$id.read_2.trimmed_fastqc.zip
# TrimGalore
- name: "--trim_log_1"
type: file
direction: output
required: false
must_exist: false
default: trimgalore/$id.read_1.trimming_report.txt
- name: "--trim_log_2"
type: file
direction: output
required: false
must_exist: false
default: trimgalore/$id.read_2.trimming_report.txt
# fastp
- name: --fastp_trim_json
type: file
description: The fastp json format report file name
default: fastp/$id_out.json
direction: output
- name: --fastp_trim_html
type: file
description: The fastp html format report file name
default: fastp/$id_out.html
direction: output
# SortMeRNA
- name: "--sortmerna_log"
type: file
direction: output
@@ -470,18 +487,30 @@ argument_groups:
required: false
must_exist: false
description: Sortmerna log file.
# STAR
- name: "--star_alignment"
type: file
direction: output
default: STAR_alignment/$id
default: STAR/$id
- name: "--genome_bam_sorted"
type: file
direction: output
default: STAR_alignment/genome_processed/$id.genome.bam
default: STAR/genome_processed/$id.genome.bam
- name: "--genome_bam_index"
type: file
direction: output
default: STAR_alignment/genome_processed/$id.genome.bam.bai
default: STAR/genome_processed/$id.genome.bam.bai
- name: "--transcriptome_bam"
type: file
direction: output
default: STAR/transcriptome_processed/$id.transcriptome.bam
- name: "--transcriptome_bam_index"
type: file
direction: output
default: STAR/transcriptome_processed/$id.transcriptome.bam.bai
# samtools
- name: "--genome_bam_stats"
type: file
direction: output
@@ -494,14 +523,6 @@ argument_groups:
type: file
direction: output
default: samtools_stats/$id.genome.idxstats
- name: "--transcriptome_bam"
type: file
direction: output
default: STAR_alignment/transcriptome_processed/$id.transcriptome.bam
- name: "--transcriptome_bam_index"
type: file
direction: output
default: STAR_alignment/transcriptome_processed/$id.transcriptome.bam.bai
- name: "--transcriptome_bam_stats"
type: file
direction: output
@@ -514,42 +535,85 @@ argument_groups:
type: file
direction: output
default: samtools_stats/$id.transcriptome.idxstats
# Transcript quantification
- name: "--salmon_quant_results"
type: file
direction: output
default: salmon/$id
default: STAR_Salmon/$id
- name: "--salmon_quant_results_file"
type: file
direction: output
default: STAR_Salmon/$id/quant.sf
- name: "--pseudo_quant_results"
type: file
direction: output
default: Pseudo_align_quant/$id
# RSEM
- name: "--rsem_counts_gene"
type: file
description: Expression counts on gene level
default: RSEM/$id.genes.results
direction: output
- name: "--rsem_counts_transcripts"
type: file
description: Expression counts on transcript level
default: RSEM/$id.isoforms.results
direction: output
- name: "--bam_star_rsem"
type: file
description: BAM file generated by STAR (from RSEM)
default: RSEM/$id.STAR.genome.bam
direction: output
- name: "--bam_genome_rsem"
type: file
description: Genome BAM file (from RSEM)
default: RSEM/$id.genome.bam
direction: output
- name: "--bam_transcript_rsem"
type: file
description: Transcript BAM file (from RSEM)
default: RSEM/$id.transcript.bam
direction: output
# Quantification (alignment)
- name: "--tpm_gene"
type: file
direction: output
default: salmon/gene_tpm.tsv
default: transcript_quantification/gene_tpm.tsv
- name: "--counts_gene"
type: file
direction: output
default: salmon/gene_counts.tsv
default: transcript_quantification/gene_counts.tsv
- name: "--counts_gene_length_scaled"
type: file
direction: output
default: salmon/gene_counts_length_scaled.tsv
default: transcript_quantification/gene_counts_length_scaled.tsv
- name: "--counts_gene_scaled"
type: file
direction: output
default: salmon/gene_counts_scaled.tsv
default: transcript_quantification/gene_counts_scaled.tsv
- name: "--tpm_transcript"
type: file
direction: output
default: salmon/transcript_tpm.tsv
default: transcript_quantification/transcript_tpm.tsv
- name: "--counts_transcript"
type: file
direction: output
default: salmon/transcript_counts.tsv
- name: "--salmon_merged_summarizedexperiment"
default: transcript_quantification/transcript_counts.tsv
- name: "--quant_merged_summarizedexperiment"
type: file
direction: output
default: salmon/summarizedexperiment
default: transcript_quantification/summarizedexperiment
# MarkDuplicates
- name: "--markduplicates_metrics"
type: file
direction: output
default: picard/$id.sorted.MarkDuplicates.metrics.txt
default: picard/$id.MarkDuplicates.metrics.txt
# StringTie
- name: "--stringtie_transcript_gtf"
type: file
direction: output
@@ -566,6 +630,8 @@ argument_groups:
type: file
direction: output
default: stringtie/$id.ballgown
# featureCounts
- name: "--featurecounts"
type: file
direction: output
@@ -584,6 +650,8 @@ argument_groups:
direction: output
must_exist: false
default: featurecounts/$id.featureCounts_rrna_mqc.tsv
# bedGraph
- name: "--bedgraph_forward"
type: file
direction: output
@@ -592,6 +660,8 @@ argument_groups:
type: file
direction: output
default: bedgraph/$id.reverse.bedgraph
# bigWig
- name: "--bigwig_forward"
type: file
direction: output
@@ -600,10 +670,14 @@ argument_groups:
type: file
direction: output
default: bigwig/$id.reverse.bigwig
# preseq lc_extrap
- name: "--preseq_output"
type: file
direction: output
default: preseq/$id.lc_extrap.txt
# RSeQC
- name: "--bamstat_output"
type: file
direction: output
@@ -742,6 +816,8 @@ argument_groups:
required: false
default: RSeQC/tin/xls/$id.tin.xls
description: file with TIN metrics (xls)
# DupRadar
- name: "--dupradar_output_dupmatrix"
type: file
direction: output
@@ -783,6 +859,8 @@ argument_groups:
direction: output
required: false
default: dupradar/intercept_slope/$id.intercept_slope.txt
# Qualimap
- name: "--qualimap_output_pdf"
type: file
direction: output
@@ -794,10 +872,14 @@ argument_groups:
direction: output
required: false
default: qualimap/$id
# DESeq2
- name: "--deseq2_output"
type: file
direction: output
default: deseq2_qc
# MultiQC
- name: "--multiqc_report"
type: file
direction: output
@@ -813,10 +895,32 @@ argument_groups:
- name: "--multiqc_versions"
type: file
direction: output
- name: "--versions"
# Quantification (pseudo alignment)
- name: "--pseudo_counts_gene"
type: file
must_exist: false
direction: output
default: pseudo_alignment_quantification/gene_counts.tsv
- name: "--pseudo_counts_gene_length_scaled"
type: file
direction: output
default: pseudo_alignment_quantification/gene_counts_length_scaled.tsv
- name: "--pseudo_counts_gene_scaled"
type: file
direction: output
default: pseudo_alignment_quantification/gene_counts_scaled.tsv
- name: "--pseudo_tpm_transcript"
type: file
direction: output
default: pseudo_alignment_quantification/transcript_tpm.tsv
- name: "--pseudo_counts_transcript"
type: file
direction: output
default: pseudo_alignment_quantification/transcript_counts.tsv
- name: "--pseudo_quant_merged_summarizedexperiment"
type: file
direction: output
default: pseudo_alignment_quantification/quant_merged_summarizedexperiment
resources:
- type: nextflow_script

87
src/workflows/rnaseq/main.nf
View File

@@ -22,27 +22,27 @@ workflow run_wf {
| map { list ->
[ "ref",
[ fasta: list[1][-1].fasta,
gtf: list[1][-1].gtf,
gff: list[1][-1].gff,
additional_fasta: list[1][-1].additional_fasta,
transcript_fasta: list[1][-1].transcript_fasta,
gene_bed: list[1][-1].gene_bed,
bbsplit_fasta_list: list[1][-1].bbsplit_fasta_list,
aligner: list[1][-1].aligner,
pseudo_aligner: list[1][-1].pseudo_aligner,
star_index: list[1][-1].star_index,
rsem_index: list[1][-1].rsem_index,
salmon_index: list[1][-1].salmon_index,
kallisto_index: list[1][-1].kallisto_index,
// splicesites: list[1][-1].splicesites,
// hisat2_index: list[1][-1].hisat2_index,
bbsplit_index: list[1][-1].bbsplit_index,
skip_bbsplit: list[1][-1].skip_bbsplit,
gencode: list[1][-1].gencode,
biotype: list[1][-1].biotype,
filter_gtf: list[1][-1].filter_gtf,
pseudo_aligner_kmer_size: list[1][-1].pseudo_aligner_kmer_size ]
[ fasta: list.collect { id, state -> state.fasta }.unique()[0],
gtf: list.collect { id, state -> state.gtf }.unique()[0],
gff: list.collect { id, state -> state.gff }.unique()[0],
additional_fasta: list.collect { id, state -> state.additional_fasta }.unique()[0],
transcript_fasta:list.collect { id, state -> state.transcript_fasta }.unique()[0],
gene_bed: list.collect { id, state -> state.gene_bed }.unique()[0],
bbsplit_fasta_list: list.collect { id, state -> state.bbsplit_fasta_list }.unique()[0],
aligner: list.collect { id, state -> state.aligner }.unique()[0],
pseudo_aligner: list.collect { id, state -> state.pseudo_aligner }.unique()[0],
star_index: list.collect { id, state -> state.star_index }.unique()[0],
rsem_index: list.collect { id, state -> state.rsem_index }.unique()[0],
salmon_index: list.collect { id, state -> state.salmon_index }.unique()[0],
kallisto_index: list.collect { id, state -> state.kallisto_index }.unique()[0],
// splicesites: list.collect { id, state -> state.splicesites }.unique()[0],
// hisat2_index: list.collect { id, state -> state.hisat2_index }.unique()[0],
bbsplit_index: list.collect { id, state -> state.bbsplit_index }.unique()[0],
skip_bbsplit: list.collect { id, state -> state.skip_bbsplit }.unique()[0],
gencode: list.collect { id, state -> state.gencode }.unique()[0],
biotype: list.collect { id, state -> state.biotype }.unique()[0],
filter_gtf: list.collect { id, state -> state.filter_gtf }.unique()[0],
pseudo_aligner_kmer_size: list.collect { id, state -> state.pseudo_aligner_kmer_size }.unique()[0] ]
]
}
@@ -213,11 +213,14 @@ workflow run_wf {
"gtf_group_features": "gtf_group_features",
"gtf_extra_attributes": "gtf_extra_attributes",
"salmon_quant_libtype": "salmon_quant_libtype",
"salmon_index": "salmon_index"
"salmon_index": "salmon_index",
"extra_rsem_calculate_expression_args": "extra_rsem_calculate_expression_args"
],
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",
@@ -229,7 +232,11 @@ workflow run_wf {
"transcriptome_bam_flagstat": "transcriptome_bam_flagstat",
"transcriptome_bam_idxstats": "transcriptome_bam_idxstats",
"quant_out_dir": "quant_out_dir",
"quant_results_file": "quant_results_file"
"quant_results_file": "quant_results_file",
"rsem_counts_gene": "rsem_counts_gene",
"rsem_counts_transcripts": "rsem_counts_transcripts",
"bam_genome_rsem": "bam_genome_rsem",
"bam_transcript_rsem": "bam_transcript_rsem"
]
)
@@ -331,16 +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",
@@ -368,11 +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",
@@ -418,7 +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",
@@ -457,15 +467,17 @@ workflow run_wf {
"star_alignment": "star_alignment",
"genome_bam_sorted": "genome_bam_sorted",
"genome_bam_index": "genome_bam_index",
"genome_bam_stats": "samtools_stats",
"genome_bam_flagstat": "samtools_flagstat",
"genome_bam_idxstats": "samtools_idxstats",
"genome_bam_stats": "genome_bam_stats",
"genome_bam_flagstat": "genome_bam_flagstat",
"genome_bam_idxstats": "genome_bam_idxstats",
"transcriptome_bam": "transcriptome_bam",
"transcriptome_bam_index": "transcriptome_bam_index",
"transcriptome_bam_stats": "transcriptome_bam_stats",
"transcriptome_bam_flagstat": "transcriptome_bam_flagstat",
"transcriptome_bam_idxstats": "transcriptome_bam_idxstats",
"salmon_quant_results": "salmon_quant_results",
"salmon_quant_results": "quant_out_dir",
"pseudo_quant_results": "pseudo_quant_out_dir",
"markduplicates_metrics": "markduplicates_metrics",
"stringtie_transcript_gtf": "stringtie_transcript_gtf",
"stringtie_coverage_gtf": "stringtie_coverage_gtf",
"stringtie_abundance": "stringtie_abundance",
@@ -531,8 +543,7 @@ 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"
]
)
@@ -611,7 +622,7 @@ 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

30
src/workflows/rnaseq/test_run.sh
View File

@@ -1,30 +1,34 @@
#!/bin/bash
viash ns build --setup cb --parallel
# viash ns build --setup cb --parallel
cat > testData/minimal_test/input_fastq/sample_sheet.csv << HERE
id,fastq_1,fastq_2,strandedness
WT_REP1,SRR6357070_1.fastq.gz;SRR6357071_1.fastq.gz,SRR6357070_2.fastq.gz;SRR6357071_2.fastq.gz,reverse
WT_REP2,SRR6357072_1.fastq.gz,SRR6357072_2.fastq.gz,reverse
RAP1_IAA_30M_REP1,SRR6357076_1.fastq.gz,SRR6357076_2.fastq.gz,reverse
RAP1_UNINDUCED_REP1,SRR6357073_1.fastq.gz,,reverse
RAP1_UNINDUCED_REP2,SRR6357074_1.fastq.gz;SRR6357075_1.fastq.gz,,reverse
HERE
echo ">> Test 1: Trimming reads with Trim galore; alignment with STAR and quantification with Salmon"
nextflow run target/nextflow/workflows/rnaseq/main.nf \
--param_list testData/minimal_test/input_fastq/sample_sheet.csv \
--publish_dir "test_results/full_pipeline_test1" \
--publish_dir test_results/full_pipeline_test1 \
--fasta testData/minimal_test/reference/genome.fasta \
--gtf testData/minimal_test/reference/genes.gtf.gz \
--additional_fasta testData/minimal_test/reference/gfp.fa.gz \
--transcript_fasta testData/minimal_test/reference/transcriptome.fasta \
--bbsplit_fasta_list testData/minimal_test/reference/bbsplit_fasta_list.txt \
--skip_pseudo_alignment \
-profile docker --resume
-profile docker \
--resume
# echo ">> Test 2: Trimming reads with Trim galore; alignment with STAR and quantification with Salmon; pseudo-alignment and quantification with Kallisto"
# nextflow run target/nextflow/workflows/rnaseq/main.nf \
# --param_list testData/minimal_test/input_fastq/sample_sheet.csv \
# --publish_dir "test_results/full_pipeline_test2" \
# --publish_dir test_results/full_pipeline_test2 \
# --fasta testData/minimal_test/reference/genome.fasta \
# --gtf testData/minimal_test/reference/genes.gtf.gz \
# --additional_fasta testData/minimal_test/reference/gfp.fa.gz \
@@ -35,10 +39,11 @@ nextflow run target/nextflow/workflows/rnaseq/main.nf \
# --kallisto_quant_fragment_length_sd 10 \
# -profile docker --resume
# echo ">> Test 3: Trimming reads with fastp; skip alignment; pseudo alignment and quantification with Salmon"
# nextflow run target/nextflow/workflows/rnaseq/main.nf \
# --param_list testData/minimal_test/input_fastq/sample_sheet.csv \
# --publish_dir "test_results/full_pipeline_test3" \
# --publish_dir test_results/full_pipeline_test3 \
# --fasta testData/minimal_test/reference/genome.fasta \
# --gtf testData/minimal_test/reference/genes.gtf.gz \
# --additional_fasta testData/minimal_test/reference/gfp.fa.gz \
@@ -47,3 +52,18 @@ nextflow run target/nextflow/workflows/rnaseq/main.nf \
# --trimmer fastp \
# --skip_alignment \
# -profile docker --resume
# echo ">> Test 4: Trimming reads with Trim galore; alignment and quantification with RSEM (STAR)"
# nextflow run target/nextflow/workflows/rnaseq/main.nf \
# --param_list testData/minimal_test/input_fastq/sample_sheet.csv \
# --publish_dir test_results/full_pipeline_test4 \
# --fasta testData/minimal_test/reference/genome.fasta \
# --gtf testData/minimal_test/reference/genes.gtf.gz \
# --additional_fasta testData/minimal_test/reference/gfp.fa.gz \
# --transcript_fasta testData/minimal_test/reference/transcriptome.fasta \
# --bbsplit_fasta_list testData/minimal_test/reference/bbsplit_fasta_list.txt \
# --aligner star_rsem \
# --skip_pseudo_alignment \
# -profile docker \
# --resume

475
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml Normal file
View File

@@ -0,0 +1,475 @@
name: "umi_tools_extract"
namespace: "umi_tools"
version: "v0.2.0"
argument_groups:
- name: "Input"
arguments:
- type: "file"
name: "--input"
description: "File containing the input data."
info: null
example:
- "sample.fastq"
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--read2_in"
description: "File containing the input data for the R2 reads (if paired). If\
\ provided, a <list of other required arguments> need to be provided."
info: null
example:
- "sample_R2.fastq"
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--bc_pattern"
alternatives:
- "-p"
description: "The UMI barcode pattern to use e.g. 'NNNNNN' indicates that the\
\ first 6 nucleotides \nof the read are from the UMI.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--bc_pattern2"
description: "The UMI barcode pattern to use for read 2."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Output"
arguments:
- type: "file"
name: "--output"
description: "Output file for read 1."
info: null
must_exist: true
create_parent: true
required: true
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--read2_out"
description: "Output file for read 2."
info: null
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--filtered_out"
description: "Write out reads not matching regex pattern or cell barcode whitelist\
\ to this file.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--filtered_out2"
description: "Write out read pairs not matching regex pattern or cell barcode\
\ whitelist to this file.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Extract Options"
arguments:
- type: "string"
name: "--extract_method"
description: "UMI pattern to use. Default: `string`.\n"
info: null
example:
- "string"
required: false
choices:
- "string"
- "regex"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--error_correct_cell"
description: "Error correct cell barcodes to the whitelist."
info: null
direction: "input"
- type: "file"
name: "--whitelist"
description: "Whitelist of accepted cell barcodes tab-separated format, where\
\ column 1 is the whitelisted\ncell barcodes and column 2 is the list (comma-separated)\
\ of other cell barcodes which should \nbe corrected to the barcode in column\
\ 1. If the --error_correct_cell option is not used, this\ncolumn will be ignored.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--blacklist"
description: "BlackWhitelist of cell barcodes to discard."
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--subset_reads"
description: "Only parse the first N reads."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--quality_filter_threshold"
description: "Remove reads where any UMI base quality score falls below this threshold."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--quality_filter_mask"
description: "If a UMI base has a quality below this threshold, replace the base\
\ with 'N'.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--quality_encoding"
description: "Quality score encoding. Choose from:\n * phred33 [33-77]\n * phred64\
\ [64-106]\n * solexa [59-106]\n"
info: null
required: false
choices:
- "phred33"
- "phred64"
- "solexa"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--reconcile_pairs"
description: "Allow read 2 infile to contain reads not in read 1 infile. This\
\ enables support for upstream protocols\nwhere read one contains cell barcodes,\
\ and the read pairs have been filtered and corrected without regard\nto the\
\ read2.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--three_prime"
alternatives:
- "--3prime"
description: "By default the barcode is assumed to be on the 5' end of the read,\
\ but use this option to sepecify that it is\non the 3' end instead. This option\
\ only works with --extract_method=string since 3' encoding can be specified\n\
explicitly with a regex, e.g `.*(?P<umi_1>.{5})$`.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--ignore_read_pair_suffixes"
description: "Ignore \"/1\" and \"/2\" read name suffixes. Note that this options\
\ is required if the suffixes are not whitespace\nseparated from the rest of\
\ the read name.\narguments:\n"
info: null
direction: "input"
- type: "string"
name: "--umi_separator"
description: "The character that separates the UMI in the read name. Most likely\
\ a colon if you skipped the extraction with\nUMI-tools and used other software.\
\ Default: `_`\n"
info: null
example:
- "_"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--grouping_method"
description: "Method to use to determine read groups by subsuming those with similar\
\ UMIs. All methods start by identifying\nthe reads with the same mapping position,\
\ but treat similar yet nonidentical UMIs differently. Default: `directional`\n"
info: null
example:
- "directional"
required: false
choices:
- "unique"
- "percentile"
- "cluster"
- "adjacency"
- "directional"
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--umi_discard_read"
description: "After UMI barcode extraction discard either R1 or R2 by setting\
\ this parameter to 1 or 2, respectively. Default: `0`\n"
info: null
example:
- 0
required: false
choices:
- 0
- 1
- 2
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Common Options"
arguments:
- type: "file"
name: "--log"
description: "File with logging information."
info: null
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--log2stderr"
description: "Send logging information to stderr."
info: null
direction: "output"
- type: "integer"
name: "--verbose"
description: "Log level. The higher, the more output."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--error"
description: "File with error information."
info: null
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--temp_dir"
description: "Directory for temporary files. If not set, the bash environmental\
\ variable TMPDIR is used.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--compresslevel"
description: "Level of Gzip compression to use. Default=6 matches GNU gzip rather\
\ than python gzip default (which is 9).\nDefault `6`.\n"
info: null
example:
- 6
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--timeit"
description: "Store timing information in file."
info: null
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--timeit_name"
description: "Name in timing file for this class of jobs."
info: null
default:
- "all"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--timeit_header"
description: "Add header for timing information."
info: null
direction: "input"
- type: "integer"
name: "--random_seed"
description: "Random seed to initialize number generator with."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
resources:
- type: "bash_script"
path: "script.sh"
is_executable: true
description: "Flexible removal of UMI sequences from fastq reads.\nUMIs are removed\
\ and appended to the read name. Any other barcode, for example a library barcode,\n\
is left on the read. Can also filter reads by quality or against a whitelist.\n"
test_resources:
- type: "bash_script"
path: "test.sh"
is_executable: true
- type: "file"
path: "test_data"
info: null
status: "enabled"
requirements:
commands:
- "ps"
keywords:
- "extract"
- "umi-tools"
- "umi"
- "fastq"
license: "MIT"
references:
doi:
- "10.1101/gr.209601.116"
links:
repository: "https://github.com/CGATOxford/UMI-tools"
homepage: "https://umi-tools.readthedocs.io/en/latest/"
documentation: "https://umi-tools.readthedocs.io/en/latest/reference/extract.html"
runners:
- type: "executable"
id: "executable"
docker_setup_strategy: "ifneedbepullelsecachedbuild"
- type: "nextflow"
id: "nextflow"
directives:
tag: "$id"
auto:
simplifyInput: true
simplifyOutput: false
transcript: false
publish: false
config:
labels:
mem1gb: "memory = 1000000000.B"
mem2gb: "memory = 2000000000.B"
mem5gb: "memory = 5000000000.B"
mem10gb: "memory = 10000000000.B"
mem20gb: "memory = 20000000000.B"
mem50gb: "memory = 50000000000.B"
mem100gb: "memory = 100000000000.B"
mem200gb: "memory = 200000000000.B"
mem500gb: "memory = 500000000000.B"
mem1tb: "memory = 1000000000000.B"
mem2tb: "memory = 2000000000000.B"
mem5tb: "memory = 5000000000000.B"
mem10tb: "memory = 10000000000000.B"
mem20tb: "memory = 20000000000000.B"
mem50tb: "memory = 50000000000000.B"
mem100tb: "memory = 100000000000000.B"
mem200tb: "memory = 200000000000000.B"
mem500tb: "memory = 500000000000000.B"
mem1gib: "memory = 1073741824.B"
mem2gib: "memory = 2147483648.B"
mem4gib: "memory = 4294967296.B"
mem8gib: "memory = 8589934592.B"
mem16gib: "memory = 17179869184.B"
mem32gib: "memory = 34359738368.B"
mem64gib: "memory = 68719476736.B"
mem128gib: "memory = 137438953472.B"
mem256gib: "memory = 274877906944.B"
mem512gib: "memory = 549755813888.B"
mem1tib: "memory = 1099511627776.B"
mem2tib: "memory = 2199023255552.B"
mem4tib: "memory = 4398046511104.B"
mem8tib: "memory = 8796093022208.B"
mem16tib: "memory = 17592186044416.B"
mem32tib: "memory = 35184372088832.B"
mem64tib: "memory = 70368744177664.B"
mem128tib: "memory = 140737488355328.B"
mem256tib: "memory = 281474976710656.B"
mem512tib: "memory = 562949953421312.B"
cpu1: "cpus = 1"
cpu2: "cpus = 2"
cpu5: "cpus = 5"
cpu10: "cpus = 10"
cpu20: "cpus = 20"
cpu50: "cpus = 50"
cpu100: "cpus = 100"
cpu200: "cpus = 200"
cpu500: "cpus = 500"
cpu1000: "cpus = 1000"
debug: false
container: "docker"
engines:
- type: "docker"
id: "docker"
image: "quay.io/biocontainers/umi_tools:1.1.4--py310h4b81fae_2"
target_registry: "images.viash-hub.com"
target_tag: "v0.2.0"
namespace_separator: "/"
setup:
- type: "docker"
run:
- "umi_tools -v | sed 's/ version//g' > /var/software_versions.txt\n"
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/umi_tools/umi_tools_extract/config.vsh.yaml"
runner: "nextflow"
engine: "docker|native"
output: "target/nextflow/umi_tools/umi_tools_extract"
executable: "target/nextflow/umi_tools/umi_tools_extract/main.nf"
viash_version: "0.9.0"
git_commit: "7e530218844c373048bc33de58f021b6460642e5"
git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
package_config:
name: "biobox"
version: "v0.2.0"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0"
source: "src"
target: "target"
config_mods:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
keywords:
- "bioinformatics"
- "modules"
- "sequencing"
license: "MIT"
organization: "vsh"
links:
repository: "https://github.com/viash-hub/biobox"
issue_tracker: "https://github.com/viash-hub/biobox/issues"

3983
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/umi_tools/umi_tools_extract/main.nf Normal file
View File

File diff suppressed because it is too large Load Diff

125
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/umi_tools/umi_tools_extract/nextflow.config Normal file
View File

@@ -0,0 +1,125 @@
manifest {
name = 'umi_tools/umi_tools_extract'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.2.0'
description = 'Flexible removal of UMI sequences from fastq reads.\nUMIs are removed and appended to the read name. Any other barcode, for example a library barcode,\nis left on the read. Can also filter reads by quality or against a whitelist.\n'
}
process.container = 'nextflow/bash:latest'
// detect tempdir
tempDir = java.nio.file.Paths.get(
System.getenv('NXF_TEMP') ?:
System.getenv('VIASH_TEMP') ?:
System.getenv('TEMPDIR') ?:
System.getenv('TMPDIR') ?:
'/tmp'
).toAbsolutePath()
profiles {
no_publish {
process {
withName: '.*' {
publishDir = [
enabled: false
]
}
}
}
mount_temp {
docker.temp = tempDir
podman.temp = tempDir
charliecloud.temp = tempDir
}
docker {
docker.enabled = true
// docker.userEmulation = true
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
podman {
podman.enabled = true
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
shifter {
shifter.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
}
charliecloud {
charliecloud.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
}
}
process{
withLabel: mem1gb { memory = 1000000000.B }
withLabel: mem2gb { memory = 2000000000.B }
withLabel: mem5gb { memory = 5000000000.B }
withLabel: mem10gb { memory = 10000000000.B }
withLabel: mem20gb { memory = 20000000000.B }
withLabel: mem50gb { memory = 50000000000.B }
withLabel: mem100gb { memory = 100000000000.B }
withLabel: mem200gb { memory = 200000000000.B }
withLabel: mem500gb { memory = 500000000000.B }
withLabel: mem1tb { memory = 1000000000000.B }
withLabel: mem2tb { memory = 2000000000000.B }
withLabel: mem5tb { memory = 5000000000000.B }
withLabel: mem10tb { memory = 10000000000000.B }
withLabel: mem20tb { memory = 20000000000000.B }
withLabel: mem50tb { memory = 50000000000000.B }
withLabel: mem100tb { memory = 100000000000000.B }
withLabel: mem200tb { memory = 200000000000000.B }
withLabel: mem500tb { memory = 500000000000000.B }
withLabel: mem1gib { memory = 1073741824.B }
withLabel: mem2gib { memory = 2147483648.B }
withLabel: mem4gib { memory = 4294967296.B }
withLabel: mem8gib { memory = 8589934592.B }
withLabel: mem16gib { memory = 17179869184.B }
withLabel: mem32gib { memory = 34359738368.B }
withLabel: mem64gib { memory = 68719476736.B }
withLabel: mem128gib { memory = 137438953472.B }
withLabel: mem256gib { memory = 274877906944.B }
withLabel: mem512gib { memory = 549755813888.B }
withLabel: mem1tib { memory = 1099511627776.B }
withLabel: mem2tib { memory = 2199023255552.B }
withLabel: mem4tib { memory = 4398046511104.B }
withLabel: mem8tib { memory = 8796093022208.B }
withLabel: mem16tib { memory = 17592186044416.B }
withLabel: mem32tib { memory = 35184372088832.B }
withLabel: mem64tib { memory = 70368744177664.B }
withLabel: mem128tib { memory = 140737488355328.B }
withLabel: mem256tib { memory = 281474976710656.B }
withLabel: mem512tib { memory = 562949953421312.B }
withLabel: cpu1 { cpus = 1 }
withLabel: cpu2 { cpus = 2 }
withLabel: cpu5 { cpus = 5 }
withLabel: cpu10 { cpus = 10 }
withLabel: cpu20 { cpus = 20 }
withLabel: cpu50 { cpus = 50 }
withLabel: cpu100 { cpus = 100 }
withLabel: cpu200 { cpus = 200 }
withLabel: cpu500 { cpus = 500 }
withLabel: cpu1000 { cpus = 1000 }
}

442
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/umi_tools/umi_tools_extract/nextflow_schema.json Normal file
View File

@@ -0,0 +1,442 @@
{
"$schema": "http://json-schema.org/draft-07/schema",
"title": "umi_tools_extract",
"description": "Flexible removal of UMI sequences from fastq reads.\nUMIs are removed and appended to the read name. Any other barcode, for example a library barcode,\nis left on the read. Can also filter reads by quality or against a whitelist.\n",
"type": "object",
"definitions": {
"input" : {
"title": "Input",
"type": "object",
"description": "No description",
"properties": {
"input": {
"type":
"string",
"description": "Type: `file`, required, example: `sample.fastq`. File containing the input data",
"help_text": "Type: `file`, required, example: `sample.fastq`. File containing the input data."
}
,
"read2_in": {
"type":
"string",
"description": "Type: `file`, example: `sample_R2.fastq`. File containing the input data for the R2 reads (if paired)",
"help_text": "Type: `file`, example: `sample_R2.fastq`. File containing the input data for the R2 reads (if paired). If provided, a \u003clist of other required arguments\u003e need to be provided."
}
,
"bc_pattern": {
"type":
"string",
"description": "Type: `string`. The UMI barcode pattern to use e",
"help_text": "Type: `string`. The UMI barcode pattern to use e.g. \u0027NNNNNN\u0027 indicates that the first 6 nucleotides \nof the read are from the UMI.\n"
}
,
"bc_pattern2": {
"type":
"string",
"description": "Type: `string`. The UMI barcode pattern to use for read 2",
"help_text": "Type: `string`. The UMI barcode pattern to use for read 2."
}
}
},
"output" : {
"title": "Output",
"type": "object",
"description": "No description",
"properties": {
"output": {
"type":
"string",
"description": "Type: `file`, required, default: `$id.$key.output.output`. Output file for read 1",
"help_text": "Type: `file`, required, default: `$id.$key.output.output`. Output file for read 1."
,
"default": "$id.$key.output.output"
}
,
"read2_out": {
"type":
"string",
"description": "Type: `file`, default: `$id.$key.read2_out.read2_out`. Output file for read 2",
"help_text": "Type: `file`, default: `$id.$key.read2_out.read2_out`. Output file for read 2."
,
"default": "$id.$key.read2_out.read2_out"
}
,
"filtered_out": {
"type":
"string",
"description": "Type: `file`. Write out reads not matching regex pattern or cell barcode whitelist to this file",
"help_text": "Type: `file`. Write out reads not matching regex pattern or cell barcode whitelist to this file.\n"
}
,
"filtered_out2": {
"type":
"string",
"description": "Type: `file`. Write out read pairs not matching regex pattern or cell barcode whitelist to this file",
"help_text": "Type: `file`. Write out read pairs not matching regex pattern or cell barcode whitelist to this file.\n"
}
}
},
"extract options" : {
"title": "Extract Options",
"type": "object",
"description": "No description",
"properties": {
"extract_method": {
"type":
"string",
"description": "Type: `string`, example: `string`, choices: ``string`, `regex``. UMI pattern to use",
"help_text": "Type: `string`, example: `string`, choices: ``string`, `regex``. UMI pattern to use. Default: `string`.\n",
"enum": ["string", "regex"]
}
,
"error_correct_cell": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Error correct cell barcodes to the whitelist",
"help_text": "Type: `boolean_true`, default: `false`. Error correct cell barcodes to the whitelist."
,
"default": "False"
}
,
"whitelist": {
"type":
"string",
"description": "Type: `file`. Whitelist of accepted cell barcodes tab-separated format, where column 1 is the whitelisted\ncell barcodes and column 2 is the list (comma-separated) of other cell barcodes which should \nbe corrected to the barcode in column 1",
"help_text": "Type: `file`. Whitelist of accepted cell barcodes tab-separated format, where column 1 is the whitelisted\ncell barcodes and column 2 is the list (comma-separated) of other cell barcodes which should \nbe corrected to the barcode in column 1. If the --error_correct_cell option is not used, this\ncolumn will be ignored.\n"
}
,
"blacklist": {
"type":
"string",
"description": "Type: `file`. BlackWhitelist of cell barcodes to discard",
"help_text": "Type: `file`. BlackWhitelist of cell barcodes to discard."
}
,
"subset_reads": {
"type":
"integer",
"description": "Type: `integer`. Only parse the first N reads",
"help_text": "Type: `integer`. Only parse the first N reads."
}
,
"quality_filter_threshold": {
"type":
"integer",
"description": "Type: `integer`. Remove reads where any UMI base quality score falls below this threshold",
"help_text": "Type: `integer`. Remove reads where any UMI base quality score falls below this threshold."
}
,
"quality_filter_mask": {
"type":
"string",
"description": "Type: `string`. If a UMI base has a quality below this threshold, replace the base with \u0027N\u0027",
"help_text": "Type: `string`. If a UMI base has a quality below this threshold, replace the base with \u0027N\u0027.\n"
}
,
"quality_encoding": {
"type":
"string",
"description": "Type: `string`, choices: ``phred33`, `phred64`, `solexa``. Quality score encoding",
"help_text": "Type: `string`, choices: ``phred33`, `phred64`, `solexa``. Quality score encoding. Choose from:\n * phred33 [33-77]\n * phred64 [64-106]\n * solexa [59-106]\n",
"enum": ["phred33", "phred64", "solexa"]
}
,
"reconcile_pairs": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Allow read 2 infile to contain reads not in read 1 infile",
"help_text": "Type: `boolean_true`, default: `false`. Allow read 2 infile to contain reads not in read 1 infile. This enables support for upstream protocols\nwhere read one contains cell barcodes, and the read pairs have been filtered and corrected without regard\nto the read2.\n"
,
"default": "False"
}
,
"three_prime": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. By default the barcode is assumed to be on the 5\u0027 end of the read, but use this option to sepecify that it is\non the 3\u0027 end instead",
"help_text": "Type: `boolean_true`, default: `false`. By default the barcode is assumed to be on the 5\u0027 end of the read, but use this option to sepecify that it is\non the 3\u0027 end instead. This option only works with --extract_method=string since 3\u0027 encoding can be specified\nexplicitly with a regex, e.g `.*(?P\u003cumi_1\u003e.{5})$`.\n"
,
"default": "False"
}
,
"ignore_read_pair_suffixes": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Ignore \"/1\" and \"/2\" read name suffixes",
"help_text": "Type: `boolean_true`, default: `false`. Ignore \"/1\" and \"/2\" read name suffixes. Note that this options is required if the suffixes are not whitespace\nseparated from the rest of the read name.\narguments:\n"
,
"default": "False"
}
,
"umi_separator": {
"type":
"string",
"description": "Type: `string`, example: `_`. The character that separates the UMI in the read name",
"help_text": "Type: `string`, example: `_`. The character that separates the UMI in the read name. Most likely a colon if you skipped the extraction with\nUMI-tools and used other software. Default: `_`\n"
}
,
"grouping_method": {
"type":
"string",
"description": "Type: `string`, example: `directional`, choices: ``unique`, `percentile`, `cluster`, `adjacency`, `directional``. Method to use to determine read groups by subsuming those with similar UMIs",
"help_text": "Type: `string`, example: `directional`, choices: ``unique`, `percentile`, `cluster`, `adjacency`, `directional``. Method to use to determine read groups by subsuming those with similar UMIs. All methods start by identifying\nthe reads with the same mapping position, but treat similar yet nonidentical UMIs differently. Default: `directional`\n",
"enum": ["unique", "percentile", "cluster", "adjacency", "directional"]
}
,
"umi_discard_read": {
"type":
"integer",
"description": "Type: `integer`, example: `0`, choices: ``0`, `1`, `2``. After UMI barcode extraction discard either R1 or R2 by setting this parameter to 1 or 2, respectively",
"help_text": "Type: `integer`, example: `0`, choices: ``0`, `1`, `2``. After UMI barcode extraction discard either R1 or R2 by setting this parameter to 1 or 2, respectively. Default: `0`\n",
"enum": [0, 1, 2]
}
}
},
"common options" : {
"title": "Common Options",
"type": "object",
"description": "No description",
"properties": {
"log": {
"type":
"string",
"description": "Type: `file`, default: `$id.$key.log.log`. File with logging information",
"help_text": "Type: `file`, default: `$id.$key.log.log`. File with logging information."
,
"default": "$id.$key.log.log"
}
,
"log2stderr": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Send logging information to stderr",
"help_text": "Type: `boolean_true`, default: `false`. Send logging information to stderr."
,
"default": "False"
}
,
"verbose": {
"type":
"integer",
"description": "Type: `integer`. Log level",
"help_text": "Type: `integer`. Log level. The higher, the more output."
}
,
"error": {
"type":
"string",
"description": "Type: `file`, default: `$id.$key.error.error`. File with error information",
"help_text": "Type: `file`, default: `$id.$key.error.error`. File with error information."
,
"default": "$id.$key.error.error"
}
,
"temp_dir": {
"type":
"string",
"description": "Type: `string`. Directory for temporary files",
"help_text": "Type: `string`. Directory for temporary files. If not set, the bash environmental variable TMPDIR is used.\n"
}
,
"compresslevel": {
"type":
"integer",
"description": "Type: `integer`, example: `6`. Level of Gzip compression to use",
"help_text": "Type: `integer`, example: `6`. Level of Gzip compression to use. Default=6 matches GNU gzip rather than python gzip default (which is 9).\nDefault `6`.\n"
}
,
"timeit": {
"type":
"string",
"description": "Type: `file`, default: `$id.$key.timeit.timeit`. Store timing information in file",
"help_text": "Type: `file`, default: `$id.$key.timeit.timeit`. Store timing information in file."
,
"default": "$id.$key.timeit.timeit"
}
,
"timeit_name": {
"type":
"string",
"description": "Type: `string`, default: `all`. Name in timing file for this class of jobs",
"help_text": "Type: `string`, default: `all`. Name in timing file for this class of jobs."
,
"default": "all"
}
,
"timeit_header": {
"type":
"boolean",
"description": "Type: `boolean_true`, default: `false`. Add header for timing information",
"help_text": "Type: `boolean_true`, default: `false`. Add header for timing information."
,
"default": "False"
}
,
"random_seed": {
"type":
"integer",
"description": "Type: `integer`. Random seed to initialize number generator with",
"help_text": "Type: `integer`. Random seed to initialize number generator with."
}
}
},
"nextflow input-output arguments" : {
"title": "Nextflow input-output arguments",
"type": "object",
"description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
"properties": {
"publish_dir": {
"type":
"string",
"description": "Type: `string`, required, example: `output/`. Path to an output directory",
"help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
}
,
"param_list": {
"type":
"string",
"description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
"help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
"hidden": true
}
}
}
},
"allOf": [
{
"$ref": "#/definitions/input"
},
{
"$ref": "#/definitions/output"
},
{
"$ref": "#/definitions/extract options"
},
{
"$ref": "#/definitions/common options"
},
{
"$ref": "#/definitions/nextflow input-output arguments"
}
]
}

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

@@ -238,8 +238,8 @@ build_info:
output: "target/executable/bbmap_bbsplit"
executable: "target/executable/bbmap_bbsplit/bbmap_bbsplit"
viash_version: "0.9.0"
git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
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="2024-09-14T08:49:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:01:50Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
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="2024-09-14T08:49:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:01:51Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
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="2024-09-14T08:49:10Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:01:59Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

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

@@ -30,7 +30,7 @@ argument_groups:
description: "Concatenated read 1 fastq"
info: null
default:
- "$id.read_1.merged.fastq"
- "$id_r1.fastq"
must_exist: true
create_parent: true
required: false
@@ -42,7 +42,7 @@ argument_groups:
description: "Concatenated read 2 fastq"
info: null
default:
- "$id.read_2.merged.fastq"
- "$id_r2.fastq"
must_exist: false
create_parent: true
required: false
@@ -169,8 +169,8 @@ build_info:
output: "target/executable/cat_fastq"
executable: "target/executable/cat_fastq/cat_fastq"
viash_version: "0.9.0"
git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

14
target/executable/cat_fastq/cat_fastq
View File

@@ -187,12 +187,12 @@ function ViashHelp {
echo "Output:"
echo " --fastq_1"
echo " type: file, output, file must exist"
echo " default: \$id.read_1.merged.fastq"
echo " default: \$id_r1.fastq"
echo " Concatenated read 1 fastq"
echo ""
echo " --fastq_2"
echo " type: file, output"
echo " default: \$id.read_2.merged.fastq"
echo " default: \$id_r2.fastq"
echo " Concatenated read 2 fastq"
}
@@ -472,9 +472,9 @@ function ViashDockerfile {
FROM ubuntu:22.04
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component cat_fastq"
LABEL org.opencontainers.image.created="2024-09-14T08:49:11Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:01:59Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -869,10 +869,10 @@ fi
# filling in defaults
if [ -z ${VIASH_PAR_FASTQ_1+x} ]; then
VIASH_PAR_FASTQ_1="\$id.read_1.merged.fastq"
VIASH_PAR_FASTQ_1="\$id_r1.fastq"
fi
if [ -z ${VIASH_PAR_FASTQ_2+x} ]; then
VIASH_PAR_FASTQ_2="\$id.read_2.merged.fastq"
VIASH_PAR_FASTQ_2="\$id_r2.fastq"
fi
# check whether required files exist

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

@@ -237,8 +237,8 @@ build_info:
output: "target/executable/deseq2_qc"
executable: "target/executable/deseq2_qc/deseq2_qc"
viash_version: "0.9.0"
git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
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="2024-09-14T08:49:21Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:10Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
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="2024-09-14T08:49:12Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:01Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

18
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="2024-09-14T08:49:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:01:52Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -1200,13 +1200,15 @@ fastqc -o \$tmpdir \${input[*]}
file1=\$(basename -- "\${input[0]}")
read1="\${file1%.fastq*}"
file2=\$(basename -- "\${input[1]}")
read2="\${file2%.fastq*}"
[[ -e "\${tmpdir}/\${read1}_fastqc.html" ]] && cp "\${tmpdir}/\${read1}_fastqc.html" \$par_fastqc_html_1
[[ -e "\${tmpdir}/\${read2}_fastqc.html" ]] && cp "\${tmpdir}/\${read2}_fastqc.html" \$par_fastqc_html_2
[[ -e "\${tmpdir}/\${read1}_fastqc.zip" ]] && cp "\${tmpdir}/\${read1}_fastqc.zip" \$par_fastqc_zip_1
[[ -e "\${tmpdir}/\${read2}_fastqc.zip" ]] && cp "\${tmpdir}/\${read2}_fastqc.zip" \$par_fastqc_zip_2
if \$par_paired; then
file2=\$(basename -- "\${input[1]}")
read2="\${file2%.fastq*}"
[[ -e "\${tmpdir}/\${read2}_fastqc.html" ]] && cp "\${tmpdir}/\${read2}_fastqc.html" \$par_fastqc_html_2
[[ -e "\${tmpdir}/\${read2}_fastqc.zip" ]] && cp "\${tmpdir}/\${read2}_fastqc.zip" \$par_fastqc_zip_2
fi
VIASHMAIN
bash "\$tempscript" &
wait "\$!"

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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
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="2024-09-14T08:49:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:01:51Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
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="2024-09-14T08:49:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:01:52Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
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="2024-09-14T08:49:16Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
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="2024-09-14T08:49:19Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:09Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
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="2024-09-14T08:49:05Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:01:52Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
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="2024-09-14T08:49:18Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:07Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

17
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="2024-09-14T08:49:17Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:07Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -1319,16 +1319,7 @@ if [[ "\$par_extra_args" != *"--fr-stranded"* ]] && [[ "\$par_extra_args" != *"-
fi
mkdir -p \$par_output
echo "kallisto quant \\
\${meta_cpus:+--threads \$meta_cpus} \\
--index \$par_index \\
\${par_gtf:+--gtf \$par_gtf} \\
\${par_chromosomes:+--chromosomes \$par_chromosomes} \\
\$single_end_params \\
\$strandedness \\
\$par_extra_args \\
-o \$par_output \\
\${input[*]} 2> >(tee -a \${par_output}/kallisto_quant.log >&2)"
kallisto quant \\
\${meta_cpus:+--threads \$meta_cpus} \\
--index \$par_index \\

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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
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="2024-09-14T08:49:12Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:01Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
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="2024-09-14T08:49:20Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:09Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

13
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="2024-09-14T08:49:16Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:05Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -2287,6 +2287,8 @@ IFS="," read -ra rsem_multiqc <<< \$par_rsem_multiqc && for file in "\${rsem_mul
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
IFS="," read -ra samtools_flagstat <<< \$par_samtools_flagstat && for file in "\${samtools_flagstat[@]}"; do [ -e "\$file" ] && cp -r "\$file" \$par_output/; done
@@ -2295,12 +2297,9 @@ 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
IFS="," read -ra featurecounts_rrna_multiqc <<< \$par_featurecounts_rrna_multiqc && for file in "\${featurecounts_rrna_multiqc[@]}"; do [ -e "\$file" ] && cp -r "\$file" "\$par_output/"; done
[ -e "\$par_aligner_pca_multiqc" ] && cp -r "\$par_aligner_pca_multiqc" "\$par_output/"

4
target/executable/preprocess_transcripts_fasta/.config.vsh.yaml
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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
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="2024-09-14T08:49:15Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
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="2024-09-14T08:49:05Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:01:53Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
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="2024-09-14T08:49:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:01:51Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

13
target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml
View File

@@ -60,15 +60,6 @@ argument_groups:
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--versions"
info: null
must_exist: false
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Output"
arguments:
- type: "file"
@@ -308,8 +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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

39
target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression
View File

@@ -201,9 +201,6 @@ function ViashHelp {
echo " type: string"
echo " Extra rsem-calculate-expression arguments in addition to the defaults."
echo ""
echo " --versions"
echo " type: file"
echo ""
echo "Output:"
echo " --counts_gene"
echo " type: file, output, file must exist"
@@ -545,9 +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="2024-09-14T08:49:17Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -759,17 +756,6 @@ while [[ $# -gt 0 ]]; do
VIASH_PAR_EXTRA_ARGS=$(ViashRemoveFlags "$1")
shift 1
;;
--versions)
[ -n "$VIASH_PAR_VERSIONS" ] && ViashError Bad arguments for option \'--versions\': \'$VIASH_PAR_VERSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_VERSIONS="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --versions. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--versions=*)
[ -n "$VIASH_PAR_VERSIONS" ] && ViashError Bad arguments for option \'--versions=*\': \'$VIASH_PAR_VERSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_VERSIONS=$(ViashRemoveFlags "$1")
shift 1
;;
--counts_gene)
[ -n "$VIASH_PAR_COUNTS_GENE" ] && ViashError Bad arguments for option \'--counts_gene\': \'$VIASH_PAR_COUNTS_GENE\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_COUNTS_GENE="$2"
@@ -1205,10 +1191,6 @@ if [ ! -z "$VIASH_PAR_INDEX" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_INDEX")" )
VIASH_PAR_INDEX=$(ViashDockerAutodetectMount "$VIASH_PAR_INDEX")
fi
if [ ! -z "$VIASH_PAR_VERSIONS" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_VERSIONS")" )
VIASH_PAR_VERSIONS=$(ViashDockerAutodetectMount "$VIASH_PAR_VERSIONS")
fi
if [ ! -z "$VIASH_PAR_COUNTS_GENE" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_COUNTS_GENE")" )
VIASH_PAR_COUNTS_GENE=$(ViashDockerAutodetectMount "$VIASH_PAR_COUNTS_GENE")
@@ -1319,7 +1301,6 @@ $( if [ ! -z ${VIASH_PAR_PAIRED+x} ]; then echo "${VIASH_PAR_PAIRED}" | sed "s#'
$( if [ ! -z ${VIASH_PAR_INPUT+x} ]; then echo "${VIASH_PAR_INPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_input='&'#" ; else echo "# par_input="; fi )
$( if [ ! -z ${VIASH_PAR_INDEX+x} ]; then echo "${VIASH_PAR_INDEX}" | sed "s#'#'\"'\"'#g;s#.*#par_index='&'#" ; else echo "# par_index="; fi )
$( if [ ! -z ${VIASH_PAR_EXTRA_ARGS+x} ]; then echo "${VIASH_PAR_EXTRA_ARGS}" | sed "s#'#'\"'\"'#g;s#.*#par_extra_args='&'#" ; else echo "# par_extra_args="; fi )
$( if [ ! -z ${VIASH_PAR_VERSIONS+x} ]; then echo "${VIASH_PAR_VERSIONS}" | sed "s#'#'\"'\"'#g;s#.*#par_versions='&'#" ; else echo "# par_versions="; fi )
$( if [ ! -z ${VIASH_PAR_COUNTS_GENE+x} ]; then echo "${VIASH_PAR_COUNTS_GENE}" | sed "s#'#'\"'\"'#g;s#.*#par_counts_gene='&'#" ; else echo "# par_counts_gene="; fi )
$( if [ ! -z ${VIASH_PAR_COUNTS_TRANSCRIPTS+x} ]; then echo "${VIASH_PAR_COUNTS_TRANSCRIPTS}" | sed "s#'#'\"'\"'#g;s#.*#par_counts_transcripts='&'#" ; else echo "# par_counts_transcripts="; fi )
$( if [ ! -z ${VIASH_PAR_STAT+x} ]; then echo "${VIASH_PAR_STAT}" | sed "s#'#'\"'\"'#g;s#.*#par_stat='&'#" ; else echo "# par_stat="; fi )
@@ -1368,10 +1349,10 @@ fi
IFS="," read -ra input <<< \$par_input
INDEX=\`find -L \$meta_resources_dir/ -name "*.grp" | sed 's/\\.grp\$//'\`
INDEX=\`find -L \$par_index/ -name "*.grp" | sed 's/\\.grp\$//'\`
rsem-calculate-expression \\
\${meta_cpus:+--num-theads \$meta_cpus} \\
\${meta_cpus:+--num-threads \$meta_cpus} \\
\$strandedness \\
\${par_paired:+--paired-end} \\
\$par_extra_args \\
@@ -1379,6 +1360,13 @@ rsem-calculate-expression \\
\$INDEX \\
\$par_id
[[ -e "\${par_id}.genes.results" ]] && mv "\${par_id}.genes.results" \$par_counts_gene
[[ -e "\${par_id}id.isoforms.results" ]] && mv "\${par_id}id.isoforms.results" \$par_counts_transcripts
[[ -e "\${par_id}.stat" ]] && mv -r "\${par_id}.stat" \$par_stat
# [[ -e "\${par_id}.log" ]] && mv "\${par_id}.log" \$par_logs
[[ -e "\${par_id}.STAR.genome.bam" ]] && mv "\${par_id}.STAR.genome.bam" \$par_bam_star
[[ -e "\${par_id}.genome.bam" ]] && mv "\${par_id}.genome.bam" \$par_bam_genome
[[ -e "\${par_id}.transcript.bam" ]] && mv "\${par_id}.transcript.bam" \$par_bam_transcript
VIASHMAIN
bash "\$tempscript" &
wait "\$!"
@@ -1405,9 +1393,6 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
if [ ! -z "$VIASH_PAR_INDEX" ]; then
VIASH_PAR_INDEX=$(ViashDockerStripAutomount "$VIASH_PAR_INDEX")
fi
if [ ! -z "$VIASH_PAR_VERSIONS" ]; then
VIASH_PAR_VERSIONS=$(ViashDockerStripAutomount "$VIASH_PAR_VERSIONS")
fi
if [ ! -z "$VIASH_PAR_COUNTS_GENE" ]; then
VIASH_PAR_COUNTS_GENE=$(ViashDockerStripAutomount "$VIASH_PAR_COUNTS_GENE")
fi

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

@@ -24,15 +24,6 @@ argument_groups:
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--versions"
info: null
must_exist: false
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Output"
arguments:
- type: "file"
@@ -83,17 +74,6 @@ argument_groups:
direction: "output"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--updated_versions"
info: null
default:
- "versions.yml"
must_exist: true
create_parent: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
resources:
- type: "bash_script"
path: "script.sh"
@@ -202,8 +182,8 @@ build_info:
output: "target/executable/rsem/rsem_merge_counts"
executable: "target/executable/rsem/rsem_merge_counts/rsem_merge_counts"
viash_version: "0.9.0"
git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

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

@@ -185,9 +185,6 @@ function ViashHelp {
echo " type: file, file must exist"
echo " Expression counts on transcript level (isoforms)"
echo ""
echo " --versions"
echo " type: file"
echo ""
echo "Output:"
echo " --merged_gene_counts"
echo " type: file, output, file must exist"
@@ -208,10 +205,6 @@ function ViashHelp {
echo " type: file, output, file must exist"
echo " default: rsem.merged.transcript_tpm.tsv"
echo " File containing transcript TPM across all samples."
echo ""
echo " --updated_versions"
echo " type: file, output, file must exist"
echo " default: versions.yml"
}
# initialise variables
@@ -490,9 +483,9 @@ function ViashDockerfile {
FROM ubuntu:22.04
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_merge_counts"
LABEL org.opencontainers.image.created="2024-09-14T08:49:17Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -654,17 +647,6 @@ while [[ $# -gt 0 ]]; do
VIASH_PAR_COUNTS_TRANSCRIPTS=$(ViashRemoveFlags "$1")
shift 1
;;
--versions)
[ -n "$VIASH_PAR_VERSIONS" ] && ViashError Bad arguments for option \'--versions\': \'$VIASH_PAR_VERSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_VERSIONS="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --versions. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--versions=*)
[ -n "$VIASH_PAR_VERSIONS" ] && ViashError Bad arguments for option \'--versions=*\': \'$VIASH_PAR_VERSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_VERSIONS=$(ViashRemoveFlags "$1")
shift 1
;;
--merged_gene_counts)
[ -n "$VIASH_PAR_MERGED_GENE_COUNTS" ] && ViashError Bad arguments for option \'--merged_gene_counts\': \'$VIASH_PAR_MERGED_GENE_COUNTS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_MERGED_GENE_COUNTS="$2"
@@ -709,17 +691,6 @@ while [[ $# -gt 0 ]]; do
VIASH_PAR_MERGED_TRANSCRIPT_TPM=$(ViashRemoveFlags "$1")
shift 1
;;
--updated_versions)
[ -n "$VIASH_PAR_UPDATED_VERSIONS" ] && ViashError Bad arguments for option \'--updated_versions\': \'$VIASH_PAR_UPDATED_VERSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_UPDATED_VERSIONS="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --updated_versions. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--updated_versions=*)
[ -n "$VIASH_PAR_UPDATED_VERSIONS" ] && ViashError Bad arguments for option \'--updated_versions=*\': \'$VIASH_PAR_UPDATED_VERSIONS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_UPDATED_VERSIONS=$(ViashRemoveFlags "$1")
shift 1
;;
---engine)
VIASH_ENGINE_ID="$2"
shift 2
@@ -930,9 +901,6 @@ fi
if [ -z ${VIASH_PAR_MERGED_TRANSCRIPT_TPM+x} ]; then
VIASH_PAR_MERGED_TRANSCRIPT_TPM="rsem.merged.transcript_tpm.tsv"
fi
if [ -z ${VIASH_PAR_UPDATED_VERSIONS+x} ]; then
VIASH_PAR_UPDATED_VERSIONS="versions.yml"
fi
# check whether required files exist
if [ ! -z "$VIASH_PAR_COUNTS_GENE" ] && [ ! -e "$VIASH_PAR_COUNTS_GENE" ]; then
@@ -1031,9 +999,6 @@ fi
if [ ! -z "$VIASH_PAR_MERGED_TRANSCRIPT_TPM" ] && [ ! -d "$(dirname "$VIASH_PAR_MERGED_TRANSCRIPT_TPM")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_MERGED_TRANSCRIPT_TPM")"
fi
if [ ! -z "$VIASH_PAR_UPDATED_VERSIONS" ] && [ ! -d "$(dirname "$VIASH_PAR_UPDATED_VERSIONS")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_UPDATED_VERSIONS")"
fi
if [ "$VIASH_ENGINE_ID" == "native" ] ; then
if [ "$VIASH_MODE" == "run" ]; then
@@ -1055,10 +1020,6 @@ if [ ! -z "$VIASH_PAR_COUNTS_TRANSCRIPTS" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_COUNTS_TRANSCRIPTS")" )
VIASH_PAR_COUNTS_TRANSCRIPTS=$(ViashDockerAutodetectMount "$VIASH_PAR_COUNTS_TRANSCRIPTS")
fi
if [ ! -z "$VIASH_PAR_VERSIONS" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_VERSIONS")" )
VIASH_PAR_VERSIONS=$(ViashDockerAutodetectMount "$VIASH_PAR_VERSIONS")
fi
if [ ! -z "$VIASH_PAR_MERGED_GENE_COUNTS" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_MERGED_GENE_COUNTS")" )
VIASH_PAR_MERGED_GENE_COUNTS=$(ViashDockerAutodetectMount "$VIASH_PAR_MERGED_GENE_COUNTS")
@@ -1079,11 +1040,6 @@ if [ ! -z "$VIASH_PAR_MERGED_TRANSCRIPT_TPM" ]; then
VIASH_PAR_MERGED_TRANSCRIPT_TPM=$(ViashDockerAutodetectMount "$VIASH_PAR_MERGED_TRANSCRIPT_TPM")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_MERGED_TRANSCRIPT_TPM" )
fi
if [ ! -z "$VIASH_PAR_UPDATED_VERSIONS" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_UPDATED_VERSIONS")" )
VIASH_PAR_UPDATED_VERSIONS=$(ViashDockerAutodetectMount "$VIASH_PAR_UPDATED_VERSIONS")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_UPDATED_VERSIONS" )
fi
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_RESOURCES_DIR")" )
VIASH_META_RESOURCES_DIR=$(ViashDockerAutodetectMount "$VIASH_META_RESOURCES_DIR")
@@ -1155,12 +1111,10 @@ cat > "\$tempscript" << 'VIASHMAIN'
# The following code has been auto-generated by Viash.
$( if [ ! -z ${VIASH_PAR_COUNTS_GENE+x} ]; then echo "${VIASH_PAR_COUNTS_GENE}" | sed "s#'#'\"'\"'#g;s#.*#par_counts_gene='&'#" ; else echo "# par_counts_gene="; fi )
$( if [ ! -z ${VIASH_PAR_COUNTS_TRANSCRIPTS+x} ]; then echo "${VIASH_PAR_COUNTS_TRANSCRIPTS}" | sed "s#'#'\"'\"'#g;s#.*#par_counts_transcripts='&'#" ; else echo "# par_counts_transcripts="; fi )
$( if [ ! -z ${VIASH_PAR_VERSIONS+x} ]; then echo "${VIASH_PAR_VERSIONS}" | sed "s#'#'\"'\"'#g;s#.*#par_versions='&'#" ; else echo "# par_versions="; fi )
$( if [ ! -z ${VIASH_PAR_MERGED_GENE_COUNTS+x} ]; then echo "${VIASH_PAR_MERGED_GENE_COUNTS}" | sed "s#'#'\"'\"'#g;s#.*#par_merged_gene_counts='&'#" ; else echo "# par_merged_gene_counts="; fi )
$( if [ ! -z ${VIASH_PAR_MERGED_GENE_TPM+x} ]; then echo "${VIASH_PAR_MERGED_GENE_TPM}" | sed "s#'#'\"'\"'#g;s#.*#par_merged_gene_tpm='&'#" ; else echo "# par_merged_gene_tpm="; fi )
$( if [ ! -z ${VIASH_PAR_MERGED_TRANSCRIPT_COUNTS+x} ]; then echo "${VIASH_PAR_MERGED_TRANSCRIPT_COUNTS}" | sed "s#'#'\"'\"'#g;s#.*#par_merged_transcript_counts='&'#" ; else echo "# par_merged_transcript_counts="; fi )
$( if [ ! -z ${VIASH_PAR_MERGED_TRANSCRIPT_TPM+x} ]; then echo "${VIASH_PAR_MERGED_TRANSCRIPT_TPM}" | sed "s#'#'\"'\"'#g;s#.*#par_merged_transcript_tpm='&'#" ; else echo "# par_merged_transcript_tpm="; fi )
$( if [ ! -z ${VIASH_PAR_UPDATED_VERSIONS+x} ]; then echo "${VIASH_PAR_UPDATED_VERSIONS}" | sed "s#'#'\"'\"'#g;s#.*#par_updated_versions='&'#" ; else echo "# par_updated_versions="; fi )
$( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
$( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi )
$( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi )
@@ -1225,9 +1179,6 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
if [ ! -z "$VIASH_PAR_COUNTS_TRANSCRIPTS" ]; then
VIASH_PAR_COUNTS_TRANSCRIPTS=$(ViashDockerStripAutomount "$VIASH_PAR_COUNTS_TRANSCRIPTS")
fi
if [ ! -z "$VIASH_PAR_VERSIONS" ]; then
VIASH_PAR_VERSIONS=$(ViashDockerStripAutomount "$VIASH_PAR_VERSIONS")
fi
if [ ! -z "$VIASH_PAR_MERGED_GENE_COUNTS" ]; then
VIASH_PAR_MERGED_GENE_COUNTS=$(ViashDockerStripAutomount "$VIASH_PAR_MERGED_GENE_COUNTS")
fi
@@ -1240,9 +1191,6 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
if [ ! -z "$VIASH_PAR_MERGED_TRANSCRIPT_TPM" ]; then
VIASH_PAR_MERGED_TRANSCRIPT_TPM=$(ViashDockerStripAutomount "$VIASH_PAR_MERGED_TRANSCRIPT_TPM")
fi
if [ ! -z "$VIASH_PAR_UPDATED_VERSIONS" ]; then
VIASH_PAR_UPDATED_VERSIONS=$(ViashDockerStripAutomount "$VIASH_PAR_UPDATED_VERSIONS")
fi
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR")
fi
@@ -1275,10 +1223,6 @@ if [ ! -z "$VIASH_PAR_MERGED_TRANSCRIPT_TPM" ] && [ ! -e "$VIASH_PAR_MERGED_TRAN
ViashError "Output file '$VIASH_PAR_MERGED_TRANSCRIPT_TPM' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_UPDATED_VERSIONS" ] && [ ! -e "$VIASH_PAR_UPDATED_VERSIONS" ]; then
ViashError "Output file '$VIASH_PAR_UPDATED_VERSIONS' does not exist."
exit 1
fi
exit 0

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

@@ -163,8 +163,8 @@ build_info:
output: "target/executable/rseqc/rseqc_bamstat"
executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat"
viash_version: "0.9.0"
git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
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="2024-09-14T08:49:15Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
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="2024-09-14T08:49:13Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:01Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
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="2024-09-14T08:49:14Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
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="2024-09-14T08:49:14Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
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="2024-09-14T08:49:14Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
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="2024-09-14T08:49:15Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:04Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
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="2024-09-14T08:49:13Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:02Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
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="2024-09-14T08:49:13Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:02Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
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="2024-09-14T08:49:19Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:09Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
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="2024-09-14T08:49:16Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:06Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
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: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
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="2024-09-14T08:49:20Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
LABEL org.opencontainers.image.created="2024-10-01T10:02:10Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

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

@@ -540,7 +540,7 @@ argument_groups:
\ files (paired-end) are specified, but not for longer lists."
info: null
example:
- "read_1.fastq"
- "read_1.fastq.gz"
must_exist: true
create_parent: true
required: false
@@ -553,7 +553,7 @@ argument_groups:
\ files (paired-end) are specified, but not for longer lists."
info: null
example:
- "read_2.fastq"
- "read_2.fastq.gz"
must_exist: true
create_parent: true
required: false
@@ -788,8 +788,8 @@ build_info:
output: "target/executable/trimgalore"
executable: "target/executable/trimgalore/trimgalore"
viash_version: "0.9.0"
git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
package_config:
version: "main"
info:

Some files were not shown because too many files have changed in this diff Show More