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Build branch main with version main (4adb388)

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Build pipeline: viash-hub.rnaseq.main-c9pqm

Source commit: 4adb388c7d

Source message: Merge pull request #29 from viash-hub/add-labels

Add labels (and then some)
This commit is contained in:
CI
2024-12-05 08:52:37 +00:00
parent b649544267
commit d69226987e
371 changed files with 11102 additions and 6497 deletions
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2
_viash.yaml
View File

@@ -12,7 +12,9 @@ info:
config_mods: | config_mods: |
.requirements.commands := ['ps'] .requirements.commands := ['ps']
.resources += {path: '/src/workflows/utils/labels.config', dest: 'nextflow_labels.config'}
.runners[.type == 'nextflow'].directives.tag := '$id' .runners[.type == 'nextflow'].directives.tag := '$id'
.runners[.type == 'nextflow'].config.script := 'includeConfig("nextflow_labels.config")'
repositories: repositories:
- name: biobox - name: biobox

27
nextflow.config
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@@ -1,27 +1,6 @@
// template nextflow.config for nested workflows
manifest { manifest {
nextflowVersion = '!>=20.12.1-edge' nextflowVersion = '!>=20.12.1-edge'
homePage = 'https://github.com/viash-hub/rnaseq'
description = 'Bulk RNAseq pipeline'
mainScript = 'target/nextflow/workflows/rnaseq/main.nf'
} }
docker {
fixOwnership = true
}
// TODO 1: unquote and adapt `rootDir` according to relative path within project
// params {
// rootDir = "$projectDir/../.."
// }
//
// workflowDir = "${params.rootDir}/workflows"
// targetDir = "${params.rootDir}/target/nextflow"
// TODO 2: insert custom imports here
// TODO 3: unquote
// docker {
// runOptions = "-v \$(realpath ${params.rootDir}):\$(realpath ${params.rootDir})"
// }

2
src/bedtools_genomecov/config.vsh.yaml
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@@ -53,4 +53,4 @@ engines:
chmod a+x /usr/local/bin/bedtools chmod a+x /usr/local/bin/bedtools
runners: runners:
- type: executable - type: executable
- type: nextflow - type: nextflow

2
src/cat_additional_fasta/config.vsh.yaml
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@@ -51,4 +51,4 @@ engines:
image: python image: python
runners: runners:
- type: executable - type: executable
- type: nextflow - type: nextflow

2
src/cat_fastq/config.vsh.yaml
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@@ -51,4 +51,4 @@ engines:
image: ubuntu:22.04 image: ubuntu:22.04
runners: runners:
- type: executable - type: executable
- type: nextflow - type: nextflow

2
src/getchromsizes/config.vsh.yaml
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@@ -54,4 +54,4 @@ engines:
make install make install
runners: runners:
- type: executable - type: executable
- type: nextflow - type: nextflow

2
src/gtf_filter/config.vsh.yaml
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@@ -42,4 +42,4 @@ engines:
image: python image: python
runners: runners:
- type: executable - type: executable
- type: nextflow - type: nextflow

2
src/picard_markduplicates/config.vsh.yaml
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@@ -66,4 +66,4 @@ engines:
env: [ PICARD=/usr/local/bin/picard.jar ] env: [ PICARD=/usr/local/bin/picard.jar ]
runners: runners:
- type: executable - type: executable
- type: nextflow - type: nextflow

9
src/prepare_multiqc_input/config.vsh.yaml
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@@ -125,7 +125,8 @@ argument_groups:
multiple_sep: "," multiple_sep: ","
- name: "--multiqc_config" - name: "--multiqc_config"
type: file type: file
description: |
Custom multiqc configuration file
- name: "Ouput" - name: "Ouput"
arguments: arguments:
@@ -133,14 +134,16 @@ argument_groups:
type: file type: file
direction: output direction: output
default: multiqc_input default: multiqc_input
resources: resources:
- type: bash_script - type: bash_script
path: script.sh path: script.sh
- path: /src/assets/multiqc_config.yml
engines: engines:
- type: docker - type: docker
image: ubuntu:22.04 image: ubuntu:22.04
runners: runners:
- type: executable - type: executable
- type: nextflow - type: nextflow

18
src/prepare_multiqc_input/script.sh
View File

@@ -70,4 +70,20 @@ IFS="," read -ra readduplication_multiqc <<< $par_readduplication_multiqc && for
IFS="," read -ra tin_multiqc <<< $par_tin_multiqc && for file in "${tin_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done IFS="," read -ra tin_multiqc <<< $par_tin_multiqc && for file in "${tin_multiqc[@]}"; do [ -e "$file" ] && cp -r "$file" "$par_output/"; done
[ -e "$par_multiqc_config" ] && cp -r $par_multiqc_config "$par_output/" echo "Checking for custom multiqc_config"
# If the variable is empty, we use the default one (registered as a resource)
if [ -z $par_multiqc_config ]; then
echo "No multiqc_config provided, using the default"
cp $meta_resources_dir/multiqc_config.yml "$par_output"
else
echo "Optional file provided"
if [ -f $par_multiqc_config ]; then
cp $par_multiqc_config "$par_output"/multiqc_config.yml
else
# Unreachable: the Viash-generated module checks this
echo "Optional file does not exist"
exit 1
fi
fi
echo "Done"

2
src/rseqc/rseqc_junctionannotation/config.vsh.yaml
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@@ -105,4 +105,4 @@ engines:
packages: [ RSeQC ] packages: [ RSeQC ]
runners: runners:
- type: executable - type: executable
- type: nextflow - type: nextflow

2
src/rseqc/rseqc_junctionsaturation/config.vsh.yaml
View File

@@ -102,4 +102,4 @@ engines:
packages: [ RSeQC ] packages: [ RSeQC ]
runners: runners:
- type: executable - type: executable
- type: nextflow - type: nextflow

2
src/rseqc/rseqc_readdistribution/config.vsh.yaml
View File

@@ -49,4 +49,4 @@ engines:
packages: [ RSeQC ] packages: [ RSeQC ]
runners: runners:
- type: executable - type: executable
- type: nextflow - type: nextflow

2
src/rseqc/rseqc_readduplication/config.vsh.yaml
View File

@@ -79,4 +79,4 @@ engines:
packages: [RSeQC] packages: [RSeQC]
runners: runners:
- type: executable - type: executable
- type: nextflow - type: nextflow

2
src/rseqc/tin/config.vsh.yaml
View File

@@ -82,4 +82,4 @@ engines:
pip3 install RSeQC pip3 install RSeQC
runners: runners:
- type: executable - type: executable
- type: nextflow - type: nextflow

2
src/sortmerna/config.vsh.yaml
View File

@@ -62,4 +62,4 @@ engines:
image: quay.io/biocontainers/sortmerna:4.3.6--h9ee0642_0 image: quay.io/biocontainers/sortmerna:4.3.6--h9ee0642_0
runners: runners:
- type: executable - type: executable
- type: nextflow - type: nextflow

2
src/summarizedexperiment/config.vsh.yaml
View File

@@ -47,4 +47,4 @@ engines:
bioc: [ SummarizedExperiment, tximeta ] bioc: [ SummarizedExperiment, tximeta ]
runners: runners:
- type: executable - type: executable
- type: nextflow - type: nextflow

2
src/tx2gene/config.vsh.yaml
View File

@@ -52,4 +52,4 @@ engines:
- type: python - type: python
runners: runners:
- type: executable - type: executable
- type: nextflow - type: nextflow

2
src/tximport/config.vsh.yaml
View File

@@ -76,4 +76,4 @@ engines:
cran: [ jsonlite ] cran: [ jsonlite ]
runners: runners:
- type: executable - type: executable
- type: nextflow - type: nextflow

366
src/workflows/genome_alignment_and_quant/main.nf
View File

@@ -10,86 +10,92 @@ workflow run_wf {
[ id, state + [ paired: paired, input: input ] ] [ id, state + [ paired: paired, input: input ] ]
} }
| star_align_reads.run ( | star_align_reads.run(
runIf: { id, state -> state.aligner == 'star_salmon' }, runIf: { id, state -> state.aligner == 'star_salmon' },
fromState: [ fromState: [
"input": "fastq_1", "input": "fastq_1",
"input_r2": "fastq_2", "input_r2": "fastq_2",
"genome_dir": "star_index", "genome_dir": "star_index",
"sjdb_gtf_file": "gtf", "sjdb_gtf_file": "gtf",
"out_sam_attr_rg_line": "star_sam_attr_rg_line", "out_sam_attr_rg_line": "star_sam_attr_rg_line",
"sjdb_gtf_feature_exon": "star_sjdb_gtf_feature_exon" "sjdb_gtf_feature_exon": "star_sjdb_gtf_feature_exon"
], ],
toState: [ toState: [
"genome_bam": "aligned_reads", "genome_bam": "aligned_reads",
"transcriptome_bam": "reads_aligned_to_transcriptome", "transcriptome_bam": "reads_aligned_to_transcriptome",
"star_multiqc": "log" "star_multiqc": "log"
], ],
args: [ args: [
quant_mode: "TranscriptomeSAM", quant_mode: "TranscriptomeSAM",
twopass_mode: "Basic", twopass_mode: "Basic",
out_sam_type: "BAM;Unsorted", out_sam_type: "BAM;Unsorted",
run_rng_seed: 0, run_rng_seed: 0,
out_filter_multimap_nmax: 20, out_filter_multimap_nmax: 20,
align_sjdb_overhang_min: 1, align_sjdb_overhang_min: 1,
out_sam_attributes: "NH;HI;AS;NM;MD", out_sam_attributes: "NH;HI;AS;NM;MD",
quant_transcriptome_sam_output: "BanSingleEnd" quant_transcriptome_sam_output: "BanSingleEnd"
] ],
directives: [ label: [ "highmem", "midcpu" ] ]
) )
// GENOME BAM // GENOME BAM
| samtools_sort.run ( | samtools_sort.run(
runIf: { id, state -> state.aligner == 'star_salmon' }, runIf: { id, state -> state.aligner == 'star_salmon' },
fromState: ["input": "genome_bam"], fromState: ["input": "genome_bam"],
toState: ["genome_bam_sorted": "output"], toState: ["genome_bam_sorted": "output"],
key: "genome_sorted" key: "genome_sorted",
directives: [ label: [ "highmem", "midcpu" ] ]
) )
| samtools_index.run ( | samtools_index.run(
runIf: { id, state -> state.aligner == 'star_salmon' }, runIf: { id, state -> state.aligner == 'star_salmon' },
fromState: [ fromState: [
"input": "genome_bam_sorted", "input": "genome_bam_sorted",
"csi": "bam_csi_index" "csi": "bam_csi_index"
], ],
toState: [ "genome_bam_index": "output" ], toState: [ "genome_bam_index": "output" ],
key: "genome_sorted" key: "genome_sorted",
directives: [ label: [ "highmem", "midcpu" ] ]
) )
| samtools_stats.run ( | samtools_stats.run(
runIf: { id, state -> state.aligner == 'star_salmon' }, runIf: { id, state -> state.aligner == 'star_salmon' },
fromState: [ fromState: [
"input": "genome_bam_sorted", "input": "genome_bam_sorted",
"bai": "genome_bam_index", "bai": "genome_bam_index",
"fasta": "fasta" "fasta": "fasta"
], ],
toState: [ "genome_bam_stats": "output" ], toState: [ "genome_bam_stats": "output" ],
key: "genome_stats" key: "genome_stats",
directives: [ label: [ "highmem", "midcpu" ] ]
) )
| samtools_flagstat.run ( | samtools_flagstat.run(
runIf: { id, state -> state.aligner == 'star_salmon' }, runIf: { id, state -> state.aligner == 'star_salmon' },
fromState: [ fromState: [
"bam": "genome_bam_sorted", "bam": "genome_bam_sorted",
"bai": "genome_bam_index", "bai": "genome_bam_index",
"fasta": "fasta" "fasta": "fasta"
], ],
toState: [ "genome_bam_flagstat": "output" ], toState: [ "genome_bam_flagstat": "output" ],
key: "genome_flagstat" key: "genome_flagstat",
directives: [ label: [ "highmem", "midcpu" ] ]
) )
| samtools_idxstats.run( | samtools_idxstats.run(
runIf: { id, state -> state.aligner == 'star_salmon' }, runIf: { id, state -> state.aligner == 'star_salmon' },
fromState: [ fromState: [
"bam": "genome_bam_sorted", "bam": "genome_bam_sorted",
"bai": "genome_bam_index", "bai": "genome_bam_index",
"fasta": "fasta" "fasta": "fasta"
], ],
toState: [ "genome_bam_idxstats": "output" ], toState: [ "genome_bam_idxstats": "output" ],
key: "genome_idxstats" key: "genome_idxstats",
directives: [ label: [ "highmem", "midcpu" ] ]
) )
// //
// Remove duplicate reads from BAM file based on UMIs // Remove duplicate reads from BAM file based on UMIs
// //
// Deduplicate genome BAM file // Deduplicate genome BAM file
| umi_tools_dedup.run ( | umi_tools_dedup.run(
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' }, runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
fromState: { id, state -> fromState: { id, state ->
def output_stats = state.umi_dedup_stats ? state.id : def output_stats = state.umi_dedup_stats ? state.id :
@@ -99,18 +105,20 @@ workflow run_wf {
output_stats: output_stats] output_stats: output_stats]
}, },
toState: [ "genome_bam_sorted": "output" ], toState: [ "genome_bam_sorted": "output" ],
key: "genome_deduped" key: "genome_deduped",
) directives: [ label: [ "highmem", "midcpu" ] ]
| samtools_index.run ( )
| samtools_index.run(
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' }, runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
fromState: [ fromState: [
"input": "genome_bam_sorted", "input": "genome_bam_sorted",
"csi": "bam_csi_index" "csi": "bam_csi_index"
], ],
toState: [ "genome_bam_index": "output" ], toState: [ "genome_bam_index": "output" ],
key: "genome_deduped" key: "genome_deduped",
) directives: [ label: [ "highmem", "midcpu" ] ]
| samtools_stats.run ( )
| samtools_stats.run(
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' }, runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
fromState: [ fromState: [
"input": "genome_bam_sorted", "input": "genome_bam_sorted",
@@ -118,9 +126,10 @@ workflow run_wf {
"fasta": "fasta" "fasta": "fasta"
], ],
toState: [ "genome_bam_stats": "output" ], toState: [ "genome_bam_stats": "output" ],
key: "genome_deduped_stats" key: "genome_deduped_stats",
) directives: [ label: [ "highmem", "midcpu" ] ]
| samtools_flagstat.run ( )
| samtools_flagstat.run(
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' }, runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
fromState: [ fromState: [
"bam": "genome_bam_sorted", "bam": "genome_bam_sorted",
@@ -128,9 +137,10 @@ workflow run_wf {
"fasta": "fasta" "fasta": "fasta"
], ],
toState: [ "genome_bam_flagstat": "output" ], toState: [ "genome_bam_flagstat": "output" ],
key: "genome_deduped_flagstat" key: "genome_deduped_flagstat",
) directives: [ label: [ "highmem", "midcpu" ] ]
| samtools_idxstats.run( )
| samtools_idxstats.run(
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' }, runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
fromState: [ fromState: [
"bam": "genome_bam_sorted", "bam": "genome_bam_sorted",
@@ -138,55 +148,61 @@ workflow run_wf {
"fasta": "fasta", "fasta": "fasta",
], ],
toState: [ "genome_bam_idxstats": "output" ], toState: [ "genome_bam_idxstats": "output" ],
key: "genome_deduped_idxstats" key: "genome_deduped_idxstats",
) directives: [ label: [ "highmem", "midcpu" ] ]
)
// Deduplicate transcriptome BAM file // Deduplicate transcriptome BAM file
| samtools_sort.run ( | samtools_sort.run(
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' }, runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
fromState: [ "input": "transcriptome_bam" ], fromState: [ "input": "transcriptome_bam" ],
toState: [ "transcriptome_bam": "output" ], toState: [ "transcriptome_bam": "output" ],
key: "transcriptome_sorted" key: "transcriptome_sorted",
) directives: [ label: [ "highmem", "midcpu" ] ]
| samtools_index.run ( )
| samtools_index.run(
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' }, runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
fromState: [ fromState: [
"input": "transcriptome_bam", "input": "transcriptome_bam",
"csi": "bam_csi_index" "csi": "bam_csi_index"
], ],
toState: [ "transcriptome_bam_index": "output" ], toState: [ "transcriptome_bam_index": "output" ],
key: "transcriptome_sorted" key: "transcriptome_sorted",
) directives: [ label: [ "highmem", "midcpu" ] ]
| samtools_stats.run ( )
| samtools_stats.run(
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' }, runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
fromState: [ fromState: [
"input": "transcriptome_bam", "input": "transcriptome_bam",
"bai": "transcriptome_bam_index", "bai": "transcriptome_bam_index",
], ],
toState: [ "transcriptome_bam_stats": "output" ], toState: [ "transcriptome_bam_stats": "output" ],
key: "transcriptome_stats" key: "transcriptome_stats",
) directives: [ label: [ "highmem", "midcpu" ] ]
| samtools_flagstat.run ( )
| samtools_flagstat.run(
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' }, runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
fromState: [ fromState: [
"bam": "transcriptome_bam", "bam": "transcriptome_bam",
"bai": "transcriptome_bam_index" "bai": "transcriptome_bam_index"
], ],
toState: [ "transcriptome_bam_flagstat": "output" ], toState: [ "transcriptome_bam_flagstat": "output" ],
key: "transcriptome_flagstat" key: "transcriptome_flagstat",
) directives: [ label: [ "highmem", "midcpu" ] ]
| samtools_idxstats.run( )
| samtools_idxstats.run(
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' }, runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
fromState: [ fromState: [
"bam": "transcriptome_bam", "bam": "transcriptome_bam",
"bai": "transcriptome_bam_index" "bai": "transcriptome_bam_index"
], ],
toState: [ "transcriptome_bam_idxstats": "output" ], toState: [ "transcriptome_bam_idxstats": "output" ],
key: "transcriptome_idxstats" key: "transcriptome_idxstats",
) directives: [ label: [ "highmem", "midcpu" ] ]
)
| umi_tools_dedup.run (
| umi_tools_dedup.run(
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' }, runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
fromState: { id, state -> fromState: { id, state ->
def output_stats = state.umi_dedup_stats ? state.id : def output_stats = state.umi_dedup_stats ? state.id :
@@ -196,57 +212,64 @@ workflow run_wf {
output_stats: output_stats] output_stats: output_stats]
}, },
toState: [ "transcriptome_bam_deduped": "output" ], toState: [ "transcriptome_bam_deduped": "output" ],
key: "transcriptome_deduped" key: "transcriptome_deduped",
) directives: [ label: [ "highmem", "midcpu" ] ]
| samtools_sort.run ( )
| samtools_sort.run(
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' }, runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
fromState: [ "input": "transcriptome_bam_deduped" ], fromState: [ "input": "transcriptome_bam_deduped" ],
toState: [ "transcriptome_bam": "output" ], toState: [ "transcriptome_bam": "output" ],
key: "transcriptome_deduped_sorted" key: "transcriptome_deduped_sorted",
) directives: [ label: [ "highmem", "midcpu" ] ]
| samtools_index.run ( )
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' }, | samtools_index.run(
fromState: [ runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
"input": "transcriptome_bam", fromState: [
"csi": "bam_csi_index" "input": "transcriptome_bam",
], "csi": "bam_csi_index"
toState: [ "transcriptome_bam_index": "output" ], ],
key: "transcriptome_deduped_sorted" toState: [ "transcriptome_bam_index": "output" ],
) key: "transcriptome_deduped_sorted",
| samtools_stats.run ( directives: [ label: [ "highmem", "midcpu" ] ]
)
| samtools_stats.run(
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' }, runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
fromState: [ fromState: [
"input": "transcriptome_bam", "input": "transcriptome_bam",
"bai": "transcriptome_bam_index" "bai": "transcriptome_bam_index"
], ],
toState: [ "transcriptome_bam_stats": "output" ], toState: [ "transcriptome_bam_stats": "output" ],
key: "transcriptome_deduped_stats" key: "transcriptome_deduped_stats",
) directives: [ label: [ "highmem", "midcpu" ] ]
| samtools_flagstat.run ( )
| samtools_flagstat.run(
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' }, runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
fromState: [ fromState: [
"bam": "transcriptome_bam", "bam": "transcriptome_bam",
"bai": "transcriptome_bam_index" "bai": "transcriptome_bam_index"
], ],
toState: [ "transcriptome_bam_flagstat": "output" ], toState: [ "transcriptome_bam_flagstat": "output" ],
key: "transcriptome_deduped_flagstat" key: "transcriptome_deduped_flagstat",
) directives: [ label: [ "highmem", "midcpu" ] ]
| samtools_idxstats.run( )
| samtools_idxstats.run(
runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' }, runIf: { id, state -> state.with_umi && state.aligner == 'star_salmon' },
fromState: [ fromState: [
"bam": "transcriptome_bam", "bam": "transcriptome_bam",
"bai": "transcriptome_bam_index" "bai": "transcriptome_bam_index"
], ],
toState: [ "transcriptome_bam_idxstats": "output" ], toState: [ "transcriptome_bam_idxstats": "output" ],
key: "transcriptome_deduped_idxstats" key: "transcriptome_deduped_idxstats",
) directives: [ label: [ "highmem", "midcpu" ] ]
)
// Fix paired-end reads in name sorted BAM file // Fix paired-end reads in name sorted BAM file
| umi_tools_prepareforrsem.run ( | umi_tools_prepareforrsem.run(
runIf: { id, state -> state.with_umi && state.paired && state.aligner == 'star_salmon' }, runIf: { id, state -> state.with_umi && state.paired && state.aligner == 'star_salmon' },
fromState: [ "input": "transcriptome_bam" ], fromState: [ "input": "transcriptome_bam" ],
toState: [ "transcriptome_bam": "output" ] toState: [ "transcriptome_bam": "output" ],
) directives: [ label: [ "highmem", "midcpu" ] ]
)
// Infer lib-type for salmon quant // Infer lib-type for salmon quant
| map { id, state -> | map { id, state ->
@@ -269,26 +292,27 @@ workflow run_wf {
} }
// Count reads from BAM alignments using Salmon // Count reads from BAM alignments using Salmon
| salmon_quant.run ( | salmon_quant.run(
runIf: { id, state -> state.aligner == 'star_salmon' }, runIf: { id, state -> state.aligner == 'star_salmon' },
fromState: [ fromState: [
"lib_type": "lib_type", "lib_type": "lib_type",
"alignments": "transcriptome_bam", "alignments": "transcriptome_bam",
"targets": "transcript_fasta", "targets": "transcript_fasta",
"gene_map": "gtf" "gene_map": "gtf"
], ],
toState: [ toState: [
"quant_out_dir": "output", "quant_out_dir": "output",
"quant_results_file": "quant_results" "quant_results_file": "quant_results"
] ],
directives: [ label: [ "highmem", "midcpu" ] ]
) )
| map { id, state -> | map { id, state ->
def mod_state = (state.aligner == 'star_salmon') ? state + [salmon_multiqc: state.quant_out_dir] : state def mod_state = (state.aligner == 'star_salmon') ? state + [salmon_multiqc: state.quant_out_dir] : state
[ id, mod_state ] [ id, mod_state ]
} }
| rsem_calculate_expression.run ( | rsem_calculate_expression.run(
runIf: { id, state -> state.aligner == 'star_rsem' }, runIf: { id, state -> state.aligner == 'star_rsem' },
fromState: [ fromState: [
"id": "id", "id": "id",
@@ -319,26 +343,29 @@ workflow run_wf {
"bam_star_rsem": "bam_star", "bam_star_rsem": "bam_star",
"bam_genome_rsem": "bam_genome", "bam_genome_rsem": "bam_genome",
"bam_transcript_rsem": "bam_transcript" "bam_transcript_rsem": "bam_transcript"
] ],
) directives: [ label: [ "highmem", "midcpu" ] ]
)
// RSEM_Star BAM
| samtools_sort.run ( // RSEM_Star BAM
| samtools_sort.run(
runIf: { id, state -> state.aligner == 'star_rsem' }, runIf: { id, state -> state.aligner == 'star_rsem' },
fromState: ["input": "bam_star_rsem"], fromState: ["input": "bam_star_rsem"],
toState: ["genome_bam_sorted": "output"], toState: ["genome_bam_sorted": "output"],
key: "genome_sorted" key: "genome_sorted",
) directives: [ label: [ "highmem", "midcpu" ] ]
| samtools_index.run ( )
| samtools_index.run(
runIf: { id, state -> state.aligner == 'star_rsem' }, runIf: { id, state -> state.aligner == 'star_rsem' },
fromState: [ fromState: [
"input": "genome_bam_sorted", "input": "genome_bam_sorted",
"csi": "bam_csi_index" "csi": "bam_csi_index"
], ],
toState: [ "genome_bam_index": "output" ], toState: [ "genome_bam_index": "output" ],
key: "genome_sorted" key: "genome_sorted",
) directives: [ label: [ "highmem", "midcpu" ] ]
| samtools_stats.run ( )
| samtools_stats.run(
runIf: { id, state -> state.aligner == 'star_rsem' }, runIf: { id, state -> state.aligner == 'star_rsem' },
fromState: [ fromState: [
"input": "genome_bam_sorted", "input": "genome_bam_sorted",
@@ -346,9 +373,10 @@ workflow run_wf {
"fasta": "fasta" "fasta": "fasta"
], ],
toState: [ "genome_bam_stats": "output" ], toState: [ "genome_bam_stats": "output" ],
key: "genome_stats" key: "genome_stats",
) directives: [ label: [ "highmem", "midcpu" ] ]
| samtools_flagstat.run ( )
| samtools_flagstat.run(
runIf: { id, state -> state.aligner == 'star_rsem' }, runIf: { id, state -> state.aligner == 'star_rsem' },
fromState: [ fromState: [
"bam": "genome_bam_sorted", "bam": "genome_bam_sorted",
@@ -356,9 +384,10 @@ workflow run_wf {
"fasta": "fasta" "fasta": "fasta"
], ],
toState: [ "genome_bam_flagstat": "output" ], toState: [ "genome_bam_flagstat": "output" ],
key: "genome_flagstat" key: "genome_flagstat",
) directives: [ label: [ "highmem", "midcpu" ] ]
| samtools_idxstats.run( )
| samtools_idxstats.run(
runIf: { id, state -> state.aligner == 'star_rsem' }, runIf: { id, state -> state.aligner == 'star_rsem' },
fromState: [ fromState: [
"bam": "genome_bam_sorted", "bam": "genome_bam_sorted",
@@ -366,9 +395,9 @@ workflow run_wf {
"fasta": "fasta" "fasta": "fasta"
], ],
toState: [ "genome_bam_idxstats": "output" ], toState: [ "genome_bam_idxstats": "output" ],
key: "genome_idxstats" key: "genome_idxstats",
) directives: [ label: [ "highmem", "midcpu" ] ]
)
| map { id, state -> | map { id, state ->
def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() } def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() }
[ id, mod_state ] [ id, mod_state ]
@@ -393,9 +422,10 @@ workflow run_wf {
"rsem_counts_gene": "rsem_counts_gene", "rsem_counts_gene": "rsem_counts_gene",
"rsem_counts_transcripts": "rsem_counts_transcripts", "rsem_counts_transcripts": "rsem_counts_transcripts",
"bam_genome_rsem": "bam_genome_rsem", "bam_genome_rsem": "bam_genome_rsem",
"bam_transcript_rsem": "bam_transcript_rsem" ] "bam_transcript_rsem": "bam_transcript_rsem"
]
) )
emit: emit:
output_ch output_ch
} }

2
src/workflows/merge_quant_results/config.vsh.yaml
View File

@@ -81,4 +81,4 @@ dependencies:
runners: runners:
- type: executable - type: executable
- type: nextflow - type: nextflow

334
src/workflows/post_processing/main.nf
View File

@@ -1,178 +1,192 @@
// Note: some helper functionality is added at the end of this file // Note: some helper functionality is added at the end of this file
workflow run_wf { workflow run_wf {
take: take:
input_ch input_ch
main: main:
output_ch = input_ch
| picard_markduplicates.run ( output_ch = input_ch
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"bam": "genome_bam",
"fasta": "fasta",
"fai": "fai",
"extra_picard_args": "extra_picard_args"
],
toState: [
"processed_genome_bam": "output_bam",
"markduplicates_metrics": "metrics"
]
)
| samtools_sort.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
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": "processed_genome_bam",
"csi": "bam_csi_index"
],
toState: [ "genome_bam_index": "output" ],
key: "genome_sorted_MarkDuplicates",
)
| samtools_stats.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"input": "processed_genome_bam",
"bai": "genome_bam_index"
],
toState: [ "genome_bam_stats": "output" ],
key: "MarkDuplicates_stats"
)
| samtools_flagstat.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"bam": "processed_genome_bam",
"bai": "genome_bam_index"
],
toState: [ "genome_bam_flagstat": "output" ],
key: "MarkDuplicates_flagstat"
)
| samtools_idxstats.run(
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"bam": "processed_genome_bam",
"bai": "genome_bam_index"
],
toState: [ "genome_bam_idxstats": "output" ],
key: "MarkDuplicates_idxstats"
)
| stringtie.run ( | picard_markduplicates.run (
runIf: { id, state -> !state.skip_stringtie }, runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [ fromState: [
"strandedness": "strandedness", "bam": "genome_bam",
"bam": "processed_genome_bam", "fasta": "fasta",
"annotation_gtf": "gtf", "fai": "fai",
"extra_stringtie_args": "extra_stringtie_args" "extra_picard_args": "extra_picard_args"
], ],
toState: [ toState: [
"stringtie_transcript_gtf": "transcript_gtf", "processed_genome_bam": "output_bam",
"stringtie_coverage_gtf": "coverage_gtf", "markduplicates_metrics": "metrics"
"stringtie_abundance": "abundance", ],
"stringtie_ballgown": "ballgown" directives: [ label: [ "midmem", "midcpu" ] ]
] )
) | samtools_sort.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [ "input": "processed_genome_bam" ],
toState: [ "processed_genome_bam": "output" ],
key: "genome_sorted_MarkDuplicates",
directives: [ label: [ "midmem", "midcpu" ] ]
)
| samtools_index.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"input": "processed_genome_bam",
"csi": "bam_csi_index"
],
toState: [ "genome_bam_index": "output" ],
key: "genome_sorted_MarkDuplicates",
directives: [ label: [ "midmem", "midcpu" ] ]
)
| samtools_stats.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"input": "processed_genome_bam",
"bai": "genome_bam_index"
],
toState: [ "genome_bam_stats": "output" ],
key: "MarkDuplicates_stats",
directives: [ label: [ "midmem", "midcpu" ] ]
)
| samtools_flagstat.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"bam": "processed_genome_bam",
"bai": "genome_bam_index"
],
toState: [ "genome_bam_flagstat": "output" ],
key: "MarkDuplicates_flagstat",
directives: [ label: [ "midmem", "midcpu" ] ]
)
| samtools_idxstats.run(
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"bam": "processed_genome_bam",
"bai": "genome_bam_index"
],
toState: [ "genome_bam_idxstats": "output" ],
key: "MarkDuplicates_idxstats",
directives: [ label: [ "midmem", "midcpu" ] ]
)
// Genome-wide coverage with BEDTools | stringtie.run (
runIf: { id, state -> !state.skip_stringtie },
fromState: [
"strandedness": "strandedness",
"bam": "processed_genome_bam",
"annotation_gtf": "gtf",
"extra_stringtie_args": "extra_stringtie_args"
],
toState: [
"stringtie_transcript_gtf": "transcript_gtf",
"stringtie_coverage_gtf": "coverage_gtf",
"stringtie_abundance": "abundance",
"stringtie_ballgown": "ballgown"
],
directives: [ label: [ "midmem", "midcpu" ] ]
)
| bedtools_genomecov.run ( // Genome-wide coverage with BEDTools
runIf: { id, state -> !state.skip_bigwig },
fromState: [
"input_bam": "processed_genome_bam",
],
args: [
split: true,
du: true,
bed_graph: true,
strand: "+"
],
toState: [ "bedgraph_forward": "output" ],
key: "bedtools_genomecov_forward"
)
| bedtools_genomecov.run ( | bedtools_genomecov.run (
runIf: { id, state -> !state.skip_bigwig }, runIf: { id, state -> !state.skip_bigwig },
fromState: [ fromState: [
"input_bam": "processed_genome_bam", "input_bam": "processed_genome_bam",
], ],
args: [ args: [
split: true, split: true,
du: true, du: true,
bed_graph: true, bed_graph: true,
strand: "-" strand: "+"
], ],
toState: [ "bedgraph_reverse": "output" ], toState: [ "bedgraph_forward": "output" ],
key: "bedtools_genomecov_reverse" key: "bedtools_genomecov_forward",
) directives: [ label: [ "midmem", "midcpu" ] ]
)
| bedclip.run ( | bedtools_genomecov.run (
runIf: { id, state -> !state.skip_bigwig }, runIf: { id, state -> !state.skip_bigwig },
fromState: [ fromState: [
"input_bedgraph": "bedgraph_forward", "input_bam": "processed_genome_bam",
"sizes": "chrom_sizes" ],
], args: [
toState: [ "bedgraph_forward": "output_bedgraph" ], split: true,
key: "bedclip_forward" du: true,
) bed_graph: true,
strand: "-"
],
toState: [ "bedgraph_reverse": "output" ],
key: "bedtools_genomecov_reverse",
directives: [ label: [ "midmem", "midcpu" ] ]
)
| bedgraphtobigwig.run ( | bedclip.run (
runIf: { id, state -> !state.skip_bigwig }, runIf: { id, state -> !state.skip_bigwig },
fromState: [ fromState: [
"bedgraph": "bedgraph_forward", "input_bedgraph": "bedgraph_forward",
"sizes": "chrom_sizes" "sizes": "chrom_sizes"
], ],
toState: [ "bigwig_forward": "bigwig" ], toState: [ "bedgraph_forward": "output_bedgraph" ],
key: "bedgraphtobigwig_forward" key: "bedclip_forward",
) directives: [ label: [ "midmem", "midcpu" ] ]
)
| bedclip.run ( | bedgraphtobigwig.run (
runIf: { id, state -> !state.skip_bigwig }, runIf: { id, state -> !state.skip_bigwig },
fromState: [ fromState: [
"input_bedgraph": "bedgraph_reverse", "bedgraph": "bedgraph_forward",
"sizes": "chrom_sizes", "sizes": "chrom_sizes"
], ],
toState: [ "bedgraph_reverse": "output_bedgraph" ], toState: [ "bigwig_forward": "bigwig" ],
key: "bedclip_reverse" key: "bedgraphtobigwig_forward",
) directives: [ label: [ "midmem", "midcpu" ] ]
)
| bedgraphtobigwig.run ( | bedclip.run (
runIf: { id, state -> !state.skip_bigwig }, runIf: { id, state -> !state.skip_bigwig },
fromState: [ fromState: [
"bedgraph": "bedgraph_reverse", "input_bedgraph": "bedgraph_reverse",
"sizes": "chrom_sizes" "sizes": "chrom_sizes",
], ],
toState: [ "bigwig_reverse": "bigwig" ], toState: [ "bedgraph_reverse": "output_bedgraph" ],
key: "bedgraphtobigwig_reverse" key: "bedclip_reverse",
) directives: [ label: [ "midmem", "midcpu" ] ]
)
| map { id, state -> | bedgraphtobigwig.run (
def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() } runIf: { id, state -> !state.skip_bigwig },
[ id, mod_state ] fromState: [
} "bedgraph": "bedgraph_reverse",
"sizes": "chrom_sizes"
],
toState: [ "bigwig_reverse": "bigwig" ],
key: "bedgraphtobigwig_reverse",
directives: [ label: [ "midmem", "midcpu" ] ]
)
| setState ( | map { id, state ->
"processed_genome_bam": "processed_genome_bam", def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() }
"genome_bam_index": "genome_bam_index", [ id, mod_state ]
"genome_bam_stats": "genome_bam_stats", }
"genome_bam_flagstat": "genome_bam_flagstat",
"genome_bam_idxstats": "genome_bam_idxstats",
"markduplicates_metrics": "markduplicates_metrics",
"stringtie_transcript_gtf": "stringtie_transcript_gtf",
"stringtie_coverage_gtf": "stringtie_coverage_gtf",
"stringtie_abundance": "stringtie_abundance",
"stringtie_ballgown": "stringtie_ballgown",
"bedgraph_forward": "bedgraph_forward",
"bedgraph_reverse": "bedgraph_reverse",
"bigwig_forward": "bigwig_forward",
"bigwig_reverse": "bigwig_reverse"
)
emit: | setState (
output_ch "processed_genome_bam": "processed_genome_bam",
"genome_bam_index": "genome_bam_index",
"genome_bam_stats": "genome_bam_stats",
"genome_bam_flagstat": "genome_bam_flagstat",
"genome_bam_idxstats": "genome_bam_idxstats",
"markduplicates_metrics": "markduplicates_metrics",
"stringtie_transcript_gtf": "stringtie_transcript_gtf",
"stringtie_coverage_gtf": "stringtie_coverage_gtf",
"stringtie_abundance": "stringtie_abundance",
"stringtie_ballgown": "stringtie_ballgown",
"bedgraph_forward": "bedgraph_forward",
"bedgraph_reverse": "bedgraph_reverse",
"bigwig_forward": "bigwig_forward",
"bigwig_reverse": "bigwig_reverse"
)
emit:
output_ch
} }

81
src/workflows/pre_processing/main.nf
View File

@@ -25,7 +25,8 @@ workflow run_wf {
def new_state = state + newKeys def new_state = state + newKeys
return new_state return new_state
}, },
args: [html: "*.html", zip: "*.zip"] args: [html: "*.html", zip: "*.zip"],
directives: [ label: [ "midmem", "highcpu" ] ]
) )
// Extract UMIs from fastq files and discard read 1 or read 2 if required // Extract UMIs from fastq files and discard read 1 or read 2 if required
@@ -48,7 +49,8 @@ workflow run_wf {
toState: [ toState: [
"fastq_1": "output", "fastq_1": "output",
"fastq_2": "read2_out" "fastq_2": "read2_out"
] ],
directives: [ label: [ "midmem", "midcpu" ] ]
) )
// Discard read if required // Discard read if required
@@ -87,7 +89,8 @@ workflow run_wf {
"trim_zip_2": "trimmed_fastqc_zip_2", "trim_zip_2": "trimmed_fastqc_zip_2",
"trim_html_1": "trimmed_fastqc_html_1", "trim_html_1": "trimmed_fastqc_html_1",
"trim_html_2": "trimmed_fastqc_html_2" "trim_html_2": "trimmed_fastqc_html_2"
] ],
directives: [ label: [ "midmem", "midcpu" ] ]
) )
// Trim reads using fastp // Trim reads using fastp
@@ -112,7 +115,8 @@ workflow run_wf {
"trim_json": "json", "trim_json": "json",
"trim_html": "html", "trim_html": "html",
"trim_merged_out": "merged_out" "trim_merged_out": "merged_out"
] ],
directives: [ label: [ "midmem", "midcpu" ] ]
) )
// Perform FASTQC on reads trimmed using fastp // Perform FASTQC on reads trimmed using fastp
@@ -133,7 +137,8 @@ workflow run_wf {
return new_state return new_state
}, },
args: [html: "*.html", zip: "*.zip"], args: [html: "*.html", zip: "*.zip"],
key: "fastqc_trimming" key: "fastqc_trimming",
directives: [ label: [ "midmem", "midcpu" ] ]
) )
// Filter out contaminant RNA // Filter out contaminant RNA
@@ -149,7 +154,8 @@ workflow run_wf {
toState: [ toState: [
"fastq_1": "fastq_1", "fastq_1": "fastq_1",
"fastq_2": "fastq_2" "fastq_2": "fastq_2"
] ],
directives: [ label: [ "midmem", "midcpu" ] ]
) )
// Sort reads by rRNA and non-rRNA // Sort reads by rRNA and non-rRNA
@@ -174,7 +180,8 @@ workflow run_wf {
] ]
def new_state = state + newKeys def new_state = state + newKeys
return new_state return new_state
} },
directives: [ label: [ "highmem", "midcpu" ] ]
) )
| map { id, state -> | map { id, state ->
if (state.remove_ribo_rna) { if (state.remove_ribo_rna) {
@@ -200,7 +207,8 @@ workflow run_wf {
toState: [ toState: [
"subsampled_fastq_1": "output_1", "subsampled_fastq_1": "output_1",
"subsampled_fastq_2": "output_2" "subsampled_fastq_2": "output_2"
] ],
directives: [ label: [ "midmem", "midcpu" ] ]
) )
// Infer lib-type for salmon quant // Infer lib-type for salmon quant
@@ -237,39 +245,40 @@ workflow run_wf {
lib_type: state.lib_type ] lib_type: state.lib_type ]
}, },
args: [ "skip_quant": true ], args: [ "skip_quant": true ],
toState: [ "salmon_quant_output": "output" ] toState: [ "salmon_quant_output": "output" ],
directives: [ label: [ "highmem", "highcpu" ] ]
) )
| map { id, state -> | map { id, state ->
def mod_state = (!state.paired) ? def mod_state = (!state.paired) ?
[trim_log_2: state.remove(state.trim_log_2), trim_zip_2: state.remove(state.trim_zip_2), trim_html_2: state.remove(state.trim_html_2), failed_trim_unpaired2: state.remove(state.failed_trim_unpaired2)] : [trim_log_2: state.remove(state.trim_log_2), trim_zip_2: state.remove(state.trim_zip_2), trim_html_2: state.remove(state.trim_html_2), failed_trim_unpaired2: state.remove(state.failed_trim_unpaired2)] :
[] []
[ id, state + mod_state ] [ id, state + mod_state ]
} }
| map { id, state -> | map { id, state ->
def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() } def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() }
[ id, mod_state ] [ id, mod_state ]
} }
| setState ( | setState (
"fastqc_html_1": "fastqc_html_1", "fastqc_html_1": "fastqc_html_1",
"fastqc_html_2": "fastqc_html_2", "fastqc_html_2": "fastqc_html_2",
"fastqc_zip_1": "fastqc_zip_1", "fastqc_zip_1": "fastqc_zip_1",
"fastqc_zip_2": "fastqc_zip_2", "fastqc_zip_2": "fastqc_zip_2",
"qc_output1": "fastq_1", "qc_output1": "fastq_1",
"qc_output2": "fastq_2", "qc_output2": "fastq_2",
"trim_log_1": "trim_log_1", "trim_log_1": "trim_log_1",
"trim_log_2": "trim_log_2", "trim_log_2": "trim_log_2",
"trim_zip_1": "trim_zip_1", "trim_zip_1": "trim_zip_1",
"trim_zip_2": "trim_zip_2", "trim_zip_2": "trim_zip_2",
"trim_html_1": "trim_html_1", "trim_html_1": "trim_html_1",
"trim_html_2": "trim_html_2", "trim_html_2": "trim_html_2",
"sortmerna_log": "sortmerna_log", "sortmerna_log": "sortmerna_log",
"trim_json": "trim_json", "trim_json": "trim_json",
"trim_html": "trim_html", "trim_html": "trim_html",
"trim_merged_out": "trim_merged_out", "trim_merged_out": "trim_merged_out",
"salmon_quant_output": "salmon_quant_output" "salmon_quant_output": "salmon_quant_output"
) )
emit: emit:

543
src/workflows/prepare_genome/main.nf
View File

@@ -1,288 +1,311 @@
workflow run_wf { workflow run_wf {
take: take:
input_ch input_ch
main: main:
output_ch = input_ch output_ch = input_ch
// Uncompress fasta
| gunzip.run (
fromState: [ "input": "fasta" ],
toState: [ "fasta": "output" ],
key: "gunzip_fasta",
args: [ output: "reference_genome.fasta" ]
)
// uncompress gtf // Uncompress fasta
| gunzip.run ( | gunzip.run (
runIf: {id, state -> state.gtf}, fromState: [ "input": "fasta" ],
fromState: [ "input": "gtf" ], toState: [ "fasta": "output" ],
toState: [ "gtf": "output" ], key: "gunzip_fasta",
key: "gunzip_gtf", args: [ output: "reference_genome.fasta" ],
args: [output: "gene_annotation.gtf"] directives: [ label: [ "lowmem", "midcpu" ] ]
) )
// uncompress gff // uncompress gtf
| gunzip.run ( | gunzip.run (
runIf: {id, state -> !state.gtf && state.gff}, runIf: {id, state -> state.gtf},
fromState: [ "input": "gff" ], fromState: [ "input": "gtf" ],
toState: [ "gff": "output" ], toState: [ "gtf": "output" ],
key: "gunzip_gff", key: "gunzip_gtf",
args: [output: "gene_annotation.gff"] args: [output: "gene_annotation.gtf"],
) directives: [ label: [ "lowmem", "midcpu" ] ]
)
// gff to gtf // uncompress gff
| gffread.run ( | gunzip.run (
runIf: {id, state -> !state.gtf && state.gff}, runIf: {id, state -> !state.gtf && state.gff},
fromState: [ fromState: [ "input": "gff" ],
"input": "gff", toState: [ "gff": "output" ],
"genome": "fasta" key: "gunzip_gff",
], args: [output: "gene_annotation.gff"],
toState: [ "gtf": "outfile" ], directives: [ label: [ "lowmem", "midcpu" ] ]
args: [ )
outfile: "gene_annotation.gtf",
gtf_output: true,
keep_attrs: true,
keep_exon_attrs: true
]
)
| gtf_filter.run( // gff to gtf
runIf: {id, state -> state.gtf && state.filter_gtf}, | gffread.run (
fromState: [ runIf: {id, state -> !state.gtf && state.gff},
"fasta": "fasta", fromState: [
"gtf": "gtf" "input": "gff",
], "genome": "fasta"
toState: [ "gtf": "filtered_gtf" ], ],
args: [filtered_gtf: "gene_annotation.gtf"] toState: [ "gtf": "outfile" ],
) args: [
outfile: "gene_annotation.gtf",
gtf_output: true,
keep_attrs: true,
keep_exon_attrs: true
],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
// uncompress additional fasta | gtf_filter.run(
| gunzip.run ( runIf: {id, state -> state.gtf && state.filter_gtf},
runIf: {id, state -> state.additional_fasta}, fromState: [
fromState: [ "input": "additional_fasta" ], "fasta": "fasta",
toState: [ "additional_fasta": "output" ], "gtf": "gtf"
key: "gunzip_additional_fasta", ],
args: [output: "additional.fasta"] toState: [ "gtf": "filtered_gtf" ],
) args: [filtered_gtf: "gene_annotation.gtf"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
// concatenate additional fasta // uncompress additional fasta
| cat_additional_fasta.run ( | gunzip.run (
runIf: {id, state -> state.additional_fasta}, runIf: {id, state -> state.additional_fasta},
fromState: [ fromState: [ "input": "additional_fasta" ],
"fasta": "fasta", toState: [ "additional_fasta": "output" ],
"gtf": "gtf", key: "gunzip_additional_fasta",
"additional_fasta": "additional_fasta", args: [output: "additional.fasta"],
"biotype": "biotype" directives: [ label: [ "lowmem", "midcpu" ] ]
], )
toState: [
"fasta": "fasta_output",
"gtf": "gtf_output"
],
args: [
fasta_output: "genome_additional.fasta",
gtf_output: "genome_additional.gtf"
]
)
// uncompress bed file // concatenate additional fasta
| gunzip.run ( | cat_additional_fasta.run (
runIf: {id, state -> state.gene_bed}, runIf: {id, state -> state.additional_fasta},
fromState: [ "input": "gene_bed" ], fromState: [
toState: [ "gene_bed": "output" ], "fasta": "fasta",
key: "gunzip_gene_bed", "gtf": "gtf",
args: [output: "genome_additional.bed"] "additional_fasta": "additional_fasta",
) "biotype": "biotype"
],
toState: [
"fasta": "fasta_output",
"gtf": "gtf_output"
],
args: [
fasta_output: "genome_additional.fasta",
gtf_output: "genome_additional.gtf"
],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
// gtf to bed // uncompress bed file
| gtf2bed.run ( | gunzip.run (
runIf: { id, state -> !state.gene_bed}, runIf: {id, state -> state.gene_bed},
fromState: [ "gtf": "gtf" ], fromState: [ "input": "gene_bed" ],
toState: [ "gene_bed": "bed_output" ], toState: [ "gene_bed": "output" ],
args: [bed_output: "genome_additional.bed"] key: "gunzip_gene_bed",
) args: [output: "genome_additional.bed"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
// uncompress transcript fasta // gtf to bed
| gunzip.run ( | gtf2bed.run (
runIf: {id, state -> state.transcript_fasta}, runIf: { id, state -> !state.gene_bed},
fromState: [ "input": "transcript_fasta" ], fromState: [ "gtf": "gtf" ],
toState: [ "transcript_fasta": "output" ], toState: [ "gene_bed": "bed_output" ],
key: "transcript_fasta", args: [bed_output: "genome_additional.bed"],
args: [output: "transcriptome.fasta"] directives: [ label: [ "lowmem", "midcpu" ] ]
) )
// preprocess transcripts fasta if gtf is in gencode format // uncompress transcript fasta
| preprocess_transcripts_fasta.run ( | gunzip.run (
runIf: {id, state -> state.transcript_fasta && state.gencode}, runIf: {id, state -> state.transcript_fasta},
fromState: [ "transcript_fasta": "transcript_fasta" ], fromState: [ "input": "transcript_fasta" ],
toState: [ "transcript_fasta": "output" ], toState: [ "transcript_fasta": "output" ],
args: [output: "transcriptome.fasta"] key: "transcript_fasta",
) args: [output: "transcriptome.fasta"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
// make transcript FASTA if not provided // preprocess transcripts fasta if gtf is in gencode format
| rsem_prepare_reference.run ( | preprocess_transcripts_fasta.run (
runIf: {id, state -> !state.transcript_fasta}, runIf: {id, state -> state.transcript_fasta && state.gencode},
fromState: [ fromState: [ "transcript_fasta": "transcript_fasta" ],
"reference_fasta_files": "fasta", toState: [ "transcript_fasta": "output" ],
"gtf": "gtf" args: [output: "transcriptome.fasta"],
], directives: [ label: [ "lowmem", "midcpu" ] ]
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 // make transcript FASTA if not provided
| getchromsizes.run ( | rsem_prepare_reference.run (
fromState: [ "fasta": "fasta" ], runIf: {id, state -> !state.transcript_fasta},
toState: [ fromState: [
"fai": "fai", "reference_fasta_files": "fasta",
"sizes": "sizes" "gtf": "gtf"
], ],
key: "chromsizes", toState: [ "make_transcript_fasta_output": "output" ],
args: [ key: "make_transcript_fasta",
fai: "genome_additional.fasta.fai", args: [reference_name: "genome"],
sizes: "genome_additional.fasta.sizes" directives: [ label: [ "lowmem", "midcpu" ] ]
] )
) | map { id, state ->
def transcript_fasta = (!state.transcript_fasta) ?
// untar bbsplit index, if available state.make_transcript_fasta_output.listFiles().find{it.name == "genome.transcripts.fa"} :
| untar.run ( state.transcript_fasta
runIf: {id, state -> state.bbsplit_index}, [ id, state + [transcript_fasta: transcript_fasta] ]
fromState: [ "input": "bbsplit_index" ], }
toState: [ "bbsplit_index": "output" ],
key: "untar_bbsplit_index",
args: [output: "BBSplit_index"]
)
| map {id, state -> // chromosome size and fai index
def ref = [state.fasta] + state.bbsplit_fasta_list | getchromsizes.run (
[id, state + [bbsplit_ref: ref] ] fromState: [ "fasta": "fasta" ],
} toState: [
"fai": "fai",
"sizes": "sizes"
],
key: "chromsizes",
args: [
fai: "genome_additional.fasta.fai",
sizes: "genome_additional.fasta.sizes"
],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
// create bbsplit index, if not already availble // untar bbsplit index, if available
| bbmap_bbsplit.run ( | untar.run (
runIf: {id, state -> !state.skip_bbsplit && !state.bbsplit_index}, runIf: {id, state -> state.bbsplit_index},
fromState: ["ref": "bbsplit_ref"], fromState: [ "input": "bbsplit_index" ],
toState: [ "bbsplit_index": "index" ], toState: [ "bbsplit_index": "output" ],
args: [ key: "untar_bbsplit_index",
only_build_index: true, directives: [ label: [ "lowmem", "midcpu" ] ]
index: "BBSplit_index" )
],
key: "generate_bbsplit_index"
)
// Uncompress STAR index or generate from scratch if required | map { id, state ->
| untar.run ( // Check if bbsplit_fasta_list is defined
runIf: {id, state -> state.star_index}, def ref = (state.bbsplit_fasta_list) ?
fromState: [ "input": "star_index" ], [state.fasta] + state.bbsplit_fasta_list :
toState: [ "star_index": "output" ], [state.fasta]
key: "untar_star_index", [id, state + [bbsplit_ref: ref] ]
args: [output: "STAR_index"] }
)
// TODO: Add to viah-hub or adapt star_align_reads to enable the generateGenome runMode
| star_genome_generate.run (
runIf: {id, state -> !state.star_index && !state.skip_alignment},
fromState: [
"genome_fasta_files": "fasta",
"sjdb_gtf_file": "gtf",
"sjdb_gtf_feature_exon": "star_sjdb_gtf_feature_exon"
],
toState: [ "star_index": "index" ],
key: "generate_star_index",
args: [index: "STAR_index"]
)
// Uncompress RSEM index or generate from scratch if required // create bbsplit index, if not already available
| untar.run ( | bbmap_bbsplit.run (
runIf: {id, state -> state.rsem_index}, runIf: {id, state -> !state.skip_bbsplit && !state.bbsplit_index},
fromState: [ "input": "rsem_index" ], fromState: ["ref": "bbsplit_ref"],
toState: [ "rsem_index": "output" ], toState: [ "bbsplit_index": "index" ],
key: "untar_rsem_index", args: [
args: [output: "RSEM_index"] only_build_index: true,
) index: "BBSplit_index"
],
key: "generate_bbsplit_index"
)
| rsem_prepare_reference.run ( // Uncompress STAR index or generate from scratch if required
runIf: {id, state -> !state.rsem_index && state.aligner == 'star_rsem'}, | untar.run (
fromState: [ runIf: {id, state -> state.star_index},
"reference_fasta_files": "fasta", fromState: [ "input": "star_index" ],
"gtf": "gtf" toState: [ "star_index": "output" ],
], key: "untar_star_index",
toState: [ "rsem_index": "output" ], args: [output: "STAR_index"],
key: "generate_rsem_index", directives: [ label: [ "lowmem", "midcpu" ] ]
args: [reference_name: "genome"] )
)
// TODO: Uncompress HISAT2 index or generate from scratch if required
// Uncompress Salmon index or generate from scratch if required | star_genome_generate.run (
| untar.run ( runIf: {id, state -> !state.star_index && !state.skip_alignment},
runIf: {id, state -> state.salmon_index}, fromState: [
fromState: [ "input": "salmon_index" ], "genome_fasta_files": "fasta",
toState: [ "salmon_index": "output" ], "sjdb_gtf_file": "gtf",
key: "untar_salmon_index", "sjdb_gtf_feature_exon": "star_sjdb_gtf_feature_exon"
args: [output: "Salmon_index"] ],
) toState: [ "star_index": "index" ],
key: "generate_star_index",
args: [index: "STAR_index"],
directives: [ label: [ "highmem", "highcpu" ] ]
)
| salmon_index.run ( // Uncompress RSEM index or generate from scratch if required
runIf: {id, state -> (state.aligner == 'star_salmon' || state.pseudo_aligner == "salmon") && !state.salmon_index}, | untar.run (
fromState: [ runIf: {id, state -> state.rsem_index},
"genome": "fasta", fromState: [ "input": "rsem_index" ],
"transcripts": "transcript_fasta", toState: [ "rsem_index": "output" ],
"kmer_len": "pseudo_aligner_kmer_size", key: "untar_rsem_index",
"gencode": "gencode" args: [output: "RSEM_index"],
], directives: [ label: [ "lowmem", "midcpu" ] ]
toState: [ "salmon_index": "index" ], )
key: "generate_salmon_index",
args: [index: "Salmon_index"]
)
// Uncompress Kallisto index or generate from scratch if required | rsem_prepare_reference.run (
| untar.run ( runIf: {id, state -> !state.rsem_index && state.aligner == 'star_rsem'},
runIf: {id, state -> state.kallisto_index}, fromState: [
fromState: [ "input": "kallisto_index" ], "reference_fasta_files": "fasta",
toState: [ "kallisto_index": "output" ], "gtf": "gtf"
key: "untar_kallisto_index", ],
args: [output: "Kallisto_index"] toState: [ "rsem_index": "output" ],
) key: "generate_rsem_index",
args: [reference_name: "genome"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
// TODO: Uncompress HISAT2 index or generate from scratch if required
| kallisto_index.run( // Uncompress Salmon index or generate from scratch if required
runIf: {id, state -> state.pseudo_aligner == "kallisto" && !state.kallisto_index}, | untar.run (
fromState: [ runIf: {id, state -> state.salmon_index},
"input": "transcript_fasta", fromState: [ "input": "salmon_index" ],
"kmer_size": "pseudo_aligner_kmer_size" toState: [ "salmon_index": "output" ],
], key: "untar_salmon_index",
toState: [ "kallisto_index": "index" ], args: [output: "Salmon_index"],
key: "generate_kallisto_index", directives: [ label: [ "lowmem", "midcpu" ] ]
args: [index: "Kallisto_index"] )
)
| map { id, state -> | salmon_index.run (
def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() } runIf: {id, state -> (state.aligner == 'star_salmon' || state.pseudo_aligner == "salmon") && !state.salmon_index},
[ id, mod_state ] fromState: [
} "genome": "fasta",
"transcripts": "transcript_fasta",
"kmer_len": "pseudo_aligner_kmer_size",
"gencode": "gencode"
],
toState: [ "salmon_index": "index" ],
key: "generate_salmon_index",
args: [index: "Salmon_index"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
| setState ( // Uncompress Kallisto index or generate from scratch if required
"fasta_uncompressed": "fasta", | untar.run (
"gtf_uncompressed": "gtf", runIf: {id, state -> state.kallisto_index},
"transcript_fasta_uncompressed": "transcript_fasta", fromState: [ "input": "kallisto_index" ],
"gene_bed_uncompressed": "gene_bed", toState: [ "kallisto_index": "output" ],
"star_index_uncompressed": "star_index", key: "untar_kallisto_index",
"salmon_index_uncompressed": "salmon_index", args: [output: "Kallisto_index"],
"kallisto_index_uncompressed": "kallisto_index", directives: [ label: [ "lowmem", "midcpu" ] ]
"bbsplit_index_uncompressed": "bbsplit_index", )
"rsem_index_uncompressed": "rsem_index",
"chrom_sizes": "sizes",
"fai": "fai"
)
emit: | kallisto_index.run(
output_ch runIf: {id, state -> state.pseudo_aligner == "kallisto" && !state.kallisto_index},
fromState: [
"input": "transcript_fasta",
"kmer_size": "pseudo_aligner_kmer_size"
],
toState: [ "kallisto_index": "index" ],
key: "generate_kallisto_index",
args: [index: "Kallisto_index"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
| map { id, state ->
def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() }
[ id, mod_state ]
}
| setState (
"fasta_uncompressed": "fasta",
"gtf_uncompressed": "gtf",
"transcript_fasta_uncompressed": "transcript_fasta",
"gene_bed_uncompressed": "gene_bed",
"star_index_uncompressed": "star_index",
"salmon_index_uncompressed": "salmon_index",
"kallisto_index_uncompressed": "kallisto_index",
"bbsplit_index_uncompressed": "bbsplit_index",
"rsem_index_uncompressed": "rsem_index",
"chrom_sizes": "sizes",
"fai": "fai"
)
emit:
output_ch
} }

43
src/workflows/pseudo_alignment_and_quant/main.nf
View File

@@ -34,22 +34,23 @@ workflow run_wf {
// Count reads from BAM alignments using Salmon // Count reads from BAM alignments using Salmon
| salmon_quant.run ( | salmon_quant.run (
runIf: { id, state -> state.pseudo_aligner == 'salmon' }, runIf: { id, state -> state.pseudo_aligner == 'salmon' },
fromState: { id, state -> fromState: { id, state ->
def unmated_reads = !state.paired ? state.fastq_1 : null def unmated_reads = !state.paired ? state.fastq_1 : null
def mates1 = state.paired ? state.fastq_1 : null def mates1 = state.paired ? state.fastq_1 : null
def mates2 = state.paired ? state.fastq_2 : null def mates2 = state.paired ? state.fastq_2 : null
[ unmated_reads: unmated_reads, [ unmated_reads: unmated_reads,
mates1: mates1, mates1: mates1,
mates2: mates2, mates2: mates2,
gene_map: state.gtf, gene_map: state.gtf,
index: state.salmon_index, index: state.salmon_index,
lib_type: state.lib_type ] lib_type: state.lib_type ]
}, },
toState: [ toState: [
"quant_out_dir": "output", "quant_out_dir": "output",
"salmon_quant_results_file": "quant_results" "salmon_quant_results_file": "quant_results"
] ],
directives: [ label: [ "midmem", "highcpu" ] ]
) )
| map { id, state -> | map { id, state ->
@@ -57,7 +58,7 @@ workflow run_wf {
[ id, mod_state ] [ id, mod_state ]
} }
| kallisto_quant.run ( | kallisto_quant.run (
runIf: { id, state -> state.pseudo_aligner == 'kallisto'}, runIf: { id, state -> state.pseudo_aligner == 'kallisto'},
fromState: { id, state -> fromState: { id, state ->
def fr_stranded = state.strandedness == 'forward' def fr_stranded = state.strandedness == 'forward'
@@ -81,8 +82,9 @@ workflow run_wf {
] ]
def new_state = state + newKeys def new_state = state + newKeys
return new_state return new_state
} },
) directives: [ label: [ "midmem", "highcpu" ] ]
)
| map { id, state -> | map { id, state ->
def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() } def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() }
@@ -93,7 +95,8 @@ workflow run_wf {
[ "pseudo_multiqc": "quant_results", [ "pseudo_multiqc": "quant_results",
"quant_out_dir": "quant_out_dir", "quant_out_dir": "quant_out_dir",
"salmon_quant_results_file": "salmon_quant_results_file", "salmon_quant_results_file": "salmon_quant_results_file",
"kallisto_quant_results_file": "kallisto_quant_results_file" ] "kallisto_quant_results_file": "kallisto_quant_results_file"
]
) )
emit: emit:

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

@@ -246,8 +246,12 @@ argument_groups:
# MultiQC # MultiQC
- name: "--multiqc_custom_config" - name: "--multiqc_custom_config"
type: file type: file
description: |
Custom multiqc configuration file
- name: "--multiqc_title" - name: "--multiqc_title"
type: string type: string
description: |
Custom multiqc title
- name: "--multiqc_methods_description" - name: "--multiqc_methods_description"
type: file type: file
- name: "--passed_trimmed_reads" - name: "--passed_trimmed_reads"

1558
src/workflows/quality_control/main.nf
View File

File diff suppressed because it is too large Load Diff

28
src/workflows/rnaseq/config.vsh.yaml
View File

@@ -218,9 +218,10 @@ argument_groups:
type: boolean type: boolean
description: Skip the adapter trimming step. description: Skip the adapter trimming step.
default: false default: false
- name: "--skip_bbsplit" # See:
type: boolean_true # - name: "--skip_bbsplit"
description: Skip BBSplit for removal of non-reference genome reads. # type: boolean_true
# description: Skip BBSplit for removal of non-reference genome reads.
- name: "--skip_umi_extract" - name: "--skip_umi_extract"
type: boolean type: boolean
description: Skip umi_tools extract step. description: Skip umi_tools extract step.
@@ -243,9 +244,9 @@ argument_groups:
- name: "--skip_preseq" - name: "--skip_preseq"
type: boolean_true type: boolean_true
description: Skip Preseq. description: Skip Preseq.
- name: "--skip_deseq2_qc" # - name: "--skip_deseq2_qc"
type: boolean_true # type: boolean_true
description: Skip DESeq2 PCA and heatmap plotting. # description: Skip DESeq2 PCA and heatmap plotting.
- name: --skip_dupradar - name: --skip_dupradar
type: boolean_true type: boolean_true
description: Skip dupRadar. description: Skip dupRadar.
@@ -285,13 +286,15 @@ argument_groups:
arguments: arguments:
- name: "--multiqc_custom_config" - name: "--multiqc_custom_config"
type: file type: file
default: src/assets/multiqc_config.yml description: |
Custom multiqc configuration file
- name: "--multiqc_title" - name: "--multiqc_title"
type: string type: string
description: |
Custom multiqc title
- name: "--multiqc_methods_description" - name: "--multiqc_methods_description"
type: file type: file
default: src/assets/methods_description_template.yml
- name: Output - name: Output
arguments: arguments:
# Reference files # Reference files
@@ -886,12 +889,17 @@ argument_groups:
type: file type: file
direction: output direction: output
default: pseudo_alignment_quantification/quant_merged_summarizedexperiment default: pseudo_alignment_quantification/quant_merged_summarizedexperiment
resources: resources:
- type: nextflow_script - type: nextflow_script
path: main.nf path: main.nf
entrypoint: run_wf entrypoint: run_wf
test_resources:
- type: nextflow_script
path: test.nf
entrypoint: test_wf
dependencies: dependencies:
- name: workflows/prepare_genome - name: workflows/prepare_genome
- name: cat_fastq - name: cat_fastq

665
src/workflows/rnaseq/main.nf
View File

@@ -3,6 +3,7 @@ workflow run_wf {
input_ch input_ch
main: main:
reference_ch = input_ch reference_ch = input_ch
| map { id, state -> | map { id, state ->
@@ -21,8 +22,8 @@ workflow run_wf {
| toSortedList | toSortedList
| map { list -> | map { list ->
[ "ref", [ "ref", [
[ fasta: list.collect { id, state -> state.fasta }.unique()[0], fasta: list.collect { id, state -> state.fasta }.unique()[0],
gtf: list.collect { id, state -> state.gtf }.unique()[0], gtf: list.collect { id, state -> state.gtf }.unique()[0],
gff: list.collect { id, state -> state.gff }.unique()[0], gff: list.collect { id, state -> state.gff }.unique()[0],
additional_fasta: list.collect { id, state -> state.additional_fasta }.unique()[0], additional_fasta: list.collect { id, state -> state.additional_fasta }.unique()[0],
@@ -38,7 +39,8 @@ workflow run_wf {
// splicesites: list.collect { id, state -> state.splicesites }.unique()[0], // splicesites: list.collect { id, state -> state.splicesites }.unique()[0],
// hisat2_index: list.collect { id, state -> state.hisat2_index }.unique()[0], // hisat2_index: list.collect { id, state -> state.hisat2_index }.unique()[0],
bbsplit_index: list.collect { id, state -> state.bbsplit_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], // See:
skip_bbsplit: true, // list.collect { id, state -> state.skip_bbsplit }.unique()[0],
skip_alignment: list.collect { id, state -> state.skip_alignment }.unique()[0], skip_alignment: list.collect { id, state -> state.skip_alignment }.unique()[0],
gencode: list.collect { id, state -> state.gencode }.unique()[0], gencode: list.collect { id, state -> state.gencode }.unique()[0],
biotype: list.collect { id, state -> state.biotype }.unique()[0], biotype: list.collect { id, state -> state.biotype }.unique()[0],
@@ -50,43 +52,43 @@ workflow run_wf {
// prepare all the necessary files for reference genome // prepare all the necessary files for reference genome
| prepare_genome.run ( | prepare_genome.run (
fromState: [ fromState: [
"fasta": "fasta", "fasta": "fasta",
"gtf": "gtf", "gtf": "gtf",
"gff": "gff", "gff": "gff",
"additional_fasta": "additional_fasta", "additional_fasta": "additional_fasta",
"transcript_fasta": "transcript_fasta", "transcript_fasta": "transcript_fasta",
"gene_bed": "gene_bed", "gene_bed": "gene_bed",
"bbsplit_fasta_list": "bbsplit_fasta_list", "bbsplit_fasta_list": "bbsplit_fasta_list",
"star_index": "star_index", "star_index": "star_index",
"rsem_index": "rsem_index", "rsem_index": "rsem_index",
"salmon_index": "salmon_index", "salmon_index": "salmon_index",
"kallisto_index": "kallisto_index", "kallisto_index": "kallisto_index",
"pseudo_aligner_kmer_size": "pseudo_aligner_kmer_size", "pseudo_aligner_kmer_size": "pseudo_aligner_kmer_size",
// "splicesites": "splicesites", // "splicesites": "splicesites",
// "hisat2_index": "hisat2_index", // "hisat2_index": "hisat2_index",
"bbsplit_index": "bbsplit_index", "bbsplit_index": "bbsplit_index",
"skip_bbsplit": "skip_bbsplit", "skip_bbsplit": "skip_bbsplit",
"gencode": "gencode", "gencode": "gencode",
"biotype": "biotype", "biotype": "biotype",
"filter_gtf": "filter_gtf", "filter_gtf": "filter_gtf",
"aligner": "aligner", "aligner": "aligner",
"pseudo_aligner": "pseudo_aligner", "pseudo_aligner": "pseudo_aligner",
"skip_alignment": "skip_alignment", "skip_alignment": "skip_alignment",
"star_sjdb_gtf_feature_exon": "star_sjdb_gtf_feature_exon" "star_sjdb_gtf_feature_exon": "star_sjdb_gtf_feature_exon"
], ],
toState: [ toState: [
"fasta": "uncompressed_fasta", "fasta": "uncompressed_fasta",
"gtf": "gtf_uncompressed", "gtf": "gtf_uncompressed",
"transcript_fasta": "transcript_fasta_uncompressed", "transcript_fasta": "transcript_fasta_uncompressed",
"fai": "fai", "fai": "fai",
"chrom_sizes": "chrom_sizes", "chrom_sizes": "chrom_sizes",
"bbsplit_index": "bbsplit_index_uncompressed", "bbsplit_index": "bbsplit_index_uncompressed",
"star_index": "star_index_uncompressed", "star_index": "star_index_uncompressed",
"salmon_index": "salmon_index_uncompressed", "salmon_index": "salmon_index_uncompressed",
"kallisto_index": "kallisto_index_uncompressed", "kallisto_index": "kallisto_index_uncompressed",
"gene_bed": "gene_bed_uncompressed" "gene_bed": "gene_bed_uncompressed"
] ]
) )
// Check if contigs in genome fasta file > 512 Mbp // Check if contigs in genome fasta file > 512 Mbp
@@ -94,6 +96,7 @@ workflow run_wf {
(isBelowMaxContigSize(state.fai)) ? [id, state] : [id, state + [bam_csi_index: true]] (isBelowMaxContigSize(state.fai)) ? [id, state] : [id, state + [bam_csi_index: true]]
} }
// Pick out the state
| map { list -> list[1]} | map { list -> list[1]}
analysis_ch = input_ch analysis_ch = input_ch
@@ -104,73 +107,74 @@ workflow run_wf {
// Concatenate FastQ files from same sample if required // Concatenate FastQ files from same sample if required
| cat_fastq.run ( | cat_fastq.run (
fromState: [ fromState: [
"read_1": "fastq_1", "read_1": "fastq_1",
"read_2": "fastq_2" "read_2": "fastq_2"
], ],
toState: [ toState: [
"fastq_1": "fastq_1", "fastq_1": "fastq_1",
"fastq_2": "fastq_2" "fastq_2": "fastq_2"
] ],
directives: [ label: [ "lowmem", "midcpu" ] ]
) )
// Pre-process fastq files // Pre-process fastq files
| pre_processing.run ( | pre_processing.run (
fromState: [ fromState: [
"id": "id", "id": "id",
"fastq_1": "fastq_1", "fastq_1": "fastq_1",
"fastq_2": "fastq_2", "fastq_2": "fastq_2",
"umitools_bc_pattern": "umitools_bc_pattern", "umitools_bc_pattern": "umitools_bc_pattern",
"umitools_bc_pattern2": "umitools_bc_pattern2", "umitools_bc_pattern2": "umitools_bc_pattern2",
"strandedness": "strandedness", "strandedness": "strandedness",
"transcript_fasta": "transcript_fasta", "transcript_fasta": "transcript_fasta",
"gtf": "gtf", "gtf": "gtf",
"with_umi": "with_umi", "with_umi": "with_umi",
"bbsplit_index": "bbsplit_index", "bbsplit_index": "bbsplit_index",
"bbsplit_fasta_list": "bbsplit_fasta_list", "bbsplit_fasta_list": "bbsplit_fasta_list",
"bc_pattern": "bc_pattern", "bc_pattern": "bc_pattern",
"ribo_database_manifest": "ribo_database_manifest", "ribo_database_manifest": "ribo_database_manifest",
"salmon_index": "salmon_index", "salmon_index": "salmon_index",
"skip_qc": "skip_qc", "skip_qc": "skip_qc",
"skip_fastqc": "skip_fastqc", "skip_fastqc": "skip_fastqc",
"skip_skip_umi_extract": "skip_umi_extract", "skip_skip_umi_extract": "skip_umi_extract",
"umi_discard_read": "umi_discard_read", "umi_discard_read": "umi_discard_read",
"skip_trimming": "skip_trimming", "skip_trimming": "skip_trimming",
"trimmer": "trimmer", "trimmer": "trimmer",
"skip_bbsplit": "skip_bbsplit", "skip_bbsplit": "skip_bbsplit",
"remove_ribo_rna": "remove_ribo_rna" "remove_ribo_rna": "remove_ribo_rna"
], ],
toState: [ toState: [
"fastqc_html_1": "fastqc_html_1", "fastqc_html_1": "fastqc_html_1",
"fastqc_html_2": "fastqc_html_2", "fastqc_html_2": "fastqc_html_2",
"fastqc_zip_1": "fastqc_zip_1", "fastqc_zip_1": "fastqc_zip_1",
"fastqc_zip_2": "fastqc_zip_2", "fastqc_zip_2": "fastqc_zip_2",
"fastq_1": "qc_output1", "fastq_1": "qc_output1",
"fastq_2": "qc_output2", "fastq_2": "qc_output2",
"trim_log_1": "trim_log_1", "trim_log_1": "trim_log_1",
"trim_log_2": "trim_log_2", "trim_log_2": "trim_log_2",
"trim_zip_1": "trim_zip_1", "trim_zip_1": "trim_zip_1",
"trim_zip_2": "trim_zip_2", "trim_zip_2": "trim_zip_2",
"trim_html_1": "trim_html_1", "trim_html_1": "trim_html_1",
"trim_html_2": "trim_html_2", "trim_html_2": "trim_html_2",
"passed_trimmed_reads": "passed_trimmed_reads", "passed_trimmed_reads": "passed_trimmed_reads",
"num_trimmed_reads": "num_trimmed_reads", "num_trimmed_reads": "num_trimmed_reads",
"sortmerna_log": "sortmerna_log", "sortmerna_log": "sortmerna_log",
"salmon_quant_output": "salmon_quant_output", "salmon_quant_output": "salmon_quant_output",
"fastp_failed_trim": "failed_trim", "fastp_failed_trim": "failed_trim",
"fastp_failed_trim_unpaired1": "failed_trim_unpaired1", "fastp_failed_trim_unpaired1": "failed_trim_unpaired1",
"fastp_failed_trim_unpaired2": "failed_trim_unpaired2", "fastp_failed_trim_unpaired2": "failed_trim_unpaired2",
"fastp_trim_json": "trim_json", "fastp_trim_json": "trim_json",
"fastp_trim_html": "trim_html", "fastp_trim_html": "trim_html",
"fastp_trim_merged_out": "trim_merged_out" "fastp_trim_merged_out": "trim_merged_out"
] ]
) )
// Infer strandedness from Salmon pseudo-alignment results // Infer strandedness from Salmon pseudo-alignment results
| map { id, state -> | map { id, state ->
(state.strandedness == 'auto') ? (state.strandedness == 'auto') ?
[ id, state + [strandedness: getSalmonInferredStrandedness(state.salmon_quant_output)] ] : [ id, state + [strandedness: getSalmonInferredStrandedness(state.salmon_quant_output)] ] :
[id, state] [id, state]
} }
// Filter FastQ files based on minimum trimmed read count after adapter trimming // Filter FastQ files based on minimum trimmed read count after adapter trimming
@@ -196,49 +200,49 @@ workflow run_wf {
// Genome alignment and quantification // Genome alignment and quantification
| genome_alignment_and_quant.run ( | genome_alignment_and_quant.run (
runIf: { id, state -> !state.skip_alignment && state.passed_trimmed_reads }, runIf: { id, state -> !state.skip_alignment && state.passed_trimmed_reads },
fromState: [ fromState: [
"id": "id", "id": "id",
"fastq_1": "fastq_1", "fastq_1": "fastq_1",
"fastq_2": "fastq_2", "fastq_2": "fastq_2",
"strandedness": "strandedness", "strandedness": "strandedness",
"gtf": "gtf", "gtf": "gtf",
"transcript_fasta": "transcript_fasta", "transcript_fasta": "transcript_fasta",
"bam_csi_index": "bam_csi_index", "bam_csi_index": "bam_csi_index",
"aligner": "aligner", "aligner": "aligner",
"rsem_index": "rsem_index", "rsem_index": "rsem_index",
"star_index": "star_index", "star_index": "star_index",
"star_sjdb_gtf_feature_exon": "star_sjdb_gtf_feature_exon", "star_sjdb_gtf_feature_exon": "star_sjdb_gtf_feature_exon",
"star_ignore_sjdbgtf": "star_ignore_sjdbgtf", "star_ignore_sjdbgtf": "star_ignore_sjdbgtf",
"with_umi": "with_umi", "with_umi": "with_umi",
"umi_dedup_stats": "umi_dedup_stats", "umi_dedup_stats": "umi_dedup_stats",
"gtf_group_features": "gtf_group_features", "gtf_group_features": "gtf_group_features",
"gtf_extra_attributes": "gtf_extra_attributes", "gtf_extra_attributes": "gtf_extra_attributes",
"salmon_quant_libtype": "salmon_quant_libtype", "salmon_quant_libtype": "salmon_quant_libtype",
"salmon_index": "salmon_index", "salmon_index": "salmon_index",
"extra_rsem_calculate_expression_args": "extra_rsem_calculate_expression_args" "extra_rsem_calculate_expression_args": "extra_rsem_calculate_expression_args"
], ],
toState: [ toState: [
"star_multiqc": "star_multiqc", "star_multiqc": "star_multiqc",
"rsem_multiqc": "rsem_multiqc", "rsem_multiqc": "rsem_multiqc",
"salmon_multiqc": "salmon_multiqc", "salmon_multiqc": "salmon_multiqc",
"genome_bam_sorted": "genome_bam_sorted", "genome_bam_sorted": "genome_bam_sorted",
"genome_bam_index": "genome_bam_index", "genome_bam_index": "genome_bam_index",
"genome_bam_stats": "genome_bam_stats", "genome_bam_stats": "genome_bam_stats",
"genome_bam_flagstat": "genome_bam_flagstat", "genome_bam_flagstat": "genome_bam_flagstat",
"genome_bam_idxstats": "genome_bam_idxstats", "genome_bam_idxstats": "genome_bam_idxstats",
"transcriptome_bam": "transcriptome_bam", "transcriptome_bam": "transcriptome_bam",
"transcriptome_bam_index": "transcriptome_bam_index", "transcriptome_bam_index": "transcriptome_bam_index",
"transcriptome_bam_stats": "transcriptome_bam_stats", "transcriptome_bam_stats": "transcriptome_bam_stats",
"transcriptome_bam_flagstat": "transcriptome_bam_flagstat", "transcriptome_bam_flagstat": "transcriptome_bam_flagstat",
"transcriptome_bam_idxstats": "transcriptome_bam_idxstats", "transcriptome_bam_idxstats": "transcriptome_bam_idxstats",
"quant_out_dir": "quant_out_dir", "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_gene": "rsem_counts_gene",
"rsem_counts_transcripts": "rsem_counts_transcripts", "rsem_counts_transcripts": "rsem_counts_transcripts",
"bam_genome_rsem": "bam_genome_rsem", "bam_genome_rsem": "bam_genome_rsem",
"bam_transcript_rsem": "bam_transcript_rsem" "bam_transcript_rsem": "bam_transcript_rsem"
] ]
) )
// Filter channels to get samples that passed STAR minimum mapping percentage // Filter channels to get samples that passed STAR minimum mapping percentage
@@ -250,35 +254,35 @@ workflow run_wf {
// Pseudo-alignment and quantification // Pseudo-alignment and quantification
| pseudo_alignment_and_quant.run ( | pseudo_alignment_and_quant.run (
runIf: { id, state -> !state.skip_pseudo_alignment && state.passed_trimmed_reads }, runIf: { id, state -> !state.skip_pseudo_alignment && state.passed_trimmed_reads },
fromState: [ fromState: [
"id": "id", "id": "id",
"fastq_1": "fastq_1", "fastq_1": "fastq_1",
"fastq_2": "fastq_2", "fastq_2": "fastq_2",
"strandedness": "strandedness", "strandedness": "strandedness",
"gtf": "gtf", "gtf": "gtf",
"transcript_fasta": "transcript_fasta", "transcript_fasta": "transcript_fasta",
"pseudo_aligner": "pseudo_aligner", "pseudo_aligner": "pseudo_aligner",
"salmon_index": "salmon_index", "salmon_index": "salmon_index",
"kallisto_index": "kallisto_index", "kallisto_index": "kallisto_index",
"extra_star_align_args": "extra_star_align_args", "extra_star_align_args": "extra_star_align_args",
"star_ignore_sjdbgtf": "star_ignore_sjdbgtf", "star_ignore_sjdbgtf": "star_ignore_sjdbgtf",
"seq_platform": "seq_platform", "seq_platform": "seq_platform",
"seq_center": "seq_center", "seq_center": "seq_center",
"with_umi": "with_umi", "with_umi": "with_umi",
"umi_dedup_stats": "umi_dedup_stats", "umi_dedup_stats": "umi_dedup_stats",
"gtf_group_features": "gtf_group_features", "gtf_group_features": "gtf_group_features",
"gtf_extra_attributes": "gtf_extra_attributes", "gtf_extra_attributes": "gtf_extra_attributes",
"lib_type": "salmon_quant_libtype", "lib_type": "salmon_quant_libtype",
"kallisto_quant_fragment_length": "kallisto_quant_fragment_length", "kallisto_quant_fragment_length": "kallisto_quant_fragment_length",
"kallisto_quant_fragment_length_sd": "kallisto_quant_fragment_length_sd" "kallisto_quant_fragment_length_sd": "kallisto_quant_fragment_length_sd"
], ],
toState: [ toState: [
"pseudo_quant_out_dir": "quant_out_dir", "pseudo_quant_out_dir": "quant_out_dir",
"pseudo_salmon_quant_results_file": "salmon_quant_results_file", "pseudo_salmon_quant_results_file": "salmon_quant_results_file",
"pseudo_kallisto_quant_results_file": "kallisto_quant_results_file", "pseudo_kallisto_quant_results_file": "kallisto_quant_results_file",
"pseudo_multiqc": "pseudo_multiqc" "pseudo_multiqc": "pseudo_multiqc"
] ]
) )
| map { id, state -> | map { id, state ->
@@ -289,165 +293,170 @@ workflow run_wf {
// Post-processing // Post-processing
| post_processing.run ( | post_processing.run (
runIf: { id, state -> !state.skip_alignment && state.passed_trimmed_reads && state.passed_mapping }, runIf: { id, state -> !state.skip_alignment && state.passed_trimmed_reads && state.passed_mapping },
fromState: [ fromState: [
"id": "id", "id": "id",
"paired": "paired", "paired": "paired",
"strandedness": "strandedness", "strandedness": "strandedness",
"fasta": "fasta", "fasta": "fasta",
"fai": "fai", "fai": "fai",
"gtf": "gtf", "gtf": "gtf",
"genome_bam": "genome_bam_sorted", "genome_bam": "genome_bam_sorted",
"chrom_sizes": "chrom_sizes", "chrom_sizes": "chrom_sizes",
"star_multiqc": "star_multiqc", "star_multiqc": "star_multiqc",
"extra_picard_args": "extra_picard_args", "extra_picard_args": "extra_picard_args",
"extra_stringtie_args": "extra_stringtie_args", "extra_stringtie_args": "extra_stringtie_args",
"stringtie_ignore_gtf": "stringtie_ignore_gtf", "stringtie_ignore_gtf": "stringtie_ignore_gtf",
"extra_bedtools_args": "extra_bedtools_args", "extra_bedtools_args": "extra_bedtools_args",
"bam_csi_index": "bam_csi_index", "bam_csi_index": "bam_csi_index",
"min_mapped_reads": "min_mapped_reads", "min_mapped_reads": "min_mapped_reads",
"with_umi": "with_umi", "with_umi": "with_umi",
"skip_qc": "skip_qc", "skip_qc": "skip_qc",
"skip_markduplicates": "skip_markduplicates", "skip_markduplicates": "skip_markduplicates",
"skip_stringtie": "skip_stringtie", "skip_stringtie": "skip_stringtie",
"skip_bigwig":"gencode" "skip_bigwig":"gencode"
], ],
toState: [ toState: [
"genome_bam_sorted": "processed_genome_bam", "genome_bam_sorted": "processed_genome_bam",
"genome_bam_index": "genome_bam_index", "genome_bam_index": "genome_bam_index",
"genome_bam_stats": "genome_bam_stats", "genome_bam_stats": "genome_bam_stats",
"genome_bam_flagstat": "genome_bam_flagstat", "genome_bam_flagstat": "genome_bam_flagstat",
"genome_bam_idxstats": "genome_bam_idxstats", "genome_bam_idxstats": "genome_bam_idxstats",
"markduplicates_metrics": "markduplicates_metrics", "markduplicates_metrics": "markduplicates_metrics",
"stringtie_transcript_gtf": "stringtie_transcript_gtf", "stringtie_transcript_gtf": "stringtie_transcript_gtf",
"stringtie_coverage_gtf": "stringtie_coverage_gtf", "stringtie_coverage_gtf": "stringtie_coverage_gtf",
"stringtie_abundance": "stringtie_abundance", "stringtie_abundance": "stringtie_abundance",
"stringtie_ballgown": "stringtie_ballgown", "stringtie_ballgown": "stringtie_ballgown",
"bedgraph_forward": "bedgraph_forward", "bedgraph_forward": "bedgraph_forward",
"bedgraph_reverse": "bedgraph_reverse", "bedgraph_reverse": "bedgraph_reverse",
"bigwig_forward": "bigwig_forward", "bigwig_forward": "bigwig_forward",
"bigwig_reverse": "bigwig_reverse" "bigwig_reverse": "bigwig_reverse"
] ]
) )
// Final QC // Final QC
// Temporarily skip DESeq2 QC for now
// https://github.com/viash-hub/rnaseq/issues/31
| map{ id, state -> [ id, state + [ skip_deseq2_qc: true ] ] }
| quality_control.run ( | quality_control.run (
fromState: [ fromState: [
"id": "id", "id": "id",
"paired": "paired", "paired": "paired",
"strandedness": "strandedness", "strandedness": "strandedness",
"skip_align": "skip_alignment", "skip_align": "skip_alignment",
"skip_pseudo_align": "skip_pseudo_alignment", "skip_pseudo_align": "skip_pseudo_alignment",
"skip_dupradar": "skip_dupradar", "skip_dupradar": "skip_dupradar",
"skip_qualimap": "skip_qualimap", "skip_qualimap": "skip_qualimap",
"skip_rseqc": "skip_rseqc", "skip_rseqc": "skip_rseqc",
"skip_multiqc": "skip_multiqc", "skip_multiqc": "skip_multiqc",
"skip_preseq": "skip_preseq", "skip_preseq": "skip_preseq",
"gtf": "gtf", "gtf": "gtf",
"num_trimmed_reads": "num_trimmed_reads", "num_trimmed_reads": "num_trimmed_reads",
"passed_trimmed_reads": "passed_trimmed_reads", "passed_trimmed_reads": "passed_trimmed_reads",
"passed_mapping": "passed_mapping", "passed_mapping": "passed_mapping",
"percent_mapped": "percent_mapped", "percent_mapped": "percent_mapped",
"genome_bam": "genome_bam_sorted", "genome_bam": "genome_bam_sorted",
"genome_bam_index": "genome_bam_index", "genome_bam_index": "genome_bam_index",
"salmon_multiqc": "salmon_multiqc", "salmon_multiqc": "salmon_multiqc",
"quant_results_file": "quant_results_file", "quant_results_file": "quant_results_file",
"rsem_multiqc": "rsem_multiqc", "rsem_multiqc": "rsem_multiqc",
"rsem_counts_gene": "rsem_counts_gene", "rsem_counts_gene": "rsem_counts_gene",
"rsem_counts_transcripts": "rsem_counts_transcripts", "rsem_counts_transcripts": "rsem_counts_transcripts",
"pseudo_multiqc": "pseudo_multiqc", "pseudo_multiqc": "pseudo_multiqc",
"pseudo_quant_out_dir": "pseudo_quant_out_dir", "pseudo_quant_out_dir": "pseudo_quant_out_dir",
"pseudo_salmon_quant_results_file": "pseudo_salmon_quant_results_file", "pseudo_salmon_quant_results_file": "pseudo_salmon_quant_results_file",
"pseudo_kallisto_quant_results_file": "pseudo_kallisto_quant_results_file", "pseudo_kallisto_quant_results_file": "pseudo_kallisto_quant_results_file",
"aligner": "aligner", "aligner": "aligner",
"pseudo_aligner": "pseudo_aligner", "pseudo_aligner": "pseudo_aligner",
"gene_bed": "gene_bed", "gene_bed": "gene_bed",
"extra_preseq_args": "extra_preseq_args", "extra_preseq_args": "extra_preseq_args",
"biotype": "biotype", "biotype": "biotype",
"skip_biotype_qc": "skip_biotype_qc", "skip_biotype_qc": "skip_biotype_qc",
"featurecounts_group_type": "featurecounts_group_type", "featurecounts_group_type": "featurecounts_group_type",
"featurecounts_feature_type": "featurecounts_feature_type", "featurecounts_feature_type": "featurecounts_feature_type",
"gencode": "gencode", "gencode": "gencode",
"skip_deseq2_qc": "skip_deseq2_qc", "skip_deseq2_qc": "skip_deseq2_qc",
"deseq2_vst": "deseq2_vst", "deseq2_vst": "deseq2_vst",
"multiqc_custom_config": "multiqc_custom_config", "multiqc_custom_config": "multiqc_custom_config",
"multiqc_title": "multiqc_title", "multiqc_title": "multiqc_title",
"multiqc_methods_description": "multiqc_methods_description", "multiqc_methods_description": "multiqc_methods_description",
"fastqc_zip_1": "fastqc_zip_1", "fastqc_zip_1": "fastqc_zip_1",
"fastqc_zip_2": "fastqc_zip_2", "fastqc_zip_2": "fastqc_zip_2",
"trim_log_1": "trim_log_1", "trim_log_1": "trim_log_1",
"trim_log_2": "trim_log_2", "trim_log_2": "trim_log_2",
"trim_zip_1": "trim_zip_1", "trim_zip_1": "trim_zip_1",
"trim_zip_2": "trim_zip_2", "trim_zip_2": "trim_zip_2",
"sortmerna_multiqc": "sortmerna_log", "sortmerna_multiqc": "sortmerna_log",
"star_multiqc": "star_multiqc", "star_multiqc": "star_multiqc",
"genome_bam_stats": "genome_bam_stats", "genome_bam_stats": "genome_bam_stats",
"genome_bam_flagstat": "genome_bam_flagstat", "genome_bam_flagstat": "genome_bam_flagstat",
"genome_bam_idxstats": "genome_bam_idxstats", "genome_bam_idxstats": "genome_bam_idxstats",
"markduplicates_multiqc": "markduplicates_metrics", "markduplicates_multiqc": "markduplicates_metrics",
"rseqc_modules": "rseqc_modules" "rseqc_modules": "rseqc_modules"
], ],
toState: [ toState: [
"preseq_output": "preseq_output", "preseq_output": "preseq_output",
"bamstat_output": "bamstat_output", "bamstat_output": "bamstat_output",
"strandedness_output": "strandedness_output", "strandedness_output": "strandedness_output",
"inner_dist_output_stats": "inner_dist_output_stats", "inner_dist_output_stats": "inner_dist_output_stats",
"inner_dist_output_dist": "inner_dist_output_dist", "inner_dist_output_dist": "inner_dist_output_dist",
"inner_dist_output_freq": "inner_dist_output_freq", "inner_dist_output_freq": "inner_dist_output_freq",
"inner_dist_output_plot": "inner_dist_output_plot", "inner_dist_output_plot": "inner_dist_output_plot",
"inner_dist_output_plot_r": "inner_dist_output_plot_r", "inner_dist_output_plot_r": "inner_dist_output_plot_r",
"junction_annotation_output_log": "junction_annotation_output_log", "junction_annotation_output_log": "junction_annotation_output_log",
"junction_annotation_output_plot_r": "junction_annotation_output_plot_r", "junction_annotation_output_plot_r": "junction_annotation_output_plot_r",
"junction_annotation_output_junction_bed": "junction_annotation_output_junction_bed", "junction_annotation_output_junction_bed": "junction_annotation_output_junction_bed",
"junction_annotation_output_junction_interact": "junction_annotation_output_junction_interact", "junction_annotation_output_junction_interact": "junction_annotation_output_junction_interact",
"junction_annotation_output_junction_sheet": "junction_annotation_output_junction_sheet", "junction_annotation_output_junction_sheet": "junction_annotation_output_junction_sheet",
"junction_annotation_output_splice_events_plot": "junction_annotation_output_splice_events_plot", "junction_annotation_output_splice_events_plot": "junction_annotation_output_splice_events_plot",
"junction_annotation_output_splice_junctions_plot": "junction_annotation_output_splice_junctions_plot", "junction_annotation_output_splice_junctions_plot": "junction_annotation_output_splice_junctions_plot",
"junction_saturation_output_plot_r": "junction_saturation_output_plot_r", "junction_saturation_output_plot_r": "junction_saturation_output_plot_r",
"junction_saturation_output_plot": "junction_saturation_output_plot", "junction_saturation_output_plot": "junction_saturation_output_plot",
"read_distribution_output": "read_distribution_output", "read_distribution_output": "read_distribution_output",
"read_duplication_output_duplication_rate_plot_r": "read_duplication_output_duplication_rate_plot_r", "read_duplication_output_duplication_rate_plot_r": "read_duplication_output_duplication_rate_plot_r",
"read_duplication_output_duplication_rate_plot": "read_duplication_output_duplication_rate_plot", "read_duplication_output_duplication_rate_plot": "read_duplication_output_duplication_rate_plot",
"read_duplication_output_duplication_rate_mapping": "read_duplication_output_duplication_rate_mapping", "read_duplication_output_duplication_rate_mapping": "read_duplication_output_duplication_rate_mapping",
"read_duplication_output_duplication_rate_sequence": "read_duplication_output_duplication_rate_sequence", "read_duplication_output_duplication_rate_sequence": "read_duplication_output_duplication_rate_sequence",
"tin_output_summary": "tin_output_summary", "tin_output_summary": "tin_output_summary",
"tin_output_metrics": "tin_output_metrics", "tin_output_metrics": "tin_output_metrics",
"dupradar_output_dupmatrix": "dupradar_output_dupmatrix", "dupradar_output_dupmatrix": "dupradar_output_dupmatrix",
"dupradar_output_dup_intercept_mqc": "dupradar_output_dup_intercept_mqc", "dupradar_output_dup_intercept_mqc": "dupradar_output_dup_intercept_mqc",
"dupradar_output_duprate_exp_boxplot": "dupradar_output_duprate_exp_boxplot", "dupradar_output_duprate_exp_boxplot": "dupradar_output_duprate_exp_boxplot",
"dupradar_output_duprate_exp_densplot": "dupradar_output_duprate_exp_densplot", "dupradar_output_duprate_exp_densplot": "dupradar_output_duprate_exp_densplot",
"dupradar_output_duprate_exp_denscurve_mqc": "dupradar_output_duprate_exp_denscurve_mqc", "dupradar_output_duprate_exp_denscurve_mqc": "dupradar_output_duprate_exp_denscurve_mqc",
"dupradar_output_expression_histogram": "dupradar_output_expression_histogram", "dupradar_output_expression_histogram": "dupradar_output_expression_histogram",
"dupradar_output_intercept_slope": "dupradar_output_intercept_slope", "dupradar_output_intercept_slope": "dupradar_output_intercept_slope",
"qualimap_report": "qualimap_report", "qualimap_report": "qualimap_report",
"qualimap_qc_report": "qualimap_qc_report", "qualimap_qc_report": "qualimap_qc_report",
"qualimap_counts": "qualimap_counts", "qualimap_counts": "qualimap_counts",
"featurecounts": "featurecounts", "featurecounts": "featurecounts",
"featurecounts_summary": "featurecounts_summary", "featurecounts_summary": "featurecounts_summary",
"featurecounts_multiqc": "featurecounts_multiqc", "featurecounts_multiqc": "featurecounts_multiqc",
"featurecounts_rrna_multiqc": "featurecounts_rrna_multiqc", "featurecounts_rrna_multiqc": "featurecounts_rrna_multiqc",
"tpm_gene": "tpm_gene", "tpm_gene": "tpm_gene",
"counts_gene": "counts_gene", "counts_gene": "counts_gene",
"counts_gene_length_scaled": "counts_gene_length_scaled", "counts_gene_length_scaled": "counts_gene_length_scaled",
"counts_gene_scaled": "counts_gene_scaled", "counts_gene_scaled": "counts_gene_scaled",
"tpm_transcript": "tpm_transcript", "tpm_transcript": "tpm_transcript",
"counts_transcript": "counts_transcript", "counts_transcript": "counts_transcript",
"qunat_merged_summarizedexperiment": "quant_merged_summarizedexperiment", "quant_merged_summarizedexperiment": "quant_merged_summarizedexperiment",
"deseq2_output": "deseq2_output", "deseq2_output": "deseq2_output",
"pseudo_tpm_gene": "pseudo_tpm_gene", "pseudo_tpm_gene": "pseudo_tpm_gene",
"pseudo_counts_gene": "pseudo_counts_gene", "pseudo_counts_gene": "pseudo_counts_gene",
"pseudo_counts_gene_length_scaled": "pseudo_counts_gene_length_scaled", "pseudo_counts_gene_length_scaled": "pseudo_counts_gene_length_scaled",
"pseudo_counts_gene_scaled": "pseudo_counts_gene_scaled", "pseudo_counts_gene_scaled": "pseudo_counts_gene_scaled",
"pseudo_tpm_transcript": "pseudo_tpm_transcript", "pseudo_tpm_transcript": "pseudo_tpm_transcript",
"pseudo_counts_transcript": "pseudo_counts_transcript", "pseudo_counts_transcript": "pseudo_counts_transcript",
"pseudo_lengths_gene": "pseudo_lengths_gene", "pseudo_lengths_gene": "pseudo_lengths_gene",
"pseudo_lengths_transcript": "pseudo_lengths_transcript", "pseudo_lengths_transcript": "pseudo_lengths_transcript",
"pseudo_quant_merged_summarizedexperiment": "pseudo_quant_merged_summarizedexperiment", "pseudo_quant_merged_summarizedexperiment": "pseudo_quant_merged_summarizedexperiment",
"deseq2_output_pseudo": "deseq2_output_pseudo", "deseq2_output_pseudo": "deseq2_output_pseudo",
"multiqc_report": "multiqc_report", "multiqc_report": "multiqc_report",
"multiqc_data": "multiqc_data", "multiqc_data": "multiqc_data",
"multiqc_plots": "multiqc_plots" "multiqc_plots": "multiqc_plots"
] ]
) )
| map { id, state -> | map { id, state ->
@@ -639,8 +648,8 @@ def getTrimGaloreReadsAfterFiltering(log_file) {
// Function that parses fastp json output file to get total number of reads after trimming // Function that parses fastp json output file to get total number of reads after trimming
// //
def getFastpReadsAfterFiltering(json_file) { def getFastpReadsAfterFiltering(json_file) {
def Map json = (Map) new JsonSlurper().parseText(json_file.text).get('summary') def Map json = (Map) new JsonSlurper().parseText(json_file.text).get('summary')
return json['after_filtering']['total_reads'].toLong() return json['after_filtering']['total_reads'].toLong()
} }
// //

14
src/workflows/rnaseq/nextflow.config Normal file
View File

@@ -0,0 +1,14 @@
manifest {
nextflowVersion = '!>=20.12.1-edge'
}
params {
rootDir = java.nio.file.Paths.get("$projectDir/../../../").toAbsolutePath().normalize().toString()
}
// Some important settings
docker.fixOwnership = true
process.container = "nextflow/nextflow:24.04.2"
// include common settings
includeConfig("${params.rootDir}/src/workflows/utils/labels.config")

53
src/workflows/rnaseq/test.nf Normal file
View File

@@ -0,0 +1,53 @@
include { rnaseq } from params.rootDir + "/target/nextflow/workflows/rnaseq/main.nf"
params.resources_test = params.rootDir + "/resources_test"
workflow test_wf {
resources_test = file(params.resources_test)
output_ch =
Channel.fromList([
[
id: "_test",
fastq_1: "https://github.com/nf-core/test-datasets/raw/refs/heads/rnaseq/testdata/GSE110004/SRR6357070_1.fastq.gz;" +
"https://github.com/nf-core/test-datasets/raw/refs/heads/rnaseq/testdata/GSE110004/SRR6357071_1.fastq.gz" ,
fastq_2: "https://github.com/nf-core/test-datasets/raw/refs/heads/rnaseq/testdata/GSE110004/SRR6357070_2.fastq.gz;" +
"https://github.com/nf-core/test-datasets/raw/refs/heads/rnaseq/testdata/GSE110004/SRR6357071_2.fastq.gz",
strandedness: "reverse",
fasta: "https://github.com/nf-core/test-datasets/raw/refs/heads/rnaseq/reference/genome.fasta",
gtf: "https://github.com/nf-core/test-datasets/raw/refs/heads/rnaseq/reference/genes.gtf.gz",
additional_fasta: "https://github.com/nf-core/test-datasets/raw/refs/heads/rnaseq/reference/gfp.fa.gz",
transcript_fasta: "https://github.com/nf-core/test-datasets/raw/refs/heads/rnaseq/reference/transcriptome.fasta",
salmon_index: "https://github.com/nf-core/test-datasets/raw/refs/heads/rnaseq/reference/salmon.tar.gz",
publish_dir: "output/",
skip_deseq2_qc: true
]
])
| map { state -> [state.id, state] }
| rnaseq.run(
fromState: { id, state -> state },
toState: { id, output, state -> output }
)
| view { output ->
assert output.size() == 2 : "Outputs should contain two elements; [id, state]"
// check id
def id = output[0]
assert id.endsWith("_test")
// check output
def state = output[1]
assert state instanceof Map : "State should be a map. Found: ${state}"
assert state.containsKey("output_fasta") : "Output should contain key 'output_fasta'."
assert state.output_fasta.isFile() : "'output_fasta' should be a file."
assert state.containsKey("output_gtf") : "Output should contain key 'output_gtf'."
assert state.output_gtf.isFile() : "'output_gtf' should be a file."
"Output: $output"
}
}

44
src/workflows/utils/labels.config Normal file
View File

@@ -0,0 +1,44 @@
process {
// Default resources for components that hardly do any processing
memory = { 2.GB * task.attempt }
cpus = 1
// Retry for exit codes that have something to do with memory issues
errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
maxRetries = 3
maxMemory = null
// Resource labels
withLabel: singlecpu { cpus = 1 }
withLabel: lowcpu { cpus = 2 }
withLabel: midcpu { cpus = 4 }
withLabel: highcpu { cpus = 8 }
withLabel: veryhighcpu { cpus = 16 }
withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
withLabel: highmem { memory = { get_memory( 24.GB * task.attempt ) } }
withLabel: veryhighmem { memory = { get_memory( 48.GB * task.attempt ) } }
}
def get_memory(to_compare) {
if (!process.containsKey("maxMemory") || !process.maxMemory) {
return to_compare
}
try {
if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
return process.maxMemory
}
else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
return max_memory as nextflow.util.MemoryUnit
}
else {
return to_compare
}
} catch (all) {
println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
System.exit(1)
}
}

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

@@ -368,9 +368,9 @@ build_info:
output: "target/nextflow/bbmap/bbmap_bbsplit" output: "target/nextflow/bbmap/bbmap_bbsplit"
executable: "target/nextflow/bbmap/bbmap_bbsplit/main.nf" executable: "target/nextflow/bbmap/bbmap_bbsplit/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d" git_tag: "v0.2.0-27-g952ff08"
package_config: package_config:
name: "biobox" name: "biobox"
version: "main" version: "main"

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

@@ -3220,9 +3220,9 @@ meta = [
"engine" : "docker|native", "engine" : "docker|native",
"output" : "target/nextflow/bbmap/bbmap_bbsplit", "output" : "target/nextflow/bbmap/bbmap_bbsplit",
"viash_version" : "0.9.0", "viash_version" : "0.9.0",
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d" "git_tag" : "v0.2.0-27-g952ff08"
}, },
"package_config" : { "package_config" : {
"name" : "biobox", "name" : "biobox",

22
target/dependencies/vsh/vsh/biobox/main/nextflow/bbmap/bbmap_bbsplit/nextflow_schema.json
View File

@@ -30,7 +30,7 @@
"description": "Type: `boolean_true`, default: `false`. Paired fastq files or not?", "description": "Type: `boolean_true`, default: `false`. Paired fastq files or not?",
"help_text": "Type: `boolean_true`, default: `false`. Paired fastq files or not?" "help_text": "Type: `boolean_true`, default: `false`. Paired fastq files or not?"
, ,
"default": "False" "default":false
} }
@@ -61,7 +61,7 @@
"description": "Type: `boolean_true`, default: `false`. If set, only builds the index", "description": "Type: `boolean_true`, default: `false`. If set, only builds the index",
"help_text": "Type: `boolean_true`, default: `false`. If set, only builds the index. Otherwise, mapping is performed." "help_text": "Type: `boolean_true`, default: `false`. If set, only builds the index. Otherwise, mapping is performed."
, ,
"default": "False" "default":false
} }
@@ -92,7 +92,7 @@
"description": "Type: `boolean_true`, default: `false`. True forces paired/interleaved input; false forces single-ended mapping", "description": "Type: `boolean_true`, default: `false`. True forces paired/interleaved input; false forces single-ended mapping",
"help_text": "Type: `boolean_true`, default: `false`. True forces paired/interleaved input; false forces single-ended mapping.\nIf not specified, interleaved status will be autodetected from read names.\n" "help_text": "Type: `boolean_true`, default: `false`. True forces paired/interleaved input; false forces single-ended mapping.\nIf not specified, interleaved status will be autodetected from read names.\n"
, ,
"default": "False" "default":false
} }
@@ -169,7 +169,7 @@
"description": "Type: `boolean_true`, default: `false`. Undo trimming after mapping", "description": "Type: `boolean_true`, default: `false`. Undo trimming after mapping",
"help_text": "Type: `boolean_true`, default: `false`. Undo trimming after mapping. Untrimmed bases will be soft-clipped in cigar strings." "help_text": "Type: `boolean_true`, default: `false`. Undo trimming after mapping. Untrimmed bases will be soft-clipped in cigar strings."
, ,
"default": "False" "default":false
} }
@@ -190,7 +190,7 @@
"description": "Type: `file`, default: `$id.$key.index.index`, example: `BBSplit_index`. Location to write the index", "description": "Type: `file`, default: `$id.$key.index.index`, example: `BBSplit_index`. Location to write the index",
"help_text": "Type: `file`, default: `$id.$key.index.index`, example: `BBSplit_index`. Location to write the index.\n" "help_text": "Type: `file`, default: `$id.$key.index.index`, example: `BBSplit_index`. Location to write the index.\n"
, ,
"default": "$id.$key.index.index" "default":"$id.$key.index.index"
} }
@@ -201,7 +201,7 @@
"description": "Type: `file`, default: `$id.$key.fastq_1.fastq`, example: `read_out1.fastq`. Output file for read 1", "description": "Type: `file`, default: `$id.$key.fastq_1.fastq`, example: `read_out1.fastq`. Output file for read 1",
"help_text": "Type: `file`, default: `$id.$key.fastq_1.fastq`, example: `read_out1.fastq`. Output file for read 1.\n" "help_text": "Type: `file`, default: `$id.$key.fastq_1.fastq`, example: `read_out1.fastq`. Output file for read 1.\n"
, ,
"default": "$id.$key.fastq_1.fastq" "default":"$id.$key.fastq_1.fastq"
} }
@@ -212,7 +212,7 @@
"description": "Type: `file`, default: `$id.$key.fastq_2.fastq`, example: `read_out2.fastq`. Output file for read 2", "description": "Type: `file`, default: `$id.$key.fastq_2.fastq`, example: `read_out2.fastq`. Output file for read 2",
"help_text": "Type: `file`, default: `$id.$key.fastq_2.fastq`, example: `read_out2.fastq`. Output file for read 2.\n" "help_text": "Type: `file`, default: `$id.$key.fastq_2.fastq`, example: `read_out2.fastq`. Output file for read 2.\n"
, ,
"default": "$id.$key.fastq_2.fastq" "default":"$id.$key.fastq_2.fastq"
} }
@@ -223,7 +223,7 @@
"description": "Type: `file`, default: `$id.$key.sam2bam.sh`, example: `script.sh`. Write a shell script to \u0027file\u0027 that will turn the sam output into a sorted, indexed bam file", "description": "Type: `file`, default: `$id.$key.sam2bam.sh`, example: `script.sh`. Write a shell script to \u0027file\u0027 that will turn the sam output into a sorted, indexed bam file",
"help_text": "Type: `file`, default: `$id.$key.sam2bam.sh`, example: `script.sh`. Write a shell script to \u0027file\u0027 that will turn the sam output into a sorted, indexed bam file.\n" "help_text": "Type: `file`, default: `$id.$key.sam2bam.sh`, example: `script.sh`. Write a shell script to \u0027file\u0027 that will turn the sam output into a sorted, indexed bam file.\n"
, ,
"default": "$id.$key.sam2bam.sh" "default":"$id.$key.sam2bam.sh"
} }
@@ -234,7 +234,7 @@
"description": "Type: `file`, default: `$id.$key.scafstats.txt`, example: `scaffold_stats.txt`. Write statistics on how many reads mapped to which scaffold to this file", "description": "Type: `file`, default: `$id.$key.scafstats.txt`, example: `scaffold_stats.txt`. Write statistics on how many reads mapped to which scaffold to this file",
"help_text": "Type: `file`, default: `$id.$key.scafstats.txt`, example: `scaffold_stats.txt`. Write statistics on how many reads mapped to which scaffold to this file.\n" "help_text": "Type: `file`, default: `$id.$key.scafstats.txt`, example: `scaffold_stats.txt`. Write statistics on how many reads mapped to which scaffold to this file.\n"
, ,
"default": "$id.$key.scafstats.txt" "default":"$id.$key.scafstats.txt"
} }
@@ -245,7 +245,7 @@
"description": "Type: `file`, default: `$id.$key.refstats.txt`, example: `reference_stats.txt`. Write statistics on how many reads were assigned to which reference to this file", "description": "Type: `file`, default: `$id.$key.refstats.txt`, example: `reference_stats.txt`. Write statistics on how many reads were assigned to which reference to this file",
"help_text": "Type: `file`, default: `$id.$key.refstats.txt`, example: `reference_stats.txt`. Write statistics on how many reads were assigned to which reference to this file.\nUnmapped reads whose mate mapped to a reference are considered assigned and will be counted.\n" "help_text": "Type: `file`, default: `$id.$key.refstats.txt`, example: `reference_stats.txt`. Write statistics on how many reads were assigned to which reference to this file.\nUnmapped reads whose mate mapped to a reference are considered assigned and will be counted.\n"
, ,
"default": "$id.$key.refstats.txt" "default":"$id.$key.refstats.txt"
} }
@@ -256,7 +256,7 @@
"description": "Type: `boolean_true`, default: `false`. Only print lines with nonzero coverage", "description": "Type: `boolean_true`, default: `false`. Only print lines with nonzero coverage",
"help_text": "Type: `boolean_true`, default: `false`. Only print lines with nonzero coverage." "help_text": "Type: `boolean_true`, default: `false`. Only print lines with nonzero coverage."
, ,
"default": "False" "default":false
} }

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

@@ -337,9 +337,9 @@ build_info:
output: "target/nextflow/bedtools/bedtools_genomecov" output: "target/nextflow/bedtools/bedtools_genomecov"
executable: "target/nextflow/bedtools/bedtools_genomecov/main.nf" executable: "target/nextflow/bedtools/bedtools_genomecov/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d" git_tag: "v0.2.0-27-g952ff08"
package_config: package_config:
name: "biobox" name: "biobox"
version: "main" version: "main"

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

@@ -3207,9 +3207,9 @@ meta = [
"engine" : "docker|native", "engine" : "docker|native",
"output" : "target/nextflow/bedtools/bedtools_genomecov", "output" : "target/nextflow/bedtools/bedtools_genomecov",
"viash_version" : "0.9.0", "viash_version" : "0.9.0",
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d" "git_tag" : "v0.2.0-27-g952ff08"
}, },
"package_config" : { "package_config" : {
"name" : "biobox", "name" : "biobox",

26
target/dependencies/vsh/vsh/biobox/main/nextflow/bedtools/bedtools_genomecov/nextflow_schema.json
View File

@@ -60,7 +60,7 @@
"description": "Type: `file`, required, default: `$id.$key.output.bed`, example: `output.bed`. The output BED file", "description": "Type: `file`, required, default: `$id.$key.output.bed`, example: `output.bed`. The output BED file",
"help_text": "Type: `file`, required, default: `$id.$key.output.bed`, example: `output.bed`. The output BED file. \n" "help_text": "Type: `file`, required, default: `$id.$key.output.bed`, example: `output.bed`. The output BED file. \n"
, ,
"default": "$id.$key.output.bed" "default":"$id.$key.output.bed"
} }
@@ -81,7 +81,7 @@
"description": "Type: `boolean_true`, default: `false`. Report the depth at each genome position (with one-based coordinates)", "description": "Type: `boolean_true`, default: `false`. Report the depth at each genome position (with one-based coordinates)",
"help_text": "Type: `boolean_true`, default: `false`. Report the depth at each genome position (with one-based coordinates).\nDefault behavior is to report a histogram.\n" "help_text": "Type: `boolean_true`, default: `false`. Report the depth at each genome position (with one-based coordinates).\nDefault behavior is to report a histogram.\n"
, ,
"default": "False" "default":false
} }
@@ -92,7 +92,7 @@
"description": "Type: `boolean_true`, default: `false`. Report the depth at each genome position (with zero-based coordinates)", "description": "Type: `boolean_true`, default: `false`. Report the depth at each genome position (with zero-based coordinates)",
"help_text": "Type: `boolean_true`, default: `false`. Report the depth at each genome position (with zero-based coordinates).\nReports only non-zero positions.\nDefault behavior is to report a histogram.\n" "help_text": "Type: `boolean_true`, default: `false`. Report the depth at each genome position (with zero-based coordinates).\nReports only non-zero positions.\nDefault behavior is to report a histogram.\n"
, ,
"default": "False" "default":false
} }
@@ -103,7 +103,7 @@
"description": "Type: `boolean_true`, default: `false`. Report depth in BedGraph format", "description": "Type: `boolean_true`, default: `false`. Report depth in BedGraph format",
"help_text": "Type: `boolean_true`, default: `false`. Report depth in BedGraph format. For details, see:\ngenome.ucsc.edu/goldenPath/help/bedgraph.html\n" "help_text": "Type: `boolean_true`, default: `false`. Report depth in BedGraph format. For details, see:\ngenome.ucsc.edu/goldenPath/help/bedgraph.html\n"
, ,
"default": "False" "default":false
} }
@@ -114,7 +114,7 @@
"description": "Type: `boolean_true`, default: `false`. Report depth in BedGraph format, as above (-bg)", "description": "Type: `boolean_true`, default: `false`. Report depth in BedGraph format, as above (-bg)",
"help_text": "Type: `boolean_true`, default: `false`. Report depth in BedGraph format, as above (-bg).\nHowever with this option, regions with zero \ncoverage are also reported. This allows one to\nquickly extract all regions of a genome with 0 \ncoverage by applying: \"grep -w 0$\" to the output.\n" "help_text": "Type: `boolean_true`, default: `false`. Report depth in BedGraph format, as above (-bg).\nHowever with this option, regions with zero \ncoverage are also reported. This allows one to\nquickly extract all regions of a genome with 0 \ncoverage by applying: \"grep -w 0$\" to the output.\n"
, ,
"default": "False" "default":false
} }
@@ -125,7 +125,7 @@
"description": "Type: `boolean_true`, default: `false`. Treat \"split\" BAM or BED12 entries as distinct BED intervals", "description": "Type: `boolean_true`, default: `false`. Treat \"split\" BAM or BED12 entries as distinct BED intervals",
"help_text": "Type: `boolean_true`, default: `false`. Treat \"split\" BAM or BED12 entries as distinct BED intervals.\nwhen computing coverage.\nFor BAM files, this uses the CIGAR \"N\" and \"D\" operations \nto infer the blocks for computing coverage.\nFor BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds\nfields (i.e., columns 10,11,12).\n" "help_text": "Type: `boolean_true`, default: `false`. Treat \"split\" BAM or BED12 entries as distinct BED intervals.\nwhen computing coverage.\nFor BAM files, this uses the CIGAR \"N\" and \"D\" operations \nto infer the blocks for computing coverage.\nFor BED12 files, this uses the BlockCount, BlockStarts, and BlockEnds\nfields (i.e., columns 10,11,12).\n"
, ,
"default": "False" "default":false
} }
@@ -136,7 +136,7 @@
"description": "Type: `boolean_true`, default: `false`. Ignore local deletions (CIGAR \"D\" operations) in BAM entries\nwhen computing coverage", "description": "Type: `boolean_true`, default: `false`. Ignore local deletions (CIGAR \"D\" operations) in BAM entries\nwhen computing coverage",
"help_text": "Type: `boolean_true`, default: `false`. Ignore local deletions (CIGAR \"D\" operations) in BAM entries\nwhen computing coverage.\n" "help_text": "Type: `boolean_true`, default: `false`. Ignore local deletions (CIGAR \"D\" operations) in BAM entries\nwhen computing coverage.\n"
, ,
"default": "False" "default":false
} }
@@ -159,7 +159,7 @@
"description": "Type: `boolean_true`, default: `false`. Calculate coverage of pair-end fragments", "description": "Type: `boolean_true`, default: `false`. Calculate coverage of pair-end fragments",
"help_text": "Type: `boolean_true`, default: `false`. Calculate coverage of pair-end fragments.\nWorks for BAM files only\n" "help_text": "Type: `boolean_true`, default: `false`. Calculate coverage of pair-end fragments.\nWorks for BAM files only\n"
, ,
"default": "False" "default":false
} }
@@ -170,7 +170,7 @@
"description": "Type: `boolean_true`, default: `false`. Force to use provided fragment size instead of read length\nWorks for BAM files only\n", "description": "Type: `boolean_true`, default: `false`. Force to use provided fragment size instead of read length\nWorks for BAM files only\n",
"help_text": "Type: `boolean_true`, default: `false`. Force to use provided fragment size instead of read length\nWorks for BAM files only\n" "help_text": "Type: `boolean_true`, default: `false`. Force to use provided fragment size instead of read length\nWorks for BAM files only\n"
, ,
"default": "False" "default":false
} }
@@ -181,7 +181,7 @@
"description": "Type: `boolean_true`, default: `false`. Change strand af the mate read (so both reads from the same strand) useful for strand specific\nWorks for BAM files only\n", "description": "Type: `boolean_true`, default: `false`. Change strand af the mate read (so both reads from the same strand) useful for strand specific\nWorks for BAM files only\n",
"help_text": "Type: `boolean_true`, default: `false`. Change strand af the mate read (so both reads from the same strand) useful for strand specific\nWorks for BAM files only\n" "help_text": "Type: `boolean_true`, default: `false`. Change strand af the mate read (so both reads from the same strand) useful for strand specific\nWorks for BAM files only\n"
, ,
"default": "False" "default":false
} }
@@ -192,7 +192,7 @@
"description": "Type: `boolean_true`, default: `false`. Calculate coverage of 5\" positions (instead of entire interval)", "description": "Type: `boolean_true`, default: `false`. Calculate coverage of 5\" positions (instead of entire interval)",
"help_text": "Type: `boolean_true`, default: `false`. Calculate coverage of 5\" positions (instead of entire interval).\n" "help_text": "Type: `boolean_true`, default: `false`. Calculate coverage of 5\" positions (instead of entire interval).\n"
, ,
"default": "False" "default":false
} }
@@ -203,7 +203,7 @@
"description": "Type: `boolean_true`, default: `false`. Calculate coverage of 3\" positions (instead of entire interval)", "description": "Type: `boolean_true`, default: `false`. Calculate coverage of 3\" positions (instead of entire interval)",
"help_text": "Type: `boolean_true`, default: `false`. Calculate coverage of 3\" positions (instead of entire interval).\n" "help_text": "Type: `boolean_true`, default: `false`. Calculate coverage of 3\" positions (instead of entire interval).\n"
, ,
"default": "False" "default":false
} }
@@ -234,7 +234,7 @@
"description": "Type: `boolean_true`, default: `false`. Adds a UCSC/Genome-Browser track line definition in the first line of the output", "description": "Type: `boolean_true`, default: `false`. Adds a UCSC/Genome-Browser track line definition in the first line of the output",
"help_text": "Type: `boolean_true`, default: `false`. Adds a UCSC/Genome-Browser track line definition in the first line of the output.\n- See here for more details about track line definition:\n http://genome.ucsc.edu/goldenPath/help/bedgraph.html\n- NOTE: When adding a trackline definition, the output BedGraph can be easily\n uploaded to the Genome Browser as a custom track,\n BUT CAN NOT be converted into a BigWig file (w/o removing the first line).\n" "help_text": "Type: `boolean_true`, default: `false`. Adds a UCSC/Genome-Browser track line definition in the first line of the output.\n- See here for more details about track line definition:\n http://genome.ucsc.edu/goldenPath/help/bedgraph.html\n- NOTE: When adding a trackline definition, the output BedGraph can be easily\n uploaded to the Genome Browser as a custom track,\n BUT CAN NOT be converted into a BigWig file (w/o removing the first line).\n"
, ,
"default": "False" "default":false
} }

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

@@ -1083,9 +1083,9 @@ build_info:
output: "target/nextflow/fastp" output: "target/nextflow/fastp"
executable: "target/nextflow/fastp/main.nf" executable: "target/nextflow/fastp/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d" git_tag: "v0.2.0-27-g952ff08"
package_config: package_config:
name: "biobox" name: "biobox"
version: "main" version: "main"

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

@@ -4023,9 +4023,9 @@ meta = [
"engine" : "docker|native", "engine" : "docker|native",
"output" : "target/nextflow/fastp", "output" : "target/nextflow/fastp",
"viash_version" : "0.9.0", "viash_version" : "0.9.0",
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d" "git_tag" : "v0.2.0-27-g952ff08"
}, },
"package_config" : { "package_config" : {
"name" : "biobox", "name" : "biobox",

58
target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/nextflow_schema.json
View File

@@ -50,7 +50,7 @@
"description": "Type: `file`, required, default: `$id.$key.out1.gz`, example: `out.R1.fq.gz`. The single-end or paired-end R1 reads that pass QC", "description": "Type: `file`, required, default: `$id.$key.out1.gz`, example: `out.R1.fq.gz`. The single-end or paired-end R1 reads that pass QC",
"help_text": "Type: `file`, required, default: `$id.$key.out1.gz`, example: `out.R1.fq.gz`. The single-end or paired-end R1 reads that pass QC. Will be gzipped if its file name ends with `.gz`." "help_text": "Type: `file`, required, default: `$id.$key.out1.gz`, example: `out.R1.fq.gz`. The single-end or paired-end R1 reads that pass QC. Will be gzipped if its file name ends with `.gz`."
, ,
"default": "$id.$key.out1.gz" "default":"$id.$key.out1.gz"
} }
@@ -61,7 +61,7 @@
"description": "Type: `file`, default: `$id.$key.out2.gz`, example: `out.R2.fq.gz`. The paired-end R2 reads that pass QC", "description": "Type: `file`, default: `$id.$key.out2.gz`, example: `out.R2.fq.gz`. The paired-end R2 reads that pass QC",
"help_text": "Type: `file`, default: `$id.$key.out2.gz`, example: `out.R2.fq.gz`. The paired-end R2 reads that pass QC. Will be gzipped if its file name ends with `.gz`." "help_text": "Type: `file`, default: `$id.$key.out2.gz`, example: `out.R2.fq.gz`. The paired-end R2 reads that pass QC. Will be gzipped if its file name ends with `.gz`."
, ,
"default": "$id.$key.out2.gz" "default":"$id.$key.out2.gz"
} }
@@ -72,7 +72,7 @@
"description": "Type: `file`, default: `$id.$key.unpaired1.gz`, example: `unpaired.R1.fq.gz`. Store the reads that `read1` passes filters but its paired `read2` doesn\u0027t", "description": "Type: `file`, default: `$id.$key.unpaired1.gz`, example: `unpaired.R1.fq.gz`. Store the reads that `read1` passes filters but its paired `read2` doesn\u0027t",
"help_text": "Type: `file`, default: `$id.$key.unpaired1.gz`, example: `unpaired.R1.fq.gz`. Store the reads that `read1` passes filters but its paired `read2` doesn\u0027t." "help_text": "Type: `file`, default: `$id.$key.unpaired1.gz`, example: `unpaired.R1.fq.gz`. Store the reads that `read1` passes filters but its paired `read2` doesn\u0027t."
, ,
"default": "$id.$key.unpaired1.gz" "default":"$id.$key.unpaired1.gz"
} }
@@ -83,7 +83,7 @@
"description": "Type: `file`, default: `$id.$key.unpaired2.gz`, example: `unpaired.R2.fq.gz`. Store the reads that `read2` passes filters but its paired `read1` doesn\u0027t", "description": "Type: `file`, default: `$id.$key.unpaired2.gz`, example: `unpaired.R2.fq.gz`. Store the reads that `read2` passes filters but its paired `read1` doesn\u0027t",
"help_text": "Type: `file`, default: `$id.$key.unpaired2.gz`, example: `unpaired.R2.fq.gz`. Store the reads that `read2` passes filters but its paired `read1` doesn\u0027t." "help_text": "Type: `file`, default: `$id.$key.unpaired2.gz`, example: `unpaired.R2.fq.gz`. Store the reads that `read2` passes filters but its paired `read1` doesn\u0027t."
, ,
"default": "$id.$key.unpaired2.gz" "default":"$id.$key.unpaired2.gz"
} }
@@ -94,7 +94,7 @@
"description": "Type: `file`, default: `$id.$key.failed_out.gz`, example: `failed.fq.gz`. Store the reads that fail filters", "description": "Type: `file`, default: `$id.$key.failed_out.gz`, example: `failed.fq.gz`. Store the reads that fail filters",
"help_text": "Type: `file`, default: `$id.$key.failed_out.gz`, example: `failed.fq.gz`. Store the reads that fail filters.\n\nIf one read failed and is written to --failed_out, its failure reason will be appended to its read name. For example, failed_quality_filter, failed_too_short etc.\nFor PE data, if unpaired reads are not stored (by giving --unpaired1 or --unpaired2), the failed pair of reads will be put together. If one read passes the filters but its pair doesn\u0027t, the failure reason will be paired_read_is_failing.\n" "help_text": "Type: `file`, default: `$id.$key.failed_out.gz`, example: `failed.fq.gz`. Store the reads that fail filters.\n\nIf one read failed and is written to --failed_out, its failure reason will be appended to its read name. For example, failed_quality_filter, failed_too_short etc.\nFor PE data, if unpaired reads are not stored (by giving --unpaired1 or --unpaired2), the failed pair of reads will be put together. If one read passes the filters but its pair doesn\u0027t, the failure reason will be paired_read_is_failing.\n"
, ,
"default": "$id.$key.failed_out.gz" "default":"$id.$key.failed_out.gz"
} }
@@ -105,7 +105,7 @@
"description": "Type: `file`, default: `$id.$key.overlapped_out.overlapped_out`. For each read pair, output the overlapped region if it has no any mismatched base", "description": "Type: `file`, default: `$id.$key.overlapped_out.overlapped_out`. For each read pair, output the overlapped region if it has no any mismatched base",
"help_text": "Type: `file`, default: `$id.$key.overlapped_out.overlapped_out`. For each read pair, output the overlapped region if it has no any mismatched base.\n" "help_text": "Type: `file`, default: `$id.$key.overlapped_out.overlapped_out`. For each read pair, output the overlapped region if it has no any mismatched base.\n"
, ,
"default": "$id.$key.overlapped_out.overlapped_out" "default":"$id.$key.overlapped_out.overlapped_out"
} }
@@ -126,7 +126,7 @@
"description": "Type: `file`, default: `$id.$key.json.json`, example: `out.json`. The json format report file name\n", "description": "Type: `file`, default: `$id.$key.json.json`, example: `out.json`. The json format report file name\n",
"help_text": "Type: `file`, default: `$id.$key.json.json`, example: `out.json`. The json format report file name\n" "help_text": "Type: `file`, default: `$id.$key.json.json`, example: `out.json`. The json format report file name\n"
, ,
"default": "$id.$key.json.json" "default":"$id.$key.json.json"
} }
@@ -137,7 +137,7 @@
"description": "Type: `file`, default: `$id.$key.html.html`, example: `out.html`. The html format report file name\n", "description": "Type: `file`, default: `$id.$key.html.html`, example: `out.html`. The html format report file name\n",
"help_text": "Type: `file`, default: `$id.$key.html.html`, example: `out.html`. The html format report file name\n" "help_text": "Type: `file`, default: `$id.$key.html.html`, example: `out.html`. The html format report file name\n"
, ,
"default": "$id.$key.html.html" "default":"$id.$key.html.html"
} }
@@ -168,7 +168,7 @@
"description": "Type: `boolean_true`, default: `false`. Disable adapter trimming", "description": "Type: `boolean_true`, default: `false`. Disable adapter trimming",
"help_text": "Type: `boolean_true`, default: `false`. Disable adapter trimming.\n" "help_text": "Type: `boolean_true`, default: `false`. Disable adapter trimming.\n"
, ,
"default": "False" "default":false
} }
@@ -179,7 +179,7 @@
"description": "Type: `boolean_true`, default: `false`. By default, the auto-detection for adapter is for SE data input only, turn on this option to enable it for PE data", "description": "Type: `boolean_true`, default: `false`. By default, the auto-detection for adapter is for SE data input only, turn on this option to enable it for PE data",
"help_text": "Type: `boolean_true`, default: `false`. By default, the auto-detection for adapter is for SE data input only, turn on this option to enable it for PE data.\n" "help_text": "Type: `boolean_true`, default: `false`. By default, the auto-detection for adapter is for SE data input only, turn on this option to enable it for PE data.\n"
, ,
"default": "False" "default":false
} }
@@ -300,7 +300,7 @@
"description": "Type: `boolean_true`, default: `false`. For paired-end input, merge each pair of reads into a single read if they are overlapped", "description": "Type: `boolean_true`, default: `false`. For paired-end input, merge each pair of reads into a single read if they are overlapped",
"help_text": "Type: `boolean_true`, default: `false`. For paired-end input, merge each pair of reads into a single read if they are overlapped. The merged reads will be written to the file given by --merged_out, the unmerged reads will be written to the files specified by --out1 and --out2. The merging mode is disabled by default.\n" "help_text": "Type: `boolean_true`, default: `false`. For paired-end input, merge each pair of reads into a single read if they are overlapped. The merged reads will be written to the file given by --merged_out, the unmerged reads will be written to the files specified by --out1 and --out2. The merging mode is disabled by default.\n"
, ,
"default": "False" "default":false
} }
@@ -311,7 +311,7 @@
"description": "Type: `file`, default: `$id.$key.merged_out.gz`, example: `merged.fq.gz`. In the merging mode, specify the file name to store merged output, or specify --stdout to stream the merged output", "description": "Type: `file`, default: `$id.$key.merged_out.gz`, example: `merged.fq.gz`. In the merging mode, specify the file name to store merged output, or specify --stdout to stream the merged output",
"help_text": "Type: `file`, default: `$id.$key.merged_out.gz`, example: `merged.fq.gz`. In the merging mode, specify the file name to store merged output, or specify --stdout to stream the merged output.\n" "help_text": "Type: `file`, default: `$id.$key.merged_out.gz`, example: `merged.fq.gz`. In the merging mode, specify the file name to store merged output, or specify --stdout to stream the merged output.\n"
, ,
"default": "$id.$key.merged_out.gz" "default":"$id.$key.merged_out.gz"
} }
@@ -322,7 +322,7 @@
"description": "Type: `boolean_true`, default: `false`. In the merging mode, write the unmerged or unpaired reads to the file specified by --merge", "description": "Type: `boolean_true`, default: `false`. In the merging mode, write the unmerged or unpaired reads to the file specified by --merge",
"help_text": "Type: `boolean_true`, default: `false`. In the merging mode, write the unmerged or unpaired reads to the file specified by --merge. Disabled by default.\n" "help_text": "Type: `boolean_true`, default: `false`. In the merging mode, write the unmerged or unpaired reads to the file specified by --merge. Disabled by default.\n"
, ,
"default": "False" "default":false
} }
@@ -343,7 +343,7 @@
"description": "Type: `boolean_true`, default: `false`. Indicate that \u003cin1\u003e is an interleaved FASTQ which contains both read1 and read2", "description": "Type: `boolean_true`, default: `false`. Indicate that \u003cin1\u003e is an interleaved FASTQ which contains both read1 and read2",
"help_text": "Type: `boolean_true`, default: `false`. Indicate that \u003cin1\u003e is an interleaved FASTQ which contains both read1 and read2. Disabled by default.\n" "help_text": "Type: `boolean_true`, default: `false`. Indicate that \u003cin1\u003e is an interleaved FASTQ which contains both read1 and read2. Disabled by default.\n"
, ,
"default": "False" "default":false
} }
@@ -354,7 +354,7 @@
"description": "Type: `boolean_true`, default: `false`. The MGI FASTQ ID format is not compatible with many BAM operation tools, enable this option to fix it", "description": "Type: `boolean_true`, default: `false`. The MGI FASTQ ID format is not compatible with many BAM operation tools, enable this option to fix it",
"help_text": "Type: `boolean_true`, default: `false`. The MGI FASTQ ID format is not compatible with many BAM operation tools, enable this option to fix it.\n" "help_text": "Type: `boolean_true`, default: `false`. The MGI FASTQ ID format is not compatible with many BAM operation tools, enable this option to fix it.\n"
, ,
"default": "False" "default":false
} }
@@ -365,7 +365,7 @@
"description": "Type: `boolean_true`, default: `false`. Indicate the input is using phred64 scoring (it\u0027ll be converted to phred33, so the output will still be phred33)\n", "description": "Type: `boolean_true`, default: `false`. Indicate the input is using phred64 scoring (it\u0027ll be converted to phred33, so the output will still be phred33)\n",
"help_text": "Type: `boolean_true`, default: `false`. Indicate the input is using phred64 scoring (it\u0027ll be converted to phred33, so the output will still be phred33)\n" "help_text": "Type: `boolean_true`, default: `false`. Indicate the input is using phred64 scoring (it\u0027ll be converted to phred33, so the output will still be phred33)\n"
, ,
"default": "False" "default":false
} }
@@ -396,7 +396,7 @@
"description": "Type: `boolean_true`, default: `false`. Don\u0027t overwrite existing files", "description": "Type: `boolean_true`, default: `false`. Don\u0027t overwrite existing files",
"help_text": "Type: `boolean_true`, default: `false`. Don\u0027t overwrite existing files. Overwritting is allowed by default.\n" "help_text": "Type: `boolean_true`, default: `false`. Don\u0027t overwrite existing files. Overwritting is allowed by default.\n"
, ,
"default": "False" "default":false
} }
@@ -417,7 +417,7 @@
"description": "Type: `boolean_true`, default: `false`. Output verbose log information (i", "description": "Type: `boolean_true`, default: `false`. Output verbose log information (i",
"help_text": "Type: `boolean_true`, default: `false`. Output verbose log information (i.e. when every 1M reads are processed)." "help_text": "Type: `boolean_true`, default: `false`. Output verbose log information (i.e. when every 1M reads are processed)."
, ,
"default": "False" "default":false
} }
@@ -458,7 +458,7 @@
"description": "Type: `boolean_true`, default: `false`. Enable deduplication to drop the duplicated reads/pairs\n", "description": "Type: `boolean_true`, default: `false`. Enable deduplication to drop the duplicated reads/pairs\n",
"help_text": "Type: `boolean_true`, default: `false`. Enable deduplication to drop the duplicated reads/pairs\n" "help_text": "Type: `boolean_true`, default: `false`. Enable deduplication to drop the duplicated reads/pairs\n"
, ,
"default": "False" "default":false
} }
@@ -479,7 +479,7 @@
"description": "Type: `boolean_true`, default: `false`. Don\u0027t evaluate duplication rate to save time and use less memory", "description": "Type: `boolean_true`, default: `false`. Don\u0027t evaluate duplication rate to save time and use less memory",
"help_text": "Type: `boolean_true`, default: `false`. Don\u0027t evaluate duplication rate to save time and use less memory.\n" "help_text": "Type: `boolean_true`, default: `false`. Don\u0027t evaluate duplication rate to save time and use less memory.\n"
, ,
"default": "False" "default":false
} }
@@ -500,7 +500,7 @@
"description": "Type: `boolean_true`, default: `false`. Force polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data\n", "description": "Type: `boolean_true`, default: `false`. Force polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data\n",
"help_text": "Type: `boolean_true`, default: `false`. Force polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data\n" "help_text": "Type: `boolean_true`, default: `false`. Force polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data\n"
, ,
"default": "False" "default":false
} }
@@ -521,7 +521,7 @@
"description": "Type: `boolean_true`, default: `false`. Disable polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data\n", "description": "Type: `boolean_true`, default: `false`. Disable polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data\n",
"help_text": "Type: `boolean_true`, default: `false`. Disable polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data\n" "help_text": "Type: `boolean_true`, default: `false`. Disable polyG tail trimming, by default trimming is automatically enabled for Illumina NextSeq/NovaSeq data\n"
, ,
"default": "False" "default":false
} }
@@ -542,7 +542,7 @@
"description": "Type: `boolean_true`, default: `false`. Enable polyX trimming in 3\u0027 ends", "description": "Type: `boolean_true`, default: `false`. Enable polyX trimming in 3\u0027 ends",
"help_text": "Type: `boolean_true`, default: `false`. Enable polyX trimming in 3\u0027 ends.\n" "help_text": "Type: `boolean_true`, default: `false`. Enable polyX trimming in 3\u0027 ends.\n"
, ,
"default": "False" "default":false
} }
@@ -693,7 +693,7 @@
"description": "Type: `boolean_true`, default: `false`. Quality filtering is enabled by default", "description": "Type: `boolean_true`, default: `false`. Quality filtering is enabled by default",
"help_text": "Type: `boolean_true`, default: `false`. Quality filtering is enabled by default. If this option is specified, quality filtering is disabled.\n" "help_text": "Type: `boolean_true`, default: `false`. Quality filtering is enabled by default. If this option is specified, quality filtering is disabled.\n"
, ,
"default": "False" "default":false
} }
@@ -754,7 +754,7 @@
"description": "Type: `boolean_true`, default: `false`. Length filtering is enabled by default", "description": "Type: `boolean_true`, default: `false`. Length filtering is enabled by default",
"help_text": "Type: `boolean_true`, default: `false`. Length filtering is enabled by default. If this option is specified, length filtering is disabled.\n" "help_text": "Type: `boolean_true`, default: `false`. Length filtering is enabled by default. If this option is specified, length filtering is disabled.\n"
, ,
"default": "False" "default":false
} }
@@ -795,7 +795,7 @@
"description": "Type: `boolean_true`, default: `false`. Enable low complexity filter", "description": "Type: `boolean_true`, default: `false`. Enable low complexity filter",
"help_text": "Type: `boolean_true`, default: `false`. Enable low complexity filter. The complexity is defined as the percentage of base that is different from its next base (base[i] != base[i+1]).\n" "help_text": "Type: `boolean_true`, default: `false`. Enable low complexity filter. The complexity is defined as the percentage of base that is different from its next base (base[i] != base[i+1]).\n"
, ,
"default": "False" "default":false
} }
@@ -866,7 +866,7 @@
"description": "Type: `boolean_true`, default: `false`. Enable base correction in overlapped regions (only for PE data), default is disabled", "description": "Type: `boolean_true`, default: `false`. Enable base correction in overlapped regions (only for PE data), default is disabled",
"help_text": "Type: `boolean_true`, default: `false`. Enable base correction in overlapped regions (only for PE data), default is disabled.\n" "help_text": "Type: `boolean_true`, default: `false`. Enable base correction in overlapped regions (only for PE data), default is disabled.\n"
, ,
"default": "False" "default":false
} }
@@ -917,7 +917,7 @@
"description": "Type: `boolean_true`, default: `false`. Enable unique molecular identifier (UMI) preprocessing", "description": "Type: `boolean_true`, default: `false`. Enable unique molecular identifier (UMI) preprocessing",
"help_text": "Type: `boolean_true`, default: `false`. Enable unique molecular identifier (UMI) preprocessing.\n" "help_text": "Type: `boolean_true`, default: `false`. Enable unique molecular identifier (UMI) preprocessing.\n"
, ,
"default": "False" "default":false
} }
@@ -990,7 +990,7 @@
"description": "Type: `boolean_true`, default: `false`. Enable overrepresentation analysis", "description": "Type: `boolean_true`, default: `false`. Enable overrepresentation analysis",
"help_text": "Type: `boolean_true`, default: `false`. Enable overrepresentation analysis.\n" "help_text": "Type: `boolean_true`, default: `false`. Enable overrepresentation analysis.\n"
, ,
"default": "False" "default":false
} }

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

@@ -340,9 +340,9 @@ build_info:
output: "target/nextflow/fastqc" output: "target/nextflow/fastqc"
executable: "target/nextflow/fastqc/main.nf" executable: "target/nextflow/fastqc/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d" git_tag: "v0.2.0-27-g952ff08"
package_config: package_config:
name: "biobox" name: "biobox"
version: "main" version: "main"

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

@@ -3182,9 +3182,9 @@ meta = [
"engine" : "docker|native", "engine" : "docker|native",
"output" : "target/nextflow/fastqc", "output" : "target/nextflow/fastqc",
"viash_version" : "0.9.0", "viash_version" : "0.9.0",
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d" "git_tag" : "v0.2.0-27-g952ff08"
}, },
"package_config" : { "package_config" : {
"name" : "biobox", "name" : "biobox",

18
target/dependencies/vsh/vsh/biobox/main/nextflow/fastqc/nextflow_schema.json
View File

@@ -40,7 +40,7 @@
"description": "Type: List of `file`, default: `$id.$key.html_*.html`, example: `*.html`, multiple_sep: `\";\"`. Create the HTML report of the results", "description": "Type: List of `file`, default: `$id.$key.html_*.html`, example: `*.html`, multiple_sep: `\";\"`. Create the HTML report of the results",
"help_text": "Type: List of `file`, default: `$id.$key.html_*.html`, example: `*.html`, multiple_sep: `\";\"`. Create the HTML report of the results. \n\u0027*\u0027 wild card must be provided in the output file name. \nWild card will be replaced by the input file basename.\ne.g. \n --input \"sample_1.fq\"\n --html \"*.html\"\n would create an output html file named sample_1.html\n" "help_text": "Type: List of `file`, default: `$id.$key.html_*.html`, example: `*.html`, multiple_sep: `\";\"`. Create the HTML report of the results. \n\u0027*\u0027 wild card must be provided in the output file name. \nWild card will be replaced by the input file basename.\ne.g. \n --input \"sample_1.fq\"\n --html \"*.html\"\n would create an output html file named sample_1.html\n"
, ,
"default": "$id.$key.html_*.html" "default":"$id.$key.html_*.html"
} }
@@ -51,7 +51,7 @@
"description": "Type: List of `file`, default: `$id.$key.zip_*.zip`, example: `*.zip`, multiple_sep: `\";\"`. Create the zip file(s) containing: html report, data, images, icons, summary, etc", "description": "Type: List of `file`, default: `$id.$key.zip_*.zip`, example: `*.zip`, multiple_sep: `\";\"`. Create the zip file(s) containing: html report, data, images, icons, summary, etc",
"help_text": "Type: List of `file`, default: `$id.$key.zip_*.zip`, example: `*.zip`, multiple_sep: `\";\"`. Create the zip file(s) containing: html report, data, images, icons, summary, etc.\n\u0027*\u0027 wild card must be provided in the output file name.\nWild card will be replaced by the input basename.\ne.g. \n --input \"sample_1.fq\"\n --html \"*.zip\"\n would create an output zip file named sample_1.zip\n" "help_text": "Type: List of `file`, default: `$id.$key.zip_*.zip`, example: `*.zip`, multiple_sep: `\";\"`. Create the zip file(s) containing: html report, data, images, icons, summary, etc.\n\u0027*\u0027 wild card must be provided in the output file name.\nWild card will be replaced by the input basename.\ne.g. \n --input \"sample_1.fq\"\n --html \"*.zip\"\n would create an output zip file named sample_1.zip\n"
, ,
"default": "$id.$key.zip_*.zip" "default":"$id.$key.zip_*.zip"
} }
@@ -62,7 +62,7 @@
"description": "Type: List of `file`, default: `$id.$key.summary_*.txt`, example: `*_summary.txt`, multiple_sep: `\";\"`. Create the summary file(s)", "description": "Type: List of `file`, default: `$id.$key.summary_*.txt`, example: `*_summary.txt`, multiple_sep: `\";\"`. Create the summary file(s)",
"help_text": "Type: List of `file`, default: `$id.$key.summary_*.txt`, example: `*_summary.txt`, multiple_sep: `\";\"`. Create the summary file(s).\n\u0027*\u0027 wild card must be provided in the output file name.\nWild card will be replaced by the input basename.\ne.g. \n --input \"sample_1.fq\"\n --summary \"*_summary.txt\"\n would create an output summary.txt file named sample_1_summary.txt\n" "help_text": "Type: List of `file`, default: `$id.$key.summary_*.txt`, example: `*_summary.txt`, multiple_sep: `\";\"`. Create the summary file(s).\n\u0027*\u0027 wild card must be provided in the output file name.\nWild card will be replaced by the input basename.\ne.g. \n --input \"sample_1.fq\"\n --summary \"*_summary.txt\"\n would create an output summary.txt file named sample_1_summary.txt\n"
, ,
"default": "$id.$key.summary_*.txt" "default":"$id.$key.summary_*.txt"
} }
@@ -73,7 +73,7 @@
"description": "Type: List of `file`, default: `$id.$key.data_*.txt`, example: `*_data.txt`, multiple_sep: `\";\"`. Create the data file(s)", "description": "Type: List of `file`, default: `$id.$key.data_*.txt`, example: `*_data.txt`, multiple_sep: `\";\"`. Create the data file(s)",
"help_text": "Type: List of `file`, default: `$id.$key.data_*.txt`, example: `*_data.txt`, multiple_sep: `\";\"`. Create the data file(s).\n\u0027*\u0027 wild card must be provided in the output file name.\nWild card will be replaced by the input basename.\ne.g. \n --input \"sample_1.fq\"\n --summary \"*_data.txt\"\n would create an output data.txt file named sample_1_data.txt\n" "help_text": "Type: List of `file`, default: `$id.$key.data_*.txt`, example: `*_data.txt`, multiple_sep: `\";\"`. Create the data file(s).\n\u0027*\u0027 wild card must be provided in the output file name.\nWild card will be replaced by the input basename.\ne.g. \n --input \"sample_1.fq\"\n --summary \"*_data.txt\"\n would create an output data.txt file named sample_1_data.txt\n"
, ,
"default": "$id.$key.data_*.txt" "default":"$id.$key.data_*.txt"
} }
@@ -94,7 +94,7 @@
"description": "Type: `boolean_true`, default: `false`. Files come from raw casava output", "description": "Type: `boolean_true`, default: `false`. Files come from raw casava output",
"help_text": "Type: `boolean_true`, default: `false`. Files come from raw casava output. Files in the same sample\ngroup (differing only by the group number) will be analysed\nas a set rather than individually. Sequences with the filter\nflag set in the header will be excluded from the analysis.\nFiles must have the same names given to them by casava\n(including being gzipped and ending with .gz) otherwise they\nwon\u0027t be grouped together correctly.\n" "help_text": "Type: `boolean_true`, default: `false`. Files come from raw casava output. Files in the same sample\ngroup (differing only by the group number) will be analysed\nas a set rather than individually. Sequences with the filter\nflag set in the header will be excluded from the analysis.\nFiles must have the same names given to them by casava\n(including being gzipped and ending with .gz) otherwise they\nwon\u0027t be grouped together correctly.\n"
, ,
"default": "False" "default":false
} }
@@ -105,7 +105,7 @@
"description": "Type: `boolean_true`, default: `false`. Files come from nanopore sequences and are in fast5 format", "description": "Type: `boolean_true`, default: `false`. Files come from nanopore sequences and are in fast5 format",
"help_text": "Type: `boolean_true`, default: `false`. Files come from nanopore sequences and are in fast5 format. In\nthis mode you can pass in directories to process and the program\nwill take in all fast5 files within those directories and produce\na single output file from the sequences found in all files.\n" "help_text": "Type: `boolean_true`, default: `false`. Files come from nanopore sequences and are in fast5 format. In\nthis mode you can pass in directories to process and the program\nwill take in all fast5 files within those directories and produce\na single output file from the sequences found in all files.\n"
, ,
"default": "False" "default":false
} }
@@ -116,7 +116,7 @@
"description": "Type: `boolean_true`, default: `false`. If running with --casava then don\u0027t remove read flagged by\ncasava as poor quality when performing the QC analysis", "description": "Type: `boolean_true`, default: `false`. If running with --casava then don\u0027t remove read flagged by\ncasava as poor quality when performing the QC analysis",
"help_text": "Type: `boolean_true`, default: `false`. If running with --casava then don\u0027t remove read flagged by\ncasava as poor quality when performing the QC analysis.\n" "help_text": "Type: `boolean_true`, default: `false`. If running with --casava then don\u0027t remove read flagged by\ncasava as poor quality when performing the QC analysis.\n"
, ,
"default": "False" "default":false
} }
@@ -127,7 +127,7 @@
"description": "Type: `boolean_true`, default: `false`. Disable grouping of bases for reads \u003e50bp", "description": "Type: `boolean_true`, default: `false`. Disable grouping of bases for reads \u003e50bp",
"help_text": "Type: `boolean_true`, default: `false`. Disable grouping of bases for reads \u003e50bp. \nAll reports will show data for every base in the read. \nWARNING: Using this option will cause fastqc to crash \nand burn if you use it on really long reads, and your \nplots may end up a ridiculous size. You have been warned!\n" "help_text": "Type: `boolean_true`, default: `false`. Disable grouping of bases for reads \u003e50bp. \nAll reports will show data for every base in the read. \nWARNING: Using this option will cause fastqc to crash \nand burn if you use it on really long reads, and your \nplots may end up a ridiculous size. You have been warned!\n"
, ,
"default": "False" "default":false
} }
@@ -198,7 +198,7 @@
"description": "Type: `boolean_true`, default: `false`. Suppress all progress messages on stdout and only report errors", "description": "Type: `boolean_true`, default: `false`. Suppress all progress messages on stdout and only report errors",
"help_text": "Type: `boolean_true`, default: `false`. Suppress all progress messages on stdout and only report errors.\n" "help_text": "Type: `boolean_true`, default: `false`. Suppress all progress messages on stdout and only report errors.\n"
, ,
"default": "False" "default":false
} }

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

@@ -645,9 +645,9 @@ build_info:
output: "target/nextflow/featurecounts" output: "target/nextflow/featurecounts"
executable: "target/nextflow/featurecounts/main.nf" executable: "target/nextflow/featurecounts/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d" git_tag: "v0.2.0-27-g952ff08"
package_config: package_config:
name: "biobox" name: "biobox"
version: "main" version: "main"

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

@@ -3549,9 +3549,9 @@ meta = [
"engine" : "docker|native", "engine" : "docker|native",
"output" : "target/nextflow/featurecounts", "output" : "target/nextflow/featurecounts",
"viash_version" : "0.9.0", "viash_version" : "0.9.0",
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d" "git_tag" : "v0.2.0-27-g952ff08"
}, },
"package_config" : { "package_config" : {
"name" : "biobox", "name" : "biobox",

44
target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/nextflow_schema.json
View File

@@ -50,7 +50,7 @@
"description": "Type: `file`, required, default: `$id.$key.counts.tsv`, example: `features.tsv`. Name of output file including read counts in tab delimited format", "description": "Type: `file`, required, default: `$id.$key.counts.tsv`, example: `features.tsv`. Name of output file including read counts in tab delimited format",
"help_text": "Type: `file`, required, default: `$id.$key.counts.tsv`, example: `features.tsv`. Name of output file including read counts in tab delimited format.\n" "help_text": "Type: `file`, required, default: `$id.$key.counts.tsv`, example: `features.tsv`. Name of output file including read counts in tab delimited format.\n"
, ,
"default": "$id.$key.counts.tsv" "default":"$id.$key.counts.tsv"
} }
@@ -61,7 +61,7 @@
"description": "Type: `file`, default: `$id.$key.summary.tsv`, example: `summary.tsv`. Summary statistics of counting results in tab delimited format", "description": "Type: `file`, default: `$id.$key.summary.tsv`, example: `summary.tsv`. Summary statistics of counting results in tab delimited format",
"help_text": "Type: `file`, default: `$id.$key.summary.tsv`, example: `summary.tsv`. Summary statistics of counting results in tab delimited format.\n" "help_text": "Type: `file`, default: `$id.$key.summary.tsv`, example: `summary.tsv`. Summary statistics of counting results in tab delimited format.\n"
, ,
"default": "$id.$key.summary.tsv" "default":"$id.$key.summary.tsv"
} }
@@ -72,7 +72,7 @@
"description": "Type: `file`, default: `$id.$key.junctions.txt`, example: `junctions.txt`. Count number of reads supporting each exon-exon junction", "description": "Type: `file`, default: `$id.$key.junctions.txt`, example: `junctions.txt`. Count number of reads supporting each exon-exon junction",
"help_text": "Type: `file`, default: `$id.$key.junctions.txt`, example: `junctions.txt`. Count number of reads supporting each exon-exon junction. Junctions were identified from those exon-spanning reads in the input (containing \u0027N\u0027 in CIGAR string).\n" "help_text": "Type: `file`, default: `$id.$key.junctions.txt`, example: `junctions.txt`. Count number of reads supporting each exon-exon junction. Junctions were identified from those exon-spanning reads in the input (containing \u0027N\u0027 in CIGAR string).\n"
, ,
"default": "$id.$key.junctions.txt" "default":"$id.$key.junctions.txt"
} }
@@ -155,7 +155,7 @@
"description": "Type: `boolean_true`, default: `false`. Perform read counting at feature level (eg", "description": "Type: `boolean_true`, default: `false`. Perform read counting at feature level (eg",
"help_text": "Type: `boolean_true`, default: `false`. Perform read counting at feature level (eg. counting reads for exons rather than genes).\n" "help_text": "Type: `boolean_true`, default: `false`. Perform read counting at feature level (eg. counting reads for exons rather than genes).\n"
, ,
"default": "False" "default":false
} }
@@ -176,7 +176,7 @@
"description": "Type: `boolean_true`, default: `false`. Assign reads to all their overlapping meta-features (or features if \u0027--feature_level\u0027 is specified)", "description": "Type: `boolean_true`, default: `false`. Assign reads to all their overlapping meta-features (or features if \u0027--feature_level\u0027 is specified)",
"help_text": "Type: `boolean_true`, default: `false`. Assign reads to all their overlapping meta-features (or features if \u0027--feature_level\u0027 is specified).\n" "help_text": "Type: `boolean_true`, default: `false`. Assign reads to all their overlapping meta-features (or features if \u0027--feature_level\u0027 is specified).\n"
, ,
"default": "False" "default":false
} }
@@ -217,7 +217,7 @@
"description": "Type: `boolean_true`, default: `false`. Assign reads to a meta-feature/feature that has the largest number of overlapping bases", "description": "Type: `boolean_true`, default: `false`. Assign reads to a meta-feature/feature that has the largest number of overlapping bases",
"help_text": "Type: `boolean_true`, default: `false`. Assign reads to a meta-feature/feature that has the largest number of overlapping bases.\n" "help_text": "Type: `boolean_true`, default: `false`. Assign reads to a meta-feature/feature that has the largest number of overlapping bases.\n"
, ,
"default": "False" "default":false
} }
@@ -290,7 +290,7 @@
"description": "Type: `boolean_true`, default: `false`. Multi-mapping reads will also be counted", "description": "Type: `boolean_true`, default: `false`. Multi-mapping reads will also be counted",
"help_text": "Type: `boolean_true`, default: `false`. Multi-mapping reads will also be counted. For a multi-mapping read, all its reported alignments will be counted. The \u0027NH\u0027 tag in BAM/SAM input is used to detect multi-mapping reads.\n" "help_text": "Type: `boolean_true`, default: `false`. Multi-mapping reads will also be counted. For a multi-mapping read, all its reported alignments will be counted. The \u0027NH\u0027 tag in BAM/SAM input is used to detect multi-mapping reads.\n"
, ,
"default": "False" "default":false
} }
@@ -311,7 +311,7 @@
"description": "Type: `boolean_true`, default: `false`. Assign fractional counts to features", "description": "Type: `boolean_true`, default: `false`. Assign fractional counts to features",
"help_text": "Type: `boolean_true`, default: `false`. Assign fractional counts to features. This option must be used together with \u0027--multi_mapping\u0027 or \u0027--overlapping\u0027 or both. When \u0027--multi_mapping\u0027 is specified, each reported alignment from a multi-mapping read (identified via \u0027NH\u0027 tag) will carry a fractional count of 1/x, instead of 1 (one), where x is the total number of alignments reported for the same read. When \u0027--overlapping\u0027 is specified, each overlapping feature will receive a fractional count of 1/y, where y is the total number of features overlapping with the read. When both \u0027--multi_mapping\u0027 and \u0027--overlapping\u0027 are specified, each alignment will carry a fractional count of 1/(x*y).\n" "help_text": "Type: `boolean_true`, default: `false`. Assign fractional counts to features. This option must be used together with \u0027--multi_mapping\u0027 or \u0027--overlapping\u0027 or both. When \u0027--multi_mapping\u0027 is specified, each reported alignment from a multi-mapping read (identified via \u0027NH\u0027 tag) will carry a fractional count of 1/x, instead of 1 (one), where x is the total number of alignments reported for the same read. When \u0027--overlapping\u0027 is specified, each overlapping feature will receive a fractional count of 1/y, where y is the total number of features overlapping with the read. When both \u0027--multi_mapping\u0027 and \u0027--overlapping\u0027 are specified, each alignment will carry a fractional count of 1/(x*y).\n"
, ,
"default": "False" "default":false
} }
@@ -342,7 +342,7 @@
"description": "Type: `boolean_true`, default: `false`. Count split alignments only (ie", "description": "Type: `boolean_true`, default: `false`. Count split alignments only (ie",
"help_text": "Type: `boolean_true`, default: `false`. Count split alignments only (ie. alignments with CIGAR string containing \u0027N\u0027). An example of split alignments is exon-spanning reads in RNA-seq data.\n" "help_text": "Type: `boolean_true`, default: `false`. Count split alignments only (ie. alignments with CIGAR string containing \u0027N\u0027). An example of split alignments is exon-spanning reads in RNA-seq data.\n"
, ,
"default": "False" "default":false
} }
@@ -353,7 +353,7 @@
"description": "Type: `boolean_true`, default: `false`. If specified, only non-split alignments (CIGAR strings do not contain letter \u0027N\u0027) will be counted", "description": "Type: `boolean_true`, default: `false`. If specified, only non-split alignments (CIGAR strings do not contain letter \u0027N\u0027) will be counted",
"help_text": "Type: `boolean_true`, default: `false`. If specified, only non-split alignments (CIGAR strings do not contain letter \u0027N\u0027) will be counted. All the other alignments will be ignored.\n" "help_text": "Type: `boolean_true`, default: `false`. If specified, only non-split alignments (CIGAR strings do not contain letter \u0027N\u0027) will be counted. All the other alignments will be ignored.\n"
, ,
"default": "False" "default":false
} }
@@ -364,7 +364,7 @@
"description": "Type: `boolean_true`, default: `false`. Count primary alignments only", "description": "Type: `boolean_true`, default: `false`. Count primary alignments only",
"help_text": "Type: `boolean_true`, default: `false`. Count primary alignments only. Primary alignments are identified using bit 0x100 in SAM/BAM FLAG field.\n" "help_text": "Type: `boolean_true`, default: `false`. Count primary alignments only. Primary alignments are identified using bit 0x100 in SAM/BAM FLAG field.\n"
, ,
"default": "False" "default":false
} }
@@ -375,7 +375,7 @@
"description": "Type: `boolean_true`, default: `false`. Ignore duplicate reads in read counting", "description": "Type: `boolean_true`, default: `false`. Ignore duplicate reads in read counting",
"help_text": "Type: `boolean_true`, default: `false`. Ignore duplicate reads in read counting. Duplicate reads are identified using bit Ox400 in BAM/SAM FLAG field. The whole read pair is ignored if one of the reads is a duplicate read for paired end data.\n" "help_text": "Type: `boolean_true`, default: `false`. Ignore duplicate reads in read counting. Duplicate reads are identified using bit Ox400 in BAM/SAM FLAG field. The whole read pair is ignored if one of the reads is a duplicate read for paired end data.\n"
, ,
"default": "False" "default":false
} }
@@ -438,7 +438,7 @@
"description": "Type: `boolean_true`, default: `false`. Specify that input data contain paired-end reads", "description": "Type: `boolean_true`, default: `false`. Specify that input data contain paired-end reads",
"help_text": "Type: `boolean_true`, default: `false`. Specify that input data contain paired-end reads. To perform fragment counting (ie. counting read pairs), the \u0027--countReadPairs\u0027 parameter should also be specified in addition to this parameter.\n" "help_text": "Type: `boolean_true`, default: `false`. Specify that input data contain paired-end reads. To perform fragment counting (ie. counting read pairs), the \u0027--countReadPairs\u0027 parameter should also be specified in addition to this parameter.\n"
, ,
"default": "False" "default":false
} }
@@ -449,7 +449,7 @@
"description": "Type: `boolean_true`, default: `false`. Count read pairs (fragments) instead of reads", "description": "Type: `boolean_true`, default: `false`. Count read pairs (fragments) instead of reads",
"help_text": "Type: `boolean_true`, default: `false`. Count read pairs (fragments) instead of reads. This option is only applicable for paired-end reads.\n" "help_text": "Type: `boolean_true`, default: `false`. Count read pairs (fragments) instead of reads. This option is only applicable for paired-end reads.\n"
, ,
"default": "False" "default":false
} }
@@ -460,7 +460,7 @@
"description": "Type: `boolean_true`, default: `false`. Count read pairs (fragments) instead of reads", "description": "Type: `boolean_true`, default: `false`. Count read pairs (fragments) instead of reads",
"help_text": "Type: `boolean_true`, default: `false`. Count read pairs (fragments) instead of reads. This option is only applicable for paired-end reads.\n" "help_text": "Type: `boolean_true`, default: `false`. Count read pairs (fragments) instead of reads. This option is only applicable for paired-end reads.\n"
, ,
"default": "False" "default":false
} }
@@ -471,7 +471,7 @@
"description": "Type: `boolean_true`, default: `false`. Check validity of paired-end distance when counting read pairs", "description": "Type: `boolean_true`, default: `false`. Check validity of paired-end distance when counting read pairs",
"help_text": "Type: `boolean_true`, default: `false`. Check validity of paired-end distance when counting read pairs. Use \u0027--min_length\u0027 and \u0027--max_length\u0027 to set thresholds.\n" "help_text": "Type: `boolean_true`, default: `false`. Check validity of paired-end distance when counting read pairs. Use \u0027--min_length\u0027 and \u0027--max_length\u0027 to set thresholds.\n"
, ,
"default": "False" "default":false
} }
@@ -502,7 +502,7 @@
"description": "Type: `boolean_true`, default: `false`. Do not count read pairs that have their two ends mapping to different chromosomes or mapping to same chromosome but on different strands", "description": "Type: `boolean_true`, default: `false`. Do not count read pairs that have their two ends mapping to different chromosomes or mapping to same chromosome but on different strands",
"help_text": "Type: `boolean_true`, default: `false`. Do not count read pairs that have their two ends mapping to different chromosomes or mapping to same chromosome but on different strands.\n" "help_text": "Type: `boolean_true`, default: `false`. Do not count read pairs that have their two ends mapping to different chromosomes or mapping to same chromosome but on different strands.\n"
, ,
"default": "False" "default":false
} }
@@ -513,7 +513,7 @@
"description": "Type: `boolean_true`, default: `false`. Do not sort reads in BAM/SAM input", "description": "Type: `boolean_true`, default: `false`. Do not sort reads in BAM/SAM input",
"help_text": "Type: `boolean_true`, default: `false`. Do not sort reads in BAM/SAM input. Note that reads from the same pair are required to be located next to each other in the input.\n" "help_text": "Type: `boolean_true`, default: `false`. Do not sort reads in BAM/SAM input. Note that reads from the same pair are required to be located next to each other in the input.\n"
, ,
"default": "False" "default":false
} }
@@ -534,7 +534,7 @@
"description": "Type: `boolean_true`, default: `false`. Assign reads by read group", "description": "Type: `boolean_true`, default: `false`. Assign reads by read group",
"help_text": "Type: `boolean_true`, default: `false`. Assign reads by read group. \"RG\" tag is required to be present in the input BAM/SAM files.\n" "help_text": "Type: `boolean_true`, default: `false`. Assign reads by read group. \"RG\" tag is required to be present in the input BAM/SAM files.\n"
, ,
"default": "False" "default":false
} }
@@ -555,7 +555,7 @@
"description": "Type: `boolean_true`, default: `false`. Count long reads such as Nanopore and PacBio reads", "description": "Type: `boolean_true`, default: `false`. Count long reads such as Nanopore and PacBio reads",
"help_text": "Type: `boolean_true`, default: `false`. Count long reads such as Nanopore and PacBio reads. Long read counting can only run in one thread and only reads (not read-pairs) can be counted. There is no limitation on the number of \u0027M\u0027 operations allowed in a CIGAR string in long read counting.\n" "help_text": "Type: `boolean_true`, default: `false`. Count long reads such as Nanopore and PacBio reads. Long read counting can only run in one thread and only reads (not read-pairs) can be counted. There is no limitation on the number of \u0027M\u0027 operations allowed in a CIGAR string in long read counting.\n"
, ,
"default": "False" "default":false
} }
@@ -576,7 +576,7 @@
"description": "Type: `file`, default: `$id.$key.detailed_results.detailed_results`, example: `detailed_results`. Directory to save the detailed assignment results", "description": "Type: `file`, default: `$id.$key.detailed_results.detailed_results`, example: `detailed_results`. Directory to save the detailed assignment results",
"help_text": "Type: `file`, default: `$id.$key.detailed_results.detailed_results`, example: `detailed_results`. Directory to save the detailed assignment results. Use `--detailed_results_format` to determine the format of the detailed results.\n" "help_text": "Type: `file`, default: `$id.$key.detailed_results.detailed_results`, example: `detailed_results`. Directory to save the detailed assignment results. Use `--detailed_results_format` to determine the format of the detailed results.\n"
, ,
"default": "$id.$key.detailed_results.detailed_results" "default":"$id.$key.detailed_results.detailed_results"
} }
@@ -619,7 +619,7 @@
"description": "Type: `boolean_true`, default: `false`. Output verbose information for debugging, such as un-matched chromosome/contig names", "description": "Type: `boolean_true`, default: `false`. Output verbose information for debugging, such as un-matched chromosome/contig names",
"help_text": "Type: `boolean_true`, default: `false`. Output verbose information for debugging, such as un-matched chromosome/contig names.\n" "help_text": "Type: `boolean_true`, default: `false`. Output verbose information for debugging, such as un-matched chromosome/contig names.\n"
, ,
"default": "False" "default":false
} }

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

@@ -190,9 +190,9 @@ build_info:
output: "target/nextflow/fq_subsample" output: "target/nextflow/fq_subsample"
executable: "target/nextflow/fq_subsample/main.nf" executable: "target/nextflow/fq_subsample/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d" git_tag: "v0.2.0-27-g952ff08"
package_config: package_config:
name: "biobox" name: "biobox"
version: "main" version: "main"

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

@@ -3032,9 +3032,9 @@ meta = [
"engine" : "docker|native", "engine" : "docker|native",
"output" : "target/nextflow/fq_subsample", "output" : "target/nextflow/fq_subsample",
"viash_version" : "0.9.0", "viash_version" : "0.9.0",
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d" "git_tag" : "v0.2.0-27-g952ff08"
}, },
"package_config" : { "package_config" : {
"name" : "biobox", "name" : "biobox",

4
target/dependencies/vsh/vsh/biobox/main/nextflow/fq_subsample/nextflow_schema.json
View File

@@ -50,7 +50,7 @@
"description": "Type: `file`, default: `$id.$key.output_1.output_1`. Sampled read 1 fastq files", "description": "Type: `file`, default: `$id.$key.output_1.output_1`. Sampled read 1 fastq files",
"help_text": "Type: `file`, default: `$id.$key.output_1.output_1`. Sampled read 1 fastq files. Output will be gzipped if ends in `.gz`." "help_text": "Type: `file`, default: `$id.$key.output_1.output_1`. Sampled read 1 fastq files. Output will be gzipped if ends in `.gz`."
, ,
"default": "$id.$key.output_1.output_1" "default":"$id.$key.output_1.output_1"
} }
@@ -61,7 +61,7 @@
"description": "Type: `file`, default: `$id.$key.output_2.output_2`. Sampled read 2 fastq files", "description": "Type: `file`, default: `$id.$key.output_2.output_2`. Sampled read 2 fastq files",
"help_text": "Type: `file`, default: `$id.$key.output_2.output_2`. Sampled read 2 fastq files. Output will be gzipped if ends in `.gz`." "help_text": "Type: `file`, default: `$id.$key.output_2.output_2`. Sampled read 2 fastq files. Output will be gzipped if ends in `.gz`."
, ,
"default": "$id.$key.output_2.output_2" "default":"$id.$key.output_2.output_2"
} }

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

@@ -685,9 +685,9 @@ build_info:
output: "target/nextflow/gffread" output: "target/nextflow/gffread"
executable: "target/nextflow/gffread/main.nf" executable: "target/nextflow/gffread/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d" git_tag: "v0.2.0-27-g952ff08"
package_config: package_config:
name: "biobox" name: "biobox"
version: "main" version: "main"

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

@@ -3606,9 +3606,9 @@ meta = [
"engine" : "docker|native", "engine" : "docker|native",
"output" : "target/nextflow/gffread", "output" : "target/nextflow/gffread",
"viash_version" : "0.9.0", "viash_version" : "0.9.0",
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d" "git_tag" : "v0.2.0-27-g952ff08"
}, },
"package_config" : { "package_config" : {
"name" : "biobox", "name" : "biobox",

92
target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/nextflow_schema.json
View File

@@ -70,7 +70,7 @@
"description": "Type: `file`, required, default: `$id.$key.outfile.gff`, example: `output.gff`. Write the output records into \u003coutfile\u003e", "description": "Type: `file`, required, default: `$id.$key.outfile.gff`, example: `output.gff`. Write the output records into \u003coutfile\u003e",
"help_text": "Type: `file`, required, default: `$id.$key.outfile.gff`, example: `output.gff`. Write the output records into \u003coutfile\u003e.\n" "help_text": "Type: `file`, required, default: `$id.$key.outfile.gff`, example: `output.gff`. Write the output records into \u003coutfile\u003e.\n"
, ,
"default": "$id.$key.outfile.gff" "default":"$id.$key.outfile.gff"
} }
@@ -81,7 +81,7 @@
"description": "Type: `boolean_true`, default: `false`. Make sure that the lowest level GFF features are considered \"exon\" features", "description": "Type: `boolean_true`, default: `false`. Make sure that the lowest level GFF features are considered \"exon\" features",
"help_text": "Type: `boolean_true`, default: `false`. Make sure that the lowest level GFF features are considered \"exon\" features.\n" "help_text": "Type: `boolean_true`, default: `false`. Make sure that the lowest level GFF features are considered \"exon\" features.\n"
, ,
"default": "False" "default":false
} }
@@ -92,7 +92,7 @@
"description": "Type: `boolean_true`, default: `false`. For single-line genes not parenting any transcripts, add an exon feature spanning \nthe entire gene (treat it as a transcript)", "description": "Type: `boolean_true`, default: `false`. For single-line genes not parenting any transcripts, add an exon feature spanning \nthe entire gene (treat it as a transcript)",
"help_text": "Type: `boolean_true`, default: `false`. For single-line genes not parenting any transcripts, add an exon feature spanning \nthe entire gene (treat it as a transcript).\n" "help_text": "Type: `boolean_true`, default: `false`. For single-line genes not parenting any transcripts, add an exon feature spanning \nthe entire gene (treat it as a transcript).\n"
, ,
"default": "False" "default":false
} }
@@ -103,7 +103,7 @@
"description": "Type: `boolean_true`, default: `false`. Try to find a parent gene overlapping/containing a transcript that does not have \nany explicit gene Parent", "description": "Type: `boolean_true`, default: `false`. Try to find a parent gene overlapping/containing a transcript that does not have \nany explicit gene Parent",
"help_text": "Type: `boolean_true`, default: `false`. Try to find a parent gene overlapping/containing a transcript that does not have \nany explicit gene Parent.\n" "help_text": "Type: `boolean_true`, default: `false`. Try to find a parent gene overlapping/containing a transcript that does not have \nany explicit gene Parent.\n"
, ,
"default": "False" "default":false
} }
@@ -114,7 +114,7 @@
"description": "Type: `boolean_true`, default: `false`. Decode url encoded characters within attributes", "description": "Type: `boolean_true`, default: `false`. Decode url encoded characters within attributes",
"help_text": "Type: `boolean_true`, default: `false`. Decode url encoded characters within attributes.\n" "help_text": "Type: `boolean_true`, default: `false`. Decode url encoded characters within attributes.\n"
, ,
"default": "False" "default":false
} }
@@ -125,7 +125,7 @@
"description": "Type: `boolean_true`, default: `false`. Merge very close exons into a single exon (when intron size\u003c4)", "description": "Type: `boolean_true`, default: `false`. Merge very close exons into a single exon (when intron size\u003c4)",
"help_text": "Type: `boolean_true`, default: `false`. Merge very close exons into a single exon (when intron size\u003c4).\n" "help_text": "Type: `boolean_true`, default: `false`. Merge very close exons into a single exon (when intron size\u003c4).\n"
, ,
"default": "False" "default":false
} }
@@ -136,7 +136,7 @@
"description": "Type: `boolean_true`, default: `false`. Output the junctions and the corresponding transcripts", "description": "Type: `boolean_true`, default: `false`. Output the junctions and the corresponding transcripts",
"help_text": "Type: `boolean_true`, default: `false`. Output the junctions and the corresponding transcripts.\n" "help_text": "Type: `boolean_true`, default: `false`. Output the junctions and the corresponding transcripts.\n"
, ,
"default": "False" "default":false
} }
@@ -147,7 +147,7 @@
"description": "Type: `file`, default: `$id.$key.spliced_exons.fa`, example: `exons.fa`. Write a fasta file with spliced exons for each transcript", "description": "Type: `file`, default: `$id.$key.spliced_exons.fa`, example: `exons.fa`. Write a fasta file with spliced exons for each transcript",
"help_text": "Type: `file`, default: `$id.$key.spliced_exons.fa`, example: `exons.fa`. Write a fasta file with spliced exons for each transcript.\n" "help_text": "Type: `file`, default: `$id.$key.spliced_exons.fa`, example: `exons.fa`. Write a fasta file with spliced exons for each transcript.\n"
, ,
"default": "$id.$key.spliced_exons.fa" "default":"$id.$key.spliced_exons.fa"
} }
@@ -168,7 +168,7 @@
"description": "Type: `boolean_true`, default: `false`. For --spliced_exons, disable the output of CDS info in the FASTA file", "description": "Type: `boolean_true`, default: `false`. For --spliced_exons, disable the output of CDS info in the FASTA file",
"help_text": "Type: `boolean_true`, default: `false`. For --spliced_exons, disable the output of CDS info in the FASTA file.\n" "help_text": "Type: `boolean_true`, default: `false`. For --spliced_exons, disable the output of CDS info in the FASTA file.\n"
, ,
"default": "False" "default":false
} }
@@ -199,7 +199,7 @@
"description": "Type: `boolean_true`, default: `false`. For --spliced_exons, --spliced_cds and -tr_cds options, write in the FASTA defline \nall the exon coordinates projected onto the spliced sequence", "description": "Type: `boolean_true`, default: `false`. For --spliced_exons, --spliced_cds and -tr_cds options, write in the FASTA defline \nall the exon coordinates projected onto the spliced sequence",
"help_text": "Type: `boolean_true`, default: `false`. For --spliced_exons, --spliced_cds and -tr_cds options, write in the FASTA defline \nall the exon coordinates projected onto the spliced sequence.\n" "help_text": "Type: `boolean_true`, default: `false`. For --spliced_exons, --spliced_cds and -tr_cds options, write in the FASTA defline \nall the exon coordinates projected onto the spliced sequence.\n"
, ,
"default": "False" "default":false
} }
@@ -210,7 +210,7 @@
"description": "Type: `boolean_true`, default: `false`. For --tr_cds option, use \u0027*\u0027 instead of \u0027", "description": "Type: `boolean_true`, default: `false`. For --tr_cds option, use \u0027*\u0027 instead of \u0027",
"help_text": "Type: `boolean_true`, default: `false`. For --tr_cds option, use \u0027*\u0027 instead of \u0027.\u0027 as stop codon translation.\n" "help_text": "Type: `boolean_true`, default: `false`. For --tr_cds option, use \u0027*\u0027 instead of \u0027.\u0027 as stop codon translation.\n"
, ,
"default": "False" "default":false
} }
@@ -221,7 +221,7 @@
"description": "Type: `boolean_true`, default: `false`. Ensembl GTF to GFF3 conversion, adds version to IDs", "description": "Type: `boolean_true`, default: `false`. Ensembl GTF to GFF3 conversion, adds version to IDs",
"help_text": "Type: `boolean_true`, default: `false`. Ensembl GTF to GFF3 conversion, adds version to IDs.\n" "help_text": "Type: `boolean_true`, default: `false`. Ensembl GTF to GFF3 conversion, adds version to IDs.\n"
, ,
"default": "False" "default":false
} }
@@ -242,7 +242,7 @@
"description": "Type: `boolean_true`, default: `false`. Main output will be GTF instead of GFF3", "description": "Type: `boolean_true`, default: `false`. Main output will be GTF instead of GFF3",
"help_text": "Type: `boolean_true`, default: `false`. Main output will be GTF instead of GFF3.\n" "help_text": "Type: `boolean_true`, default: `false`. Main output will be GTF instead of GFF3.\n"
, ,
"default": "False" "default":false
} }
@@ -253,7 +253,7 @@
"description": "Type: `boolean_true`, default: `false`. Output records in BED format instead of default GFF3", "description": "Type: `boolean_true`, default: `false`. Output records in BED format instead of default GFF3",
"help_text": "Type: `boolean_true`, default: `false`. Output records in BED format instead of default GFF3.\n" "help_text": "Type: `boolean_true`, default: `false`. Output records in BED format instead of default GFF3.\n"
, ,
"default": "False" "default":false
} }
@@ -264,7 +264,7 @@
"description": "Type: `boolean_true`, default: `false`. Output \"transcript line format\" which is like GFF but with exons and CDS related \nfeatures stored as GFF attributes in the transcript feature line, like this:\n exoncount=N;exons=\u003cexons\u003e;CDSphase=\u003cN\u003e;CDS=\u003cCDScoords\u003e\n\u003cexons\u003e is a comma-delimited list of exon_start-exon_end coordinates;\n\u003cCDScoords\u003e is CDS_start:CDS_end coordinates or a list like \u003cexons\u003e", "description": "Type: `boolean_true`, default: `false`. Output \"transcript line format\" which is like GFF but with exons and CDS related \nfeatures stored as GFF attributes in the transcript feature line, like this:\n exoncount=N;exons=\u003cexons\u003e;CDSphase=\u003cN\u003e;CDS=\u003cCDScoords\u003e\n\u003cexons\u003e is a comma-delimited list of exon_start-exon_end coordinates;\n\u003cCDScoords\u003e is CDS_start:CDS_end coordinates or a list like \u003cexons\u003e",
"help_text": "Type: `boolean_true`, default: `false`. Output \"transcript line format\" which is like GFF but with exons and CDS related \nfeatures stored as GFF attributes in the transcript feature line, like this:\n exoncount=N;exons=\u003cexons\u003e;CDSphase=\u003cN\u003e;CDS=\u003cCDScoords\u003e\n\u003cexons\u003e is a comma-delimited list of exon_start-exon_end coordinates;\n\u003cCDScoords\u003e is CDS_start:CDS_end coordinates or a list like \u003cexons\u003e.\n" "help_text": "Type: `boolean_true`, default: `false`. Output \"transcript line format\" which is like GFF but with exons and CDS related \nfeatures stored as GFF attributes in the transcript feature line, like this:\n exoncount=N;exons=\u003cexons\u003e;CDSphase=\u003cN\u003e;CDS=\u003cCDScoords\u003e\n\u003cexons\u003e is a comma-delimited list of exon_start-exon_end coordinates;\n\u003cCDScoords\u003e is CDS_start:CDS_end coordinates or a list like \u003cexons\u003e.\n"
, ,
"default": "False" "default":false
} }
@@ -285,7 +285,7 @@
"description": "Type: `boolean_true`, default: `false`. Expose (warn about) duplicate transcript IDs and other potential problems with the \ngiven GFF/GTF records", "description": "Type: `boolean_true`, default: `false`. Expose (warn about) duplicate transcript IDs and other potential problems with the \ngiven GFF/GTF records",
"help_text": "Type: `boolean_true`, default: `false`. Expose (warn about) duplicate transcript IDs and other potential problems with the \ngiven GFF/GTF records.\n" "help_text": "Type: `boolean_true`, default: `false`. Expose (warn about) duplicate transcript IDs and other potential problems with the \ngiven GFF/GTF records.\n"
, ,
"default": "False" "default":false
} }
@@ -356,7 +356,7 @@
"description": "Type: `boolean_true`, default: `false`. For --range option, discard all transcripts that are not fully contained within the given \nrange", "description": "Type: `boolean_true`, default: `false`. For --range option, discard all transcripts that are not fully contained within the given \nrange",
"help_text": "Type: `boolean_true`, default: `false`. For --range option, discard all transcripts that are not fully contained within the given \nrange.\n" "help_text": "Type: `boolean_true`, default: `false`. For --range option, discard all transcripts that are not fully contained within the given \nrange.\n"
, ,
"default": "False" "default":false
} }
@@ -377,7 +377,7 @@
"description": "Type: `boolean_true`, default: `false`. Discard single-exon transcripts", "description": "Type: `boolean_true`, default: `false`. Discard single-exon transcripts",
"help_text": "Type: `boolean_true`, default: `false`. Discard single-exon transcripts.\n" "help_text": "Type: `boolean_true`, default: `false`. Discard single-exon transcripts.\n"
, ,
"default": "False" "default":false
} }
@@ -388,7 +388,7 @@
"description": "Type: `boolean_true`, default: `false`. Coding only: discard mRNAs that have no CDS features", "description": "Type: `boolean_true`, default: `false`. Coding only: discard mRNAs that have no CDS features",
"help_text": "Type: `boolean_true`, default: `false`. Coding only: discard mRNAs that have no CDS features.\n" "help_text": "Type: `boolean_true`, default: `false`. Coding only: discard mRNAs that have no CDS features.\n"
, ,
"default": "False" "default":false
} }
@@ -399,7 +399,7 @@
"description": "Type: `boolean_true`, default: `false`. Non-coding only: discard mRNAs that have CDS features", "description": "Type: `boolean_true`, default: `false`. Non-coding only: discard mRNAs that have CDS features",
"help_text": "Type: `boolean_true`, default: `false`. Non-coding only: discard mRNAs that have CDS features.\n" "help_text": "Type: `boolean_true`, default: `false`. Non-coding only: discard mRNAs that have CDS features.\n"
, ,
"default": "False" "default":false
} }
@@ -410,7 +410,7 @@
"description": "Type: `boolean_true`, default: `false`. Discard locus features and attributes found in the input", "description": "Type: `boolean_true`, default: `false`. Discard locus features and attributes found in the input",
"help_text": "Type: `boolean_true`, default: `false`. Discard locus features and attributes found in the input.\n" "help_text": "Type: `boolean_true`, default: `false`. Discard locus features and attributes found in the input.\n"
, ,
"default": "False" "default":false
} }
@@ -421,7 +421,7 @@
"description": "Type: `boolean_true`, default: `false`. Use the description field from \u003cseq_info", "description": "Type: `boolean_true`, default: `false`. Use the description field from \u003cseq_info",
"help_text": "Type: `boolean_true`, default: `false`. Use the description field from \u003cseq_info.fsize\u003e and add it as the value for a \u0027descr\u0027 \nattribute to the GFF record.\n" "help_text": "Type: `boolean_true`, default: `false`. Use the description field from \u003cseq_info.fsize\u003e and add it as the value for a \u0027descr\u0027 \nattribute to the GFF record.\n"
, ,
"default": "False" "default":false
} }
@@ -442,7 +442,7 @@
"description": "Type: `boolean_true`, default: `false`. Chromosomes (reference sequences) are sorted alphabetically", "description": "Type: `boolean_true`, default: `false`. Chromosomes (reference sequences) are sorted alphabetically",
"help_text": "Type: `boolean_true`, default: `false`. Chromosomes (reference sequences) are sorted alphabetically.\n" "help_text": "Type: `boolean_true`, default: `false`. Chromosomes (reference sequences) are sorted alphabetically.\n"
, ,
"default": "False" "default":false
} }
@@ -473,7 +473,7 @@
"description": "Type: `boolean_true`, default: `false`. Keep all GFF attributes (for non-exon features)", "description": "Type: `boolean_true`, default: `false`. Keep all GFF attributes (for non-exon features)",
"help_text": "Type: `boolean_true`, default: `false`. Keep all GFF attributes (for non-exon features).\n" "help_text": "Type: `boolean_true`, default: `false`. Keep all GFF attributes (for non-exon features).\n"
, ,
"default": "False" "default":false
} }
@@ -484,7 +484,7 @@
"description": "Type: `boolean_true`, default: `false`. For -F option, do not attempt to reduce redundant exon/CDS attributes", "description": "Type: `boolean_true`, default: `false`. For -F option, do not attempt to reduce redundant exon/CDS attributes",
"help_text": "Type: `boolean_true`, default: `false`. For -F option, do not attempt to reduce redundant exon/CDS attributes.\n" "help_text": "Type: `boolean_true`, default: `false`. For -F option, do not attempt to reduce redundant exon/CDS attributes.\n"
, ,
"default": "False" "default":false
} }
@@ -495,7 +495,7 @@
"description": "Type: `boolean_true`, default: `false`. Do not keep exon attributes, move them to the transcript feature (for GFF3 output)", "description": "Type: `boolean_true`, default: `false`. Do not keep exon attributes, move them to the transcript feature (for GFF3 output)",
"help_text": "Type: `boolean_true`, default: `false`. Do not keep exon attributes, move them to the transcript feature (for GFF3 output).\n" "help_text": "Type: `boolean_true`, default: `false`. Do not keep exon attributes, move them to the transcript feature (for GFF3 output).\n"
, ,
"default": "False" "default":false
} }
@@ -516,7 +516,7 @@
"description": "Type: `boolean_true`, default: `false`. In transcript-only mode (default), also preserve gene records", "description": "Type: `boolean_true`, default: `false`. In transcript-only mode (default), also preserve gene records",
"help_text": "Type: `boolean_true`, default: `false`. In transcript-only mode (default), also preserve gene records.\n" "help_text": "Type: `boolean_true`, default: `false`. In transcript-only mode (default), also preserve gene records.\n"
, ,
"default": "False" "default":false
} }
@@ -527,7 +527,7 @@
"description": "Type: `boolean_true`, default: `false`. For GFF3 input/output, try to preserve comments", "description": "Type: `boolean_true`, default: `false`. For GFF3 input/output, try to preserve comments",
"help_text": "Type: `boolean_true`, default: `false`. For GFF3 input/output, try to preserve comments.\n" "help_text": "Type: `boolean_true`, default: `false`. For GFF3 input/output, try to preserve comments.\n"
, ,
"default": "False" "default":false
} }
@@ -538,7 +538,7 @@
"description": "Type: `boolean_true`, default: `false`. process other non-transcript GFF records (by default non-transcript records are ignored)", "description": "Type: `boolean_true`, default: `false`. process other non-transcript GFF records (by default non-transcript records are ignored)",
"help_text": "Type: `boolean_true`, default: `false`. process other non-transcript GFF records (by default non-transcript records are ignored).\n" "help_text": "Type: `boolean_true`, default: `false`. process other non-transcript GFF records (by default non-transcript records are ignored).\n"
, ,
"default": "False" "default":false
} }
@@ -549,7 +549,7 @@
"description": "Type: `boolean_true`, default: `false`. Discard any mRNAs with CDS having in-frame stop codons (requires --genome)", "description": "Type: `boolean_true`, default: `false`. Discard any mRNAs with CDS having in-frame stop codons (requires --genome)",
"help_text": "Type: `boolean_true`, default: `false`. Discard any mRNAs with CDS having in-frame stop codons (requires --genome).\n" "help_text": "Type: `boolean_true`, default: `false`. Discard any mRNAs with CDS having in-frame stop codons (requires --genome).\n"
, ,
"default": "False" "default":false
} }
@@ -560,7 +560,7 @@
"description": "Type: `boolean_true`, default: `false`. For --rm_stop_codons option, check and adjust the starting CDS phase if the original phase\nleads to a translation with an in-frame stop codon", "description": "Type: `boolean_true`, default: `false`. For --rm_stop_codons option, check and adjust the starting CDS phase if the original phase\nleads to a translation with an in-frame stop codon",
"help_text": "Type: `boolean_true`, default: `false`. For --rm_stop_codons option, check and adjust the starting CDS phase if the original phase\nleads to a translation with an in-frame stop codon.\n" "help_text": "Type: `boolean_true`, default: `false`. For --rm_stop_codons option, check and adjust the starting CDS phase if the original phase\nleads to a translation with an in-frame stop codon.\n"
, ,
"default": "False" "default":false
} }
@@ -571,7 +571,7 @@
"description": "Type: `boolean_true`, default: `false`. For -V option, single-exon transcripts are also checked on the opposite strand (requires \n--genome)", "description": "Type: `boolean_true`, default: `false`. For -V option, single-exon transcripts are also checked on the opposite strand (requires \n--genome)",
"help_text": "Type: `boolean_true`, default: `false`. For -V option, single-exon transcripts are also checked on the opposite strand (requires \n--genome). \n" "help_text": "Type: `boolean_true`, default: `false`. For -V option, single-exon transcripts are also checked on the opposite strand (requires \n--genome). \n"
, ,
"default": "False" "default":false
} }
@@ -582,7 +582,7 @@
"description": "Type: `boolean_true`, default: `false`. Add transcript level GFF attributes about the coding status of each transcript, including \npartialness or in-frame stop codons (requires --genome)", "description": "Type: `boolean_true`, default: `false`. Add transcript level GFF attributes about the coding status of each transcript, including \npartialness or in-frame stop codons (requires --genome)",
"help_text": "Type: `boolean_true`, default: `false`. Add transcript level GFF attributes about the coding status of each transcript, including \npartialness or in-frame stop codons (requires --genome).\n" "help_text": "Type: `boolean_true`, default: `false`. Add transcript level GFF attributes about the coding status of each transcript, including \npartialness or in-frame stop codons (requires --genome).\n"
, ,
"default": "False" "default":false
} }
@@ -593,7 +593,7 @@
"description": "Type: `boolean_true`, default: `false`. Add a \"hasCDS\" attribute with value \"true\" for transcripts that have CDS features", "description": "Type: `boolean_true`, default: `false`. Add a \"hasCDS\" attribute with value \"true\" for transcripts that have CDS features",
"help_text": "Type: `boolean_true`, default: `false`. Add a \"hasCDS\" attribute with value \"true\" for transcripts that have CDS features. \n" "help_text": "Type: `boolean_true`, default: `false`. Add a \"hasCDS\" attribute with value \"true\" for transcripts that have CDS features. \n"
, ,
"default": "False" "default":false
} }
@@ -604,7 +604,7 @@
"description": "Type: `boolean_true`, default: `false`. Stop codon adjustment: enables --coding_status and performs automatic adjustment of the CDS stop \ncoordinate if premature or downstream", "description": "Type: `boolean_true`, default: `false`. Stop codon adjustment: enables --coding_status and performs automatic adjustment of the CDS stop \ncoordinate if premature or downstream",
"help_text": "Type: `boolean_true`, default: `false`. Stop codon adjustment: enables --coding_status and performs automatic adjustment of the CDS stop \ncoordinate if premature or downstream.\n" "help_text": "Type: `boolean_true`, default: `false`. Stop codon adjustment: enables --coding_status and performs automatic adjustment of the CDS stop \ncoordinate if premature or downstream.\n"
, ,
"default": "False" "default":false
} }
@@ -615,7 +615,7 @@
"description": "Type: `boolean_true`, default: `false`. Discard multi-exon mRNAs that have any intron with a non-canonical splice site consensus \n(i", "description": "Type: `boolean_true`, default: `false`. Discard multi-exon mRNAs that have any intron with a non-canonical splice site consensus \n(i",
"help_text": "Type: `boolean_true`, default: `false`. Discard multi-exon mRNAs that have any intron with a non-canonical splice site consensus \n(i.e. not GT-AG, GC-AG or AT-AC).\n" "help_text": "Type: `boolean_true`, default: `false`. Discard multi-exon mRNAs that have any intron with a non-canonical splice site consensus \n(i.e. not GT-AG, GC-AG or AT-AC).\n"
, ,
"default": "False" "default":false
} }
@@ -626,7 +626,7 @@
"description": "Type: `boolean_true`, default: `false`. Discard any mRNAs that either lack initial START codon or the terminal STOP codon, or \nhave an in-frame stop codon (i", "description": "Type: `boolean_true`, default: `false`. Discard any mRNAs that either lack initial START codon or the terminal STOP codon, or \nhave an in-frame stop codon (i",
"help_text": "Type: `boolean_true`, default: `false`. Discard any mRNAs that either lack initial START codon or the terminal STOP codon, or \nhave an in-frame stop codon (i.e. only print mRNAs with a complete CDS).\n" "help_text": "Type: `boolean_true`, default: `false`. Discard any mRNAs that either lack initial START codon or the terminal STOP codon, or \nhave an in-frame stop codon (i.e. only print mRNAs with a complete CDS).\n"
, ,
"default": "False" "default":false
} }
@@ -637,7 +637,7 @@
"description": "Type: `boolean_true`, default: `false`. Filter out records matching the \u0027pseudo\u0027 keyword", "description": "Type: `boolean_true`, default: `false`. Filter out records matching the \u0027pseudo\u0027 keyword",
"help_text": "Type: `boolean_true`, default: `false`. Filter out records matching the \u0027pseudo\u0027 keyword.\n" "help_text": "Type: `boolean_true`, default: `false`. Filter out records matching the \u0027pseudo\u0027 keyword.\n"
, ,
"default": "False" "default":false
} }
@@ -648,7 +648,7 @@
"description": "Type: `boolean_true`, default: `false`. Input should be parsed as BED format (automatic if the input filename ends with ", "description": "Type: `boolean_true`, default: `false`. Input should be parsed as BED format (automatic if the input filename ends with ",
"help_text": "Type: `boolean_true`, default: `false`. Input should be parsed as BED format (automatic if the input filename ends with .bed*).\n" "help_text": "Type: `boolean_true`, default: `false`. Input should be parsed as BED format (automatic if the input filename ends with .bed*).\n"
, ,
"default": "False" "default":false
} }
@@ -659,7 +659,7 @@
"description": "Type: `boolean_true`, default: `false`. Input GFF-like one-line-per-transcript format without exon/CDS features (see --tlf option \nbelow); automatic if the input filename ends with ", "description": "Type: `boolean_true`, default: `false`. Input GFF-like one-line-per-transcript format without exon/CDS features (see --tlf option \nbelow); automatic if the input filename ends with ",
"help_text": "Type: `boolean_true`, default: `false`. Input GFF-like one-line-per-transcript format without exon/CDS features (see --tlf option \nbelow); automatic if the input filename ends with .tlf).\n" "help_text": "Type: `boolean_true`, default: `false`. Input GFF-like one-line-per-transcript format without exon/CDS features (see --tlf option \nbelow); automatic if the input filename ends with .tlf).\n"
, ,
"default": "False" "default":false
} }
@@ -670,7 +670,7 @@
"description": "Type: `boolean_true`, default: `false`. Fast processing of input GFF/BED transcripts as they are received (no sorting, exons must \nbe grouped by transcript in the input data)", "description": "Type: `boolean_true`, default: `false`. Fast processing of input GFF/BED transcripts as they are received (no sorting, exons must \nbe grouped by transcript in the input data)",
"help_text": "Type: `boolean_true`, default: `false`. Fast processing of input GFF/BED transcripts as they are received (no sorting, exons must \nbe grouped by transcript in the input data).\n" "help_text": "Type: `boolean_true`, default: `false`. Fast processing of input GFF/BED transcripts as they are received (no sorting, exons must \nbe grouped by transcript in the input data).\n"
, ,
"default": "False" "default":false
} }
@@ -691,7 +691,7 @@
"description": "Type: `boolean_true`, default: `false`. Cluster the input transcripts into loci, discarding \"redundant\" transcripts (those with \nthe same exact introns and fully contained or equal boundaries)", "description": "Type: `boolean_true`, default: `false`. Cluster the input transcripts into loci, discarding \"redundant\" transcripts (those with \nthe same exact introns and fully contained or equal boundaries)",
"help_text": "Type: `boolean_true`, default: `false`. Cluster the input transcripts into loci, discarding \"redundant\" transcripts (those with \nthe same exact introns and fully contained or equal boundaries).\n" "help_text": "Type: `boolean_true`, default: `false`. Cluster the input transcripts into loci, discarding \"redundant\" transcripts (those with \nthe same exact introns and fully contained or equal boundaries).\n"
, ,
"default": "False" "default":false
} }
@@ -712,7 +712,7 @@
"description": "Type: `boolean_true`, default: `false`. Same as --merge but without discarding any of the \"duplicate\" transcripts, only create \n\"locus\" features", "description": "Type: `boolean_true`, default: `false`. Same as --merge but without discarding any of the \"duplicate\" transcripts, only create \n\"locus\" features",
"help_text": "Type: `boolean_true`, default: `false`. Same as --merge but without discarding any of the \"duplicate\" transcripts, only create \n\"locus\" features.\n" "help_text": "Type: `boolean_true`, default: `false`. Same as --merge but without discarding any of the \"duplicate\" transcripts, only create \n\"locus\" features.\n"
, ,
"default": "False" "default":false
} }
@@ -723,7 +723,7 @@
"description": "Type: `boolean_true`, default: `false`. For --merge option: also discard as redundant the shorter, fully contained transcripts (intron \nchains matching a part of the container)", "description": "Type: `boolean_true`, default: `false`. For --merge option: also discard as redundant the shorter, fully contained transcripts (intron \nchains matching a part of the container)",
"help_text": "Type: `boolean_true`, default: `false`. For --merge option: also discard as redundant the shorter, fully contained transcripts (intron \nchains matching a part of the container).\n" "help_text": "Type: `boolean_true`, default: `false`. For --merge option: also discard as redundant the shorter, fully contained transcripts (intron \nchains matching a part of the container).\n"
, ,
"default": "False" "default":false
} }
@@ -734,7 +734,7 @@
"description": "Type: `boolean_true`, default: `false`. For --merge option, no longer require boundary containment when assessing redundancy (can be \ncombined with --rm_redundant); only introns have to match for multi-exon transcripts, and \u003e=80%\noverlap for single-exon transcripts", "description": "Type: `boolean_true`, default: `false`. For --merge option, no longer require boundary containment when assessing redundancy (can be \ncombined with --rm_redundant); only introns have to match for multi-exon transcripts, and \u003e=80%\noverlap for single-exon transcripts",
"help_text": "Type: `boolean_true`, default: `false`. For --merge option, no longer require boundary containment when assessing redundancy (can be \ncombined with --rm_redundant); only introns have to match for multi-exon transcripts, and \u003e=80%\noverlap for single-exon transcripts.\n" "help_text": "Type: `boolean_true`, default: `false`. For --merge option, no longer require boundary containment when assessing redundancy (can be \ncombined with --rm_redundant); only introns have to match for multi-exon transcripts, and \u003e=80%\noverlap for single-exon transcripts.\n"
, ,
"default": "False" "default":false
} }
@@ -745,7 +745,7 @@
"description": "Type: `boolean_true`, default: `false`. For --merge option, enforce --no_boundary but also discard overlapping single-exon transcripts,\neven on the opposite strand (can be combined with --rm_redudant)", "description": "Type: `boolean_true`, default: `false`. For --merge option, enforce --no_boundary but also discard overlapping single-exon transcripts,\neven on the opposite strand (can be combined with --rm_redudant)",
"help_text": "Type: `boolean_true`, default: `false`. For --merge option, enforce --no_boundary but also discard overlapping single-exon transcripts,\neven on the opposite strand (can be combined with --rm_redudant).\n" "help_text": "Type: `boolean_true`, default: `false`. For --merge option, enforce --no_boundary but also discard overlapping single-exon transcripts,\neven on the opposite strand (can be combined with --rm_redudant).\n"
, ,
"default": "False" "default":false
} }

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

@@ -218,9 +218,9 @@ build_info:
output: "target/nextflow/kallisto/kallisto_index" output: "target/nextflow/kallisto/kallisto_index"
executable: "target/nextflow/kallisto/kallisto_index/main.nf" executable: "target/nextflow/kallisto/kallisto_index/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d" git_tag: "v0.2.0-27-g952ff08"
package_config: package_config:
name: "biobox" name: "biobox"
version: "main" version: "main"

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

@@ -3071,9 +3071,9 @@ meta = [
"engine" : "docker|native", "engine" : "docker|native",
"output" : "target/nextflow/kallisto/kallisto_index", "output" : "target/nextflow/kallisto/kallisto_index",
"viash_version" : "0.9.0", "viash_version" : "0.9.0",
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d" "git_tag" : "v0.2.0-27-g952ff08"
}, },
"package_config" : { "package_config" : {
"name" : "biobox", "name" : "biobox",

8
target/dependencies/vsh/vsh/biobox/main/nextflow/kallisto/kallisto_index/nextflow_schema.json
View File

@@ -50,7 +50,7 @@
"description": "Type: `file`, default: `$id.$key.index.index`, example: `Kallisto_index`. ", "description": "Type: `file`, default: `$id.$key.index.index`, example: `Kallisto_index`. ",
"help_text": "Type: `file`, default: `$id.$key.index.index`, example: `Kallisto_index`. " "help_text": "Type: `file`, default: `$id.$key.index.index`, example: `Kallisto_index`. "
, ,
"default": "$id.$key.index.index" "default":"$id.$key.index.index"
} }
@@ -81,7 +81,7 @@
"description": "Type: `boolean_true`, default: `false`. Replace repeated target names with unique names", "description": "Type: `boolean_true`, default: `false`. Replace repeated target names with unique names",
"help_text": "Type: `boolean_true`, default: `false`. Replace repeated target names with unique names.\n" "help_text": "Type: `boolean_true`, default: `false`. Replace repeated target names with unique names.\n"
, ,
"default": "False" "default":false
} }
@@ -92,7 +92,7 @@
"description": "Type: `boolean_true`, default: `false`. Generate index from a FASTA-file containing amino acid sequences", "description": "Type: `boolean_true`, default: `false`. Generate index from a FASTA-file containing amino acid sequences",
"help_text": "Type: `boolean_true`, default: `false`. Generate index from a FASTA-file containing amino acid sequences.\n" "help_text": "Type: `boolean_true`, default: `false`. Generate index from a FASTA-file containing amino acid sequences.\n"
, ,
"default": "False" "default":false
} }
@@ -103,7 +103,7 @@
"description": "Type: `boolean_true`, default: `false`. Generate index where sequences are distinguished by the sequence names", "description": "Type: `boolean_true`, default: `false`. Generate index where sequences are distinguished by the sequence names",
"help_text": "Type: `boolean_true`, default: `false`. Generate index where sequences are distinguished by the sequence names.\n" "help_text": "Type: `boolean_true`, default: `false`. Generate index where sequences are distinguished by the sequence names.\n"
, ,
"default": "False" "default":false
} }

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

@@ -246,9 +246,9 @@ build_info:
output: "target/nextflow/kallisto/kallisto_quant" output: "target/nextflow/kallisto/kallisto_quant"
executable: "target/nextflow/kallisto/kallisto_quant/main.nf" executable: "target/nextflow/kallisto/kallisto_quant/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d" git_tag: "v0.2.0-27-g952ff08"
package_config: package_config:
name: "biobox" name: "biobox"
version: "main" version: "main"

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

@@ -3105,9 +3105,9 @@ meta = [
"engine" : "docker|native", "engine" : "docker|native",
"output" : "target/nextflow/kallisto/kallisto_quant", "output" : "target/nextflow/kallisto/kallisto_quant",
"viash_version" : "0.9.0", "viash_version" : "0.9.0",
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d" "git_tag" : "v0.2.0-27-g952ff08"
}, },
"package_config" : { "package_config" : {
"name" : "biobox", "name" : "biobox",

14
target/dependencies/vsh/vsh/biobox/main/nextflow/kallisto/kallisto_quant/nextflow_schema.json
View File

@@ -50,7 +50,7 @@
"description": "Type: `file`, required, default: `$id.$key.output_dir.output_dir`. Directory to write output to", "description": "Type: `file`, required, default: `$id.$key.output_dir.output_dir`. Directory to write output to",
"help_text": "Type: `file`, required, default: `$id.$key.output_dir.output_dir`. Directory to write output to." "help_text": "Type: `file`, required, default: `$id.$key.output_dir.output_dir`. Directory to write output to."
, ,
"default": "$id.$key.output_dir.output_dir" "default":"$id.$key.output_dir.output_dir"
} }
@@ -61,7 +61,7 @@
"description": "Type: `file`, default: `$id.$key.log.log`. File containing log information from running kallisto quant", "description": "Type: `file`, default: `$id.$key.log.log`. File containing log information from running kallisto quant",
"help_text": "Type: `file`, default: `$id.$key.log.log`. File containing log information from running kallisto quant" "help_text": "Type: `file`, default: `$id.$key.log.log`. File containing log information from running kallisto quant"
, ,
"default": "$id.$key.log.log" "default":"$id.$key.log.log"
} }
@@ -82,7 +82,7 @@
"description": "Type: `boolean_true`, default: `false`. Single end mode", "description": "Type: `boolean_true`, default: `false`. Single end mode",
"help_text": "Type: `boolean_true`, default: `false`. Single end mode." "help_text": "Type: `boolean_true`, default: `false`. Single end mode."
, ,
"default": "False" "default":false
} }
@@ -93,7 +93,7 @@
"description": "Type: `boolean_true`, default: `false`. Include reads where unobserved rest of fragment is predicted to lie outside a transcript", "description": "Type: `boolean_true`, default: `false`. Include reads where unobserved rest of fragment is predicted to lie outside a transcript",
"help_text": "Type: `boolean_true`, default: `false`. Include reads where unobserved rest of fragment is predicted to lie outside a transcript." "help_text": "Type: `boolean_true`, default: `false`. Include reads where unobserved rest of fragment is predicted to lie outside a transcript."
, ,
"default": "False" "default":false
} }
@@ -104,7 +104,7 @@
"description": "Type: `boolean_true`, default: `false`. Strand specific reads, first read forward", "description": "Type: `boolean_true`, default: `false`. Strand specific reads, first read forward",
"help_text": "Type: `boolean_true`, default: `false`. Strand specific reads, first read forward." "help_text": "Type: `boolean_true`, default: `false`. Strand specific reads, first read forward."
, ,
"default": "False" "default":false
} }
@@ -115,7 +115,7 @@
"description": "Type: `boolean_true`, default: `false`. Strand specific reads, first read reverse", "description": "Type: `boolean_true`, default: `false`. Strand specific reads, first read reverse",
"help_text": "Type: `boolean_true`, default: `false`. Strand specific reads, first read reverse." "help_text": "Type: `boolean_true`, default: `false`. Strand specific reads, first read reverse."
, ,
"default": "False" "default":false
} }
@@ -146,7 +146,7 @@
"description": "Type: `boolean_true`, default: `false`. Output plaintext instead of HDF5", "description": "Type: `boolean_true`, default: `false`. Output plaintext instead of HDF5",
"help_text": "Type: `boolean_true`, default: `false`. Output plaintext instead of HDF5." "help_text": "Type: `boolean_true`, default: `false`. Output plaintext instead of HDF5."
, ,
"default": "False" "default":false
} }

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

@@ -456,9 +456,9 @@ build_info:
output: "target/nextflow/multiqc" output: "target/nextflow/multiqc"
executable: "target/nextflow/multiqc/main.nf" executable: "target/nextflow/multiqc/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d" git_tag: "v0.2.0-27-g952ff08"
package_config: package_config:
name: "biobox" name: "biobox"
version: "main" version: "main"

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

@@ -3366,9 +3366,9 @@ meta = [
"engine" : "docker|native", "engine" : "docker|native",
"output" : "target/nextflow/multiqc", "output" : "target/nextflow/multiqc",
"viash_version" : "0.9.0", "viash_version" : "0.9.0",
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d" "git_tag" : "v0.2.0-27-g952ff08"
}, },
"package_config" : { "package_config" : {
"name" : "biobox", "name" : "biobox",

42
target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/nextflow_schema.json
View File

@@ -40,7 +40,7 @@
"description": "Type: `file`, default: `$id.$key.output_report.html`, example: `multiqc_report.html`. Filepath of the generated report", "description": "Type: `file`, default: `$id.$key.output_report.html`, example: `multiqc_report.html`. Filepath of the generated report",
"help_text": "Type: `file`, default: `$id.$key.output_report.html`, example: `multiqc_report.html`. Filepath of the generated report.\n" "help_text": "Type: `file`, default: `$id.$key.output_report.html`, example: `multiqc_report.html`. Filepath of the generated report.\n"
, ,
"default": "$id.$key.output_report.html" "default":"$id.$key.output_report.html"
} }
@@ -51,7 +51,7 @@
"description": "Type: `file`, default: `$id.$key.output_data.output_data`, example: `multiqc_data`. Output directory for parsed data files", "description": "Type: `file`, default: `$id.$key.output_data.output_data`, example: `multiqc_data`. Output directory for parsed data files",
"help_text": "Type: `file`, default: `$id.$key.output_data.output_data`, example: `multiqc_data`. Output directory for parsed data files. If not provided, parsed data will not be published.\n" "help_text": "Type: `file`, default: `$id.$key.output_data.output_data`, example: `multiqc_data`. Output directory for parsed data files. If not provided, parsed data will not be published.\n"
, ,
"default": "$id.$key.output_data.output_data" "default":"$id.$key.output_data.output_data"
} }
@@ -62,7 +62,7 @@
"description": "Type: `file`, default: `$id.$key.output_plots.output_plots`, example: `multiqc_plots`. Output directory for generated plots", "description": "Type: `file`, default: `$id.$key.output_plots.output_plots`, example: `multiqc_plots`. Output directory for generated plots",
"help_text": "Type: `file`, default: `$id.$key.output_plots.output_plots`, example: `multiqc_plots`. Output directory for generated plots. If not provided, plots will not be published.\n" "help_text": "Type: `file`, default: `$id.$key.output_plots.output_plots`, example: `multiqc_plots`. Output directory for generated plots. If not provided, plots will not be published.\n"
, ,
"default": "$id.$key.output_plots.output_plots" "default":"$id.$key.output_plots.output_plots"
} }
@@ -123,7 +123,7 @@
"description": "Type: `boolean_true`, default: `false`. Ignore symlinked directories and files", "description": "Type: `boolean_true`, default: `false`. Ignore symlinked directories and files",
"help_text": "Type: `boolean_true`, default: `false`. Ignore symlinked directories and files" "help_text": "Type: `boolean_true`, default: `false`. Ignore symlinked directories and files"
, ,
"default": "False" "default":false
} }
@@ -144,7 +144,7 @@
"description": "Type: `boolean_true`, default: `false`. Prepend directory to sample names to avoid clashing filenames", "description": "Type: `boolean_true`, default: `false`. Prepend directory to sample names to avoid clashing filenames",
"help_text": "Type: `boolean_true`, default: `false`. Prepend directory to sample names to avoid clashing filenames" "help_text": "Type: `boolean_true`, default: `false`. Prepend directory to sample names to avoid clashing filenames"
, ,
"default": "False" "default":false
} }
@@ -165,7 +165,7 @@
"description": "Type: `boolean_true`, default: `false`. Do not clean the sample names (leave as full file name)", "description": "Type: `boolean_true`, default: `false`. Do not clean the sample names (leave as full file name)",
"help_text": "Type: `boolean_true`, default: `false`. Do not clean the sample names (leave as full file name)" "help_text": "Type: `boolean_true`, default: `false`. Do not clean the sample names (leave as full file name)"
, ,
"default": "False" "default":false
} }
@@ -176,7 +176,7 @@
"description": "Type: `boolean_true`, default: `false`. Use the log filename as the sample name", "description": "Type: `boolean_true`, default: `false`. Use the log filename as the sample name",
"help_text": "Type: `boolean_true`, default: `false`. Use the log filename as the sample name" "help_text": "Type: `boolean_true`, default: `false`. Use the log filename as the sample name"
, ,
"default": "False" "default":false
} }
@@ -269,7 +269,7 @@
"description": "Type: `boolean_true`, default: `false`. Add analysis of how long MultiQC takes to run to the report\n", "description": "Type: `boolean_true`, default: `false`. Add analysis of how long MultiQC takes to run to the report\n",
"help_text": "Type: `boolean_true`, default: `false`. Add analysis of how long MultiQC takes to run to the report\n" "help_text": "Type: `boolean_true`, default: `false`. Add analysis of how long MultiQC takes to run to the report\n"
, ,
"default": "False" "default":false
} }
@@ -290,7 +290,7 @@
"description": "Type: `boolean_true`, default: `false`. Increase output verbosity", "description": "Type: `boolean_true`, default: `false`. Increase output verbosity",
"help_text": "Type: `boolean_true`, default: `false`. Increase output verbosity.\n" "help_text": "Type: `boolean_true`, default: `false`. Increase output verbosity.\n"
, ,
"default": "False" "default":false
} }
@@ -301,7 +301,7 @@
"description": "Type: `boolean_true`, default: `false`. Only show log warnings\n", "description": "Type: `boolean_true`, default: `false`. Only show log warnings\n",
"help_text": "Type: `boolean_true`, default: `false`. Only show log warnings\n" "help_text": "Type: `boolean_true`, default: `false`. Only show log warnings\n"
, ,
"default": "False" "default":false
} }
@@ -312,7 +312,7 @@
"description": "Type: `boolean_true`, default: `false`. Don\u0027t catch exceptions, run additional code checks to help development", "description": "Type: `boolean_true`, default: `false`. Don\u0027t catch exceptions, run additional code checks to help development",
"help_text": "Type: `boolean_true`, default: `false`. Don\u0027t catch exceptions, run additional code checks to help development.\n" "help_text": "Type: `boolean_true`, default: `false`. Don\u0027t catch exceptions, run additional code checks to help development.\n"
, ,
"default": "False" "default":false
} }
@@ -323,7 +323,7 @@
"description": "Type: `boolean_true`, default: `false`. Development mode", "description": "Type: `boolean_true`, default: `false`. Development mode",
"help_text": "Type: `boolean_true`, default: `false`. Development mode. Do not compress and minimise JS, export uncompressed plot data.\n" "help_text": "Type: `boolean_true`, default: `false`. Development mode. Do not compress and minimise JS, export uncompressed plot data.\n"
, ,
"default": "False" "default":false
} }
@@ -334,7 +334,7 @@
"description": "Type: `boolean_true`, default: `false`. Require all explicitly requested modules to have log files", "description": "Type: `boolean_true`, default: `false`. Require all explicitly requested modules to have log files",
"help_text": "Type: `boolean_true`, default: `false`. Require all explicitly requested modules to have log files. If not, MultiQC will exit with an error.\n" "help_text": "Type: `boolean_true`, default: `false`. Require all explicitly requested modules to have log files. If not, MultiQC will exit with an error.\n"
, ,
"default": "False" "default":false
} }
@@ -345,7 +345,7 @@
"description": "Type: `boolean_true`, default: `false`. Don\u0027t upload generated report to MegaQC, even if MegaQC options are found", "description": "Type: `boolean_true`, default: `false`. Don\u0027t upload generated report to MegaQC, even if MegaQC options are found",
"help_text": "Type: `boolean_true`, default: `false`. Don\u0027t upload generated report to MegaQC, even if MegaQC options are found.\n" "help_text": "Type: `boolean_true`, default: `false`. Don\u0027t upload generated report to MegaQC, even if MegaQC options are found.\n"
, ,
"default": "False" "default":false
} }
@@ -356,7 +356,7 @@
"description": "Type: `boolean_true`, default: `false`. Disable coloured log output", "description": "Type: `boolean_true`, default: `false`. Disable coloured log output",
"help_text": "Type: `boolean_true`, default: `false`. Disable coloured log output.\n" "help_text": "Type: `boolean_true`, default: `false`. Disable coloured log output.\n"
, ,
"default": "False" "default":false
} }
@@ -387,7 +387,7 @@
"description": "Type: `boolean_true`, default: `false`. Use only flat plots (static images)", "description": "Type: `boolean_true`, default: `false`. Use only flat plots (static images)",
"help_text": "Type: `boolean_true`, default: `false`. Use only flat plots (static images).\n" "help_text": "Type: `boolean_true`, default: `false`. Use only flat plots (static images).\n"
, ,
"default": "False" "default":false
} }
@@ -398,7 +398,7 @@
"description": "Type: `boolean_true`, default: `false`. Use only interactive plots (in-browser Javascript)", "description": "Type: `boolean_true`, default: `false`. Use only interactive plots (in-browser Javascript)",
"help_text": "Type: `boolean_true`, default: `false`. Use only interactive plots (in-browser Javascript).\n" "help_text": "Type: `boolean_true`, default: `false`. Use only interactive plots (in-browser Javascript).\n"
, ,
"default": "False" "default":false
} }
@@ -409,7 +409,7 @@
"description": "Type: `boolean_true`, default: `false`. Force the parsed data directory to be created", "description": "Type: `boolean_true`, default: `false`. Force the parsed data directory to be created",
"help_text": "Type: `boolean_true`, default: `false`. Force the parsed data directory to be created.\n" "help_text": "Type: `boolean_true`, default: `false`. Force the parsed data directory to be created.\n"
, ,
"default": "False" "default":false
} }
@@ -420,7 +420,7 @@
"description": "Type: `boolean_true`, default: `false`. Prevent the parsed data directory from being created", "description": "Type: `boolean_true`, default: `false`. Prevent the parsed data directory from being created",
"help_text": "Type: `boolean_true`, default: `false`. Prevent the parsed data directory from being created.\n" "help_text": "Type: `boolean_true`, default: `false`. Prevent the parsed data directory from being created.\n"
, ,
"default": "False" "default":false
} }
@@ -431,7 +431,7 @@
"description": "Type: `boolean_true`, default: `false`. Compress the data directory", "description": "Type: `boolean_true`, default: `false`. Compress the data directory",
"help_text": "Type: `boolean_true`, default: `false`. Compress the data directory.\n" "help_text": "Type: `boolean_true`, default: `false`. Compress the data directory.\n"
, ,
"default": "False" "default":false
} }
@@ -454,7 +454,7 @@
"description": "Type: `boolean_true`, default: `false`. Creates PDF report with the \u0027simple\u0027 template", "description": "Type: `boolean_true`, default: `false`. Creates PDF report with the \u0027simple\u0027 template",
"help_text": "Type: `boolean_true`, default: `false`. Creates PDF report with the \u0027simple\u0027 template. Requires Pandoc to be installed.\n" "help_text": "Type: `boolean_true`, default: `false`. Creates PDF report with the \u0027simple\u0027 template. Requires Pandoc to be installed.\n"
, ,
"default": "False" "default":false
} }

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

@@ -264,9 +264,9 @@ build_info:
output: "target/nextflow/qualimap/qualimap_rnaseq" output: "target/nextflow/qualimap/qualimap_rnaseq"
executable: "target/nextflow/qualimap/qualimap_rnaseq/main.nf" executable: "target/nextflow/qualimap/qualimap_rnaseq/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d" git_tag: "v0.2.0-27-g952ff08"
package_config: package_config:
name: "biobox" name: "biobox"
version: "main" version: "main"

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

@@ -3129,9 +3129,9 @@ meta = [
"engine" : "docker|native", "engine" : "docker|native",
"output" : "target/nextflow/qualimap/qualimap_rnaseq", "output" : "target/nextflow/qualimap/qualimap_rnaseq",
"viash_version" : "0.9.0", "viash_version" : "0.9.0",
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d" "git_tag" : "v0.2.0-27-g952ff08"
}, },
"package_config" : { "package_config" : {
"name" : "biobox", "name" : "biobox",

10
target/dependencies/vsh/vsh/biobox/main/nextflow/qualimap/qualimap_rnaseq/nextflow_schema.json
View File

@@ -50,7 +50,7 @@
"description": "Type: `file`, required, default: `$id.$key.qc_results.txt`, example: `rnaseq_qc_results.txt`. Text file containing the RNAseq QC results", "description": "Type: `file`, required, default: `$id.$key.qc_results.txt`, example: `rnaseq_qc_results.txt`. Text file containing the RNAseq QC results",
"help_text": "Type: `file`, required, default: `$id.$key.qc_results.txt`, example: `rnaseq_qc_results.txt`. Text file containing the RNAseq QC results." "help_text": "Type: `file`, required, default: `$id.$key.qc_results.txt`, example: `rnaseq_qc_results.txt`. Text file containing the RNAseq QC results."
, ,
"default": "$id.$key.qc_results.txt" "default":"$id.$key.qc_results.txt"
} }
@@ -61,7 +61,7 @@
"description": "Type: `file`, default: `$id.$key.counts.counts`. Output file for computed counts", "description": "Type: `file`, default: `$id.$key.counts.counts`. Output file for computed counts",
"help_text": "Type: `file`, default: `$id.$key.counts.counts`. Output file for computed counts." "help_text": "Type: `file`, default: `$id.$key.counts.counts`. Output file for computed counts."
, ,
"default": "$id.$key.counts.counts" "default":"$id.$key.counts.counts"
} }
@@ -72,7 +72,7 @@
"description": "Type: `file`, default: `$id.$key.report.html`, example: `report.html`. Report output file", "description": "Type: `file`, default: `$id.$key.report.html`, example: `report.html`. Report output file",
"help_text": "Type: `file`, default: `$id.$key.report.html`, example: `report.html`. Report output file. Supported formats are PDF or HTML." "help_text": "Type: `file`, default: `$id.$key.report.html`, example: `report.html`. Report output file. Supported formats are PDF or HTML."
, ,
"default": "$id.$key.report.html" "default":"$id.$key.report.html"
} }
@@ -137,7 +137,7 @@
"description": "Type: `boolean_true`, default: `false`. Setting this flag for paired-end experiments will result in counting fragments instead of reads", "description": "Type: `boolean_true`, default: `false`. Setting this flag for paired-end experiments will result in counting fragments instead of reads",
"help_text": "Type: `boolean_true`, default: `false`. Setting this flag for paired-end experiments will result in counting fragments instead of reads." "help_text": "Type: `boolean_true`, default: `false`. Setting this flag for paired-end experiments will result in counting fragments instead of reads."
, ,
"default": "False" "default":false
} }
@@ -148,7 +148,7 @@
"description": "Type: `boolean_true`, default: `false`. Setting this flag indicates that the input file is already sorted by name", "description": "Type: `boolean_true`, default: `false`. Setting this flag indicates that the input file is already sorted by name",
"help_text": "Type: `boolean_true`, default: `false`. Setting this flag indicates that the input file is already sorted by name. If flag is not set, additional sorting by name will be performed. Only requiredfor paired-end analysis." "help_text": "Type: `boolean_true`, default: `false`. Setting this flag indicates that the input file is already sorted by name. If flag is not set, additional sorting by name will be performed. Only requiredfor paired-end analysis."
, ,
"default": "False" "default":false
} }

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

@@ -852,9 +852,9 @@ build_info:
output: "target/nextflow/rsem/rsem_calculate_expression" output: "target/nextflow/rsem/rsem_calculate_expression"
executable: "target/nextflow/rsem/rsem_calculate_expression/main.nf" executable: "target/nextflow/rsem/rsem_calculate_expression/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d" git_tag: "v0.2.0-27-g952ff08"
package_config: package_config:
name: "biobox" name: "biobox"
version: "main" version: "main"

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

@@ -3661,9 +3661,9 @@ meta = [
"engine" : "docker|native", "engine" : "docker|native",
"output" : "target/nextflow/rsem/rsem_calculate_expression", "output" : "target/nextflow/rsem/rsem_calculate_expression",
"viash_version" : "0.9.0", "viash_version" : "0.9.0",
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d" "git_tag" : "v0.2.0-27-g952ff08"
}, },
"package_config" : { "package_config" : {
"name" : "biobox", "name" : "biobox",

66
target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_calculate_expression/nextflow_schema.json
View File

@@ -42,7 +42,7 @@
"description": "Type: `boolean_true`, default: `false`. Paired-end reads or not?", "description": "Type: `boolean_true`, default: `false`. Paired-end reads or not?",
"help_text": "Type: `boolean_true`, default: `false`. Paired-end reads or not?" "help_text": "Type: `boolean_true`, default: `false`. Paired-end reads or not?"
, ,
"default": "False" "default":false
} }
@@ -93,7 +93,7 @@
"description": "Type: `file`, default: `$id.$key.counts_gene.results`, example: `$id.genes.results`. Expression counts on gene level", "description": "Type: `file`, default: `$id.$key.counts_gene.results`, example: `$id.genes.results`. Expression counts on gene level",
"help_text": "Type: `file`, default: `$id.$key.counts_gene.results`, example: `$id.genes.results`. Expression counts on gene level" "help_text": "Type: `file`, default: `$id.$key.counts_gene.results`, example: `$id.genes.results`. Expression counts on gene level"
, ,
"default": "$id.$key.counts_gene.results" "default":"$id.$key.counts_gene.results"
} }
@@ -104,7 +104,7 @@
"description": "Type: `file`, default: `$id.$key.counts_transcripts.results`, example: `$id.isoforms.results`. Expression counts on transcript level", "description": "Type: `file`, default: `$id.$key.counts_transcripts.results`, example: `$id.isoforms.results`. Expression counts on transcript level",
"help_text": "Type: `file`, default: `$id.$key.counts_transcripts.results`, example: `$id.isoforms.results`. Expression counts on transcript level" "help_text": "Type: `file`, default: `$id.$key.counts_transcripts.results`, example: `$id.isoforms.results`. Expression counts on transcript level"
, ,
"default": "$id.$key.counts_transcripts.results" "default":"$id.$key.counts_transcripts.results"
} }
@@ -115,7 +115,7 @@
"description": "Type: `file`, default: `$id.$key.stat.stat`, example: `$id.stat`. RSEM statistics", "description": "Type: `file`, default: `$id.$key.stat.stat`, example: `$id.stat`. RSEM statistics",
"help_text": "Type: `file`, default: `$id.$key.stat.stat`, example: `$id.stat`. RSEM statistics" "help_text": "Type: `file`, default: `$id.$key.stat.stat`, example: `$id.stat`. RSEM statistics"
, ,
"default": "$id.$key.stat.stat" "default":"$id.$key.stat.stat"
} }
@@ -126,7 +126,7 @@
"description": "Type: `file`, default: `$id.$key.logs.log`, example: `$id.log`. RSEM logs", "description": "Type: `file`, default: `$id.$key.logs.log`, example: `$id.log`. RSEM logs",
"help_text": "Type: `file`, default: `$id.$key.logs.log`, example: `$id.log`. RSEM logs" "help_text": "Type: `file`, default: `$id.$key.logs.log`, example: `$id.log`. RSEM logs"
, ,
"default": "$id.$key.logs.log" "default":"$id.$key.logs.log"
} }
@@ -137,7 +137,7 @@
"description": "Type: `file`, default: `$id.$key.bam_star.bam`, example: `$id.STAR.genome.bam`. BAM file generated by STAR (optional)", "description": "Type: `file`, default: `$id.$key.bam_star.bam`, example: `$id.STAR.genome.bam`. BAM file generated by STAR (optional)",
"help_text": "Type: `file`, default: `$id.$key.bam_star.bam`, example: `$id.STAR.genome.bam`. BAM file generated by STAR (optional)" "help_text": "Type: `file`, default: `$id.$key.bam_star.bam`, example: `$id.STAR.genome.bam`. BAM file generated by STAR (optional)"
, ,
"default": "$id.$key.bam_star.bam" "default":"$id.$key.bam_star.bam"
} }
@@ -148,7 +148,7 @@
"description": "Type: `file`, default: `$id.$key.bam_genome.bam`, example: `$id.genome.bam`. Genome BAM file (optional)", "description": "Type: `file`, default: `$id.$key.bam_genome.bam`, example: `$id.genome.bam`. Genome BAM file (optional)",
"help_text": "Type: `file`, default: `$id.$key.bam_genome.bam`, example: `$id.genome.bam`. Genome BAM file (optional)" "help_text": "Type: `file`, default: `$id.$key.bam_genome.bam`, example: `$id.genome.bam`. Genome BAM file (optional)"
, ,
"default": "$id.$key.bam_genome.bam" "default":"$id.$key.bam_genome.bam"
} }
@@ -159,7 +159,7 @@
"description": "Type: `file`, default: `$id.$key.bam_transcript.bam`, example: `$id.transcript.bam`. Transcript BAM file (optional)", "description": "Type: `file`, default: `$id.$key.bam_transcript.bam`, example: `$id.transcript.bam`. Transcript BAM file (optional)",
"help_text": "Type: `file`, default: `$id.$key.bam_transcript.bam`, example: `$id.transcript.bam`. Transcript BAM file (optional)" "help_text": "Type: `file`, default: `$id.$key.bam_transcript.bam`, example: `$id.transcript.bam`. Transcript BAM file (optional)"
, ,
"default": "$id.$key.bam_transcript.bam" "default":"$id.$key.bam_transcript.bam"
} }
@@ -170,7 +170,7 @@
"description": "Type: `boolean_true`, default: `false`. Sort BAM file aligned under transcript coordidate by read name", "description": "Type: `boolean_true`, default: `false`. Sort BAM file aligned under transcript coordidate by read name",
"help_text": "Type: `boolean_true`, default: `false`. Sort BAM file aligned under transcript coordidate by read name. Setting this option on will produce \ndeterministic maximum likelihood estimations from independent runs. Note that sorting will take long \ntime and lots of memory.\n" "help_text": "Type: `boolean_true`, default: `false`. Sort BAM file aligned under transcript coordidate by read name. Setting this option on will produce \ndeterministic maximum likelihood estimations from independent runs. Note that sorting will take long \ntime and lots of memory.\n"
, ,
"default": "False" "default":false
} }
@@ -181,7 +181,7 @@
"description": "Type: `boolean_true`, default: `false`. Do not output any BAM file", "description": "Type: `boolean_true`, default: `false`. Do not output any BAM file",
"help_text": "Type: `boolean_true`, default: `false`. Do not output any BAM file." "help_text": "Type: `boolean_true`, default: `false`. Do not output any BAM file."
, ,
"default": "False" "default":false
} }
@@ -192,7 +192,7 @@
"description": "Type: `boolean_true`, default: `false`. When RSEM generates a BAM file, instead of outputting all alignments a read has with their posterior \nprobabilities, one alignment is sampled according to the posterior probabilities", "description": "Type: `boolean_true`, default: `false`. When RSEM generates a BAM file, instead of outputting all alignments a read has with their posterior \nprobabilities, one alignment is sampled according to the posterior probabilities",
"help_text": "Type: `boolean_true`, default: `false`. When RSEM generates a BAM file, instead of outputting all alignments a read has with their posterior \nprobabilities, one alignment is sampled according to the posterior probabilities. The sampling procedure \nincludes the alignment to the \"noise\" transcript, which does not appear in the BAM file. Only the \nsampled alignment has a weight of 1. All other alignments have weight 0. If the \"noise\" transcript is \nsampled, all alignments appeared in the BAM file should have weight 0.\n" "help_text": "Type: `boolean_true`, default: `false`. When RSEM generates a BAM file, instead of outputting all alignments a read has with their posterior \nprobabilities, one alignment is sampled according to the posterior probabilities. The sampling procedure \nincludes the alignment to the \"noise\" transcript, which does not appear in the BAM file. Only the \nsampled alignment has a weight of 1. All other alignments have weight 0. If the \"noise\" transcript is \nsampled, all alignments appeared in the BAM file should have weight 0.\n"
, ,
"default": "False" "default":false
} }
@@ -203,7 +203,7 @@
"description": "Type: `boolean_true`, default: `false`. Generate a BAM file, \u0027sample_name", "description": "Type: `boolean_true`, default: `false`. Generate a BAM file, \u0027sample_name",
"help_text": "Type: `boolean_true`, default: `false`. Generate a BAM file, \u0027sample_name.genome.bam\u0027, with alignments mapped to genomic coordinates and \nannotated with their posterior probabilities. In addition, RSEM will call samtools (included in RSEM \npackage) to sort and index the bam file. \u0027sample_name.genome.sorted.bam\u0027 and \u0027sample_name.genome.sorted.bam.bai\u0027 \nwill be generated.\n" "help_text": "Type: `boolean_true`, default: `false`. Generate a BAM file, \u0027sample_name.genome.bam\u0027, with alignments mapped to genomic coordinates and \nannotated with their posterior probabilities. In addition, RSEM will call samtools (included in RSEM \npackage) to sort and index the bam file. \u0027sample_name.genome.sorted.bam\u0027 and \u0027sample_name.genome.sorted.bam.bai\u0027 \nwill be generated.\n"
, ,
"default": "False" "default":false
} }
@@ -214,7 +214,7 @@
"description": "Type: `boolean_true`, default: `false`. Sort RSEM generated transcript and genome BAM files by coordinates and build associated indices", "description": "Type: `boolean_true`, default: `false`. Sort RSEM generated transcript and genome BAM files by coordinates and build associated indices",
"help_text": "Type: `boolean_true`, default: `false`. Sort RSEM generated transcript and genome BAM files by coordinates and build associated indices.\n" "help_text": "Type: `boolean_true`, default: `false`. Sort RSEM generated transcript and genome BAM files by coordinates and build associated indices.\n"
, ,
"default": "False" "default":false
} }
@@ -235,7 +235,7 @@
"description": "Type: `boolean_true`, default: `false`. Input reads do not contain quality scores", "description": "Type: `boolean_true`, default: `false`. Input reads do not contain quality scores",
"help_text": "Type: `boolean_true`, default: `false`. Input reads do not contain quality scores." "help_text": "Type: `boolean_true`, default: `false`. Input reads do not contain quality scores."
, ,
"default": "False" "default":false
} }
@@ -246,7 +246,7 @@
"description": "Type: `boolean_true`, default: `false`. Input file contains alignments in SAM/BAM/CRAM format", "description": "Type: `boolean_true`, default: `false`. Input file contains alignments in SAM/BAM/CRAM format",
"help_text": "Type: `boolean_true`, default: `false`. Input file contains alignments in SAM/BAM/CRAM format. The exact file format will be determined \nautomatically.\n" "help_text": "Type: `boolean_true`, default: `false`. Input file contains alignments in SAM/BAM/CRAM format. The exact file format will be determined \nautomatically.\n"
, ,
"default": "False" "default":false
} }
@@ -267,7 +267,7 @@
"description": "Type: `boolean_true`, default: `false`. Use Bowtie 2 instead of Bowtie to align reads", "description": "Type: `boolean_true`, default: `false`. Use Bowtie 2 instead of Bowtie to align reads",
"help_text": "Type: `boolean_true`, default: `false`. Use Bowtie 2 instead of Bowtie to align reads. Since currently RSEM does not handle indel, local \nand discordant alignments, the Bowtie2 parameters are set in a way to avoid those alignments. In \nparticular, we use options \u0027--sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score_min L,0,-0.1\u0027 \nby default. The last parameter of \u0027--score_min\u0027, \u0027-0.1\u0027, is the negative of maximum mismatch rate. \nThis rate can be set by option \u0027--bowtie2_mismatch_rate\u0027. If reads are paired-end, we additionally \nuse options \u0027--no_mixed\u0027 and \u0027--no_discordant\u0027.\n" "help_text": "Type: `boolean_true`, default: `false`. Use Bowtie 2 instead of Bowtie to align reads. Since currently RSEM does not handle indel, local \nand discordant alignments, the Bowtie2 parameters are set in a way to avoid those alignments. In \nparticular, we use options \u0027--sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score_min L,0,-0.1\u0027 \nby default. The last parameter of \u0027--score_min\u0027, \u0027-0.1\u0027, is the negative of maximum mismatch rate. \nThis rate can be set by option \u0027--bowtie2_mismatch_rate\u0027. If reads are paired-end, we additionally \nuse options \u0027--no_mixed\u0027 and \u0027--no_discordant\u0027.\n"
, ,
"default": "False" "default":false
} }
@@ -278,7 +278,7 @@
"description": "Type: `boolean_true`, default: `false`. Use STAR to align reads", "description": "Type: `boolean_true`, default: `false`. Use STAR to align reads",
"help_text": "Type: `boolean_true`, default: `false`. Use STAR to align reads. Alignment parameters are from ENCODE3\u0027s STAR-RSEM pipeline. To save \ncomputational time and memory resources, STAR\u0027s Output BAM file is unsorted. It is stored in RSEM\u0027s \ntemporary directory with name as \u0027sample_name.bam\u0027. Each STAR job will have its own private copy of \nthe genome in memory.\n" "help_text": "Type: `boolean_true`, default: `false`. Use STAR to align reads. Alignment parameters are from ENCODE3\u0027s STAR-RSEM pipeline. To save \ncomputational time and memory resources, STAR\u0027s Output BAM file is unsorted. It is stored in RSEM\u0027s \ntemporary directory with name as \u0027sample_name.bam\u0027. Each STAR job will have its own private copy of \nthe genome in memory.\n"
, ,
"default": "False" "default":false
} }
@@ -289,7 +289,7 @@
"description": "Type: `boolean_true`, default: `false`. Use HISAT2 to align reads to the transcriptome according to Human Cell Atlast", "description": "Type: `boolean_true`, default: `false`. Use HISAT2 to align reads to the transcriptome according to Human Cell Atlast",
"help_text": "Type: `boolean_true`, default: `false`. Use HISAT2 to align reads to the transcriptome according to Human Cell Atlast.\n" "help_text": "Type: `boolean_true`, default: `false`. Use HISAT2 to align reads to the transcriptome according to Human Cell Atlast.\n"
, ,
"default": "False" "default":false
} }
@@ -300,7 +300,7 @@
"description": "Type: `boolean_true`, default: `false`. If gene_name/transcript_name is available, append it to the end of gene_id/transcript_id (separated \nby \u0027_\u0027) in files \u0027sample_name", "description": "Type: `boolean_true`, default: `false`. If gene_name/transcript_name is available, append it to the end of gene_id/transcript_id (separated \nby \u0027_\u0027) in files \u0027sample_name",
"help_text": "Type: `boolean_true`, default: `false`. If gene_name/transcript_name is available, append it to the end of gene_id/transcript_id (separated \nby \u0027_\u0027) in files \u0027sample_name.isoforms.results\u0027 and \u0027sample_name.genes.results\u0027.\n" "help_text": "Type: `boolean_true`, default: `false`. If gene_name/transcript_name is available, append it to the end of gene_id/transcript_id (separated \nby \u0027_\u0027) in files \u0027sample_name.isoforms.results\u0027 and \u0027sample_name.genes.results\u0027.\n"
, ,
"default": "False" "default":false
} }
@@ -321,7 +321,7 @@
"description": "Type: `boolean_true`, default: `false`. By default, RSEM uses Dirichlet(1) as the prior to calculate posterior mean estimates and credibility \nintervals", "description": "Type: `boolean_true`, default: `false`. By default, RSEM uses Dirichlet(1) as the prior to calculate posterior mean estimates and credibility \nintervals",
"help_text": "Type: `boolean_true`, default: `false`. By default, RSEM uses Dirichlet(1) as the prior to calculate posterior mean estimates and credibility \nintervals. However, much less genes are expressed in single cell RNA-Seq data. Thus, if you want to \ncompute posterior mean estimates and/or credibility intervals and you have single-cell RNA-Seq data, \nyou are recommended to turn on this option. Then RSEM will use Dirichlet(0.1) as the prior which \nencourage the sparsity of the expression levels.\n" "help_text": "Type: `boolean_true`, default: `false`. By default, RSEM uses Dirichlet(1) as the prior to calculate posterior mean estimates and credibility \nintervals. However, much less genes are expressed in single cell RNA-Seq data. Thus, if you want to \ncompute posterior mean estimates and/or credibility intervals and you have single-cell RNA-Seq data, \nyou are recommended to turn on this option. Then RSEM will use Dirichlet(0.1) as the prior which \nencourage the sparsity of the expression levels.\n"
, ,
"default": "False" "default":false
} }
@@ -332,7 +332,7 @@
"description": "Type: `boolean_true`, default: `false`. Run RSEM\u0027s collapsed Gibbs sampler to calculate posterior mean estimates", "description": "Type: `boolean_true`, default: `false`. Run RSEM\u0027s collapsed Gibbs sampler to calculate posterior mean estimates",
"help_text": "Type: `boolean_true`, default: `false`. Run RSEM\u0027s collapsed Gibbs sampler to calculate posterior mean estimates." "help_text": "Type: `boolean_true`, default: `false`. Run RSEM\u0027s collapsed Gibbs sampler to calculate posterior mean estimates."
, ,
"default": "False" "default":false
} }
@@ -343,7 +343,7 @@
"description": "Type: `boolean_true`, default: `false`. Calculate 95% credibility intervals and posterior mean estimates", "description": "Type: `boolean_true`, default: `false`. Calculate 95% credibility intervals and posterior mean estimates",
"help_text": "Type: `boolean_true`, default: `false`. Calculate 95% credibility intervals and posterior mean estimates. The credibility level can be \nchanged by setting \u0027--ci_credibility_level\u0027.\n" "help_text": "Type: `boolean_true`, default: `false`. Calculate 95% credibility intervals and posterior mean estimates. The credibility level can be \nchanged by setting \u0027--ci_credibility_level\u0027.\n"
, ,
"default": "False" "default":false
} }
@@ -354,7 +354,7 @@
"description": "Type: `boolean_true`, default: `false`. Suppress the output of logging information", "description": "Type: `boolean_true`, default: `false`. Suppress the output of logging information",
"help_text": "Type: `boolean_true`, default: `false`. Suppress the output of logging information." "help_text": "Type: `boolean_true`, default: `false`. Suppress the output of logging information."
, ,
"default": "False" "default":false
} }
@@ -385,7 +385,7 @@
"description": "Type: `boolean_true`, default: `false`. Input quality scores are encoded as Phred+64 (default for GA Pipeline ver", "description": "Type: `boolean_true`, default: `false`. Input quality scores are encoded as Phred+64 (default for GA Pipeline ver",
"help_text": "Type: `boolean_true`, default: `false`. Input quality scores are encoded as Phred+64 (default for GA Pipeline ver. \u003e= 1.3). This option is \nused by Bowtie, Bowtie 2 and HISAT2. Otherwise, quality score will be encoded as Phred+33. (Default: false)\n" "help_text": "Type: `boolean_true`, default: `false`. Input quality scores are encoded as Phred+64 (default for GA Pipeline ver. \u003e= 1.3). This option is \nused by Bowtie, Bowtie 2 and HISAT2. Otherwise, quality score will be encoded as Phred+33. (Default: false)\n"
, ,
"default": "False" "default":false
} }
@@ -396,7 +396,7 @@
"description": "Type: `boolean_true`, default: `false`. Input quality scores are solexa encoded (from GA Pipeline ver", "description": "Type: `boolean_true`, default: `false`. Input quality scores are solexa encoded (from GA Pipeline ver",
"help_text": "Type: `boolean_true`, default: `false`. Input quality scores are solexa encoded (from GA Pipeline ver. \u003c 1.3). This option is used by \nBowtie, Bowtie 2 and HISAT2. Otherwise, quality score will be encoded as Phred+33. (Default: false)\n" "help_text": "Type: `boolean_true`, default: `false`. Input quality scores are solexa encoded (from GA Pipeline ver. \u003c 1.3). This option is used by \nBowtie, Bowtie 2 and HISAT2. Otherwise, quality score will be encoded as Phred+33. (Default: false)\n"
, ,
"default": "False" "default":false
} }
@@ -481,7 +481,7 @@
"description": "Type: `boolean_true`, default: `false`. Input read file(s) is compressed by gzip", "description": "Type: `boolean_true`, default: `false`. Input read file(s) is compressed by gzip",
"help_text": "Type: `boolean_true`, default: `false`. Input read file(s) is compressed by gzip. (Default: false)\n" "help_text": "Type: `boolean_true`, default: `false`. Input read file(s) is compressed by gzip. (Default: false)\n"
, ,
"default": "False" "default":false
} }
@@ -492,7 +492,7 @@
"description": "Type: `boolean_true`, default: `false`. Input read file(s) is compressed by bzip2", "description": "Type: `boolean_true`, default: `false`. Input read file(s) is compressed by bzip2",
"help_text": "Type: `boolean_true`, default: `false`. Input read file(s) is compressed by bzip2. (Default: false)\n" "help_text": "Type: `boolean_true`, default: `false`. Input read file(s) is compressed by bzip2. (Default: false)\n"
, ,
"default": "False" "default":false
} }
@@ -503,7 +503,7 @@
"description": "Type: `boolean_true`, default: `false`. Save the BAM file from STAR alignment under genomic coordinate to \u0027sample_name", "description": "Type: `boolean_true`, default: `false`. Save the BAM file from STAR alignment under genomic coordinate to \u0027sample_name",
"help_text": "Type: `boolean_true`, default: `false`. Save the BAM file from STAR alignment under genomic coordinate to \u0027sample_name.STAR.genome.bam\u0027. \nThis file is NOT sorted by genomic coordinate. In this file, according to STAR\u0027s manual, \u0027paired \nends of an alignment are always adjacent, and multiple alignments of a read are adjacent as well\u0027. \n(Default: false)\n" "help_text": "Type: `boolean_true`, default: `false`. Save the BAM file from STAR alignment under genomic coordinate to \u0027sample_name.STAR.genome.bam\u0027. \nThis file is NOT sorted by genomic coordinate. In this file, according to STAR\u0027s manual, \u0027paired \nends of an alignment are always adjacent, and multiple alignments of a read are adjacent as well\u0027. \n(Default: false)\n"
, ,
"default": "False" "default":false
} }
@@ -574,7 +574,7 @@
"description": "Type: `boolean_true`, default: `false`. Set this option if you want to estimate the read start position distribution (RSPD) from data", "description": "Type: `boolean_true`, default: `false`. Set this option if you want to estimate the read start position distribution (RSPD) from data",
"help_text": "Type: `boolean_true`, default: `false`. Set this option if you want to estimate the read start position distribution (RSPD) from data.\nOtherwise, RSEM will use a uniform RSPD.\n" "help_text": "Type: `boolean_true`, default: `false`. Set this option if you want to estimate the read start position distribution (RSPD) from data.\nOtherwise, RSEM will use a uniform RSPD.\n"
, ,
"default": "False" "default":false
} }
@@ -645,7 +645,7 @@
"description": "Type: `boolean_true`, default: `false`. Keep temporary files generated by RSEM", "description": "Type: `boolean_true`, default: `false`. Keep temporary files generated by RSEM",
"help_text": "Type: `boolean_true`, default: `false`. Keep temporary files generated by RSEM. RSEM creates a temporary directory, \u0027sample_name.temp\u0027, \ninto which it puts all intermediate output files. If this directory already exists, RSEM overwrites \nall files generated by previous RSEM runs inside of it. By default, after RSEM finishes, the \ntemporary directory is deleted. Set this option to prevent the deletion of this directory and the \nintermediate files inside of it.\n" "help_text": "Type: `boolean_true`, default: `false`. Keep temporary files generated by RSEM. RSEM creates a temporary directory, \u0027sample_name.temp\u0027, \ninto which it puts all intermediate output files. If this directory already exists, RSEM overwrites \nall files generated by previous RSEM runs inside of it. By default, after RSEM finishes, the \ntemporary directory is deleted. Set this option to prevent the deletion of this directory and the \nintermediate files inside of it.\n"
, ,
"default": "False" "default":false
} }
@@ -666,7 +666,7 @@
"description": "Type: `boolean_true`, default: `false`. Output time consumed by each step of RSEM to \u0027sample_name", "description": "Type: `boolean_true`, default: `false`. Output time consumed by each step of RSEM to \u0027sample_name",
"help_text": "Type: `boolean_true`, default: `false`. Output time consumed by each step of RSEM to \u0027sample_name.time\u0027.\n" "help_text": "Type: `boolean_true`, default: `false`. Output time consumed by each step of RSEM to \u0027sample_name.time\u0027.\n"
, ,
"default": "False" "default":false
} }
@@ -687,7 +687,7 @@
"description": "Type: `boolean_true`, default: `false`. Running prior-enhanced RSEM (pRSEM)", "description": "Type: `boolean_true`, default: `false`. Running prior-enhanced RSEM (pRSEM)",
"help_text": "Type: `boolean_true`, default: `false`. Running prior-enhanced RSEM (pRSEM). Prior parameters, i.e. isoform\u0027s initial pseudo-count for \nRSEM\u0027s Gibbs sampling, will be learned from input RNA-seq data and an external data set. When pRSEM \nneeds and only needs ChIP-seq peak information to partition isoforms (e.g. in pRSEM\u0027s default \npartition model), either ChIP-seq peak file (with the \u0027--chipseq_peak_file\u0027 option) or ChIP-seq \nFASTQ files for target and input and the path for Bowtie executables are required (with the \n\u0027--chipseq_target_read_files \u003cstring\u003e\u0027, \u0027--chipseq_control_read_files \u003cstring\u003e\u0027, and \u0027--bowtie_path \n\u003cpath\u003e options), otherwise, ChIP-seq FASTQ files for target and control and the path to Bowtie \nexecutables are required.\n" "help_text": "Type: `boolean_true`, default: `false`. Running prior-enhanced RSEM (pRSEM). Prior parameters, i.e. isoform\u0027s initial pseudo-count for \nRSEM\u0027s Gibbs sampling, will be learned from input RNA-seq data and an external data set. When pRSEM \nneeds and only needs ChIP-seq peak information to partition isoforms (e.g. in pRSEM\u0027s default \npartition model), either ChIP-seq peak file (with the \u0027--chipseq_peak_file\u0027 option) or ChIP-seq \nFASTQ files for target and input and the path for Bowtie executables are required (with the \n\u0027--chipseq_target_read_files \u003cstring\u003e\u0027, \u0027--chipseq_control_read_files \u003cstring\u003e\u0027, and \u0027--bowtie_path \n\u003cpath\u003e options), otherwise, ChIP-seq FASTQ files for target and control and the path to Bowtie \nexecutables are required.\n"
, ,
"default": "False" "default":false
} }
@@ -748,7 +748,7 @@
"description": "Type: `boolean_true`, default: `false`. Keep a maximum number of ChIP-seq reads that aligned to the same genomic interval", "description": "Type: `boolean_true`, default: `false`. Keep a maximum number of ChIP-seq reads that aligned to the same genomic interval",
"help_text": "Type: `boolean_true`, default: `false`. Keep a maximum number of ChIP-seq reads that aligned to the same genomic interval. This option is used \nwhen running prior-enhanced RSEM, where prior is learned from multiple complementary data sets. This \noption is only in use when either \u0027--chipseq_read_files_multi_targets \u003cstring\u003e\u0027 or \n\u0027--chipseq_bed_files_multi_targets \u003cstring\u003e\u0027 is specified.\n" "help_text": "Type: `boolean_true`, default: `false`. Keep a maximum number of ChIP-seq reads that aligned to the same genomic interval. This option is used \nwhen running prior-enhanced RSEM, where prior is learned from multiple complementary data sets. This \noption is only in use when either \u0027--chipseq_read_files_multi_targets \u003cstring\u003e\u0027 or \n\u0027--chipseq_bed_files_multi_targets \u003cstring\u003e\u0027 is specified.\n"
, ,
"default": "False" "default":false
} }

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

@@ -416,9 +416,9 @@ build_info:
output: "target/nextflow/rsem/rsem_prepare_reference" output: "target/nextflow/rsem/rsem_prepare_reference"
executable: "target/nextflow/rsem/rsem_prepare_reference/main.nf" executable: "target/nextflow/rsem/rsem_prepare_reference/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d" git_tag: "v0.2.0-27-g952ff08"
package_config: package_config:
name: "biobox" name: "biobox"
version: "main" version: "main"

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

@@ -3245,9 +3245,9 @@ meta = [
"engine" : "docker|native", "engine" : "docker|native",
"output" : "target/nextflow/rsem/rsem_prepare_reference", "output" : "target/nextflow/rsem/rsem_prepare_reference",
"viash_version" : "0.9.0", "viash_version" : "0.9.0",
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d" "git_tag" : "v0.2.0-27-g952ff08"
}, },
"package_config" : { "package_config" : {
"name" : "biobox", "name" : "biobox",

18
target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/nextflow_schema.json
View File

@@ -50,7 +50,7 @@
"description": "Type: `file`, required, default: `$id.$key.output.output`. Directory containing reference files generated by RSEM", "description": "Type: `file`, required, default: `$id.$key.output.output`. Directory containing reference files generated by RSEM",
"help_text": "Type: `file`, required, default: `$id.$key.output.output`. Directory containing reference files generated by RSEM." "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Directory containing reference files generated by RSEM."
, ,
"default": "$id.$key.output.output" "default":"$id.$key.output.output"
} }
@@ -101,7 +101,7 @@
"description": "Type: `boolean_true`, default: `false`. This option is designed for untypical organisms, such as viruses, whose GFF3 files only contain genes", "description": "Type: `boolean_true`, default: `false`. This option is designed for untypical organisms, such as viruses, whose GFF3 files only contain genes",
"help_text": "Type: `boolean_true`, default: `false`. This option is designed for untypical organisms, such as viruses, whose GFF3 files only contain genes. RSEM will assume each gene as a unique transcript when it converts the GFF3 file into GTF format." "help_text": "Type: `boolean_true`, default: `false`. This option is designed for untypical organisms, such as viruses, whose GFF3 files only contain genes. RSEM will assume each gene as a unique transcript when it converts the GFF3 file into GTF format."
, ,
"default": "False" "default":false
} }
@@ -142,7 +142,7 @@
"description": "Type: `boolean_true`, default: `false`. Add poly(A) tails to the end of all reference isoforms", "description": "Type: `boolean_true`, default: `false`. Add poly(A) tails to the end of all reference isoforms",
"help_text": "Type: `boolean_true`, default: `false`. Add poly(A) tails to the end of all reference isoforms. The length of poly(A) tail added is specified by \u0027--polyA-length\u0027 option. STAR aligner users may not want to use this option." "help_text": "Type: `boolean_true`, default: `false`. Add poly(A) tails to the end of all reference isoforms. The length of poly(A) tail added is specified by \u0027--polyA-length\u0027 option. STAR aligner users may not want to use this option."
, ,
"default": "False" "default":false
} }
@@ -173,7 +173,7 @@
"description": "Type: `boolean_true`, default: `false`. Build Bowtie indices", "description": "Type: `boolean_true`, default: `false`. Build Bowtie indices",
"help_text": "Type: `boolean_true`, default: `false`. Build Bowtie indices." "help_text": "Type: `boolean_true`, default: `false`. Build Bowtie indices."
, ,
"default": "False" "default":false
} }
@@ -184,7 +184,7 @@
"description": "Type: `boolean_true`, default: `false`. Build Bowtie 2 indices", "description": "Type: `boolean_true`, default: `false`. Build Bowtie 2 indices",
"help_text": "Type: `boolean_true`, default: `false`. Build Bowtie 2 indices." "help_text": "Type: `boolean_true`, default: `false`. Build Bowtie 2 indices."
, ,
"default": "False" "default":false
} }
@@ -195,7 +195,7 @@
"description": "Type: `boolean_true`, default: `false`. Build STAR indices", "description": "Type: `boolean_true`, default: `false`. Build STAR indices",
"help_text": "Type: `boolean_true`, default: `false`. Build STAR indices." "help_text": "Type: `boolean_true`, default: `false`. Build STAR indices."
, ,
"default": "False" "default":false
} }
@@ -216,7 +216,7 @@
"description": "Type: `boolean_true`, default: `false`. Build HISAT2 indices on the transcriptome according to Human Cell Atlas (HCA) SMART-Seq2 pipeline", "description": "Type: `boolean_true`, default: `false`. Build HISAT2 indices on the transcriptome according to Human Cell Atlas (HCA) SMART-Seq2 pipeline",
"help_text": "Type: `boolean_true`, default: `false`. Build HISAT2 indices on the transcriptome according to Human Cell Atlas (HCA) SMART-Seq2 pipeline." "help_text": "Type: `boolean_true`, default: `false`. Build HISAT2 indices on the transcriptome according to Human Cell Atlas (HCA) SMART-Seq2 pipeline."
, ,
"default": "False" "default":false
} }
@@ -227,7 +227,7 @@
"description": "Type: `boolean_true`, default: `false`. Suppress the output of logging information", "description": "Type: `boolean_true`, default: `false`. Suppress the output of logging information",
"help_text": "Type: `boolean_true`, default: `false`. Suppress the output of logging information." "help_text": "Type: `boolean_true`, default: `false`. Suppress the output of logging information."
, ,
"default": "False" "default":false
} }
@@ -248,7 +248,7 @@
"description": "Type: `boolean_true`, default: `false`. A Boolean indicating whether to prepare reference files for pRSEM, including building Bowtie indices for a genome and selecting training set isoforms", "description": "Type: `boolean_true`, default: `false`. A Boolean indicating whether to prepare reference files for pRSEM, including building Bowtie indices for a genome and selecting training set isoforms",
"help_text": "Type: `boolean_true`, default: `false`. A Boolean indicating whether to prepare reference files for pRSEM, including building Bowtie indices for a genome and selecting training set isoforms. The index files will be used for aligning ChIP-seq reads in prior-enhanced RSEM and the training set isoforms will be used for learning prior. A path to Bowtie executables and a mappability file in bigWig format are required when this option is on. Currently, Bowtie2 is not supported for prior-enhanced RSEM." "help_text": "Type: `boolean_true`, default: `false`. A Boolean indicating whether to prepare reference files for pRSEM, including building Bowtie indices for a genome and selecting training set isoforms. The index files will be used for aligning ChIP-seq reads in prior-enhanced RSEM and the training set isoforms will be used for learning prior. A path to Bowtie executables and a mappability file in bigWig format are required when this option is on. Currently, Bowtie2 is not supported for prior-enhanced RSEM."
, ,
"default": "False" "default":false
} }

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

@@ -175,9 +175,9 @@ build_info:
output: "target/nextflow/rseqc/rseqc_bamstat" output: "target/nextflow/rseqc/rseqc_bamstat"
executable: "target/nextflow/rseqc/rseqc_bamstat/main.nf" executable: "target/nextflow/rseqc/rseqc_bamstat/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d" git_tag: "v0.2.0-27-g952ff08"
package_config: package_config:
name: "biobox" name: "biobox"
version: "main" version: "main"

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

@@ -3036,9 +3036,9 @@ meta = [
"engine" : "docker|native", "engine" : "docker|native",
"output" : "target/nextflow/rseqc/rseqc_bamstat", "output" : "target/nextflow/rseqc/rseqc_bamstat",
"viash_version" : "0.9.0", "viash_version" : "0.9.0",
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d" "git_tag" : "v0.2.0-27-g952ff08"
}, },
"package_config" : { "package_config" : {
"name" : "biobox", "name" : "biobox",

2
target/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_bamstat/nextflow_schema.json
View File

@@ -50,7 +50,7 @@
"description": "Type: `file`, default: `$id.$key.output.output`. Output file (txt) with mapping quality statistics", "description": "Type: `file`, default: `$id.$key.output.output`. Output file (txt) with mapping quality statistics",
"help_text": "Type: `file`, default: `$id.$key.output.output`. Output file (txt) with mapping quality statistics." "help_text": "Type: `file`, default: `$id.$key.output.output`. Output file (txt) with mapping quality statistics."
, ,
"default": "$id.$key.output.output" "default":"$id.$key.output.output"
} }

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

@@ -201,9 +201,9 @@ build_info:
output: "target/nextflow/rseqc/rseqc_inferexperiment" output: "target/nextflow/rseqc/rseqc_inferexperiment"
executable: "target/nextflow/rseqc/rseqc_inferexperiment/main.nf" executable: "target/nextflow/rseqc/rseqc_inferexperiment/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d" git_tag: "v0.2.0-27-g952ff08"
package_config: package_config:
name: "biobox" name: "biobox"
version: "main" version: "main"

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

@@ -3069,9 +3069,9 @@ meta = [
"engine" : "docker|native", "engine" : "docker|native",
"output" : "target/nextflow/rseqc/rseqc_inferexperiment", "output" : "target/nextflow/rseqc/rseqc_inferexperiment",
"viash_version" : "0.9.0", "viash_version" : "0.9.0",
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d" "git_tag" : "v0.2.0-27-g952ff08"
}, },
"package_config" : { "package_config" : {
"name" : "biobox", "name" : "biobox",

2
target/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_inferexperiment/nextflow_schema.json
View File

@@ -50,7 +50,7 @@
"description": "Type: `file`, required, default: `$id.$key.output.txt`, example: `$id.strandedness.txt`. Output file (txt) of strandness report", "description": "Type: `file`, required, default: `$id.$key.output.txt`, example: `$id.strandedness.txt`. Output file (txt) of strandness report",
"help_text": "Type: `file`, required, default: `$id.$key.output.txt`, example: `$id.strandedness.txt`. Output file (txt) of strandness report." "help_text": "Type: `file`, required, default: `$id.$key.output.txt`, example: `$id.strandedness.txt`. Output file (txt) of strandness report."
, ,
"default": "$id.$key.output.txt" "default":"$id.$key.output.txt"
} }

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

@@ -294,9 +294,9 @@ build_info:
output: "target/nextflow/rseqc/rseqc_inner_distance" output: "target/nextflow/rseqc/rseqc_inner_distance"
executable: "target/nextflow/rseqc/rseqc_inner_distance/main.nf" executable: "target/nextflow/rseqc/rseqc_inner_distance/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d" git_tag: "v0.2.0-27-g952ff08"
package_config: package_config:
name: "biobox" name: "biobox"
version: "main" version: "main"

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

@@ -3169,9 +3169,9 @@ meta = [
"engine" : "docker|native", "engine" : "docker|native",
"output" : "target/nextflow/rseqc/rseqc_inner_distance", "output" : "target/nextflow/rseqc/rseqc_inner_distance",
"viash_version" : "0.9.0", "viash_version" : "0.9.0",
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d" "git_tag" : "v0.2.0-27-g952ff08"
}, },
"package_config" : { "package_config" : {
"name" : "biobox", "name" : "biobox",

10
target/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_inner_distance/nextflow_schema.json
View File

@@ -110,7 +110,7 @@
"description": "Type: `file`, default: `$id.$key.output_stats.output_stats`. output file (txt) with summary statistics of inner distances of paired reads", "description": "Type: `file`, default: `$id.$key.output_stats.output_stats`. output file (txt) with summary statistics of inner distances of paired reads",
"help_text": "Type: `file`, default: `$id.$key.output_stats.output_stats`. output file (txt) with summary statistics of inner distances of paired reads" "help_text": "Type: `file`, default: `$id.$key.output_stats.output_stats`. output file (txt) with summary statistics of inner distances of paired reads"
, ,
"default": "$id.$key.output_stats.output_stats" "default":"$id.$key.output_stats.output_stats"
} }
@@ -121,7 +121,7 @@
"description": "Type: `file`, default: `$id.$key.output_dist.output_dist`. output file (txt) with inner distances of all paired reads", "description": "Type: `file`, default: `$id.$key.output_dist.output_dist`. output file (txt) with inner distances of all paired reads",
"help_text": "Type: `file`, default: `$id.$key.output_dist.output_dist`. output file (txt) with inner distances of all paired reads" "help_text": "Type: `file`, default: `$id.$key.output_dist.output_dist`. output file (txt) with inner distances of all paired reads"
, ,
"default": "$id.$key.output_dist.output_dist" "default":"$id.$key.output_dist.output_dist"
} }
@@ -132,7 +132,7 @@
"description": "Type: `file`, default: `$id.$key.output_freq.output_freq`. output file (txt) with frequencies of inner distances of all paired reads", "description": "Type: `file`, default: `$id.$key.output_freq.output_freq`. output file (txt) with frequencies of inner distances of all paired reads",
"help_text": "Type: `file`, default: `$id.$key.output_freq.output_freq`. output file (txt) with frequencies of inner distances of all paired reads" "help_text": "Type: `file`, default: `$id.$key.output_freq.output_freq`. output file (txt) with frequencies of inner distances of all paired reads"
, ,
"default": "$id.$key.output_freq.output_freq" "default":"$id.$key.output_freq.output_freq"
} }
@@ -143,7 +143,7 @@
"description": "Type: `file`, default: `$id.$key.output_plot.output_plot`. output file (pdf) with histogram plot of of inner distances of all paired reads", "description": "Type: `file`, default: `$id.$key.output_plot.output_plot`. output file (pdf) with histogram plot of of inner distances of all paired reads",
"help_text": "Type: `file`, default: `$id.$key.output_plot.output_plot`. output file (pdf) with histogram plot of of inner distances of all paired reads" "help_text": "Type: `file`, default: `$id.$key.output_plot.output_plot`. output file (pdf) with histogram plot of of inner distances of all paired reads"
, ,
"default": "$id.$key.output_plot.output_plot" "default":"$id.$key.output_plot.output_plot"
} }
@@ -154,7 +154,7 @@
"description": "Type: `file`, default: `$id.$key.output_plot_r.output_plot_r`. output file (R) with script of histogram plot of of inner distances of all paired reads", "description": "Type: `file`, default: `$id.$key.output_plot_r.output_plot_r`. output file (R) with script of histogram plot of of inner distances of all paired reads",
"help_text": "Type: `file`, default: `$id.$key.output_plot_r.output_plot_r`. output file (R) with script of histogram plot of of inner distances of all paired reads" "help_text": "Type: `file`, default: `$id.$key.output_plot_r.output_plot_r`. output file (R) with script of histogram plot of of inner distances of all paired reads"
, ,
"default": "$id.$key.output_plot_r.output_plot_r" "default":"$id.$key.output_plot_r.output_plot_r"
} }

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

@@ -277,9 +277,9 @@ build_info:
output: "target/nextflow/salmon/salmon_index" output: "target/nextflow/salmon/salmon_index"
executable: "target/nextflow/salmon/salmon_index/main.nf" executable: "target/nextflow/salmon/salmon_index/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d" git_tag: "v0.2.0-27-g952ff08"
package_config: package_config:
name: "biobox" name: "biobox"
version: "main" version: "main"

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

@@ -3129,9 +3129,9 @@ meta = [
"engine" : "docker|native", "engine" : "docker|native",
"output" : "target/nextflow/salmon/salmon_index", "output" : "target/nextflow/salmon/salmon_index",
"viash_version" : "0.9.0", "viash_version" : "0.9.0",
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d" "git_tag" : "v0.2.0-27-g952ff08"
}, },
"package_config" : { "package_config" : {
"name" : "biobox", "name" : "biobox",

14
target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/nextflow_schema.json
View File

@@ -50,7 +50,7 @@
"description": "Type: `boolean_true`, default: `false`. This flag will expect the input transcript fasta to be in GENCODE format, and will split the transcript name at the first \u0027|\u0027 character", "description": "Type: `boolean_true`, default: `false`. This flag will expect the input transcript fasta to be in GENCODE format, and will split the transcript name at the first \u0027|\u0027 character",
"help_text": "Type: `boolean_true`, default: `false`. This flag will expect the input transcript fasta to be in GENCODE format, and will split the transcript name at the first \u0027|\u0027 character. These reduced names will be used in the output and when looking for these transcripts in a gene to transcript GTF.\n" "help_text": "Type: `boolean_true`, default: `false`. This flag will expect the input transcript fasta to be in GENCODE format, and will split the transcript name at the first \u0027|\u0027 character. These reduced names will be used in the output and when looking for these transcripts in a gene to transcript GTF.\n"
, ,
"default": "False" "default":false
} }
@@ -61,7 +61,7 @@
"description": "Type: `boolean_true`, default: `false`. This flag will expect the input reference to be in the tsv file format, and will split the feature name at the first \u0027tab\u0027 character", "description": "Type: `boolean_true`, default: `false`. This flag will expect the input reference to be in the tsv file format, and will split the feature name at the first \u0027tab\u0027 character",
"help_text": "Type: `boolean_true`, default: `false`. This flag will expect the input reference to be in the tsv file format, and will split the feature name at the first \u0027tab\u0027 character. These reduced names will be used in the output and when looking for the sequence of the features.GTF.\n" "help_text": "Type: `boolean_true`, default: `false`. This flag will expect the input reference to be in the tsv file format, and will split the feature name at the first \u0027tab\u0027 character. These reduced names will be used in the output and when looking for the sequence of the features.GTF.\n"
, ,
"default": "False" "default":false
} }
@@ -72,7 +72,7 @@
"description": "Type: `boolean_true`, default: `false`. This flag will disable the default indexing behavior of discarding sequence-identical duplicate transcripts", "description": "Type: `boolean_true`, default: `false`. This flag will disable the default indexing behavior of discarding sequence-identical duplicate transcripts",
"help_text": "Type: `boolean_true`, default: `false`. This flag will disable the default indexing behavior of discarding sequence-identical duplicate transcripts. If this flag is passed, then duplicate transcripts that appear in the input will be retained and quantified separately.\n" "help_text": "Type: `boolean_true`, default: `false`. This flag will disable the default indexing behavior of discarding sequence-identical duplicate transcripts. If this flag is passed, then duplicate transcripts that appear in the input will be retained and quantified separately.\n"
, ,
"default": "False" "default":false
} }
@@ -83,7 +83,7 @@
"description": "Type: `boolean_true`, default: `false`. Retain the fixed fasta file (without short transcripts and duplicates, clipped, etc", "description": "Type: `boolean_true`, default: `false`. Retain the fixed fasta file (without short transcripts and duplicates, clipped, etc",
"help_text": "Type: `boolean_true`, default: `false`. Retain the fixed fasta file (without short transcripts and duplicates, clipped, etc.) generated during indexing.\n" "help_text": "Type: `boolean_true`, default: `false`. Retain the fixed fasta file (without short transcripts and duplicates, clipped, etc.) generated during indexing.\n"
, ,
"default": "False" "default":false
} }
@@ -104,7 +104,7 @@
"description": "Type: `boolean_true`, default: `false`. Build the index using a sparse sampling of k-mer positions This will require less memory (especially during quantification), but will take longer to construct and can slow down mapping / alignment", "description": "Type: `boolean_true`, default: `false`. Build the index using a sparse sampling of k-mer positions This will require less memory (especially during quantification), but will take longer to construct and can slow down mapping / alignment",
"help_text": "Type: `boolean_true`, default: `false`. Build the index using a sparse sampling of k-mer positions This will require less memory (especially during quantification), but will take longer to construct and can slow down mapping / alignment.\n" "help_text": "Type: `boolean_true`, default: `false`. Build the index using a sparse sampling of k-mer positions This will require less memory (especially during quantification), but will take longer to construct and can slow down mapping / alignment.\n"
, ,
"default": "False" "default":false
} }
@@ -125,7 +125,7 @@
"description": "Type: `boolean_true`, default: `false`. Don\u0027t clip poly-A tails from the ends of target sequences", "description": "Type: `boolean_true`, default: `false`. Don\u0027t clip poly-A tails from the ends of target sequences",
"help_text": "Type: `boolean_true`, default: `false`. Don\u0027t clip poly-A tails from the ends of target sequences.\n" "help_text": "Type: `boolean_true`, default: `false`. Don\u0027t clip poly-A tails from the ends of target sequences.\n"
, ,
"default": "False" "default":false
} }
@@ -156,7 +156,7 @@
"description": "Type: `file`, required, default: `$id.$key.index.index`, example: `Salmon_index`. Salmon index\n", "description": "Type: `file`, required, default: `$id.$key.index.index`, example: `Salmon_index`. Salmon index\n",
"help_text": "Type: `file`, required, default: `$id.$key.index.index`, example: `Salmon_index`. Salmon index\n" "help_text": "Type: `file`, required, default: `$id.$key.index.index`, example: `Salmon_index`. Salmon index\n"
, ,
"default": "$id.$key.index.index" "default":"$id.$key.index.index"
} }

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

@@ -1173,9 +1173,9 @@ build_info:
output: "target/nextflow/salmon/salmon_quant" output: "target/nextflow/salmon/salmon_quant"
executable: "target/nextflow/salmon/salmon_quant/main.nf" executable: "target/nextflow/salmon/salmon_quant/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d" git_tag: "v0.2.0-27-g952ff08"
package_config: package_config:
name: "biobox" name: "biobox"
version: "main" version: "main"

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

@@ -3964,9 +3964,9 @@ meta = [
"engine" : "docker|native", "engine" : "docker|native",
"output" : "target/nextflow/salmon/salmon_quant", "output" : "target/nextflow/salmon/salmon_quant",
"viash_version" : "0.9.0", "viash_version" : "0.9.0",
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d" "git_tag" : "v0.2.0-27-g952ff08"
}, },
"package_config" : { "package_config" : {
"name" : "biobox", "name" : "biobox",

94
target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/nextflow_schema.json
View File

@@ -22,7 +22,7 @@
"enum": ["A", "U", "SF", "SR", "IU", "IS", "ISF", "ISR", "OU", "OS", "OSF", "OSR", "MU", "MS", "MSF", "MSR"] "enum": ["A", "U", "SF", "SR", "IU", "IS", "ISF", "ISR", "OU", "OS", "OSF", "OSR", "MU", "MS", "MSF", "MSR"]
, ,
"default": "A" "default":"A"
} }
@@ -93,7 +93,7 @@
"description": "Type: `boolean_true`, default: `false`. Discard orphan alignments in the input [for alignment-based mode only]", "description": "Type: `boolean_true`, default: `false`. Discard orphan alignments in the input [for alignment-based mode only]",
"help_text": "Type: `boolean_true`, default: `false`. Discard orphan alignments in the input [for alignment-based mode only]. If this flag is passed, then only paired alignments will be considered toward quantification estimates. The default behavior is to consider orphan alignments if no valid paired mappings exist.\n" "help_text": "Type: `boolean_true`, default: `false`. Discard orphan alignments in the input [for alignment-based mode only]. If this flag is passed, then only paired alignments will be considered toward quantification estimates. The default behavior is to consider orphan alignments if no valid paired mappings exist.\n"
, ,
"default": "False" "default":false
} }
@@ -134,7 +134,7 @@
"description": "Type: `boolean_true`, default: `false`. Use alignment model for Oxford Nanopore long reads\n", "description": "Type: `boolean_true`, default: `false`. Use alignment model for Oxford Nanopore long reads\n",
"help_text": "Type: `boolean_true`, default: `false`. Use alignment model for Oxford Nanopore long reads\n" "help_text": "Type: `boolean_true`, default: `false`. Use alignment model for Oxford Nanopore long reads\n"
, ,
"default": "False" "default":false
} }
@@ -155,7 +155,7 @@
"description": "Type: `file`, required, default: `$id.$key.output.output`, example: `quant_output`. Output quantification directory", "description": "Type: `file`, required, default: `$id.$key.output.output`, example: `quant_output`. Output quantification directory",
"help_text": "Type: `file`, required, default: `$id.$key.output.output`, example: `quant_output`. Output quantification directory.\n" "help_text": "Type: `file`, required, default: `$id.$key.output.output`, example: `quant_output`. Output quantification directory.\n"
, ,
"default": "$id.$key.output.output" "default":"$id.$key.output.output"
} }
@@ -166,7 +166,7 @@
"description": "Type: `file`, default: `$id.$key.quant_results.sf`, example: `quant.sf`. Salmon quantification file", "description": "Type: `file`, default: `$id.$key.quant_results.sf`, example: `quant.sf`. Salmon quantification file",
"help_text": "Type: `file`, default: `$id.$key.quant_results.sf`, example: `quant.sf`. Salmon quantification file.\n" "help_text": "Type: `file`, default: `$id.$key.quant_results.sf`, example: `quant.sf`. Salmon quantification file.\n"
, ,
"default": "$id.$key.quant_results.sf" "default":"$id.$key.quant_results.sf"
} }
@@ -187,7 +187,7 @@
"description": "Type: `boolean_true`, default: `false`. Perform sequence-specific bias correction", "description": "Type: `boolean_true`, default: `false`. Perform sequence-specific bias correction",
"help_text": "Type: `boolean_true`, default: `false`. Perform sequence-specific bias correction.\n" "help_text": "Type: `boolean_true`, default: `false`. Perform sequence-specific bias correction.\n"
, ,
"default": "False" "default":false
} }
@@ -198,7 +198,7 @@
"description": "Type: `boolean_true`, default: `false`. Perform fragment GC bias correction [beta for single-end reads]", "description": "Type: `boolean_true`, default: `false`. Perform fragment GC bias correction [beta for single-end reads]",
"help_text": "Type: `boolean_true`, default: `false`. Perform fragment GC bias correction [beta for single-end reads].\n" "help_text": "Type: `boolean_true`, default: `false`. Perform fragment GC bias correction [beta for single-end reads].\n"
, ,
"default": "False" "default":false
} }
@@ -209,7 +209,7 @@
"description": "Type: `boolean_true`, default: `false`. Perform positional bias correction", "description": "Type: `boolean_true`, default: `false`. Perform positional bias correction",
"help_text": "Type: `boolean_true`, default: `false`. Perform positional bias correction.\n" "help_text": "Type: `boolean_true`, default: `false`. Perform positional bias correction.\n"
, ,
"default": "False" "default":false
} }
@@ -250,7 +250,7 @@
"description": "Type: `boolean_true`, default: `false`. If you\u0027re using Salmon on a metagenomic dataset, consider setting this flag to disable parts of the abundance estimation model that make less sense for metagenomic data", "description": "Type: `boolean_true`, default: `false`. If you\u0027re using Salmon on a metagenomic dataset, consider setting this flag to disable parts of the abundance estimation model that make less sense for metagenomic data",
"help_text": "Type: `boolean_true`, default: `false`. If you\u0027re using Salmon on a metagenomic dataset, consider setting this flag to disable parts of the abundance estimation model that make less sense for metagenomic data.\n" "help_text": "Type: `boolean_true`, default: `false`. If you\u0027re using Salmon on a metagenomic dataset, consider setting this flag to disable parts of the abundance estimation model that make less sense for metagenomic data.\n"
, ,
"default": "False" "default":false
} }
@@ -281,7 +281,7 @@
"description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nDiscard orphan mappings in selective-alignment mode", "description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nDiscard orphan mappings in selective-alignment mode",
"help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nDiscard orphan mappings in selective-alignment mode. If this flag is passed then only paired mappings will be considered toward quantification estimates. The default behavior is to consider orphan mappings if no valid paired mappings exist. This flag is independent of the option to write the orphaned mappings to file (--writeOrphanLinks).\n" "help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nDiscard orphan mappings in selective-alignment mode. If this flag is passed then only paired mappings will be considered toward quantification estimates. The default behavior is to consider orphan mappings if no valid paired mappings exist. This flag is independent of the option to write the orphaned mappings to file (--writeOrphanLinks).\n"
, ,
"default": "False" "default":false
} }
@@ -352,7 +352,7 @@
"description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nBy default, the heuristic of (Li 2018) is implemented, which terminates the chaining DP once a given number of valid backpointers are found", "description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nBy default, the heuristic of (Li 2018) is implemented, which terminates the chaining DP once a given number of valid backpointers are found",
"help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nBy default, the heuristic of (Li 2018) is implemented, which terminates the chaining DP once a given number of valid backpointers are found. This speeds up the seed (MEM) chaining step, but may result in sub-optimal chains in complex situations (e.g. sequences with many repeats and overlapping repeats). Passing this flag will disable the chaining heuristic, and perform the full chaining dynamic program, guaranteeing the optimal chain is found in this step.\n" "help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nBy default, the heuristic of (Li 2018) is implemented, which terminates the chaining DP once a given number of valid backpointers are found. This speeds up the seed (MEM) chaining step, but may result in sub-optimal chains in complex situations (e.g. sequences with many repeats and overlapping repeats). Passing this flag will disable the chaining heuristic, and perform the full chaining dynamic program, guaranteeing the optimal chain is found in this step.\n"
, ,
"default": "False" "default":false
} }
@@ -423,7 +423,7 @@
"description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAllow dovetailing mappings", "description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAllow dovetailing mappings",
"help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAllow dovetailing mappings.\n" "help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAllow dovetailing mappings.\n"
, ,
"default": "False" "default":false
} }
@@ -434,7 +434,7 @@
"description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAttempt to recover the mates of orphaned reads", "description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAttempt to recover the mates of orphaned reads",
"help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAttempt to recover the mates of orphaned reads. This uses edlib for orphan recovery, and so introduces some computational overhead, but it can improve sensitivity.\n" "help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAttempt to recover the mates of orphaned reads. This uses edlib for orphan recovery, and so introduces some computational overhead, but it can improve sensitivity.\n"
, ,
"default": "False" "default":false
} }
@@ -445,7 +445,7 @@
"description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nSet flags to mimic parameters similar to Bowtie2 with --no-discordant and --no-mixed flags", "description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nSet flags to mimic parameters similar to Bowtie2 with --no-discordant and --no-mixed flags",
"help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nSet flags to mimic parameters similar to Bowtie2 with --no-discordant and --no-mixed flags. This increases disallows dovetailing reads, and discards orphans. Note, this does not impose the very strict parameters assumed by RSEM+Bowtie2, like gapless alignments. For that behavior, use the --mimic_strictBT2 flag below.\n" "help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nSet flags to mimic parameters similar to Bowtie2 with --no-discordant and --no-mixed flags. This increases disallows dovetailing reads, and discards orphans. Note, this does not impose the very strict parameters assumed by RSEM+Bowtie2, like gapless alignments. For that behavior, use the --mimic_strictBT2 flag below.\n"
, ,
"default": "False" "default":false
} }
@@ -456,7 +456,7 @@
"description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nSet flags to mimic the very strict parameters used by RSEM+Bowtie2", "description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nSet flags to mimic the very strict parameters used by RSEM+Bowtie2",
"help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nSet flags to mimic the very strict parameters used by RSEM+Bowtie2. This increases --min_score_fraction to 0.8, disallows dovetailing reads, discards orphans, and disallows gaps in alignments.\n" "help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nSet flags to mimic the very strict parameters used by RSEM+Bowtie2. This increases --min_score_fraction to 0.8, disallows dovetailing reads, discards orphans, and disallows gaps in alignments.\n"
, ,
"default": "False" "default":false
} }
@@ -467,7 +467,7 @@
"description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAllos soft-clipping of reads during selective-alignment", "description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAllos soft-clipping of reads during selective-alignment",
"help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAllos soft-clipping of reads during selective-alignment. If this option is provided, then regions at the beginning or end of the read can be withheld from alignment without any effect on the resulting score (i.e. neither adding nor removing from the score). This will drastically reduce the penalty if there are mismatches at the beginning or end of the read due to e.g. low-quality bases or adapters. NOTE: Even with soft-clipping enabled, the read must still achieve a score of at least min_score_fraction * maximum achievable score, where the maximum achievable score is computed based on the full (un-clipped) read length.\n" "help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAllos soft-clipping of reads during selective-alignment. If this option is provided, then regions at the beginning or end of the read can be withheld from alignment without any effect on the resulting score (i.e. neither adding nor removing from the score). This will drastically reduce the penalty if there are mismatches at the beginning or end of the read due to e.g. low-quality bases or adapters. NOTE: Even with soft-clipping enabled, the read must still achieve a score of at least min_score_fraction * maximum achievable score, where the maximum achievable score is computed based on the full (un-clipped) read length.\n"
, ,
"default": "False" "default":false
} }
@@ -478,7 +478,7 @@
"description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAllow soft-clipping of reads that overhang the beginning or ends of the transcript", "description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAllow soft-clipping of reads that overhang the beginning or ends of the transcript",
"help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAllow soft-clipping of reads that overhang the beginning or ends of the transcript. In this case, the overhaning section of the read will simply be unaligned, and will not contribute or detract from the alignment score. The default policy is to force an end-to-end alignment of the entire read, so that overhanings will result in some deletion of nucleotides from the read.\n" "help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nAllow soft-clipping of reads that overhang the beginning or ends of the transcript. In this case, the overhaning section of the read will simply be unaligned, and will not contribute or detract from the alignment score. The default policy is to force an end-to-end alignment of the entire read, so that overhanings will result in some deletion of nucleotides from the read.\n"
, ,
"default": "False" "default":false
} }
@@ -489,7 +489,7 @@
"description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nPerform selective alignment over the full length of the read, beginning from the (approximate) initial mapping location and using extension alignment", "description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nPerform selective alignment over the full length of the read, beginning from the (approximate) initial mapping location and using extension alignment",
"help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nPerform selective alignment over the full length of the read, beginning from the (approximate) initial mapping location and using extension alignment. This is in contrast with the default behavior which is to only perform alignment between the MEMs in the optimal chain (and before the first and after the last MEM if applicable). The default strategy forces the MEMs to belong to the alignment, but has the benefit that it can discover indels prior to the first hit shared between the read and reference. Except in very rare circumstances, the default mode should be more accurate.\n" "help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nPerform selective alignment over the full length of the read, beginning from the (approximate) initial mapping location and using extension alignment. This is in contrast with the default behavior which is to only perform alignment between the MEMs in the optimal chain (and before the first and after the last MEM if applicable). The default strategy forces the MEMs to belong to the alignment, but has the benefit that it can discover indels prior to the first hit shared between the read and reference. Except in very rare circumstances, the default mode should be more accurate.\n"
, ,
"default": "False" "default":false
} }
@@ -500,7 +500,7 @@
"description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nInstead of weighting mappings by their alignment score, this flag will discard any mappings with sub-optimal alignment score", "description": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nInstead of weighting mappings by their alignment score, this flag will discard any mappings with sub-optimal alignment score",
"help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nInstead of weighting mappings by their alignment score, this flag will discard any mappings with sub-optimal alignment score. The default option of soft-filtering (i.e. weighting mappings by their alignment score) usually yields slightly more accurate abundance estimates but this flag may be desirable if you want more accurate \u0027naive\u0027 equivalence classes, rather than range factorized equivalence classes.\n" "help_text": "Type: `boolean_true`, default: `false`. [selective-alignment mode only] \nInstead of weighting mappings by their alignment score, this flag will discard any mappings with sub-optimal alignment score. The default option of soft-filtering (i.e. weighting mappings by their alignment score) usually yields slightly more accurate abundance estimates but this flag may be desirable if you want more accurate \u0027naive\u0027 equivalence classes, rather than range factorized equivalence classes.\n"
, ,
"default": "False" "default":false
} }
@@ -521,7 +521,7 @@
"description": "Type: `boolean_true`, default: `false`. If this option is provided, then the selective-alignment results will be written out in SAM-compatible format", "description": "Type: `boolean_true`, default: `false`. If this option is provided, then the selective-alignment results will be written out in SAM-compatible format",
"help_text": "Type: `boolean_true`, default: `false`. If this option is provided, then the selective-alignment results will be written out in SAM-compatible format. By default, output will be directed to stdout, but an alternative file name can be provided instead.\n" "help_text": "Type: `boolean_true`, default: `false`. If this option is provided, then the selective-alignment results will be written out in SAM-compatible format. By default, output will be directed to stdout, but an alternative file name can be provided instead.\n"
, ,
"default": "False" "default":false
} }
@@ -532,7 +532,7 @@
"description": "Type: `file`, default: `$id.$key.mapping_sam.sam`, example: `mappings.sam`. Path to file that should output the selective-alignment results in SAM-compatible format", "description": "Type: `file`, default: `$id.$key.mapping_sam.sam`, example: `mappings.sam`. Path to file that should output the selective-alignment results in SAM-compatible format",
"help_text": "Type: `file`, default: `$id.$key.mapping_sam.sam`, example: `mappings.sam`. Path to file that should output the selective-alignment results in SAM-compatible format. This option must be provided while using --write_mappings" "help_text": "Type: `file`, default: `$id.$key.mapping_sam.sam`, example: `mappings.sam`. Path to file that should output the selective-alignment results in SAM-compatible format. This option must be provided while using --write_mappings"
, ,
"default": "$id.$key.mapping_sam.sam" "default":"$id.$key.mapping_sam.sam"
} }
@@ -543,7 +543,7 @@
"description": "Type: `boolean_true`, default: `false`. This flag only has meaning if mappings are being written (with --write_mappings/-z)", "description": "Type: `boolean_true`, default: `false`. This flag only has meaning if mappings are being written (with --write_mappings/-z)",
"help_text": "Type: `boolean_true`, default: `false`. This flag only has meaning if mappings are being written (with --write_mappings/-z). If this flag is provided, then the output SAM file will contain quality strings as well as read sequences. Note that this can greatly increase the size of the output file.\n" "help_text": "Type: `boolean_true`, default: `false`. This flag only has meaning if mappings are being written (with --write_mappings/-z). If this flag is provided, then the output SAM file will contain quality strings as well as read sequences. Note that this can greatly increase the size of the output file.\n"
, ,
"default": "False" "default":false
} }
@@ -576,7 +576,7 @@
"description": "Type: `boolean_true`, default: `false`. Use an alternative strategy (rather than simple interpolation between) the online and uniform abundance estimates to initialize the EM / VBEM algorithm", "description": "Type: `boolean_true`, default: `false`. Use an alternative strategy (rather than simple interpolation between) the online and uniform abundance estimates to initialize the EM / VBEM algorithm",
"help_text": "Type: `boolean_true`, default: `false`. Use an alternative strategy (rather than simple interpolation between) the online and uniform abundance estimates to initialize the EM / VBEM algorithm.\n" "help_text": "Type: `boolean_true`, default: `false`. Use an alternative strategy (rather than simple interpolation between) the online and uniform abundance estimates to initialize the EM / VBEM algorithm.\n"
, ,
"default": "False" "default":false
} }
@@ -587,7 +587,7 @@
"description": "Type: `file`, default: `$id.$key.aux_dir.aux_dir`, example: `aux_info`. The sub-directory of the quantification directory where auxiliary information e", "description": "Type: `file`, default: `$id.$key.aux_dir.aux_dir`, example: `aux_info`. The sub-directory of the quantification directory where auxiliary information e",
"help_text": "Type: `file`, default: `$id.$key.aux_dir.aux_dir`, example: `aux_info`. The sub-directory of the quantification directory where auxiliary information e.g. bootstraps, bias parameters, etc. will be written.\n" "help_text": "Type: `file`, default: `$id.$key.aux_dir.aux_dir`, example: `aux_info`. The sub-directory of the quantification directory where auxiliary information e.g. bootstraps, bias parameters, etc. will be written.\n"
, ,
"default": "$id.$key.aux_dir.aux_dir" "default":"$id.$key.aux_dir.aux_dir"
} }
@@ -598,7 +598,7 @@
"description": "Type: `boolean_true`, default: `false`. Skip performing the actual transcript quantification (including any Gibbs sampling or bootstrapping)", "description": "Type: `boolean_true`, default: `false`. Skip performing the actual transcript quantification (including any Gibbs sampling or bootstrapping)",
"help_text": "Type: `boolean_true`, default: `false`. Skip performing the actual transcript quantification (including any Gibbs sampling or bootstrapping).\n" "help_text": "Type: `boolean_true`, default: `false`. Skip performing the actual transcript quantification (including any Gibbs sampling or bootstrapping).\n"
, ,
"default": "False" "default":false
} }
@@ -609,7 +609,7 @@
"description": "Type: `boolean_true`, default: `false`. Dump the simple equivalence class counts that were computed during mapping or alignment", "description": "Type: `boolean_true`, default: `false`. Dump the simple equivalence class counts that were computed during mapping or alignment",
"help_text": "Type: `boolean_true`, default: `false`. Dump the simple equivalence class counts that were computed during mapping or alignment.\n" "help_text": "Type: `boolean_true`, default: `false`. Dump the simple equivalence class counts that were computed during mapping or alignment.\n"
, ,
"default": "False" "default":false
} }
@@ -620,7 +620,7 @@
"description": "Type: `boolean_true`, default: `false`. Dump conditional probabilities associated with transcripts when equivalence class information is being dumped to file", "description": "Type: `boolean_true`, default: `false`. Dump conditional probabilities associated with transcripts when equivalence class information is being dumped to file",
"help_text": "Type: `boolean_true`, default: `false`. Dump conditional probabilities associated with transcripts when equivalence class information is being dumped to file. Note, this will dump the factorization that is actually used by salmon\u0027s offline phase for inference. If you are using range-factorized equivalence classes (the default) then the same transcript set may appear multiple times with different associated conditional probabilities.\n" "help_text": "Type: `boolean_true`, default: `false`. Dump conditional probabilities associated with transcripts when equivalence class information is being dumped to file. Note, this will dump the factorization that is actually used by salmon\u0027s offline phase for inference. If you are using range-factorized equivalence classes (the default) then the same transcript set may appear multiple times with different associated conditional probabilities.\n"
, ,
"default": "False" "default":false
} }
@@ -641,7 +641,7 @@
"description": "Type: `boolean_true`, default: `false`. If this option is selected, a more memory efficient (but slightly slower) representation is used to compute fragment GC content", "description": "Type: `boolean_true`, default: `false`. If this option is selected, a more memory efficient (but slightly slower) representation is used to compute fragment GC content",
"help_text": "Type: `boolean_true`, default: `false`. If this option is selected, a more memory efficient (but slightly slower) representation is used to compute fragment GC content. Enabling this will reduce memory usage, but can also reduce speed. However, the results themselves will remain the same.\n" "help_text": "Type: `boolean_true`, default: `false`. If this option is selected, a more memory efficient (but slightly slower) representation is used to compute fragment GC content. Enabling this will reduce memory usage, but can also reduce speed. However, the results themselves will remain the same.\n"
, ,
"default": "False" "default":false
} }
@@ -702,7 +702,7 @@
"description": "Type: `boolean_true`, default: `false`. Initialize the offline inference with uniform parameters, rather than seeding with online parameters", "description": "Type: `boolean_true`, default: `false`. Initialize the offline inference with uniform parameters, rather than seeding with online parameters",
"help_text": "Type: `boolean_true`, default: `false`. Initialize the offline inference with uniform parameters, rather than seeding with online parameters.\n" "help_text": "Type: `boolean_true`, default: `false`. Initialize the offline inference with uniform parameters, rather than seeding with online parameters.\n"
, ,
"default": "False" "default":false
} }
@@ -733,7 +733,7 @@
"description": "Type: `boolean_true`, default: `false`. Entirely disables length correction when estimating the abundance of transcripts", "description": "Type: `boolean_true`, default: `false`. Entirely disables length correction when estimating the abundance of transcripts",
"help_text": "Type: `boolean_true`, default: `false`. Entirely disables length correction when estimating the abundance of transcripts. This option can be used with protocols where one expects that fragments derive from their underlying targets without regard to that target\u0027s length (e.g. QuantSeq)\n" "help_text": "Type: `boolean_true`, default: `false`. Entirely disables length correction when estimating the abundance of transcripts. This option can be used with protocols where one expects that fragments derive from their underlying targets without regard to that target\u0027s length (e.g. QuantSeq)\n"
, ,
"default": "False" "default":false
} }
@@ -744,7 +744,7 @@
"description": "Type: `boolean_true`, default: `false`. Disables effective length correction when computing the probability that a fragment was generated from a transcript", "description": "Type: `boolean_true`, default: `false`. Disables effective length correction when computing the probability that a fragment was generated from a transcript",
"help_text": "Type: `boolean_true`, default: `false`. Disables effective length correction when computing the probability that a fragment was generated from a transcript. If this flag is passed in,the fragment length distribution is not taken into account when computing this probability.\n" "help_text": "Type: `boolean_true`, default: `false`. Disables effective length correction when computing the probability that a fragment was generated from a transcript. If this flag is passed in,the fragment length distribution is not taken into account when computing this probability.\n"
, ,
"default": "False" "default":false
} }
@@ -755,7 +755,7 @@
"description": "Type: `boolean_true`, default: `false`. Disables the estimation of an associated fragment length probability for single-end reads or for orphaned mappings in paired-end libraries", "description": "Type: `boolean_true`, default: `false`. Disables the estimation of an associated fragment length probability for single-end reads or for orphaned mappings in paired-end libraries",
"help_text": "Type: `boolean_true`, default: `false`. Disables the estimation of an associated fragment length probability for single-end reads or for orphaned mappings in paired-end libraries. The default behavior is to consider the probability of all possible fragment lengths associated with the retained mapping. Enabling this flag (i.e. turning this default behavior off) will simply not attempt to estimate a fragment length probability in such cases.\n" "help_text": "Type: `boolean_true`, default: `false`. Disables the estimation of an associated fragment length probability for single-end reads or for orphaned mappings in paired-end libraries. The default behavior is to consider the probability of all possible fragment lengths associated with the retained mapping. Enabling this flag (i.e. turning this default behavior off) will simply not attempt to estimate a fragment length probability in such cases.\n"
, ,
"default": "False" "default":false
} }
@@ -766,7 +766,7 @@
"description": "Type: `boolean_true`, default: `false`. Don\u0027t consider concordance with the learned fragment length distribution when trying to determine the probability that a fragment has originated from a specified location", "description": "Type: `boolean_true`, default: `false`. Don\u0027t consider concordance with the learned fragment length distribution when trying to determine the probability that a fragment has originated from a specified location",
"help_text": "Type: `boolean_true`, default: `false`. Don\u0027t consider concordance with the learned fragment length distribution when trying to determine the probability that a fragment has originated from a specified location. Normally, Fragments with unlikely lengths will be assigned a smaller relative probability than those with more likely lengths. When this flag is passed in, the observed fragment length has no effect on that fragment\u0027s a priori probability.\n" "help_text": "Type: `boolean_true`, default: `false`. Don\u0027t consider concordance with the learned fragment length distribution when trying to determine the probability that a fragment has originated from a specified location. Normally, Fragments with unlikely lengths will be assigned a smaller relative probability than those with more likely lengths. When this flag is passed in, the observed fragment length has no effect on that fragment\u0027s a priori probability.\n"
, ,
"default": "False" "default":false
} }
@@ -777,7 +777,7 @@
"description": "Type: `boolean_true`, default: `false`. If this option is enabled, then no (lower) threshold will be set on how short bias correction can make effective lengths", "description": "Type: `boolean_true`, default: `false`. If this option is enabled, then no (lower) threshold will be set on how short bias correction can make effective lengths",
"help_text": "Type: `boolean_true`, default: `false`. If this option is enabled, then no (lower) threshold will be set on how short bias correction can make effective lengths. This can increase the precision of bias correction, but harm robustness. The default correction applies a threshold.\n" "help_text": "Type: `boolean_true`, default: `false`. If this option is enabled, then no (lower) threshold will be set on how short bias correction can make effective lengths. This can increase the precision of bias correction, but harm robustness. The default correction applies a threshold.\n"
, ,
"default": "False" "default":false
} }
@@ -818,7 +818,7 @@
"description": "Type: `boolean_true`, default: `false`. Use the traditional EM algorithm for optimization in the batch passes", "description": "Type: `boolean_true`, default: `false`. Use the traditional EM algorithm for optimization in the batch passes",
"help_text": "Type: `boolean_true`, default: `false`. Use the traditional EM algorithm for optimization in the batch passes.\n" "help_text": "Type: `boolean_true`, default: `false`. Use the traditional EM algorithm for optimization in the batch passes.\n"
, ,
"default": "False" "default":false
} }
@@ -829,7 +829,7 @@
"description": "Type: `boolean_true`, default: `false`. Use the Variational Bayesian EM [default]\n", "description": "Type: `boolean_true`, default: `false`. Use the Variational Bayesian EM [default]\n",
"help_text": "Type: `boolean_true`, default: `false`. Use the Variational Bayesian EM [default]\n" "help_text": "Type: `boolean_true`, default: `false`. Use the Variational Bayesian EM [default]\n"
, ,
"default": "False" "default":false
} }
@@ -860,7 +860,7 @@
"description": "Type: `boolean_true`, default: `false`. This switch will disable drawing transcript fractions from a Gamma distribution during Gibbs sampling", "description": "Type: `boolean_true`, default: `false`. This switch will disable drawing transcript fractions from a Gamma distribution during Gibbs sampling",
"help_text": "Type: `boolean_true`, default: `false`. This switch will disable drawing transcript fractions from a Gamma distribution during Gibbs sampling. In this case the sampler does not account for shot-noise, but only assignment ambiguity\n" "help_text": "Type: `boolean_true`, default: `false`. This switch will disable drawing transcript fractions from a Gamma distribution during Gibbs sampling. In this case the sampler does not account for shot-noise, but only assignment ambiguity\n"
, ,
"default": "False" "default":false
} }
@@ -881,7 +881,7 @@
"description": "Type: `boolean_true`, default: `false`. This switch will learn the parameter distribution from the bootstrapped counts for each sample, but will reproject those parameters onto the original equivalence class counts", "description": "Type: `boolean_true`, default: `false`. This switch will learn the parameter distribution from the bootstrapped counts for each sample, but will reproject those parameters onto the original equivalence class counts",
"help_text": "Type: `boolean_true`, default: `false`. This switch will learn the parameter distribution from the bootstrapped counts for each sample, but will reproject those parameters onto the original equivalence class counts.\n" "help_text": "Type: `boolean_true`, default: `false`. This switch will learn the parameter distribution from the bootstrapped counts for each sample, but will reproject those parameters onto the original equivalence class counts.\n"
, ,
"default": "False" "default":false
} }
@@ -902,7 +902,7 @@
"description": "Type: `boolean_true`, default: `false`. Be quiet while doing quantification (don\u0027t write informative output to the console unless something goes wrong)", "description": "Type: `boolean_true`, default: `false`. Be quiet while doing quantification (don\u0027t write informative output to the console unless something goes wrong)",
"help_text": "Type: `boolean_true`, default: `false`. Be quiet while doing quantification (don\u0027t write informative output to the console unless something goes wrong).\n" "help_text": "Type: `boolean_true`, default: `false`. Be quiet while doing quantification (don\u0027t write informative output to the console unless something goes wrong).\n"
, ,
"default": "False" "default":false
} }
@@ -913,7 +913,7 @@
"description": "Type: `boolean_true`, default: `false`. The prior (either the default or the argument provided via --vb_prior) will be interpreted as a transcript-level prior (i", "description": "Type: `boolean_true`, default: `false`. The prior (either the default or the argument provided via --vb_prior) will be interpreted as a transcript-level prior (i",
"help_text": "Type: `boolean_true`, default: `false`. The prior (either the default or the argument provided via --vb_prior) will be interpreted as a transcript-level prior (i.e. each transcript will be given a prior read count of this value)\n" "help_text": "Type: `boolean_true`, default: `false`. The prior (either the default or the argument provided via --vb_prior) will be interpreted as a transcript-level prior (i.e. each transcript will be given a prior read count of this value)\n"
, ,
"default": "False" "default":false
} }
@@ -924,7 +924,7 @@
"description": "Type: `boolean_true`, default: `false`. The prior (either the default or the argument provided via --vb_prior) will be interpreted as a nucleotide-level prior (i", "description": "Type: `boolean_true`, default: `false`. The prior (either the default or the argument provided via --vb_prior) will be interpreted as a nucleotide-level prior (i",
"help_text": "Type: `boolean_true`, default: `false`. The prior (either the default or the argument provided via --vb_prior) will be interpreted as a nucleotide-level prior (i.e. each nucleotide will be given a prior read count of this value)\n" "help_text": "Type: `boolean_true`, default: `false`. The prior (either the default or the argument provided via --vb_prior) will be interpreted as a nucleotide-level prior (i.e. each nucleotide will be given a prior read count of this value)\n"
, ,
"default": "False" "default":false
} }
@@ -955,7 +955,7 @@
"description": "Type: `boolean_true`, default: `false`. Write the transcripts that are linked by orphaned reads", "description": "Type: `boolean_true`, default: `false`. Write the transcripts that are linked by orphaned reads",
"help_text": "Type: `boolean_true`, default: `false`. Write the transcripts that are linked by orphaned reads.\n" "help_text": "Type: `boolean_true`, default: `false`. Write the transcripts that are linked by orphaned reads.\n"
, ,
"default": "False" "default":false
} }
@@ -966,7 +966,7 @@
"description": "Type: `boolean_true`, default: `false`. Write the names of un-mapped reads to the file unmapped_names", "description": "Type: `boolean_true`, default: `false`. Write the names of un-mapped reads to the file unmapped_names",
"help_text": "Type: `boolean_true`, default: `false`. Write the names of un-mapped reads to the file unmapped_names.txt in the auxiliary directory.\n" "help_text": "Type: `boolean_true`, default: `false`. Write the names of un-mapped reads to the file unmapped_names.txt in the auxiliary directory.\n"
, ,
"default": "False" "default":false
} }
@@ -987,7 +987,7 @@
"description": "Type: `boolean_true`, default: `false`. Turn off the alignment error model, which takes into account the the observed frequency of different types of mismatches / indels when computing the likelihood of a given alignment", "description": "Type: `boolean_true`, default: `false`. Turn off the alignment error model, which takes into account the the observed frequency of different types of mismatches / indels when computing the likelihood of a given alignment",
"help_text": "Type: `boolean_true`, default: `false`. Turn off the alignment error model, which takes into account the the observed frequency of different types of mismatches / indels when computing the likelihood of a given alignment. Turning this off can speed up alignment-based salmon, but can harm quantification accuracy.\n" "help_text": "Type: `boolean_true`, default: `false`. Turn off the alignment error model, which takes into account the the observed frequency of different types of mismatches / indels when computing the likelihood of a given alignment. Turning this off can speed up alignment-based salmon, but can harm quantification accuracy.\n"
, ,
"default": "False" "default":false
} }
@@ -1008,7 +1008,7 @@
"description": "Type: `boolean_true`, default: `false`. Write a \"postSample", "description": "Type: `boolean_true`, default: `false`. Write a \"postSample",
"help_text": "Type: `boolean_true`, default: `false`. Write a \"postSample.bam\" file in the output directory that will sample the input alignments according to the estimated transcript abundances. If you\u0027re going to perform downstream analysis of the alignments with tools which don\u0027t, themselves, take fragment assignment ambiguity into account, you should use this output.\n" "help_text": "Type: `boolean_true`, default: `false`. Write a \"postSample.bam\" file in the output directory that will sample the input alignments according to the estimated transcript abundances. If you\u0027re going to perform downstream analysis of the alignments with tools which don\u0027t, themselves, take fragment assignment ambiguity into account, you should use this output.\n"
, ,
"default": "False" "default":false
} }
@@ -1019,7 +1019,7 @@
"description": "Type: `boolean_true`, default: `false`. In addition to sampling the aligned reads, also write the un-aligned reads to \"postSample", "description": "Type: `boolean_true`, default: `false`. In addition to sampling the aligned reads, also write the un-aligned reads to \"postSample",
"help_text": "Type: `boolean_true`, default: `false`. In addition to sampling the aligned reads, also write the un-aligned reads to \"postSample.bam\".\n" "help_text": "Type: `boolean_true`, default: `false`. In addition to sampling the aligned reads, also write the un-aligned reads to \"postSample.bam\".\n"
, ,
"default": "False" "default":false
} }
@@ -1030,7 +1030,7 @@
"description": "Type: `boolean_true`, default: `false`. This flag will expect the input transcript fasta to be in GENCODE format, and will split the transcript name at the first \u0027|\u0027 character", "description": "Type: `boolean_true`, default: `false`. This flag will expect the input transcript fasta to be in GENCODE format, and will split the transcript name at the first \u0027|\u0027 character",
"help_text": "Type: `boolean_true`, default: `false`. This flag will expect the input transcript fasta to be in GENCODE format, and will split the transcript name at the first \u0027|\u0027 character. These reduced names will be used in the output and when looking for these transcripts in a gene to transcript GTF.\n" "help_text": "Type: `boolean_true`, default: `false`. This flag will expect the input transcript fasta to be in GENCODE format, and will split the transcript name at the first \u0027|\u0027 character. These reduced names will be used in the output and when looking for these transcripts in a gene to transcript GTF.\n"
, ,
"default": "False" "default":false
} }

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

@@ -173,9 +173,9 @@ build_info:
output: "target/nextflow/samtools/samtools_flagstat" output: "target/nextflow/samtools/samtools_flagstat"
executable: "target/nextflow/samtools/samtools_flagstat/main.nf" executable: "target/nextflow/samtools/samtools_flagstat/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d" git_tag: "v0.2.0-27-g952ff08"
package_config: package_config:
name: "biobox" name: "biobox"
version: "main" version: "main"

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

@@ -3028,9 +3028,9 @@ meta = [
"engine" : "docker|native", "engine" : "docker|native",
"output" : "target/nextflow/samtools/samtools_flagstat", "output" : "target/nextflow/samtools/samtools_flagstat",
"viash_version" : "0.9.0", "viash_version" : "0.9.0",
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d" "git_tag" : "v0.2.0-27-g952ff08"
}, },
"package_config" : { "package_config" : {
"name" : "biobox", "name" : "biobox",

2
target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/nextflow_schema.json
View File

@@ -50,7 +50,7 @@
"description": "Type: `file`, required, default: `$id.$key.output.flagstat`, example: `output.flagstat`. File containing samtools stats output", "description": "Type: `file`, required, default: `$id.$key.output.flagstat`, example: `output.flagstat`. File containing samtools stats output",
"help_text": "Type: `file`, required, default: `$id.$key.output.flagstat`, example: `output.flagstat`. File containing samtools stats output.\n" "help_text": "Type: `file`, required, default: `$id.$key.output.flagstat`, example: `output.flagstat`. File containing samtools stats output.\n"
, ,
"default": "$id.$key.output.flagstat" "default":"$id.$key.output.flagstat"
} }

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

@@ -183,9 +183,9 @@ build_info:
output: "target/nextflow/samtools/samtools_idxstats" output: "target/nextflow/samtools/samtools_idxstats"
executable: "target/nextflow/samtools/samtools_idxstats/main.nf" executable: "target/nextflow/samtools/samtools_idxstats/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d" git_tag: "v0.2.0-27-g952ff08"
package_config: package_config:
name: "biobox" name: "biobox"
version: "main" version: "main"

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

@@ -3040,9 +3040,9 @@ meta = [
"engine" : "docker|native", "engine" : "docker|native",
"output" : "target/nextflow/samtools/samtools_idxstats", "output" : "target/nextflow/samtools/samtools_idxstats",
"viash_version" : "0.9.0", "viash_version" : "0.9.0",
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d" "git_tag" : "v0.2.0-27-g952ff08"
}, },
"package_config" : { "package_config" : {
"name" : "biobox", "name" : "biobox",

2
target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/nextflow_schema.json
View File

@@ -60,7 +60,7 @@
"description": "Type: `file`, required, default: `$id.$key.output.idxstats`, example: `output.idxstats`. File containing samtools stats output in tab-delimited format", "description": "Type: `file`, required, default: `$id.$key.output.idxstats`, example: `output.idxstats`. File containing samtools stats output in tab-delimited format",
"help_text": "Type: `file`, required, default: `$id.$key.output.idxstats`, example: `output.idxstats`. File containing samtools stats output in tab-delimited format.\n" "help_text": "Type: `file`, required, default: `$id.$key.output.idxstats`, example: `output.idxstats`. File containing samtools stats output in tab-delimited format.\n"
, ,
"default": "$id.$key.output.idxstats" "default":"$id.$key.output.idxstats"
} }

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

@@ -189,9 +189,9 @@ build_info:
output: "target/nextflow/samtools/samtools_index" output: "target/nextflow/samtools/samtools_index"
executable: "target/nextflow/samtools/samtools_index/main.nf" executable: "target/nextflow/samtools/samtools_index/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d" git_tag: "v0.2.0-27-g952ff08"
package_config: package_config:
name: "biobox" name: "biobox"
version: "main" version: "main"

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

@@ -3053,9 +3053,9 @@ meta = [
"engine" : "docker|native", "engine" : "docker|native",
"output" : "target/nextflow/samtools/samtools_index", "output" : "target/nextflow/samtools/samtools_index",
"viash_version" : "0.9.0", "viash_version" : "0.9.0",
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d" "git_tag" : "v0.2.0-27-g952ff08"
}, },
"package_config" : { "package_config" : {
"name" : "biobox", "name" : "biobox",

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

@@ -40,7 +40,7 @@
"description": "Type: `file`, required, default: `$id.$key.output.bai`, example: `out.bam.bai`. Output file name", "description": "Type: `file`, required, default: `$id.$key.output.bai`, example: `out.bam.bai`. Output file name",
"help_text": "Type: `file`, required, default: `$id.$key.output.bai`, example: `out.bam.bai`. Output file name" "help_text": "Type: `file`, required, default: `$id.$key.output.bai`, example: `out.bam.bai`. Output file name"
, ,
"default": "$id.$key.output.bai" "default":"$id.$key.output.bai"
} }
@@ -61,7 +61,7 @@
"description": "Type: `boolean_true`, default: `false`. Generate BAM index", "description": "Type: `boolean_true`, default: `false`. Generate BAM index",
"help_text": "Type: `boolean_true`, default: `false`. Generate BAM index" "help_text": "Type: `boolean_true`, default: `false`. Generate BAM index"
, ,
"default": "False" "default":false
} }
@@ -72,7 +72,7 @@
"description": "Type: `boolean_true`, default: `false`. Create a CSI index for BAM files instead of the traditional BAI \nindex", "description": "Type: `boolean_true`, default: `false`. Create a CSI index for BAM files instead of the traditional BAI \nindex",
"help_text": "Type: `boolean_true`, default: `false`. Create a CSI index for BAM files instead of the traditional BAI \nindex. This will be required for genomes with larger chromosome \nsizes.\n" "help_text": "Type: `boolean_true`, default: `false`. Create a CSI index for BAM files instead of the traditional BAI \nindex. This will be required for genomes with larger chromosome \nsizes.\n"
, ,
"default": "False" "default":false
} }

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

@@ -332,9 +332,9 @@ build_info:
output: "target/nextflow/samtools/samtools_sort" output: "target/nextflow/samtools/samtools_sort"
executable: "target/nextflow/samtools/samtools_sort/main.nf" executable: "target/nextflow/samtools/samtools_sort/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d" git_tag: "v0.2.0-27-g952ff08"
package_config: package_config:
name: "biobox" name: "biobox"
version: "main" version: "main"

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

@@ -3225,9 +3225,9 @@ meta = [
"engine" : "docker|native", "engine" : "docker|native",
"output" : "target/nextflow/samtools/samtools_sort", "output" : "target/nextflow/samtools/samtools_sort",
"viash_version" : "0.9.0", "viash_version" : "0.9.0",
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d" "git_tag" : "v0.2.0-27-g952ff08"
}, },
"package_config" : { "package_config" : {
"name" : "biobox", "name" : "biobox",

22
target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/nextflow_schema.json
View File

@@ -40,7 +40,7 @@
"description": "Type: `file`, required, default: `$id.$key.output.bam`, example: `out.bam`. Write final output to file", "description": "Type: `file`, required, default: `$id.$key.output.bam`, example: `out.bam`. Write final output to file",
"help_text": "Type: `file`, required, default: `$id.$key.output.bam`, example: `out.bam`. Write final output to file.\n" "help_text": "Type: `file`, required, default: `$id.$key.output.bam`, example: `out.bam`. Write final output to file.\n"
, ,
"default": "$id.$key.output.bam" "default":"$id.$key.output.bam"
} }
@@ -81,7 +81,7 @@
"description": "Type: `boolean_true`, default: `false`. Automatically index the output files", "description": "Type: `boolean_true`, default: `false`. Automatically index the output files",
"help_text": "Type: `boolean_true`, default: `false`. Automatically index the output files.\n" "help_text": "Type: `boolean_true`, default: `false`. Automatically index the output files.\n"
, ,
"default": "False" "default":false
} }
@@ -102,7 +102,7 @@
"description": "Type: `boolean_true`, default: `false`. Do not add a PG line", "description": "Type: `boolean_true`, default: `false`. Do not add a PG line",
"help_text": "Type: `boolean_true`, default: `false`. Do not add a PG line.\n" "help_text": "Type: `boolean_true`, default: `false`. Do not add a PG line.\n"
, ,
"default": "False" "default":false
} }
@@ -113,7 +113,7 @@
"description": "Type: `boolean_true`, default: `false`. Sort by template-coordinate", "description": "Type: `boolean_true`, default: `false`. Sort by template-coordinate",
"help_text": "Type: `boolean_true`, default: `false`. Sort by template-coordinate.\n" "help_text": "Type: `boolean_true`, default: `false`. Sort by template-coordinate.\n"
, ,
"default": "False" "default":false
} }
@@ -144,7 +144,7 @@
"description": "Type: `integer`, default: `0`. Set compression level, from 0 (uncompressed) to 9 (best)", "description": "Type: `integer`, default: `0`. Set compression level, from 0 (uncompressed) to 9 (best)",
"help_text": "Type: `integer`, default: `0`. Set compression level, from 0 (uncompressed) to 9 (best).\n" "help_text": "Type: `integer`, default: `0`. Set compression level, from 0 (uncompressed) to 9 (best).\n"
, ,
"default": "0" "default":0
} }
@@ -155,7 +155,7 @@
"description": "Type: `boolean_true`, default: `false`. Output uncompressed data (equivalent to --compression 0)", "description": "Type: `boolean_true`, default: `false`. Output uncompressed data (equivalent to --compression 0)",
"help_text": "Type: `boolean_true`, default: `false`. Output uncompressed data (equivalent to --compression 0).\n" "help_text": "Type: `boolean_true`, default: `false`. Output uncompressed data (equivalent to --compression 0).\n"
, ,
"default": "False" "default":false
} }
@@ -166,7 +166,7 @@
"description": "Type: `boolean_true`, default: `false`. Use minimiser for clustering unaligned/unplaced reads", "description": "Type: `boolean_true`, default: `false`. Use minimiser for clustering unaligned/unplaced reads",
"help_text": "Type: `boolean_true`, default: `false`. Use minimiser for clustering unaligned/unplaced reads.\n" "help_text": "Type: `boolean_true`, default: `false`. Use minimiser for clustering unaligned/unplaced reads.\n"
, ,
"default": "False" "default":false
} }
@@ -177,7 +177,7 @@
"description": "Type: `boolean_true`, default: `false`. Do not use reverse strand (only compatible with --minimiser)\n", "description": "Type: `boolean_true`, default: `false`. Do not use reverse strand (only compatible with --minimiser)\n",
"help_text": "Type: `boolean_true`, default: `false`. Do not use reverse strand (only compatible with --minimiser)\n" "help_text": "Type: `boolean_true`, default: `false`. Do not use reverse strand (only compatible with --minimiser)\n"
, ,
"default": "False" "default":false
} }
@@ -218,7 +218,7 @@
"description": "Type: `boolean_true`, default: `false`. Squash homopolymers when computing minimiser", "description": "Type: `boolean_true`, default: `false`. Squash homopolymers when computing minimiser",
"help_text": "Type: `boolean_true`, default: `false`. Squash homopolymers when computing minimiser.\n" "help_text": "Type: `boolean_true`, default: `false`. Squash homopolymers when computing minimiser.\n"
, ,
"default": "False" "default":false
} }
@@ -229,7 +229,7 @@
"description": "Type: `boolean_true`, default: `false`. Sort by read name (natural): cannot be used with samtools index", "description": "Type: `boolean_true`, default: `false`. Sort by read name (natural): cannot be used with samtools index",
"help_text": "Type: `boolean_true`, default: `false`. Sort by read name (natural): cannot be used with samtools index.\n" "help_text": "Type: `boolean_true`, default: `false`. Sort by read name (natural): cannot be used with samtools index.\n"
, ,
"default": "False" "default":false
} }
@@ -240,7 +240,7 @@
"description": "Type: `boolean_true`, default: `false`. Sort by read name (ASCII): cannot be used with samtools index", "description": "Type: `boolean_true`, default: `false`. Sort by read name (ASCII): cannot be used with samtools index",
"help_text": "Type: `boolean_true`, default: `false`. Sort by read name (ASCII): cannot be used with samtools index.\n" "help_text": "Type: `boolean_true`, default: `false`. Sort by read name (ASCII): cannot be used with samtools index.\n"
, ,
"default": "False" "default":false
} }

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

@@ -401,9 +401,9 @@ build_info:
output: "target/nextflow/samtools/samtools_stats" output: "target/nextflow/samtools/samtools_stats"
executable: "target/nextflow/samtools/samtools_stats/main.nf" executable: "target/nextflow/samtools/samtools_stats/main.nf"
viash_version: "0.9.0" viash_version: "0.9.0"
git_commit: "a13b57d04a3f3741eedd1af10fd96a9bee126f55" git_commit: "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b"
git_remote: "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox" git_remote: "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-26-ga13b57d" git_tag: "v0.2.0-27-g952ff08"
package_config: package_config:
name: "biobox" name: "biobox"
version: "main" version: "main"

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

@@ -3295,9 +3295,9 @@ meta = [
"engine" : "docker|native", "engine" : "docker|native",
"output" : "target/nextflow/samtools/samtools_stats", "output" : "target/nextflow/samtools/samtools_stats",
"viash_version" : "0.9.0", "viash_version" : "0.9.0",
"git_commit" : "a13b57d04a3f3741eedd1af10fd96a9bee126f55", "git_commit" : "952ff0843093b538cbfd6fefdecf2e7a0bc9e70b",
"git_remote" : "https://x-access-token:ghs_xpDMoQpz4lF1RaGsMH4IlMbO48cLeW1cIYSF@github.com/viash-hub/biobox", "git_remote" : "https://x-access-token:ghs_EwAUAMYJ0K4VBHlAEMs4ZP2OyQYqJM0PSfEO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-26-ga13b57d" "git_tag" : "v0.2.0-27-g952ff08"
}, },
"package_config" : { "package_config" : {
"name" : "biobox", "name" : "biobox",

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