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Build branch add-labels with version add-labels (3ee9ba7)

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Build pipeline: viash-hub.rnaseq.add-labels-xf9kj

Source commit: 3ee9ba76ca

Source message: Disable bbsplit
This commit is contained in:
CI
2024-12-03 08:22:22 +00:00
parent 5f8830f4c8
commit 15c280b8fc
138 changed files with 1164 additions and 1121 deletions
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546
src/workflows/prepare_genome/main.nf
View File

@@ -1,288 +1,316 @@
workflow run_wf {
take:
input_ch
take:
input_ch
main:
output_ch = input_ch
// Uncompress fasta
| gunzip.run (
fromState: [ "input": "fasta" ],
toState: [ "fasta": "output" ],
key: "gunzip_fasta",
args: [ output: "reference_genome.fasta" ]
)
main:
output_ch = input_ch
// uncompress gtf
| gunzip.run (
runIf: {id, state -> state.gtf},
fromState: [ "input": "gtf" ],
toState: [ "gtf": "output" ],
key: "gunzip_gtf",
args: [output: "gene_annotation.gtf"]
)
// Uncompress fasta
| gunzip.run (
fromState: [ "input": "fasta" ],
toState: [ "fasta": "output" ],
key: "gunzip_fasta",
args: [ output: "reference_genome.fasta" ],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
// uncompress gff
| gunzip.run (
runIf: {id, state -> !state.gtf && state.gff},
fromState: [ "input": "gff" ],
toState: [ "gff": "output" ],
key: "gunzip_gff",
args: [output: "gene_annotation.gff"]
)
// uncompress gtf
| gunzip.run (
runIf: {id, state -> state.gtf},
fromState: [ "input": "gtf" ],
toState: [ "gtf": "output" ],
key: "gunzip_gtf",
args: [output: "gene_annotation.gtf"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
// gff to gtf
| gffread.run (
runIf: {id, state -> !state.gtf && state.gff},
fromState: [
"input": "gff",
"genome": "fasta"
],
toState: [ "gtf": "outfile" ],
args: [
outfile: "gene_annotation.gtf",
gtf_output: true,
keep_attrs: true,
keep_exon_attrs: true
]
)
// uncompress gff
| gunzip.run (
runIf: {id, state -> !state.gtf && state.gff},
fromState: [ "input": "gff" ],
toState: [ "gff": "output" ],
key: "gunzip_gff",
args: [output: "gene_annotation.gff"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
| gtf_filter.run(
runIf: {id, state -> state.gtf && state.filter_gtf},
fromState: [
"fasta": "fasta",
"gtf": "gtf"
],
toState: [ "gtf": "filtered_gtf" ],
args: [filtered_gtf: "gene_annotation.gtf"]
)
// gff to gtf
| gffread.run (
runIf: {id, state -> !state.gtf && state.gff},
fromState: [
"input": "gff",
"genome": "fasta"
],
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
| gunzip.run (
runIf: {id, state -> state.additional_fasta},
fromState: [ "input": "additional_fasta" ],
toState: [ "additional_fasta": "output" ],
key: "gunzip_additional_fasta",
args: [output: "additional.fasta"]
)
| gtf_filter.run(
runIf: {id, state -> state.gtf && state.filter_gtf},
fromState: [
"fasta": "fasta",
"gtf": "gtf"
],
toState: [ "gtf": "filtered_gtf" ],
args: [filtered_gtf: "gene_annotation.gtf"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
// concatenate additional fasta
| cat_additional_fasta.run (
runIf: {id, state -> state.additional_fasta},
fromState: [
"fasta": "fasta",
"gtf": "gtf",
"additional_fasta": "additional_fasta",
"biotype": "biotype"
],
toState: [
"fasta": "fasta_output",
"gtf": "gtf_output"
],
args: [
fasta_output: "genome_additional.fasta",
gtf_output: "genome_additional.gtf"
]
)
// uncompress additional fasta
| gunzip.run (
runIf: {id, state -> state.additional_fasta},
fromState: [ "input": "additional_fasta" ],
toState: [ "additional_fasta": "output" ],
key: "gunzip_additional_fasta",
args: [output: "additional.fasta"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
// uncompress bed file
| gunzip.run (
runIf: {id, state -> state.gene_bed},
fromState: [ "input": "gene_bed" ],
toState: [ "gene_bed": "output" ],
key: "gunzip_gene_bed",
args: [output: "genome_additional.bed"]
)
// concatenate additional fasta
| cat_additional_fasta.run (
runIf: {id, state -> state.additional_fasta},
fromState: [
"fasta": "fasta",
"gtf": "gtf",
"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
| gtf2bed.run (
runIf: { id, state -> !state.gene_bed},
fromState: [ "gtf": "gtf" ],
toState: [ "gene_bed": "bed_output" ],
args: [bed_output: "genome_additional.bed"]
)
// uncompress bed file
| gunzip.run (
runIf: {id, state -> state.gene_bed},
fromState: [ "input": "gene_bed" ],
toState: [ "gene_bed": "output" ],
key: "gunzip_gene_bed",
args: [output: "genome_additional.bed"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
// uncompress transcript fasta
| gunzip.run (
runIf: {id, state -> state.transcript_fasta},
fromState: [ "input": "transcript_fasta" ],
toState: [ "transcript_fasta": "output" ],
key: "transcript_fasta",
args: [output: "transcriptome.fasta"]
)
// gtf to bed
| gtf2bed.run (
runIf: { id, state -> !state.gene_bed},
fromState: [ "gtf": "gtf" ],
toState: [ "gene_bed": "bed_output" ],
args: [bed_output: "genome_additional.bed"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
// preprocess transcripts fasta if gtf is in gencode format
| preprocess_transcripts_fasta.run (
runIf: {id, state -> state.transcript_fasta && state.gencode},
fromState: [ "transcript_fasta": "transcript_fasta" ],
toState: [ "transcript_fasta": "output" ],
args: [output: "transcriptome.fasta"]
)
// uncompress transcript fasta
| gunzip.run (
runIf: {id, state -> state.transcript_fasta},
fromState: [ "input": "transcript_fasta" ],
toState: [ "transcript_fasta": "output" ],
key: "transcript_fasta",
args: [output: "transcriptome.fasta"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
// make transcript FASTA if not provided
| rsem_prepare_reference.run (
runIf: {id, state -> !state.transcript_fasta},
fromState: [
"reference_fasta_files": "fasta",
"gtf": "gtf"
],
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] ]
}
// preprocess transcripts fasta if gtf is in gencode format
| preprocess_transcripts_fasta.run (
runIf: {id, state -> state.transcript_fasta && state.gencode},
fromState: [ "transcript_fasta": "transcript_fasta" ],
toState: [ "transcript_fasta": "output" ],
args: [output: "transcriptome.fasta"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
// chromosome size and fai index
| getchromsizes.run (
fromState: [ "fasta": "fasta" ],
toState: [
"fai": "fai",
"sizes": "sizes"
],
key: "chromsizes",
args: [
fai: "genome_additional.fasta.fai",
sizes: "genome_additional.fasta.sizes"
]
)
// untar bbsplit index, if available
| untar.run (
runIf: {id, state -> state.bbsplit_index},
fromState: [ "input": "bbsplit_index" ],
toState: [ "bbsplit_index": "output" ],
key: "untar_bbsplit_index",
args: [output: "BBSplit_index"]
)
// make transcript FASTA if not provided
| rsem_prepare_reference.run (
runIf: {id, state -> !state.transcript_fasta},
fromState: [
"reference_fasta_files": "fasta",
"gtf": "gtf"
],
toState: [ "make_transcript_fasta_output": "output" ],
key: "make_transcript_fasta",
args: [reference_name: "genome"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
| 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] ]
}
| map {id, state ->
def ref = [state.fasta] + state.bbsplit_fasta_list
[id, state + [bbsplit_ref: ref] ]
// chromosome size and fai index
| getchromsizes.run (
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" ] ]
)
// untar bbsplit index, if available
| untar.run (
runIf: {id, state -> state.bbsplit_index},
fromState: [ "input": "bbsplit_index" ],
toState: [ "bbsplit_index": "output" ],
key: "untar_bbsplit_index",
directives: [ label: [ "lowmem", "midcpu" ] ]
)
| map { id, state ->
// Check if bbsplit_fasta_list is defined
if (state.bbsplit_fasta_list) {
def ref = [state.fasta] + state.bbsplit_fasta_list
} else {
def ref = [state.fasta]
}
[id, state + [bbsplit_ref: ref] ]
}
// create bbsplit index, if not already availble
| bbmap_bbsplit.run (
runIf: {id, state -> !state.skip_bbsplit && !state.bbsplit_index},
fromState: ["ref": "bbsplit_ref"],
toState: [ "bbsplit_index": "index" ],
args: [
only_build_index: true,
index: "BBSplit_index"
],
key: "generate_bbsplit_index"
)
| niceView()
// Uncompress STAR index or generate from scratch if required
| untar.run (
runIf: {id, state -> state.star_index},
fromState: [ "input": "star_index" ],
toState: [ "star_index": "output" ],
key: "untar_star_index",
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"]
)
// create bbsplit index, if not already available
| bbmap_bbsplit.run (
runIf: {id, state -> !state.skip_bbsplit && !state.bbsplit_index},
fromState: ["ref": "bbsplit_ref"],
toState: [ "bbsplit_index": "index" ],
args: [
only_build_index: true,
index: "BBSplit_index"
],
key: "generate_bbsplit_index"
)
// Uncompress RSEM index or generate from scratch if required
| untar.run (
runIf: {id, state -> state.rsem_index},
fromState: [ "input": "rsem_index" ],
toState: [ "rsem_index": "output" ],
key: "untar_rsem_index",
args: [output: "RSEM_index"]
)
// Uncompress STAR index or generate from scratch if required
| untar.run (
runIf: {id, state -> state.star_index},
fromState: [ "input": "star_index" ],
toState: [ "star_index": "output" ],
key: "untar_star_index",
args: [output: "STAR_index"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
| rsem_prepare_reference.run (
runIf: {id, state -> !state.rsem_index && state.aligner == 'star_rsem'},
fromState: [
"reference_fasta_files": "fasta",
"gtf": "gtf"
],
toState: [ "rsem_index": "output" ],
key: "generate_rsem_index",
args: [reference_name: "genome"]
)
// TODO: Uncompress HISAT2 index or generate from scratch if required
// 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"],
directives: [ label: [ "highmem", "highcpu" ] ]
)
// Uncompress Salmon index or generate from scratch if required
| untar.run (
runIf: {id, state -> state.salmon_index},
fromState: [ "input": "salmon_index" ],
toState: [ "salmon_index": "output" ],
key: "untar_salmon_index",
args: [output: "Salmon_index"]
)
// Uncompress RSEM index or generate from scratch if required
| untar.run (
runIf: {id, state -> state.rsem_index},
fromState: [ "input": "rsem_index" ],
toState: [ "rsem_index": "output" ],
key: "untar_rsem_index",
args: [output: "RSEM_index"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
| salmon_index.run (
runIf: {id, state -> (state.aligner == 'star_salmon' || state.pseudo_aligner == "salmon") && !state.salmon_index},
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"]
)
| rsem_prepare_reference.run (
runIf: {id, state -> !state.rsem_index && state.aligner == 'star_rsem'},
fromState: [
"reference_fasta_files": "fasta",
"gtf": "gtf"
],
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
// Uncompress Kallisto index or generate from scratch if required
| untar.run (
runIf: {id, state -> state.kallisto_index},
fromState: [ "input": "kallisto_index" ],
toState: [ "kallisto_index": "output" ],
key: "untar_kallisto_index",
args: [output: "Kallisto_index"]
)
// Uncompress Salmon index or generate from scratch if required
| untar.run (
runIf: {id, state -> state.salmon_index},
fromState: [ "input": "salmon_index" ],
toState: [ "salmon_index": "output" ],
key: "untar_salmon_index",
args: [output: "Salmon_index"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
| kallisto_index.run(
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"]
)
| salmon_index.run (
runIf: {id, state -> (state.aligner == 'star_salmon' || state.pseudo_aligner == "salmon") && !state.salmon_index},
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" ] ]
)
| map { id, state ->
def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() }
[ id, mod_state ]
}
// Uncompress Kallisto index or generate from scratch if required
| untar.run (
runIf: {id, state -> state.kallisto_index},
fromState: [ "input": "kallisto_index" ],
toState: [ "kallisto_index": "output" ],
key: "untar_kallisto_index",
args: [output: "Kallisto_index"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
| 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"
)
| kallisto_index.run(
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" ] ]
)
emit:
output_ch
| 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
}

7
src/workflows/rnaseq/config.vsh.yaml
View File

@@ -218,9 +218,10 @@ argument_groups:
type: boolean
description: Skip the adapter trimming step.
default: false
- name: "--skip_bbsplit"
type: boolean_true
description: Skip BBSplit for removal of non-reference genome reads.
# See:
# - name: "--skip_bbsplit"
# type: boolean_true
# description: Skip BBSplit for removal of non-reference genome reads.
- name: "--skip_umi_extract"
type: boolean
description: Skip umi_tools extract step.

3
src/workflows/rnaseq/main.nf
View File

@@ -39,7 +39,8 @@ workflow run_wf {
// splicesites: list.collect { id, state -> state.splicesites }.unique()[0],
// hisat2_index: list.collect { id, state -> state.hisat2_index }.unique()[0],
bbsplit_index: list.collect { id, state -> state.bbsplit_index }.unique()[0],
skip_bbsplit: list.collect { id, state -> state.skip_bbsplit }.unique()[0],
// See:
skip_bbsplit: true, // list.collect { id, state -> state.skip_bbsplit }.unique()[0],
skip_alignment: list.collect { id, state -> state.skip_alignment }.unique()[0],
gencode: list.collect { id, state -> state.gencode }.unique()[0],
biotype: list.collect { id, state -> state.biotype }.unique()[0],

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

@@ -183,8 +183,8 @@ build_info:
output: "target/executable/bedtools_genomecov"
executable: "target/executable/bedtools_genomecov/bedtools_genomecov"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

6
target/executable/bedtools_genomecov/bedtools_genomecov
View File

@@ -481,9 +481,9 @@ mv bedtools.static /usr/local/bin/bedtools && \
chmod a+x /usr/local/bin/bedtools
LABEL org.opencontainers.image.description="Companion container for running component bedtools_genomecov"
LABEL org.opencontainers.image.created="2024-12-02T15:00:02Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590"
LABEL org.opencontainers.image.created="2024-12-03T05:47:41Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -187,8 +187,8 @@ build_info:
output: "target/executable/cat_additional_fasta"
executable: "target/executable/cat_additional_fasta/cat_additional_fasta"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

6
target/executable/cat_additional_fasta/cat_additional_fasta
View File

@@ -480,9 +480,9 @@ function ViashDockerfile {
FROM python:latest
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component cat_additional_fasta"
LABEL org.opencontainers.image.created="2024-12-02T15:00:01Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590"
LABEL org.opencontainers.image.created="2024-12-03T05:47:40Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -174,8 +174,8 @@ build_info:
output: "target/executable/cat_fastq"
executable: "target/executable/cat_fastq/cat_fastq"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

6
target/executable/cat_fastq/cat_fastq
View File

@@ -472,9 +472,9 @@ function ViashDockerfile {
FROM ubuntu:22.04
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component cat_fastq"
LABEL org.opencontainers.image.created="2024-12-02T15:00:00Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590"
LABEL org.opencontainers.image.created="2024-12-03T05:47:39Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -242,8 +242,8 @@ build_info:
output: "target/executable/deseq2_qc"
executable: "target/executable/deseq2_qc/deseq2_qc"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

6
target/executable/deseq2_qc/deseq2_qc
View File

@@ -506,9 +506,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
Rscript -e 'remotes::install_cran(c("optparse", "ggplot2", "RColorBrewer", "pheatmap", "stringr", "matrixStats"), repos = "https://cran.rstudio.com")'
LABEL org.opencontainers.image.description="Companion container for running component deseq2_qc"
LABEL org.opencontainers.image.created="2024-12-02T15:00:00Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590"
LABEL org.opencontainers.image.created="2024-12-03T05:47:40Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -271,8 +271,8 @@ build_info:
output: "target/executable/dupradar"
executable: "target/executable/dupradar/dupradar"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

6
target/executable/dupradar/dupradar
View File

@@ -520,9 +520,9 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.pa
Rscript -e 'if (!requireNamespace("dupRadar", quietly = TRUE)) BiocManager::install("dupRadar")'
LABEL org.opencontainers.image.description="Companion container for running component dupradar"
LABEL org.opencontainers.image.created="2024-12-02T15:00:02Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590"
LABEL org.opencontainers.image.created="2024-12-03T05:47:42Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -172,8 +172,8 @@ build_info:
output: "target/executable/getchromsizes"
executable: "target/executable/getchromsizes/getchromsizes"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

6
target/executable/getchromsizes/getchromsizes
View File

@@ -480,9 +480,9 @@ make && \
make install
LABEL org.opencontainers.image.description="Companion container for running component getchromsizes"
LABEL org.opencontainers.image.created="2024-12-02T15:00:01Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590"
LABEL org.opencontainers.image.created="2024-12-03T05:47:40Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -150,8 +150,8 @@ build_info:
output: "target/executable/gtf2bed"
executable: "target/executable/gtf2bed/gtf2bed"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

6
target/executable/gtf2bed/gtf2bed
View File

@@ -466,9 +466,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component gtf2bed"
LABEL org.opencontainers.image.created="2024-12-02T15:00:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590"
LABEL org.opencontainers.image.created="2024-12-03T05:47:42Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -160,8 +160,8 @@ build_info:
output: "target/executable/gtf_filter"
executable: "target/executable/gtf_filter/gtf_filter"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

6
target/executable/gtf_filter/gtf_filter
View File

@@ -470,9 +470,9 @@ function ViashDockerfile {
FROM python:latest
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component gtf_filter"
LABEL org.opencontainers.image.created="2024-12-02T15:00:01Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590"
LABEL org.opencontainers.image.created="2024-12-03T05:47:41Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -149,8 +149,8 @@ build_info:
output: "target/executable/gunzip"
executable: "target/executable/gunzip/gunzip"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

6
target/executable/gunzip/gunzip
View File

@@ -466,9 +466,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component gunzip"
LABEL org.opencontainers.image.created="2024-12-02T14:59:58Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590"
LABEL org.opencontainers.image.created="2024-12-03T05:47:37Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -170,8 +170,8 @@ build_info:
output: "target/executable/multiqc_custom_biotype"
executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

6
target/executable/multiqc_custom_biotype/multiqc_custom_biotype
View File

@@ -476,9 +476,9 @@ function ViashDockerfile {
FROM python:latest
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component multiqc_custom_biotype"
LABEL org.opencontainers.image.created="2024-12-02T15:00:00Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590"
LABEL org.opencontainers.image.created="2024-12-03T05:47:40Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -212,8 +212,8 @@ build_info:
output: "target/executable/picard_markduplicates"
executable: "target/executable/picard_markduplicates/picard_markduplicates"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

6
target/executable/picard_markduplicates/picard_markduplicates
View File

@@ -494,9 +494,9 @@ wget --no-check-certificate https://github.com/broadinstitute/picard/releases/do
mv picard.jar /usr/local/bin
LABEL org.opencontainers.image.description="Companion container for running component picard_markduplicates"
LABEL org.opencontainers.image.created="2024-12-02T14:59:58Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590"
LABEL org.opencontainers.image.created="2024-12-03T05:47:37Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -417,8 +417,8 @@ build_info:
output: "target/executable/prepare_multiqc_input"
executable: "target/executable/prepare_multiqc_input/prepare_multiqc_input"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

6
target/executable/prepare_multiqc_input/prepare_multiqc_input
View File

@@ -558,9 +558,9 @@ function ViashDockerfile {
FROM ubuntu:22.04
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component prepare_multiqc_input"
LABEL org.opencontainers.image.created="2024-12-02T14:59:57Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590"
LABEL org.opencontainers.image.created="2024-12-03T05:47:36Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -143,8 +143,8 @@ build_info:
output: "target/executable/preprocess_transcripts_fasta"
executable: "target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

6
target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta
View File

@@ -462,9 +462,9 @@ function ViashDockerfile {
FROM ubuntu:22.04
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component preprocess_transcripts_fasta"
LABEL org.opencontainers.image.created="2024-12-02T14:59:59Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590"
LABEL org.opencontainers.image.created="2024-12-03T05:47:38Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -196,8 +196,8 @@ build_info:
output: "target/executable/preseq_lcextrap"
executable: "target/executable/preseq_lcextrap/preseq_lcextrap"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

6
target/executable/preseq_lcextrap/preseq_lcextrap
View File

@@ -495,9 +495,9 @@ mkdir build && cd build && \
make && make install && make HAVE_HTSLIB=1 all
LABEL org.opencontainers.image.description="Companion container for running component preseq_lcextrap"
LABEL org.opencontainers.image.created="2024-12-02T14:59:58Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590"
LABEL org.opencontainers.image.created="2024-12-03T05:47:37Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -186,8 +186,8 @@ build_info:
output: "target/executable/rsem_merge_counts"
executable: "target/executable/rsem_merge_counts/rsem_merge_counts"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

6
target/executable/rsem_merge_counts/rsem_merge_counts
View File

@@ -483,9 +483,9 @@ function ViashDockerfile {
FROM ubuntu:22.04
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component rsem_merge_counts"
LABEL org.opencontainers.image.created="2024-12-02T15:00:00Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590"
LABEL org.opencontainers.image.created="2024-12-03T05:47:39Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -265,8 +265,8 @@ build_info:
output: "target/executable/rseqc/rseqc_junctionannotation"
executable: "target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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

@@ -519,9 +519,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionannotation"
LABEL org.opencontainers.image.created="2024-12-02T14:59:59Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590"
LABEL org.opencontainers.image.created="2024-12-03T05:47:38Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -254,8 +254,8 @@ build_info:
output: "target/executable/rseqc/rseqc_junctionsaturation"
executable: "target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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

@@ -522,9 +522,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionsaturation"
LABEL org.opencontainers.image.created="2024-12-02T15:00:00Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590"
LABEL org.opencontainers.image.created="2024-12-03T05:47:39Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -167,8 +167,8 @@ build_info:
output: "target/executable/rseqc/rseqc_readdistribution"
executable: "target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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

@@ -474,9 +474,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readdistribution"
LABEL org.opencontainers.image.created="2024-12-02T15:00:00Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590"
LABEL org.opencontainers.image.created="2024-12-03T05:47:39Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -216,8 +216,8 @@ build_info:
output: "target/executable/rseqc/rseqc_readduplication"
executable: "target/executable/rseqc/rseqc_readduplication/rseqc_readduplication"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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

@@ -499,9 +499,9 @@ RUN pip install --upgrade pip && \
pip install --upgrade --no-cache-dir "RSeQC"
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readduplication"
LABEL org.opencontainers.image.created="2024-12-02T14:59:59Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590"
LABEL org.opencontainers.image.created="2024-12-03T05:47:38Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -219,8 +219,8 @@ build_info:
output: "target/executable/rseqc/rseqc_tin"
executable: "target/executable/rseqc/rseqc_tin/rseqc_tin"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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

@@ -501,9 +501,9 @@ RUN apt-get update && \
RUN pip3 install RSeQC
LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_tin"
LABEL org.opencontainers.image.created="2024-12-02T15:00:00Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590"
LABEL org.opencontainers.image.created="2024-12-03T05:47:39Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -197,8 +197,8 @@ build_info:
output: "target/executable/sortmerna"
executable: "target/executable/sortmerna/sortmerna"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

6
target/executable/sortmerna/sortmerna
View File

@@ -486,9 +486,9 @@ function ViashDockerfile {
FROM quay.io/biocontainers/sortmerna:4.3.6--h9ee0642_0
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component sortmerna"
LABEL org.opencontainers.image.created="2024-12-02T15:00:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590"
LABEL org.opencontainers.image.created="2024-12-03T05:47:43Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -221,8 +221,8 @@ build_info:
output: "target/executable/stringtie"
executable: "target/executable/stringtie/stringtie"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

6
target/executable/stringtie/stringtie
View File

@@ -496,9 +496,9 @@ tar -xzf stringtie-2.2.1.Linux_x86_64.tar.gz && \
cp stringtie-2.2.1.Linux_x86_64/stringtie /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component stringtie"
LABEL org.opencontainers.image.created="2024-12-02T15:00:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590"
LABEL org.opencontainers.image.created="2024-12-03T05:47:43Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -204,8 +204,8 @@ build_info:
output: "target/executable/summarizedexperiment"
executable: "target/executable/summarizedexperiment/summarizedexperiment"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

6
target/executable/summarizedexperiment/summarizedexperiment
View File

@@ -487,9 +487,9 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.pa
Rscript -e 'if (!requireNamespace("tximeta", quietly = TRUE)) BiocManager::install("tximeta")'
LABEL org.opencontainers.image.description="Companion container for running component summarizedexperiment"
LABEL org.opencontainers.image.created="2024-12-02T15:00:03Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590"
LABEL org.opencontainers.image.created="2024-12-03T05:47:42Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -190,8 +190,8 @@ build_info:
output: "target/executable/tx2gene"
executable: "target/executable/tx2gene/tx2gene"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

6
target/executable/tx2gene/tx2gene
View File

@@ -483,9 +483,9 @@ RUN apt-get update && \
RUN pip install --upgrade pip
LABEL org.opencontainers.image.description="Companion container for running component tx2gene"
LABEL org.opencontainers.image.created="2024-12-02T15:00:01Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590"
LABEL org.opencontainers.image.created="2024-12-03T05:47:41Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -256,8 +256,8 @@ build_info:
output: "target/executable/tximport"
executable: "target/executable/tximport/tximport"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

6
target/executable/tximport/tximport
View File

@@ -508,9 +508,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
Rscript -e 'remotes::install_cran(c("jsonlite"), repos = "https://cran.rstudio.com")'
LABEL org.opencontainers.image.description="Companion container for running component tximport"
LABEL org.opencontainers.image.created="2024-12-02T15:00:02Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590"
LABEL org.opencontainers.image.created="2024-12-03T05:47:41Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -169,8 +169,8 @@ build_info:
output: "target/executable/ucsc/bedclip"
executable: "target/executable/ucsc/bedclip/bedclip"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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

@@ -473,9 +473,9 @@ RUN apt-get update && \
RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedClip /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component ucsc bedclip"
LABEL org.opencontainers.image.created="2024-12-02T15:00:01Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590"
LABEL org.opencontainers.image.created="2024-12-03T05:47:40Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -169,8 +169,8 @@ build_info:
output: "target/executable/ucsc/bedgraphtobigwig"
executable: "target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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

@@ -473,9 +473,9 @@ RUN apt-get update && \
RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedGraphToBigWig /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component ucsc bedgraphtobigwig"
LABEL org.opencontainers.image.created="2024-12-02T15:00:01Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="59cbb30eecf218c0572104f849ab542423f0e590"
LABEL org.opencontainers.image.created="2024-12-03T05:47:40Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="3ee9ba76ca2112681c41468800aab2fa38cdf453"
LABEL org.opencontainers.image.version="add-labels"
VIASHDOCKER

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

@@ -595,8 +595,8 @@ build_info:
output: "target/executable/workflows/genome_alignment_and_quant"
executable: "target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort"

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

@@ -283,8 +283,8 @@ build_info:
output: "target/executable/workflows/merge_quant_results"
executable: "target/executable/workflows/merge_quant_results/merge_quant_results"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/tx2gene"
- "target/nextflow/tximport"

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

@@ -482,8 +482,8 @@ build_info:
output: "target/executable/workflows/post_processing"
executable: "target/executable/workflows/post_processing/post_processing"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/picard_markduplicates"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort"

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

@@ -637,8 +637,8 @@ build_info:
output: "target/executable/workflows/pre_processing"
executable: "target/executable/workflows/pre_processing/pre_processing"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/main/nextflow/fastqc"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract"

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

@@ -507,8 +507,8 @@ build_info:
output: "target/executable/workflows/prepare_genome"
executable: "target/executable/workflows/prepare_genome/prepare_genome"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/gunzip"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/gffread"

546
target/executable/workflows/prepare_genome/prepare_genome
View File

@@ -1171,291 +1171,319 @@ cat > "\$tempscript" << 'VIASHMAIN'
//// VIASH END
workflow run_wf {
take:
input_ch
take:
input_ch
main:
output_ch = input_ch
// Uncompress fasta
| gunzip.run (
fromState: [ "input": "fasta" ],
toState: [ "fasta": "output" ],
key: "gunzip_fasta",
args: [ output: "reference_genome.fasta" ]
)
main:
output_ch = input_ch
// uncompress gtf
| gunzip.run (
runIf: {id, state -> state.gtf},
fromState: [ "input": "gtf" ],
toState: [ "gtf": "output" ],
key: "gunzip_gtf",
args: [output: "gene_annotation.gtf"]
)
// Uncompress fasta
| gunzip.run (
fromState: [ "input": "fasta" ],
toState: [ "fasta": "output" ],
key: "gunzip_fasta",
args: [ output: "reference_genome.fasta" ],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
// uncompress gff
| gunzip.run (
runIf: {id, state -> !state.gtf && state.gff},
fromState: [ "input": "gff" ],
toState: [ "gff": "output" ],
key: "gunzip_gff",
args: [output: "gene_annotation.gff"]
)
// uncompress gtf
| gunzip.run (
runIf: {id, state -> state.gtf},
fromState: [ "input": "gtf" ],
toState: [ "gtf": "output" ],
key: "gunzip_gtf",
args: [output: "gene_annotation.gtf"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
// gff to gtf
| gffread.run (
runIf: {id, state -> !state.gtf && state.gff},
fromState: [
"input": "gff",
"genome": "fasta"
],
toState: [ "gtf": "outfile" ],
args: [
outfile: "gene_annotation.gtf",
gtf_output: true,
keep_attrs: true,
keep_exon_attrs: true
]
)
// uncompress gff
| gunzip.run (
runIf: {id, state -> !state.gtf && state.gff},
fromState: [ "input": "gff" ],
toState: [ "gff": "output" ],
key: "gunzip_gff",
args: [output: "gene_annotation.gff"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
| gtf_filter.run(
runIf: {id, state -> state.gtf && state.filter_gtf},
fromState: [
"fasta": "fasta",
"gtf": "gtf"
],
toState: [ "gtf": "filtered_gtf" ],
args: [filtered_gtf: "gene_annotation.gtf"]
)
// gff to gtf
| gffread.run (
runIf: {id, state -> !state.gtf && state.gff},
fromState: [
"input": "gff",
"genome": "fasta"
],
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
| gunzip.run (
runIf: {id, state -> state.additional_fasta},
fromState: [ "input": "additional_fasta" ],
toState: [ "additional_fasta": "output" ],
key: "gunzip_additional_fasta",
args: [output: "additional.fasta"]
)
| gtf_filter.run(
runIf: {id, state -> state.gtf && state.filter_gtf},
fromState: [
"fasta": "fasta",
"gtf": "gtf"
],
toState: [ "gtf": "filtered_gtf" ],
args: [filtered_gtf: "gene_annotation.gtf"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
// concatenate additional fasta
| cat_additional_fasta.run (
runIf: {id, state -> state.additional_fasta},
fromState: [
"fasta": "fasta",
"gtf": "gtf",
"additional_fasta": "additional_fasta",
"biotype": "biotype"
],
toState: [
"fasta": "fasta_output",
"gtf": "gtf_output"
],
args: [
fasta_output: "genome_additional.fasta",
gtf_output: "genome_additional.gtf"
]
)
// uncompress additional fasta
| gunzip.run (
runIf: {id, state -> state.additional_fasta},
fromState: [ "input": "additional_fasta" ],
toState: [ "additional_fasta": "output" ],
key: "gunzip_additional_fasta",
args: [output: "additional.fasta"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
// uncompress bed file
| gunzip.run (
runIf: {id, state -> state.gene_bed},
fromState: [ "input": "gene_bed" ],
toState: [ "gene_bed": "output" ],
key: "gunzip_gene_bed",
args: [output: "genome_additional.bed"]
)
// concatenate additional fasta
| cat_additional_fasta.run (
runIf: {id, state -> state.additional_fasta},
fromState: [
"fasta": "fasta",
"gtf": "gtf",
"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
| gtf2bed.run (
runIf: { id, state -> !state.gene_bed},
fromState: [ "gtf": "gtf" ],
toState: [ "gene_bed": "bed_output" ],
args: [bed_output: "genome_additional.bed"]
)
// uncompress bed file
| gunzip.run (
runIf: {id, state -> state.gene_bed},
fromState: [ "input": "gene_bed" ],
toState: [ "gene_bed": "output" ],
key: "gunzip_gene_bed",
args: [output: "genome_additional.bed"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
// uncompress transcript fasta
| gunzip.run (
runIf: {id, state -> state.transcript_fasta},
fromState: [ "input": "transcript_fasta" ],
toState: [ "transcript_fasta": "output" ],
key: "transcript_fasta",
args: [output: "transcriptome.fasta"]
)
// gtf to bed
| gtf2bed.run (
runIf: { id, state -> !state.gene_bed},
fromState: [ "gtf": "gtf" ],
toState: [ "gene_bed": "bed_output" ],
args: [bed_output: "genome_additional.bed"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
// preprocess transcripts fasta if gtf is in gencode format
| preprocess_transcripts_fasta.run (
runIf: {id, state -> state.transcript_fasta && state.gencode},
fromState: [ "transcript_fasta": "transcript_fasta" ],
toState: [ "transcript_fasta": "output" ],
args: [output: "transcriptome.fasta"]
)
// uncompress transcript fasta
| gunzip.run (
runIf: {id, state -> state.transcript_fasta},
fromState: [ "input": "transcript_fasta" ],
toState: [ "transcript_fasta": "output" ],
key: "transcript_fasta",
args: [output: "transcriptome.fasta"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
// make transcript FASTA if not provided
| rsem_prepare_reference.run (
runIf: {id, state -> !state.transcript_fasta},
fromState: [
"reference_fasta_files": "fasta",
"gtf": "gtf"
],
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] ]
}
// preprocess transcripts fasta if gtf is in gencode format
| preprocess_transcripts_fasta.run (
runIf: {id, state -> state.transcript_fasta && state.gencode},
fromState: [ "transcript_fasta": "transcript_fasta" ],
toState: [ "transcript_fasta": "output" ],
args: [output: "transcriptome.fasta"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
// chromosome size and fai index
| getchromsizes.run (
fromState: [ "fasta": "fasta" ],
toState: [
"fai": "fai",
"sizes": "sizes"
],
key: "chromsizes",
args: [
fai: "genome_additional.fasta.fai",
sizes: "genome_additional.fasta.sizes"
]
)
// untar bbsplit index, if available
| untar.run (
runIf: {id, state -> state.bbsplit_index},
fromState: [ "input": "bbsplit_index" ],
toState: [ "bbsplit_index": "output" ],
key: "untar_bbsplit_index",
args: [output: "BBSplit_index"]
)
// make transcript FASTA if not provided
| rsem_prepare_reference.run (
runIf: {id, state -> !state.transcript_fasta},
fromState: [
"reference_fasta_files": "fasta",
"gtf": "gtf"
],
toState: [ "make_transcript_fasta_output": "output" ],
key: "make_transcript_fasta",
args: [reference_name: "genome"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
| 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] ]
}
| map {id, state ->
def ref = [state.fasta] + state.bbsplit_fasta_list
[id, state + [bbsplit_ref: ref] ]
// chromosome size and fai index
| getchromsizes.run (
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" ] ]
)
// untar bbsplit index, if available
| untar.run (
runIf: {id, state -> state.bbsplit_index},
fromState: [ "input": "bbsplit_index" ],
toState: [ "bbsplit_index": "output" ],
key: "untar_bbsplit_index",
directives: [ label: [ "lowmem", "midcpu" ] ]
)
| map { id, state ->
// Check if bbsplit_fasta_list is defined
if (state.bbsplit_fasta_list) {
def ref = [state.fasta] + state.bbsplit_fasta_list
} else {
def ref = [state.fasta]
}
[id, state + [bbsplit_ref: ref] ]
}
// create bbsplit index, if not already availble
| bbmap_bbsplit.run (
runIf: {id, state -> !state.skip_bbsplit && !state.bbsplit_index},
fromState: ["ref": "bbsplit_ref"],
toState: [ "bbsplit_index": "index" ],
args: [
only_build_index: true,
index: "BBSplit_index"
],
key: "generate_bbsplit_index"
)
| niceView()
// Uncompress STAR index or generate from scratch if required
| untar.run (
runIf: {id, state -> state.star_index},
fromState: [ "input": "star_index" ],
toState: [ "star_index": "output" ],
key: "untar_star_index",
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"]
)
// create bbsplit index, if not already available
| bbmap_bbsplit.run (
runIf: {id, state -> !state.skip_bbsplit && !state.bbsplit_index},
fromState: ["ref": "bbsplit_ref"],
toState: [ "bbsplit_index": "index" ],
args: [
only_build_index: true,
index: "BBSplit_index"
],
key: "generate_bbsplit_index"
)
// Uncompress RSEM index or generate from scratch if required
| untar.run (
runIf: {id, state -> state.rsem_index},
fromState: [ "input": "rsem_index" ],
toState: [ "rsem_index": "output" ],
key: "untar_rsem_index",
args: [output: "RSEM_index"]
)
// Uncompress STAR index or generate from scratch if required
| untar.run (
runIf: {id, state -> state.star_index},
fromState: [ "input": "star_index" ],
toState: [ "star_index": "output" ],
key: "untar_star_index",
args: [output: "STAR_index"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
| rsem_prepare_reference.run (
runIf: {id, state -> !state.rsem_index && state.aligner == 'star_rsem'},
fromState: [
"reference_fasta_files": "fasta",
"gtf": "gtf"
],
toState: [ "rsem_index": "output" ],
key: "generate_rsem_index",
args: [reference_name: "genome"]
)
// TODO: Uncompress HISAT2 index or generate from scratch if required
// 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"],
directives: [ label: [ "highmem", "highcpu" ] ]
)
// Uncompress Salmon index or generate from scratch if required
| untar.run (
runIf: {id, state -> state.salmon_index},
fromState: [ "input": "salmon_index" ],
toState: [ "salmon_index": "output" ],
key: "untar_salmon_index",
args: [output: "Salmon_index"]
)
// Uncompress RSEM index or generate from scratch if required
| untar.run (
runIf: {id, state -> state.rsem_index},
fromState: [ "input": "rsem_index" ],
toState: [ "rsem_index": "output" ],
key: "untar_rsem_index",
args: [output: "RSEM_index"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
| salmon_index.run (
runIf: {id, state -> (state.aligner == 'star_salmon' || state.pseudo_aligner == "salmon") && !state.salmon_index},
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"]
)
| rsem_prepare_reference.run (
runIf: {id, state -> !state.rsem_index && state.aligner == 'star_rsem'},
fromState: [
"reference_fasta_files": "fasta",
"gtf": "gtf"
],
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
// Uncompress Kallisto index or generate from scratch if required
| untar.run (
runIf: {id, state -> state.kallisto_index},
fromState: [ "input": "kallisto_index" ],
toState: [ "kallisto_index": "output" ],
key: "untar_kallisto_index",
args: [output: "Kallisto_index"]
)
// Uncompress Salmon index or generate from scratch if required
| untar.run (
runIf: {id, state -> state.salmon_index},
fromState: [ "input": "salmon_index" ],
toState: [ "salmon_index": "output" ],
key: "untar_salmon_index",
args: [output: "Salmon_index"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
| kallisto_index.run(
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"]
)
| salmon_index.run (
runIf: {id, state -> (state.aligner == 'star_salmon' || state.pseudo_aligner == "salmon") && !state.salmon_index},
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" ] ]
)
| map { id, state ->
def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() }
[ id, mod_state ]
}
// Uncompress Kallisto index or generate from scratch if required
| untar.run (
runIf: {id, state -> state.kallisto_index},
fromState: [ "input": "kallisto_index" ],
toState: [ "kallisto_index": "output" ],
key: "untar_kallisto_index",
args: [output: "Kallisto_index"],
directives: [ label: [ "lowmem", "midcpu" ] ]
)
| 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"
)
| kallisto_index.run(
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" ] ]
)
emit:
output_ch
| 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
}
VIASHMAIN
nextflow run . -main-script "\$tempscript" &

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

@@ -290,8 +290,8 @@ build_info:
output: "target/executable/workflows/pseudo_alignment_and_quant"
executable: "target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/kallisto/kallisto_quant"

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

@@ -1561,8 +1561,8 @@ build_info:
output: "target/executable/workflows/quality_control"
executable: "target/executable/workflows/quality_control/quality_control"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
dependencies:
- "target/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_bamstat"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/rseqc/rseqc_inferexperiment"

9
target/executable/workflows/rnaseq/.config.vsh.yaml
View File

@@ -521,11 +521,6 @@ argument_groups:
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--skip_bbsplit"
description: "Skip BBSplit for removal of non-reference genome reads."
info: null
direction: "input"
- type: "boolean"
name: "--skip_umi_extract"
description: "Skip umi_tools extract step."
@@ -2064,8 +2059,8 @@ build_info:
output: "target/executable/workflows/rnaseq"
executable: "target/executable/workflows/rnaseq/rnaseq"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/workflows/prepare_genome"
- "target/nextflow/cat_fastq"

21
target/executable/workflows/rnaseq/rnaseq
View File

@@ -441,10 +441,6 @@ function ViashHelp {
echo " default: false"
echo " Skip the adapter trimming step."
echo ""
echo " --skip_bbsplit"
echo " type: boolean_true"
echo " Skip BBSplit for removal of non-reference genome reads."
echo ""
echo " --skip_umi_extract"
echo " type: boolean"
echo " default: false"
@@ -1583,11 +1579,6 @@ while [[ $# -gt 0 ]]; do
VIASH_PAR_SKIP_TRIMMING=$(ViashRemoveFlags "$1")
shift 1
;;
--skip_bbsplit)
[ -n "$VIASH_PAR_SKIP_BBSPLIT" ] && ViashError Bad arguments for option \'--skip_bbsplit\': \'$VIASH_PAR_SKIP_BBSPLIT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SKIP_BBSPLIT=true
shift 1
;;
--skip_umi_extract)
[ -n "$VIASH_PAR_SKIP_UMI_EXTRACT" ] && ViashError Bad arguments for option \'--skip_umi_extract\': \'$VIASH_PAR_SKIP_UMI_EXTRACT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SKIP_UMI_EXTRACT="$2"
@@ -3175,9 +3166,6 @@ fi
if [ -z ${VIASH_PAR_SKIP_TRIMMING+x} ]; then
VIASH_PAR_SKIP_TRIMMING="false"
fi
if [ -z ${VIASH_PAR_SKIP_BBSPLIT+x} ]; then
VIASH_PAR_SKIP_BBSPLIT="false"
fi
if [ -z ${VIASH_PAR_SKIP_UMI_EXTRACT+x} ]; then
VIASH_PAR_SKIP_UMI_EXTRACT="false"
fi
@@ -3749,12 +3737,6 @@ if [[ -n "$VIASH_PAR_SKIP_TRIMMING" ]]; then
exit 1
fi
fi
if [[ -n "$VIASH_PAR_SKIP_BBSPLIT" ]]; then
if ! [[ "$VIASH_PAR_SKIP_BBSPLIT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--skip_bbsplit' has to be a boolean_true. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_SKIP_UMI_EXTRACT" ]]; then
if ! [[ "$VIASH_PAR_SKIP_UMI_EXTRACT" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--skip_umi_extract' has to be a boolean. Use "--help" to get more information on the parameters.
@@ -4415,7 +4397,8 @@ workflow run_wf {
// splicesites: list.collect { id, state -> state.splicesites }.unique()[0],
// hisat2_index: list.collect { id, state -> state.hisat2_index }.unique()[0],
bbsplit_index: list.collect { id, state -> state.bbsplit_index }.unique()[0],
skip_bbsplit: list.collect { id, state -> state.skip_bbsplit }.unique()[0],
// See:
skip_bbsplit: true, // list.collect { id, state -> state.skip_bbsplit }.unique()[0],
skip_alignment: list.collect { id, state -> state.skip_alignment }.unique()[0],
gencode: list.collect { id, state -> state.gencode }.unique()[0],
biotype: list.collect { id, state -> state.biotype }.unique()[0],

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

@@ -183,8 +183,8 @@ build_info:
output: "target/nextflow/bedtools_genomecov"
executable: "target/nextflow/bedtools_genomecov/main.nf"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

4
target/nextflow/bedtools_genomecov/main.nf
View File

@@ -3039,8 +3039,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/bedtools_genomecov",
"viash_version" : "0.9.0",
"git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590",
"git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
"git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453",
"git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

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

@@ -187,8 +187,8 @@ build_info:
output: "target/nextflow/cat_additional_fasta"
executable: "target/nextflow/cat_additional_fasta/main.nf"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

4
target/nextflow/cat_additional_fasta/main.nf
View File

@@ -3040,8 +3040,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/cat_additional_fasta",
"viash_version" : "0.9.0",
"git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590",
"git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
"git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453",
"git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

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

@@ -174,8 +174,8 @@ build_info:
output: "target/nextflow/cat_fastq"
executable: "target/nextflow/cat_fastq/main.nf"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

4
target/nextflow/cat_fastq/main.nf
View File

@@ -3031,8 +3031,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/cat_fastq",
"viash_version" : "0.9.0",
"git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590",
"git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
"git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453",
"git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

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

@@ -242,8 +242,8 @@ build_info:
output: "target/nextflow/deseq2_qc"
executable: "target/nextflow/deseq2_qc/main.nf"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

4
target/nextflow/deseq2_qc/main.nf
View File

@@ -3112,8 +3112,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/deseq2_qc",
"viash_version" : "0.9.0",
"git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590",
"git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
"git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453",
"git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

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

@@ -271,8 +271,8 @@ build_info:
output: "target/nextflow/dupradar"
executable: "target/nextflow/dupradar/main.nf"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

4
target/nextflow/dupradar/main.nf
View File

@@ -3144,8 +3144,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/dupradar",
"viash_version" : "0.9.0",
"git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590",
"git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
"git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453",
"git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

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

@@ -172,8 +172,8 @@ build_info:
output: "target/nextflow/getchromsizes"
executable: "target/nextflow/getchromsizes/main.nf"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

4
target/nextflow/getchromsizes/main.nf
View File

@@ -3021,8 +3021,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/getchromsizes",
"viash_version" : "0.9.0",
"git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590",
"git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
"git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453",
"git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

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

@@ -150,8 +150,8 @@ build_info:
output: "target/nextflow/gtf2bed"
executable: "target/nextflow/gtf2bed/main.nf"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

4
target/nextflow/gtf2bed/main.nf
View File

@@ -3003,8 +3003,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/gtf2bed",
"viash_version" : "0.9.0",
"git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590",
"git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
"git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453",
"git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

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

@@ -160,8 +160,8 @@ build_info:
output: "target/nextflow/gtf_filter"
executable: "target/nextflow/gtf_filter/main.nf"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

4
target/nextflow/gtf_filter/main.nf
View File

@@ -3011,8 +3011,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/gtf_filter",
"viash_version" : "0.9.0",
"git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590",
"git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
"git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453",
"git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

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

@@ -149,8 +149,8 @@ build_info:
output: "target/nextflow/gunzip"
executable: "target/nextflow/gunzip/main.nf"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

4
target/nextflow/gunzip/main.nf
View File

@@ -3000,8 +3000,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/gunzip",
"viash_version" : "0.9.0",
"git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590",
"git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
"git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453",
"git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

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

@@ -170,8 +170,8 @@ build_info:
output: "target/nextflow/multiqc_custom_biotype"
executable: "target/nextflow/multiqc_custom_biotype/main.nf"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

4
target/nextflow/multiqc_custom_biotype/main.nf
View File

@@ -3020,8 +3020,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/multiqc_custom_biotype",
"viash_version" : "0.9.0",
"git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590",
"git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
"git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453",
"git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

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

@@ -212,8 +212,8 @@ build_info:
output: "target/nextflow/picard_markduplicates"
executable: "target/nextflow/picard_markduplicates/main.nf"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

4
target/nextflow/picard_markduplicates/main.nf
View File

@@ -3071,8 +3071,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/picard_markduplicates",
"viash_version" : "0.9.0",
"git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590",
"git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
"git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453",
"git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

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

@@ -417,8 +417,8 @@ build_info:
output: "target/nextflow/prepare_multiqc_input"
executable: "target/nextflow/prepare_multiqc_input/main.nf"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

4
target/nextflow/prepare_multiqc_input/main.nf
View File

@@ -3290,8 +3290,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/prepare_multiqc_input",
"viash_version" : "0.9.0",
"git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590",
"git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
"git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453",
"git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

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

@@ -143,8 +143,8 @@ build_info:
output: "target/nextflow/preprocess_transcripts_fasta"
executable: "target/nextflow/preprocess_transcripts_fasta/main.nf"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

4
target/nextflow/preprocess_transcripts_fasta/main.nf
View File

@@ -2990,8 +2990,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/preprocess_transcripts_fasta",
"viash_version" : "0.9.0",
"git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590",
"git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
"git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453",
"git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

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

@@ -196,8 +196,8 @@ build_info:
output: "target/nextflow/preseq_lcextrap"
executable: "target/nextflow/preseq_lcextrap/main.nf"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

4
target/nextflow/preseq_lcextrap/main.nf
View File

@@ -3043,8 +3043,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/preseq_lcextrap",
"viash_version" : "0.9.0",
"git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590",
"git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
"git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453",
"git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

4
target/nextflow/rsem_merge_counts/.config.vsh.yaml
View File

@@ -186,8 +186,8 @@ build_info:
output: "target/nextflow/rsem_merge_counts"
executable: "target/nextflow/rsem_merge_counts/main.nf"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

4
target/nextflow/rsem_merge_counts/main.nf
View File

@@ -3035,8 +3035,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/rsem_merge_counts",
"viash_version" : "0.9.0",
"git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590",
"git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
"git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453",
"git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

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

@@ -265,8 +265,8 @@ build_info:
output: "target/nextflow/rseqc/rseqc_junctionannotation"
executable: "target/nextflow/rseqc/rseqc_junctionannotation/main.nf"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

4
target/nextflow/rseqc/rseqc_junctionannotation/main.nf
View File

@@ -3136,8 +3136,8 @@ meta = [
"engine" : "docker|native",
"output" : "/workdir/root/repo/target/nextflow/rseqc/rseqc_junctionannotation",
"viash_version" : "0.9.0",
"git_commit" : "59cbb30eecf218c0572104f849ab542423f0e590",
"git_remote" : "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
"git_commit" : "3ee9ba76ca2112681c41468800aab2fa38cdf453",
"git_remote" : "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
},
"package_config" : {
"name" : "rnaseq",

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

@@ -254,8 +254,8 @@ build_info:
output: "target/nextflow/rseqc/rseqc_junctionsaturation"
executable: "target/nextflow/rseqc/rseqc_junctionsaturation/main.nf"
viash_version: "0.9.0"
git_commit: "59cbb30eecf218c0572104f849ab542423f0e590"
git_remote: "https://x-access-token:ghs_lWPkcchJhx5BAqplCo3R1uKbRtP5On1H5oPO@github.com/viash-hub/rnaseq"
git_commit: "3ee9ba76ca2112681c41468800aab2fa38cdf453"
git_remote: "https://x-access-token:ghs_voB56eF2OpLwoHCFv0Y7b6hOUsN5Mp3c03Em@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "add-labels"

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