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Build branch main with version main (05d48ac)

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Build pipeline: viash-hub.rnaseq.main-c7sdt

Source commit: 05d48ac2f8

Source message: Multiple fixes (#26)

* unset argument if not paired

* fix argument name

* add count_read_pairs argument

* output star log

* move biotypes header file into multiqc_custom_biotype component

* move deseq2 header files into deseq2_qc component

* update output defaults

* use biobox main

* add parameters to example

* update component

* update component

* ribo database processing moved to workflow

* clean code, remove unused arguments
This commit is contained in:
CI
2024-10-25 09:08:46 +00:00
parent 54557aa596
commit fe41adb0c7
298 changed files with 3125 additions and 3983 deletions
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13
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/fastp/.config.vsh.yaml → target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "fastp"
version: "v0.2.0"
version: "main"
authors:
- name: "Robrecht Cannoodt"
roles:
@@ -1066,7 +1066,7 @@ engines:
id: "docker"
image: "quay.io/biocontainers/fastp:0.23.4--hadf994f_2"
target_registry: "images.viash-hub.com"
target_tag: "v0.2.0"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "docker"
@@ -1083,11 +1083,12 @@ build_info:
output: "target/nextflow/fastp"
executable: "target/nextflow/fastp/main.nf"
viash_version: "0.9.0"
git_commit: "7e530218844c373048bc33de58f021b6460642e5"
git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-11-g7fb67a9"
package_config:
name: "biobox"
version: "v0.2.0"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0"
@@ -1097,7 +1098,7 @@ package_config:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "modules"

17
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/fastp/main.nf → target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/main.nf
View File

@@ -1,4 +1,4 @@
// fastp v0.2.0
// fastp main
//
// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2808,7 +2808,7 @@ meta = [
"resources_dir": moduleDir.toRealPath().normalize(),
"config": processConfig(readJsonBlob('''{
"name" : "fastp",
"version" : "v0.2.0",
"version" : "main",
"authors" : [
{
"name" : "Robrecht Cannoodt",
@@ -4001,7 +4001,7 @@ meta = [
"id" : "docker",
"image" : "quay.io/biocontainers/fastp:0.23.4--hadf994f_2",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.2.0",
"target_tag" : "main",
"namespace_separator" : "/",
"setup" : [
{
@@ -4023,12 +4023,13 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/fastp",
"viash_version" : "0.9.0",
"git_commit" : "7e530218844c373048bc33de58f021b6460642e5",
"git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
"git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7",
"git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-11-g7fb67a9"
},
"package_config" : {
"name" : "biobox",
"version" : "v0.2.0",
"version" : "main",
"description" : "A collection of bioinformatics tools for working with sequence data.\n",
"viash_version" : "0.9.0",
"source" : "src",
@@ -4037,7 +4038,7 @@ meta = [
".requirements.commands := ['ps']\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.2.0'"
".engines[.type == 'docker'].target_tag := 'main'"
],
"keywords" : [
"bioinformatics",
@@ -4632,7 +4633,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/biobox/fastp",
"tag" : "v0.2.0"
"tag" : "main"
},
"tag" : "$id"
}'''),

2
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/fastp/nextflow.config → target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'fastp'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.2.0'
version = 'main'
description = 'An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...).\n\nFeatures:\n\n - comprehensive quality profiling for both before and after filtering data (quality curves, base contents, KMER, Q20/Q30, GC Ratio, duplication, adapter contents...)\n - filter out bad reads (too low quality, too short, or too many N...)\n - cut low quality bases for per read in its 5\' and 3\' by evaluating the mean quality from a sliding window (like Trimmomatic but faster).\n - trim all reads in front and tail\n - cut adapters. Adapter sequences can be automatically detected, which means you don\'t have to input the adapter sequences to trim them.\n - correct mismatched base pairs in overlapped regions of paired end reads, if one base is with high quality while the other is with ultra low quality\n - trim polyG in 3\' ends, which is commonly seen in NovaSeq/NextSeq data. Trim polyX in 3\' ends to remove unwanted polyX tailing (i.e. polyA tailing for mRNA-Seq data)\n - preprocess unique molecular identifier (UMI) enabled data, shift UMI to sequence name.\n - report JSON format result for further interpreting.\n - visualize quality control and filtering results on a single HTML page (like FASTQC but faster and more informative).\n - split the output to multiple files (0001.R1.gz, 0002.R1.gz...) to support parallel processing. Two modes can be used, limiting the total split file number, or limitting the lines of each split file.\n - support long reads (data from PacBio / Nanopore devices).\n - support reading from STDIN and writing to STDOUT\n - support interleaved input\n - support ultra-fast FASTQ-level deduplication\n'
author = 'Robrecht Cannoodt'
}

0
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/fastp/nextflow_schema.json → target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/nextflow_schema.json
View File

13
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/featurecounts/.config.vsh.yaml → target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "featurecounts"
version: "v0.2.0"
version: "main"
authors:
- name: "Sai Nirmayi Yasa"
roles:
@@ -627,7 +627,7 @@ engines:
id: "docker"
image: "quay.io/biocontainers/subread:2.0.6--he4a0461_0"
target_registry: "images.viash-hub.com"
target_tag: "v0.2.0"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "docker"
@@ -645,11 +645,12 @@ build_info:
output: "target/nextflow/featurecounts"
executable: "target/nextflow/featurecounts/main.nf"
viash_version: "0.9.0"
git_commit: "7e530218844c373048bc33de58f021b6460642e5"
git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-11-g7fb67a9"
package_config:
name: "biobox"
version: "v0.2.0"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0"
@@ -659,7 +660,7 @@ package_config:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "modules"

17
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/featurecounts/main.nf → target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/main.nf
View File

@@ -1,4 +1,4 @@
// featurecounts v0.2.0
// featurecounts main
//
// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2808,7 +2808,7 @@ meta = [
"resources_dir": moduleDir.toRealPath().normalize(),
"config": processConfig(readJsonBlob('''{
"name" : "featurecounts",
"version" : "v0.2.0",
"version" : "main",
"authors" : [
{
"name" : "Sai Nirmayi Yasa",
@@ -3527,7 +3527,7 @@ meta = [
"id" : "docker",
"image" : "quay.io/biocontainers/subread:2.0.6--he4a0461_0",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.2.0",
"target_tag" : "main",
"namespace_separator" : "/",
"setup" : [
{
@@ -3549,12 +3549,13 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/featurecounts",
"viash_version" : "0.9.0",
"git_commit" : "7e530218844c373048bc33de58f021b6460642e5",
"git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
"git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7",
"git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-11-g7fb67a9"
},
"package_config" : {
"name" : "biobox",
"version" : "v0.2.0",
"version" : "main",
"description" : "A collection of bioinformatics tools for working with sequence data.\n",
"viash_version" : "0.9.0",
"source" : "src",
@@ -3563,7 +3564,7 @@ meta = [
".requirements.commands := ['ps']\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.2.0'"
".engines[.type == 'docker'].target_tag := 'main'"
],
"keywords" : [
"bioinformatics",
@@ -4115,7 +4116,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/biobox/featurecounts",
"tag" : "v0.2.0"
"tag" : "main"
},
"tag" : "$id"
}'''),

2
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/featurecounts/nextflow.config → target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'featurecounts'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.2.0'
version = 'main'
description = 'featureCounts is a read summarization program for counting reads generated from either RNA or genomic DNA sequencing experiments by implementing highly efficient chromosome hashing and feature blocking techniques. It works with either single or paired-end reads and provides a wide range of options appropriate for different sequencing applications.\n'
author = 'Sai Nirmayi Yasa'
}

0
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/featurecounts/nextflow_schema.json → target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/nextflow_schema.json
View File

13
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread/.config.vsh.yaml → target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "gffread"
version: "v0.2.0"
version: "main"
authors:
- name: "Emma Rousseau"
roles:
@@ -668,7 +668,7 @@ engines:
id: "docker"
image: "quay.io/biocontainers/gffread:0.12.7--hdcf5f25_3"
target_registry: "images.viash-hub.com"
target_tag: "v0.2.0"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "docker"
@@ -685,11 +685,12 @@ build_info:
output: "target/nextflow/gffread"
executable: "target/nextflow/gffread/main.nf"
viash_version: "0.9.0"
git_commit: "7e530218844c373048bc33de58f021b6460642e5"
git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-11-g7fb67a9"
package_config:
name: "biobox"
version: "v0.2.0"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0"
@@ -699,7 +700,7 @@ package_config:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "modules"

17
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread/main.nf → target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/main.nf
View File

@@ -1,4 +1,4 @@
// gffread v0.2.0
// gffread main
//
// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2808,7 +2808,7 @@ meta = [
"resources_dir": moduleDir.toRealPath().normalize(),
"config": processConfig(readJsonBlob('''{
"name" : "gffread",
"version" : "v0.2.0",
"version" : "main",
"authors" : [
{
"name" : "Emma Rousseau",
@@ -3584,7 +3584,7 @@ meta = [
"id" : "docker",
"image" : "quay.io/biocontainers/gffread:0.12.7--hdcf5f25_3",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.2.0",
"target_tag" : "main",
"namespace_separator" : "/",
"setup" : [
{
@@ -3606,12 +3606,13 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/gffread",
"viash_version" : "0.9.0",
"git_commit" : "7e530218844c373048bc33de58f021b6460642e5",
"git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
"git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7",
"git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-11-g7fb67a9"
},
"package_config" : {
"name" : "biobox",
"version" : "v0.2.0",
"version" : "main",
"description" : "A collection of bioinformatics tools for working with sequence data.\n",
"viash_version" : "0.9.0",
"source" : "src",
@@ -3620,7 +3621,7 @@ meta = [
".requirements.commands := ['ps']\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.2.0'"
".engines[.type == 'docker'].target_tag := 'main'"
],
"keywords" : [
"bioinformatics",
@@ -4218,7 +4219,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/biobox/gffread",
"tag" : "v0.2.0"
"tag" : "main"
},
"tag" : "$id"
}'''),

2
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread/nextflow.config → target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'gffread'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.2.0'
version = 'main'
description = 'Validate, filter, convert and perform various other operations on GFF files.'
author = 'Emma Rousseau'
}

0
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread/nextflow_schema.json → target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/nextflow_schema.json
View File

13
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/.config.vsh.yaml → target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/.config.vsh.yaml
View File

@@ -1,5 +1,5 @@
name: "multiqc"
version: "v0.2.0"
version: "main"
authors:
- name: "Dorien Roosen"
roles:
@@ -433,7 +433,7 @@ engines:
id: "docker"
image: "quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0"
target_registry: "images.viash-hub.com"
target_tag: "v0.2.0"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "docker"
@@ -456,11 +456,12 @@ build_info:
output: "target/nextflow/multiqc"
executable: "target/nextflow/multiqc/main.nf"
viash_version: "0.9.0"
git_commit: "7e530218844c373048bc33de58f021b6460642e5"
git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-11-g7fb67a9"
package_config:
name: "biobox"
version: "v0.2.0"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0"
@@ -470,7 +471,7 @@ package_config:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "modules"

17
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/main.nf → target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/main.nf
View File

@@ -1,4 +1,4 @@
// multiqc v0.2.0
// multiqc main
//
// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2808,7 +2808,7 @@ meta = [
"resources_dir": moduleDir.toRealPath().normalize(),
"config": processConfig(readJsonBlob('''{
"name" : "multiqc",
"version" : "v0.2.0",
"version" : "main",
"authors" : [
{
"name" : "Dorien Roosen",
@@ -3335,7 +3335,7 @@ meta = [
"id" : "docker",
"image" : "quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.2.0",
"target_tag" : "main",
"namespace_separator" : "/",
"setup" : [
{
@@ -3366,12 +3366,13 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/multiqc",
"viash_version" : "0.9.0",
"git_commit" : "7e530218844c373048bc33de58f021b6460642e5",
"git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
"git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7",
"git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-11-g7fb67a9"
},
"package_config" : {
"name" : "biobox",
"version" : "v0.2.0",
"version" : "main",
"description" : "A collection of bioinformatics tools for working with sequence data.\n",
"viash_version" : "0.9.0",
"source" : "src",
@@ -3380,7 +3381,7 @@ meta = [
".requirements.commands := ['ps']\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.2.0'"
".engines[.type == 'docker'].target_tag := 'main'"
],
"keywords" : [
"bioinformatics",
@@ -3961,7 +3962,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/biobox/multiqc",
"tag" : "v0.2.0"
"tag" : "main"
},
"tag" : "$id"
}'''),

2
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/nextflow.config → target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'multiqc'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.2.0'
version = 'main'
description = 'MultiQC aggregates results from bioinformatics analyses across many samples into a single report.\nIt searches a given directory for analysis logs and compiles a HTML report. It\'s a general use tool, perfect for summarising the output from numerous bioinformatics tools.\n'
author = 'Dorien Roosen'
}

0
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/nextflow_schema.json → target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/nextflow_schema.json
View File

13
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml → target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "rsem_prepare_reference"
namespace: "rsem"
version: "v0.2.0"
version: "main"
authors:
- name: "Sai Nirmayi Yasa"
roles:
@@ -352,7 +352,7 @@ engines:
id: "docker"
image: "ubuntu:22.04"
target_registry: "images.viash-hub.com"
target_tag: "v0.2.0"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "apt"
@@ -416,11 +416,12 @@ build_info:
output: "target/nextflow/rsem/rsem_prepare_reference"
executable: "target/nextflow/rsem/rsem_prepare_reference/main.nf"
viash_version: "0.9.0"
git_commit: "7e530218844c373048bc33de58f021b6460642e5"
git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-11-g7fb67a9"
package_config:
name: "biobox"
version: "v0.2.0"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0"
@@ -430,7 +431,7 @@ package_config:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "modules"

17
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/rsem/rsem_prepare_reference/main.nf → target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/main.nf
View File

@@ -1,4 +1,4 @@
// rsem_prepare_reference v0.2.0
// rsem_prepare_reference main
//
// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2809,7 +2809,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "rsem_prepare_reference",
"namespace" : "rsem",
"version" : "v0.2.0",
"version" : "main",
"authors" : [
{
"name" : "Sai Nirmayi Yasa",
@@ -3185,7 +3185,7 @@ meta = [
"id" : "docker",
"image" : "ubuntu:22.04",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.2.0",
"target_tag" : "main",
"namespace_separator" : "/",
"setup" : [
{
@@ -3245,12 +3245,13 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/rsem/rsem_prepare_reference",
"viash_version" : "0.9.0",
"git_commit" : "7e530218844c373048bc33de58f021b6460642e5",
"git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
"git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7",
"git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-11-g7fb67a9"
},
"package_config" : {
"name" : "biobox",
"version" : "v0.2.0",
"version" : "main",
"description" : "A collection of bioinformatics tools for working with sequence data.\n",
"viash_version" : "0.9.0",
"source" : "src",
@@ -3259,7 +3260,7 @@ meta = [
".requirements.commands := ['ps']\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.2.0'"
".engines[.type == 'docker'].target_tag := 'main'"
],
"keywords" : [
"bioinformatics",
@@ -3731,7 +3732,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/biobox/rsem/rsem_prepare_reference",
"tag" : "v0.2.0"
"tag" : "main"
},
"tag" : "$id"
}'''),

2
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/rsem/rsem_prepare_reference/nextflow.config → target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'rsem/rsem_prepare_reference'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.2.0'
version = 'main'
description = 'RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. This component prepares transcript references for RSEM.\n'
author = 'Sai Nirmayi Yasa'
}

0
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/rsem/rsem_prepare_reference/nextflow_schema.json → target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/nextflow_schema.json
View File

13
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index/.config.vsh.yaml → target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "salmon_index"
namespace: "salmon"
version: "v0.2.0"
version: "main"
authors:
- name: "Sai Nirmayi Yasa"
roles:
@@ -260,7 +260,7 @@ engines:
id: "docker"
image: "quay.io/biocontainers/salmon:1.10.2--hecfa306_0"
target_registry: "images.viash-hub.com"
target_tag: "v0.2.0"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "docker"
@@ -277,11 +277,12 @@ build_info:
output: "target/nextflow/salmon/salmon_index"
executable: "target/nextflow/salmon/salmon_index/main.nf"
viash_version: "0.9.0"
git_commit: "7e530218844c373048bc33de58f021b6460642e5"
git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-11-g7fb67a9"
package_config:
name: "biobox"
version: "v0.2.0"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0"
@@ -291,7 +292,7 @@ package_config:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "modules"

17
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index/main.nf → target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/main.nf
View File

@@ -1,4 +1,4 @@
// salmon_index v0.2.0
// salmon_index main
//
// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2809,7 +2809,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "salmon_index",
"namespace" : "salmon",
"version" : "v0.2.0",
"version" : "main",
"authors" : [
{
"name" : "Sai Nirmayi Yasa",
@@ -3107,7 +3107,7 @@ meta = [
"id" : "docker",
"image" : "quay.io/biocontainers/salmon:1.10.2--hecfa306_0",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.2.0",
"target_tag" : "main",
"namespace_separator" : "/",
"setup" : [
{
@@ -3129,12 +3129,13 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/salmon/salmon_index",
"viash_version" : "0.9.0",
"git_commit" : "7e530218844c373048bc33de58f021b6460642e5",
"git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
"git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7",
"git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-11-g7fb67a9"
},
"package_config" : {
"name" : "biobox",
"version" : "v0.2.0",
"version" : "main",
"description" : "A collection of bioinformatics tools for working with sequence data.\n",
"viash_version" : "0.9.0",
"source" : "src",
@@ -3143,7 +3144,7 @@ meta = [
".requirements.commands := ['ps']\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.2.0'"
".engines[.type == 'docker'].target_tag := 'main'"
],
"keywords" : [
"bioinformatics",
@@ -3619,7 +3620,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/biobox/salmon/salmon_index",
"tag" : "v0.2.0"
"tag" : "main"
},
"tag" : "$id"
}'''),

2
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index/nextflow.config → target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'salmon/salmon_index'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.2.0'
version = 'main'
description = 'Salmon is a tool for wicked-fast transcript quantification from RNA-seq data. It can either make use of pre-computed alignments (in the form of a SAM/BAM file) to the transcripts rather than the raw reads, or can be run in the mapping-based mode. This component creates a salmon index for the transcriptome to use Salmon in the mapping-based mode. It is generally recommend that you build a decoy-aware transcriptome file. This is done using the entire genome of the organism as the decoy sequence by concatenating the genome to the end of the transcriptome to be indexed and populating the decoys.txt file with the chromosome names.\n'
author = 'Sai Nirmayi Yasa'
}

0
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index/nextflow_schema.json → target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/nextflow_schema.json
View File

19
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/.config.vsh.yaml → target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "salmon_quant"
namespace: "salmon"
version: "v0.2.0"
version: "main"
authors:
- name: "Sai Nirmayi Yasa"
roles:
@@ -24,7 +24,7 @@ argument_groups:
- "-l"
description: "Format string describing the library.\nThe library type string consists\
\ of three parts: \n1. Relative orientation of the reads: This part is only\
\ provided if the library is paired-end, THe possible options are\n I = inward\n\
\ provided if the library is paired-end, The possible options are\n I = inward\n\
\ O = outward\n M = matching\n2. Strandedness of the library: This part specifies\
\ whether the protocol is stranded or unstranded. The options are:\n S = stranded\n\
\ U = unstranded\n3. Directionality of the reads: If the library is stranded,\
@@ -193,7 +193,7 @@ argument_groups:
- "quant.sf"
must_exist: true
create_parent: true
required: true
required: false
direction: "output"
multiple: false
multiple_sep: ";"
@@ -587,7 +587,7 @@ argument_groups:
- type: "file"
name: "--mapping_sam"
description: "Path to file that should output the selective-alignment results\
\ in SAM-compatible format. THis option must be provided while using --write_mappings"
\ in SAM-compatible format. This option must be provided while using --write_mappings"
info: null
example:
- "mappings.sam"
@@ -1156,7 +1156,7 @@ engines:
id: "docker"
image: "quay.io/biocontainers/salmon:1.10.2--hecfa306_0"
target_registry: "images.viash-hub.com"
target_tag: "v0.2.0"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "docker"
@@ -1173,11 +1173,12 @@ build_info:
output: "target/nextflow/salmon/salmon_quant"
executable: "target/nextflow/salmon/salmon_quant/main.nf"
viash_version: "0.9.0"
git_commit: "7e530218844c373048bc33de58f021b6460642e5"
git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-11-g7fb67a9"
package_config:
name: "biobox"
version: "v0.2.0"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0"
@@ -1187,7 +1188,7 @@ package_config:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "modules"

23
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/main.nf → target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/main.nf
View File

@@ -1,4 +1,4 @@
// salmon_quant v0.2.0
// salmon_quant main
//
// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2809,7 +2809,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "salmon_quant",
"namespace" : "salmon",
"version" : "v0.2.0",
"version" : "main",
"authors" : [
{
"name" : "Sai Nirmayi Yasa",
@@ -2843,7 +2843,7 @@ meta = [
"alternatives" : [
"-l"
],
"description" : "Format string describing the library.\nThe library type string consists of three parts: \n1. Relative orientation of the reads: This part is only provided if the library is paired-end, THe possible options are\n I = inward\n O = outward\n M = matching\n2. Strandedness of the library: This part specifies whether the protocol is stranded or unstranded. The options are:\n S = stranded\n U = unstranded\n3. Directionality of the reads: If the library is stranded, the final part of the library string is used to specify the strand from which the read originates. The possible values are\n F = read 1 (or single-end read) comes from the forward strand\n R = read 1 (or single-end read) comes from the reverse strand\n",
"description" : "Format string describing the library.\nThe library type string consists of three parts: \n1. Relative orientation of the reads: This part is only provided if the library is paired-end, The possible options are\n I = inward\n O = outward\n M = matching\n2. Strandedness of the library: This part specifies whether the protocol is stranded or unstranded. The options are:\n S = stranded\n U = unstranded\n3. Directionality of the reads: If the library is stranded, the final part of the library string is used to specify the strand from which the read originates. The possible values are\n F = read 1 (or single-end read) comes from the forward strand\n R = read 1 (or single-end read) comes from the reverse strand\n",
"default" : [
"A"
],
@@ -3039,7 +3039,7 @@ meta = [
],
"must_exist" : true,
"create_parent" : true,
"required" : true,
"required" : false,
"direction" : "output",
"multiple" : false,
"multiple_sep" : ";"
@@ -3375,7 +3375,7 @@ meta = [
{
"type" : "file",
"name" : "--mapping_sam",
"description" : "Path to file that should output the selective-alignment results in SAM-compatible format. THis option must be provided while using --write_mappings",
"description" : "Path to file that should output the selective-alignment results in SAM-compatible format. This option must be provided while using --write_mappings",
"example" : [
"mappings.sam"
],
@@ -3942,7 +3942,7 @@ meta = [
"id" : "docker",
"image" : "quay.io/biocontainers/salmon:1.10.2--hecfa306_0",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.2.0",
"target_tag" : "main",
"namespace_separator" : "/",
"setup" : [
{
@@ -3964,12 +3964,13 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/salmon/salmon_quant",
"viash_version" : "0.9.0",
"git_commit" : "7e530218844c373048bc33de58f021b6460642e5",
"git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
"git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7",
"git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-11-g7fb67a9"
},
"package_config" : {
"name" : "biobox",
"version" : "v0.2.0",
"version" : "main",
"description" : "A collection of bioinformatics tools for working with sequence data.\n",
"viash_version" : "0.9.0",
"source" : "src",
@@ -3978,7 +3979,7 @@ meta = [
".requirements.commands := ['ps']\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.2.0'"
".engines[.type == 'docker'].target_tag := 'main'"
],
"keywords" : [
"bioinformatics",
@@ -4634,7 +4635,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/biobox/salmon/salmon_quant",
"tag" : "v0.2.0"
"tag" : "main"
},
"tag" : "$id"
}'''),

2
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/nextflow.config → target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'salmon/salmon_quant'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.2.0'
version = 'main'
description = 'Salmon is a tool for wicked-fast transcript quantification from RNA-seq data. It can either make use of pre-computed alignments (in the form of a SAM/BAM file) to the transcripts rather than the raw reads, or can be run in the mapping-based mode. \n'
author = 'Sai Nirmayi Yasa'
}

8
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/nextflow_schema.json → target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/nextflow_schema.json
View File

@@ -18,7 +18,7 @@
"type":
"string",
"description": "Type: `string`, default: `A`, choices: ``A`, `U`, `SF`, `SR`, `IU`, `IS`, `ISF`, `ISR`, `OU`, `OS`, `OSF`, `OSR`, `MU`, `MS`, `MSF`, `MSR``. Format string describing the library",
"help_text": "Type: `string`, default: `A`, choices: ``A`, `U`, `SF`, `SR`, `IU`, `IS`, `ISF`, `ISR`, `OU`, `OS`, `OSF`, `OSR`, `MU`, `MS`, `MSF`, `MSR``. Format string describing the library.\nThe library type string consists of three parts: \n1. Relative orientation of the reads: This part is only provided if the library is paired-end, THe possible options are\n I = inward\n O = outward\n M = matching\n2. Strandedness of the library: This part specifies whether the protocol is stranded or unstranded. The options are:\n S = stranded\n U = unstranded\n3. Directionality of the reads: If the library is stranded, the final part of the library string is used to specify the strand from which the read originates. The possible values are\n F = read 1 (or single-end read) comes from the forward strand\n R = read 1 (or single-end read) comes from the reverse strand\n",
"help_text": "Type: `string`, default: `A`, choices: ``A`, `U`, `SF`, `SR`, `IU`, `IS`, `ISF`, `ISR`, `OU`, `OS`, `OSF`, `OSR`, `MU`, `MS`, `MSF`, `MSR``. Format string describing the library.\nThe library type string consists of three parts: \n1. Relative orientation of the reads: This part is only provided if the library is paired-end, The possible options are\n I = inward\n O = outward\n M = matching\n2. Strandedness of the library: This part specifies whether the protocol is stranded or unstranded. The options are:\n S = stranded\n U = unstranded\n3. Directionality of the reads: If the library is stranded, the final part of the library string is used to specify the strand from which the read originates. The possible values are\n F = read 1 (or single-end read) comes from the forward strand\n R = read 1 (or single-end read) comes from the reverse strand\n",
"enum": ["A", "U", "SF", "SR", "IU", "IS", "ISF", "ISR", "OU", "OS", "OSF", "OSR", "MU", "MS", "MSF", "MSR"]
,
@@ -163,8 +163,8 @@
"quant_results": {
"type":
"string",
"description": "Type: `file`, required, default: `$id.$key.quant_results.sf`, example: `quant.sf`. Salmon quantification file",
"help_text": "Type: `file`, required, default: `$id.$key.quant_results.sf`, example: `quant.sf`. Salmon quantification file.\n"
"description": "Type: `file`, default: `$id.$key.quant_results.sf`, example: `quant.sf`. Salmon quantification file",
"help_text": "Type: `file`, default: `$id.$key.quant_results.sf`, example: `quant.sf`. Salmon quantification file.\n"
,
"default": "$id.$key.quant_results.sf"
}
@@ -530,7 +530,7 @@
"type":
"string",
"description": "Type: `file`, default: `$id.$key.mapping_sam.sam`, example: `mappings.sam`. Path to file that should output the selective-alignment results in SAM-compatible format",
"help_text": "Type: `file`, default: `$id.$key.mapping_sam.sam`, example: `mappings.sam`. Path to file that should output the selective-alignment results in SAM-compatible format. THis option must be provided while using --write_mappings"
"help_text": "Type: `file`, default: `$id.$key.mapping_sam.sam`, example: `mappings.sam`. Path to file that should output the selective-alignment results in SAM-compatible format. This option must be provided while using --write_mappings"
,
"default": "$id.$key.mapping_sam.sam"
}

13
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat/.config.vsh.yaml → target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "samtools_flagstat"
namespace: "samtools"
version: "v0.2.0"
version: "main"
authors:
- name: "Emma Rousseau"
roles:
@@ -155,7 +155,7 @@ engines:
id: "docker"
image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1"
target_registry: "images.viash-hub.com"
target_tag: "v0.2.0"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "docker"
@@ -173,11 +173,12 @@ build_info:
output: "target/nextflow/samtools/samtools_flagstat"
executable: "target/nextflow/samtools/samtools_flagstat/main.nf"
viash_version: "0.9.0"
git_commit: "7e530218844c373048bc33de58f021b6460642e5"
git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-11-g7fb67a9"
package_config:
name: "biobox"
version: "v0.2.0"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0"
@@ -187,7 +188,7 @@ package_config:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "modules"

17
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat/main.nf → target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/main.nf
View File

@@ -1,4 +1,4 @@
// samtools_flagstat v0.2.0
// samtools_flagstat main
//
// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2809,7 +2809,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "samtools_flagstat",
"namespace" : "samtools",
"version" : "v0.2.0",
"version" : "main",
"authors" : [
{
"name" : "Emma Rousseau",
@@ -3006,7 +3006,7 @@ meta = [
"id" : "docker",
"image" : "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.2.0",
"target_tag" : "main",
"namespace_separator" : "/",
"setup" : [
{
@@ -3028,12 +3028,13 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/samtools/samtools_flagstat",
"viash_version" : "0.9.0",
"git_commit" : "7e530218844c373048bc33de58f021b6460642e5",
"git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
"git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7",
"git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-11-g7fb67a9"
},
"package_config" : {
"name" : "biobox",
"version" : "v0.2.0",
"version" : "main",
"description" : "A collection of bioinformatics tools for working with sequence data.\n",
"viash_version" : "0.9.0",
"source" : "src",
@@ -3042,7 +3043,7 @@ meta = [
".requirements.commands := ['ps']\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.2.0'"
".engines[.type == 'docker'].target_tag := 'main'"
],
"keywords" : [
"bioinformatics",
@@ -3463,7 +3464,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/biobox/samtools/samtools_flagstat",
"tag" : "v0.2.0"
"tag" : "main"
},
"tag" : "$id"
}'''),

2
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat/nextflow.config → target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'samtools/samtools_flagstat'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.2.0'
version = 'main'
description = 'Counts the number of alignments in SAM/BAM/CRAM files for each FLAG type.'
author = 'Emma Rousseau'
}

0
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat/nextflow_schema.json → target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/nextflow_schema.json
View File

13
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats/.config.vsh.yaml → target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "samtools_idxstats"
namespace: "samtools"
version: "v0.2.0"
version: "main"
authors:
- name: "Emma Rousseau"
roles:
@@ -165,7 +165,7 @@ engines:
id: "docker"
image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1"
target_registry: "images.viash-hub.com"
target_tag: "v0.2.0"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "docker"
@@ -183,11 +183,12 @@ build_info:
output: "target/nextflow/samtools/samtools_idxstats"
executable: "target/nextflow/samtools/samtools_idxstats/main.nf"
viash_version: "0.9.0"
git_commit: "7e530218844c373048bc33de58f021b6460642e5"
git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-11-g7fb67a9"
package_config:
name: "biobox"
version: "v0.2.0"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0"
@@ -197,7 +198,7 @@ package_config:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "modules"

17
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats/main.nf → target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/main.nf
View File

@@ -1,4 +1,4 @@
// samtools_idxstats v0.2.0
// samtools_idxstats main
//
// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2809,7 +2809,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "samtools_idxstats",
"namespace" : "samtools",
"version" : "v0.2.0",
"version" : "main",
"authors" : [
{
"name" : "Emma Rousseau",
@@ -3018,7 +3018,7 @@ meta = [
"id" : "docker",
"image" : "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.2.0",
"target_tag" : "main",
"namespace_separator" : "/",
"setup" : [
{
@@ -3040,12 +3040,13 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/samtools/samtools_idxstats",
"viash_version" : "0.9.0",
"git_commit" : "7e530218844c373048bc33de58f021b6460642e5",
"git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
"git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7",
"git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-11-g7fb67a9"
},
"package_config" : {
"name" : "biobox",
"version" : "v0.2.0",
"version" : "main",
"description" : "A collection of bioinformatics tools for working with sequence data.\n",
"viash_version" : "0.9.0",
"source" : "src",
@@ -3054,7 +3055,7 @@ meta = [
".requirements.commands := ['ps']\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.2.0'"
".engines[.type == 'docker'].target_tag := 'main'"
],
"keywords" : [
"bioinformatics",
@@ -3473,7 +3474,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/biobox/samtools/samtools_idxstats",
"tag" : "v0.2.0"
"tag" : "main"
},
"tag" : "$id"
}'''),

2
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats/nextflow.config → target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'samtools/samtools_idxstats'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.2.0'
version = 'main'
description = 'Reports alignment summary statistics for a BAM file.'
author = 'Emma Rousseau'
}

0
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats/nextflow_schema.json → target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/nextflow_schema.json
View File

13
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index/.config.vsh.yaml → target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "samtools_index"
namespace: "samtools"
version: "v0.2.0"
version: "main"
authors:
- name: "Emma Rousseau"
roles:
@@ -171,7 +171,7 @@ engines:
id: "docker"
image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1"
target_registry: "images.viash-hub.com"
target_tag: "v0.2.0"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "docker"
@@ -189,11 +189,12 @@ build_info:
output: "target/nextflow/samtools/samtools_index"
executable: "target/nextflow/samtools/samtools_index/main.nf"
viash_version: "0.9.0"
git_commit: "7e530218844c373048bc33de58f021b6460642e5"
git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-11-g7fb67a9"
package_config:
name: "biobox"
version: "v0.2.0"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0"
@@ -203,7 +204,7 @@ package_config:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "modules"

17
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index/main.nf → target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/main.nf
View File

@@ -1,4 +1,4 @@
// samtools_index v0.2.0
// samtools_index main
//
// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2809,7 +2809,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "samtools_index",
"namespace" : "samtools",
"version" : "v0.2.0",
"version" : "main",
"authors" : [
{
"name" : "Emma Rousseau",
@@ -3031,7 +3031,7 @@ meta = [
"id" : "docker",
"image" : "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.2.0",
"target_tag" : "main",
"namespace_separator" : "/",
"setup" : [
{
@@ -3053,12 +3053,13 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/samtools/samtools_index",
"viash_version" : "0.9.0",
"git_commit" : "7e530218844c373048bc33de58f021b6460642e5",
"git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
"git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7",
"git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-11-g7fb67a9"
},
"package_config" : {
"name" : "biobox",
"version" : "v0.2.0",
"version" : "main",
"description" : "A collection of bioinformatics tools for working with sequence data.\n",
"viash_version" : "0.9.0",
"source" : "src",
@@ -3067,7 +3068,7 @@ meta = [
".requirements.commands := ['ps']\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.2.0'"
".engines[.type == 'docker'].target_tag := 'main'"
],
"keywords" : [
"bioinformatics",
@@ -3497,7 +3498,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/biobox/samtools/samtools_index",
"tag" : "v0.2.0"
"tag" : "main"
},
"tag" : "$id"
}'''),

2
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index/nextflow.config → target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'samtools/samtools_index'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.2.0'
version = 'main'
description = 'Index SAM/BAM/CRAM files.'
author = 'Emma Rousseau'
}

0
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index/nextflow_schema.json → target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/nextflow_schema.json
View File

13
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort/.config.vsh.yaml → target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "samtools_sort"
namespace: "samtools"
version: "v0.2.0"
version: "main"
authors:
- name: "Emma Rousseau"
roles:
@@ -314,7 +314,7 @@ engines:
id: "docker"
image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1"
target_registry: "images.viash-hub.com"
target_tag: "v0.2.0"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "docker"
@@ -332,11 +332,12 @@ build_info:
output: "target/nextflow/samtools/samtools_sort"
executable: "target/nextflow/samtools/samtools_sort/main.nf"
viash_version: "0.9.0"
git_commit: "7e530218844c373048bc33de58f021b6460642e5"
git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-11-g7fb67a9"
package_config:
name: "biobox"
version: "v0.2.0"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0"
@@ -346,7 +347,7 @@ package_config:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "modules"

17
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort/main.nf → target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/main.nf
View File

@@ -1,4 +1,4 @@
// samtools_sort v0.2.0
// samtools_sort main
//
// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2809,7 +2809,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "samtools_sort",
"namespace" : "samtools",
"version" : "v0.2.0",
"version" : "main",
"authors" : [
{
"name" : "Emma Rousseau",
@@ -3203,7 +3203,7 @@ meta = [
"id" : "docker",
"image" : "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.2.0",
"target_tag" : "main",
"namespace_separator" : "/",
"setup" : [
{
@@ -3225,12 +3225,13 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/samtools/samtools_sort",
"viash_version" : "0.9.0",
"git_commit" : "7e530218844c373048bc33de58f021b6460642e5",
"git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
"git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7",
"git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-11-g7fb67a9"
},
"package_config" : {
"name" : "biobox",
"version" : "v0.2.0",
"version" : "main",
"description" : "A collection of bioinformatics tools for working with sequence data.\n",
"viash_version" : "0.9.0",
"source" : "src",
@@ -3239,7 +3240,7 @@ meta = [
".requirements.commands := ['ps']\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.2.0'"
".engines[.type == 'docker'].target_tag := 'main'"
],
"keywords" : [
"bioinformatics",
@@ -3717,7 +3718,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/biobox/samtools/samtools_sort",
"tag" : "v0.2.0"
"tag" : "main"
},
"tag" : "$id"
}'''),

2
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort/nextflow.config → target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'samtools/samtools_sort'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.2.0'
version = 'main'
description = 'Sort SAM/BAM/CRAM file.'
author = 'Emma Rousseau'
}

0
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort/nextflow_schema.json → target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/nextflow_schema.json
View File

13
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats/.config.vsh.yaml → target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "samtools_stats"
namespace: "samtools"
version: "v0.2.0"
version: "main"
authors:
- name: "Emma Rousseau"
roles:
@@ -383,7 +383,7 @@ engines:
id: "docker"
image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1"
target_registry: "images.viash-hub.com"
target_tag: "v0.2.0"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "docker"
@@ -401,11 +401,12 @@ build_info:
output: "target/nextflow/samtools/samtools_stats"
executable: "target/nextflow/samtools/samtools_stats/main.nf"
viash_version: "0.9.0"
git_commit: "7e530218844c373048bc33de58f021b6460642e5"
git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-11-g7fb67a9"
package_config:
name: "biobox"
version: "v0.2.0"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0"
@@ -415,7 +416,7 @@ package_config:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "modules"

17
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats/main.nf → target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/main.nf
View File

@@ -1,4 +1,4 @@
// samtools_stats v0.2.0
// samtools_stats main
//
// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2809,7 +2809,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "samtools_stats",
"namespace" : "samtools",
"version" : "v0.2.0",
"version" : "main",
"authors" : [
{
"name" : "Emma Rousseau",
@@ -3273,7 +3273,7 @@ meta = [
"id" : "docker",
"image" : "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.2.0",
"target_tag" : "main",
"namespace_separator" : "/",
"setup" : [
{
@@ -3295,12 +3295,13 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/samtools/samtools_stats",
"viash_version" : "0.9.0",
"git_commit" : "7e530218844c373048bc33de58f021b6460642e5",
"git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
"git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7",
"git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-11-g7fb67a9"
},
"package_config" : {
"name" : "biobox",
"version" : "v0.2.0",
"version" : "main",
"description" : "A collection of bioinformatics tools for working with sequence data.\n",
"viash_version" : "0.9.0",
"source" : "src",
@@ -3309,7 +3310,7 @@ meta = [
".requirements.commands := ['ps']\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.2.0'"
".engines[.type == 'docker'].target_tag := 'main'"
],
"keywords" : [
"bioinformatics",
@@ -3779,7 +3780,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/biobox/samtools/samtools_stats",
"tag" : "v0.2.0"
"tag" : "main"
},
"tag" : "$id"
}'''),

2
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats/nextflow.config → target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'samtools/samtools_stats'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.2.0'
version = 'main'
description = 'Reports alignment summary statistics for a BAM file.'
author = 'Emma Rousseau'
}

0
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats/nextflow_schema.json → target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/nextflow_schema.json
View File

13
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads/.config.vsh.yaml → target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "star_align_reads"
namespace: "star"
version: "v0.2.0"
version: "main"
authors:
- name: "Angela Oliveira Pisco"
roles:
@@ -2624,7 +2624,7 @@ engines:
id: "docker"
image: "python:3.12-slim"
target_registry: "images.viash-hub.com"
target_tag: "v0.2.0"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "apt"
@@ -2663,11 +2663,12 @@ build_info:
output: "target/nextflow/star/star_align_reads"
executable: "target/nextflow/star/star_align_reads/main.nf"
viash_version: "0.9.0"
git_commit: "7e530218844c373048bc33de58f021b6460642e5"
git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-11-g7fb67a9"
package_config:
name: "biobox"
version: "v0.2.0"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0"
@@ -2677,7 +2678,7 @@ package_config:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "modules"

19
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads/main.nf → target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/main.nf
View File

@@ -1,4 +1,4 @@
// star_align_reads v0.2.0
// star_align_reads main
//
// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2810,7 +2810,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "star_align_reads",
"namespace" : "star",
"version" : "v0.2.0",
"version" : "main",
"authors" : [
{
"name" : "Angela Oliveira Pisco",
@@ -4570,7 +4570,7 @@ meta = [
{
"type" : "integer",
"name" : "--seed_split_min",
"description" : "min length of the seed sequ''' + '''ences split by Ns or mate gap",
"description" : "min length of the seed sequen''' + '''ces split by Ns or mate gap",
"info" : {
"orig_name" : "--seedSplitMin"
},
@@ -5894,7 +5894,7 @@ meta = [
"id" : "docker",
"image" : "python:3.12-slim",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.2.0",
"target_tag" : "main",
"namespace_separator" : "/",
"setup" : [
{
@@ -5943,12 +5943,13 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/star/star_align_reads",
"viash_version" : "0.9.0",
"git_commit" : "7e530218844c373048bc33de58f021b6460642e5",
"git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
"git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7",
"git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-11-g7fb67a9"
},
"package_config" : {
"name" : "biobox",
"version" : "v0.2.0",
"version" : "main",
"description" : "A collection of bioinformatics tools for working with sequence data.\n",
"viash_version" : "0.9.0",
"source" : "src",
@@ -5957,7 +5958,7 @@ meta = [
".requirements.commands := ['ps']\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.2.0'"
".engines[.type == 'docker'].target_tag := 'main'"
],
"keywords" : [
"bioinformatics",
@@ -6671,7 +6672,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/biobox/star/star_align_reads",
"tag" : "v0.2.0"
"tag" : "main"
},
"tag" : "$id"
}'''),

2
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads/nextflow.config → target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'star/star_align_reads'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.2.0'
version = 'main'
description = 'Aligns reads to a reference genome using STAR.\n'
author = 'Angela Oliveira Pisco, Robrecht Cannoodt'
}

0
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads/nextflow_schema.json → target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/nextflow_schema.json
View File

13
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_genome_generate/.config.vsh.yaml → target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "star_genome_generate"
namespace: "star"
version: "v0.2.0"
version: "main"
authors:
- name: "Sai Nirmayi Yasa"
roles:
@@ -305,7 +305,7 @@ engines:
id: "docker"
image: "ubuntu:22.04"
target_registry: "images.viash-hub.com"
target_tag: "v0.2.0"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "docker"
@@ -333,11 +333,12 @@ build_info:
output: "target/nextflow/star/star_genome_generate"
executable: "target/nextflow/star/star_genome_generate/main.nf"
viash_version: "0.9.0"
git_commit: "7e530218844c373048bc33de58f021b6460642e5"
git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-11-g7fb67a9"
package_config:
name: "biobox"
version: "v0.2.0"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0"
@@ -347,7 +348,7 @@ package_config:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "modules"

17
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_genome_generate/main.nf → target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/main.nf
View File

@@ -1,4 +1,4 @@
// star_genome_generate v0.2.0
// star_genome_generate main
//
// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2809,7 +2809,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "star_genome_generate",
"namespace" : "star",
"version" : "v0.2.0",
"version" : "main",
"authors" : [
{
"name" : "Sai Nirmayi Yasa",
@@ -3163,7 +3163,7 @@ meta = [
"id" : "docker",
"image" : "ubuntu:22.04",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.2.0",
"target_tag" : "main",
"namespace_separator" : "/",
"setup" : [
{
@@ -3195,12 +3195,13 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/star/star_genome_generate",
"viash_version" : "0.9.0",
"git_commit" : "7e530218844c373048bc33de58f021b6460642e5",
"git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
"git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7",
"git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-11-g7fb67a9"
},
"package_config" : {
"name" : "biobox",
"version" : "v0.2.0",
"version" : "main",
"description" : "A collection of bioinformatics tools for working with sequence data.\n",
"viash_version" : "0.9.0",
"source" : "src",
@@ -3209,7 +3210,7 @@ meta = [
".requirements.commands := ['ps']\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.2.0'"
".engines[.type == 'docker'].target_tag := 'main'"
],
"keywords" : [
"bioinformatics",
@@ -3662,7 +3663,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/biobox/star/star_genome_generate",
"tag" : "v0.2.0"
"tag" : "main"
},
"tag" : "$id"
}'''),

2
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_genome_generate/nextflow.config → target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'star/star_genome_generate'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.2.0'
version = 'main'
description = 'Create index for STAR\n'
author = 'Sai Nirmayi Yasa'
}

0
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_genome_generate/nextflow_schema.json → target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/nextflow_schema.json
View File

13
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml → target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml
View File

@@ -1,6 +1,6 @@
name: "umi_tools_extract"
namespace: "umi_tools"
version: "v0.2.0"
version: "main"
argument_groups:
- name: "Input"
arguments:
@@ -432,7 +432,7 @@ engines:
id: "docker"
image: "quay.io/biocontainers/umi_tools:1.1.4--py310h4b81fae_2"
target_registry: "images.viash-hub.com"
target_tag: "v0.2.0"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "docker"
@@ -449,11 +449,12 @@ build_info:
output: "target/nextflow/umi_tools/umi_tools_extract"
executable: "target/nextflow/umi_tools/umi_tools_extract/main.nf"
viash_version: "0.9.0"
git_commit: "7e530218844c373048bc33de58f021b6460642e5"
git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
git_tag: "v0.2.0-11-g7fb67a9"
package_config:
name: "biobox"
version: "v0.2.0"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
info: null
viash_version: "0.9.0"
@@ -463,7 +464,7 @@ package_config:
- ".requirements.commands := ['ps']\n"
- ".engines += { type: \"native\" }"
- ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
- ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
- ".engines[.type == 'docker'].target_tag := 'main'"
keywords:
- "bioinformatics"
- "modules"

17
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/umi_tools/umi_tools_extract/main.nf → target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/main.nf
View File

@@ -1,4 +1,4 @@
// umi_tools_extract v0.2.0
// umi_tools_extract main
//
// This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
// work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2806,7 +2806,7 @@ meta = [
"config": processConfig(readJsonBlob('''{
"name" : "umi_tools_extract",
"namespace" : "umi_tools",
"version" : "v0.2.0",
"version" : "main",
"argument_groups" : [
{
"name" : "Input",
@@ -3294,7 +3294,7 @@ meta = [
"id" : "docker",
"image" : "quay.io/biocontainers/umi_tools:1.1.4--py310h4b81fae_2",
"target_registry" : "images.viash-hub.com",
"target_tag" : "v0.2.0",
"target_tag" : "main",
"namespace_separator" : "/",
"setup" : [
{
@@ -3316,12 +3316,13 @@ meta = [
"engine" : "docker|native",
"output" : "target/nextflow/umi_tools/umi_tools_extract",
"viash_version" : "0.9.0",
"git_commit" : "7e530218844c373048bc33de58f021b6460642e5",
"git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
"git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7",
"git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
"git_tag" : "v0.2.0-11-g7fb67a9"
},
"package_config" : {
"name" : "biobox",
"version" : "v0.2.0",
"version" : "main",
"description" : "A collection of bioinformatics tools for working with sequence data.\n",
"viash_version" : "0.9.0",
"source" : "src",
@@ -3330,7 +3331,7 @@ meta = [
".requirements.commands := ['ps']\n",
".engines += { type: \\"native\\" }",
".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
".engines[.type == 'docker'].target_tag := 'v0.2.0'"
".engines[.type == 'docker'].target_tag := 'main'"
],
"keywords" : [
"bioinformatics",
@@ -3861,7 +3862,7 @@ meta["defaults"] = [
"container" : {
"registry" : "images.viash-hub.com",
"image" : "vsh/biobox/umi_tools/umi_tools_extract",
"tag" : "v0.2.0"
"tag" : "main"
},
"tag" : "$id"
}'''),

2
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/umi_tools/umi_tools_extract/nextflow.config → target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/nextflow.config
View File

@@ -2,7 +2,7 @@ manifest {
name = 'umi_tools/umi_tools_extract'
mainScript = 'main.nf'
nextflowVersion = '!>=20.12.1-edge'
version = 'v0.2.0'
version = 'main'
description = 'Flexible removal of UMI sequences from fastq reads.\nUMIs are removed and appended to the read name. Any other barcode, for example a library barcode,\nis left on the read. Can also filter reads by quality or against a whitelist.\n'
}

0
target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/umi_tools/umi_tools_extract/nextflow_schema.json → target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/nextflow_schema.json
View File

9
target/executable/bbmap_bbsplit/.config.vsh.yaml
View File

@@ -144,7 +144,7 @@ repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
@@ -238,9 +238,10 @@ build_info:
output: "target/executable/bbmap_bbsplit"
executable: "target/executable/bbmap_bbsplit/bbmap_bbsplit"
viash_version: "0.9.0"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"
info:
test_resources:
@@ -250,7 +251,7 @@ package_config:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"

8
target/executable/bbmap_bbsplit/bbmap_bbsplit
View File

@@ -506,9 +506,9 @@ tar xzf BBMap_39.01.tar.gz && \
cp -r bbmap/* /usr/local/bin
LABEL org.opencontainers.image.description="Companion container for running component bbmap_bbsplit"
LABEL org.opencontainers.image.created="2024-10-04T07:06:12Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
LABEL org.opencontainers.image.created="2024-10-25T08:58:48Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -852,7 +852,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/bbmap_bbsplit:main'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/bbmap_bbsplit:main'
fi
# print dockerfile

9
target/executable/bedtools_genomecov/.config.vsh.yaml
View File

@@ -84,7 +84,7 @@ repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
@@ -178,9 +178,10 @@ build_info:
output: "target/executable/bedtools_genomecov"
executable: "target/executable/bedtools_genomecov/bedtools_genomecov"
viash_version: "0.9.0"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"
info:
test_resources:
@@ -190,7 +191,7 @@ package_config:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"

8
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="2024-10-04T07:06:12Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
LABEL org.opencontainers.image.created="2024-10-25T08:58:42Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -766,7 +766,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/bedtools_genomecov:main'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/bedtools_genomecov:main'
fi
# print dockerfile

9
target/executable/cat_additional_fasta/.config.vsh.yaml
View File

@@ -94,7 +94,7 @@ repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
@@ -182,9 +182,10 @@ build_info:
output: "target/executable/cat_additional_fasta"
executable: "target/executable/cat_additional_fasta/cat_additional_fasta"
viash_version: "0.9.0"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"
info:
test_resources:
@@ -194,7 +195,7 @@ package_config:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"

8
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="2024-10-04T07:06:20Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
LABEL org.opencontainers.image.created="2024-10-25T08:58:38Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -776,7 +776,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/cat_additional_fasta:main'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/cat_additional_fasta:main'
fi
# print dockerfile

9
target/executable/cat_fastq/.config.vsh.yaml
View File

@@ -81,7 +81,7 @@ repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
@@ -169,9 +169,10 @@ build_info:
output: "target/executable/cat_fastq"
executable: "target/executable/cat_fastq/cat_fastq"
viash_version: "0.9.0"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"
info:
test_resources:
@@ -181,7 +182,7 @@ package_config:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"

8
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="2024-10-04T07:06:21Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
LABEL org.opencontainers.image.created="2024-10-25T08:58:43Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -758,7 +758,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/cat_fastq:main'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/cat_fastq:main'
fi
# print dockerfile

106
target/executable/deseq2_qc/.config.vsh.yaml
View File

@@ -5,60 +5,69 @@ argument_groups:
arguments:
- type: "file"
name: "--counts"
description: "count file matrix where rows are genes and columns are samples"
description: "Count file matrix where rows are genes and columns are samples."
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--pca_header_multiqc"
info: null
default:
- "assets/multiqc/deseq2_pca_header.txt"
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--clustering_header_multiqc"
info: null
default:
- "assets/multiqc/deseq2_clustering_header.txt"
must_exist: true
create_parent: true
required: false
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean"
name: "--deseq2_vst"
description: "Use vst transformation instead of rlog with DESeq2"
name: "--vst"
description: "Use vst transformation instead of rlog with .DESeq2"
info: null
default:
- true
- false
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--count_col"
description: "First column containing sample count data."
info: null
default:
- 3
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--id_col"
description: "Column containing identifiers to be used."
info: null
default:
- 1
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--extra_args"
name: "--sample_suffix"
description: "Suffix to remove after sample name in columns e.g. '.rmDup.bam'\
\ if 'DRUG_R1.rmDup.bam'."
info: null
default:
- "--id_col 1 --sample_suffix '' --outprefix deseq2 --count_col 3"
- ""
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--extra_args2"
name: "--outprefix"
description: "Output prefix"
info: null
default:
- "star_salmon"
- "deseq2"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--label"
description: "Label to used in MultiQC report"
info: null
required: false
direction: "input"
multiple: false
@@ -66,7 +75,7 @@ argument_groups:
- name: "Output"
arguments:
- type: "file"
name: "--deseq2_output"
name: "--outdir"
info: null
default:
- "deseq2"
@@ -88,7 +97,7 @@ argument_groups:
multiple: false
multiple_sep: ";"
- type: "file"
name: "--dists_multiqc"
name: "--sample_dists_multiqc"
info: null
default:
- "deseq2.sample.dists_mqc.tsv"
@@ -99,17 +108,13 @@ argument_groups:
multiple: false
multiple_sep: ";"
resources:
- type: "bash_script"
path: "script.sh"
- type: "r_script"
path: "script.r"
is_executable: true
- type: "file"
path: "deseq2_qc.r"
path: "deseq2_pca_header.txt"
- type: "file"
path: "assets/multiqc/deseq2_pca_header.txt"
dest: "assets/multiqc/deseq2_pca_header.txt"
- type: "file"
path: "assets/multiqc/deseq2_clustering_header.txt"
dest: "assets/multiqc/deseq2_clustering_header.txt"
path: "deseq2_clustering_header.txt"
description: "run deseq2, perform pca, generate heatmaps and scatterplots for samples\
\ in the counts files\n"
test_resources:
@@ -132,7 +137,7 @@ repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
@@ -205,24 +210,18 @@ runners:
engines:
- type: "docker"
id: "docker"
image: "ubuntu:22.04"
image: "rocker/r2u:22.04"
target_registry: "images.viash-hub.com"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "apt"
packages:
- "r-base"
- "libcurl4-openssl-dev"
- "libssl-dev"
- "libxml2-dev"
interactive: false
- type: "r"
cran:
- "optparse"
- "ggplot2"
- "RColorBrewer"
- "pheatmap"
- "stringr"
bioc:
- "DESeq2"
url:
@@ -239,9 +238,10 @@ build_info:
output: "target/executable/deseq2_qc"
executable: "target/executable/deseq2_qc/deseq2_qc"
viash_version: "0.9.0"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"
info:
test_resources:
@@ -251,7 +251,7 @@ package_config:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"

0
target/executable/deseq2_qc/assets/multiqc/deseq2_clustering_header.txt → target/executable/deseq2_qc/deseq2_clustering_header.txt
View File

0
target/executable/deseq2_qc/assets/multiqc/deseq2_pca_header.txt → target/executable/deseq2_qc/deseq2_pca_header.txt
View File

604
target/executable/deseq2_qc/deseq2_qc
View File

@@ -178,32 +178,41 @@ function ViashHelp {
echo ""
echo "input:"
echo " --counts"
echo " type: file, file must exist"
echo " count file matrix where rows are genes and columns are samples"
echo " type: file, required parameter, file must exist"
echo " Count file matrix where rows are genes and columns are samples."
echo ""
echo " --pca_header_multiqc"
echo " type: file, file must exist"
echo " default: assets/multiqc/deseq2_pca_header.txt"
echo ""
echo " --clustering_header_multiqc"
echo " type: file, file must exist"
echo " default: assets/multiqc/deseq2_clustering_header.txt"
echo ""
echo " --deseq2_vst"
echo " --vst"
echo " type: boolean"
echo " default: true"
echo " Use vst transformation instead of rlog with DESeq2"
echo " default: false"
echo " Use vst transformation instead of rlog with .DESeq2"
echo ""
echo " --extra_args"
echo " type: string"
echo " default: --id_col 1 --sample_suffix '' --outprefix deseq2 --count_col 3"
echo " --count_col"
echo " type: integer"
echo " default: 3"
echo " First column containing sample count data."
echo ""
echo " --extra_args2"
echo " --id_col"
echo " type: integer"
echo " default: 1"
echo " Column containing identifiers to be used."
echo ""
echo " --sample_suffix"
echo " type: string"
echo " default: star_salmon"
echo " default:"
echo " Suffix to remove after sample name in columns e.g. '.rmDup.bam' if"
echo " 'DRUG_R1.rmDup.bam'."
echo ""
echo " --outprefix"
echo " type: string"
echo " default: deseq2"
echo " Output prefix"
echo ""
echo " --label"
echo " type: string"
echo " Label to used in MultiQC report"
echo ""
echo "Output:"
echo " --deseq2_output"
echo " --outdir"
echo " type: file, output, file must exist"
echo " default: deseq2"
echo ""
@@ -211,7 +220,7 @@ function ViashHelp {
echo " type: file, output, file must exist"
echo " default: deseq2.pca.vals_mqc.tsv"
echo ""
echo " --dists_multiqc"
echo " --sample_dists_multiqc"
echo " type: file, output, file must exist"
echo " default: deseq2.sample.dists_mqc.tsv"
}
@@ -489,22 +498,18 @@ function ViashDockerfile {
if [[ "$engine_id" == "docker" ]]; then
cat << 'VIASHDOCKER'
FROM ubuntu:22.04
FROM rocker/r2u:22.04
ENTRYPOINT []
RUN apt-get update && \
DEBIAN_FRONTEND=noninteractive apt-get install -y r-base libcurl4-openssl-dev libssl-dev libxml2-dev && \
rm -rf /var/lib/apt/lists/*
RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")' && \
Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")' && \
Rscript -e 'if (!requireNamespace("DESeq2", quietly = TRUE)) BiocManager::install("DESeq2")' && \
Rscript -e 'remotes::install_cran(c("optparse", "ggplot2", "RColorBrewer", "pheatmap"), repos = "https://cran.rstudio.com")' && \
Rscript -e 'remotes::install_cran(c("optparse", "ggplot2", "RColorBrewer", "pheatmap", "stringr"), repos = "https://cran.rstudio.com")' && \
Rscript -e 'remotes::install_url(c("https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz"), repos = "https://cran.rstudio.com")'
LABEL org.opencontainers.image.description="Companion container for running component deseq2_qc"
LABEL org.opencontainers.image.created="2024-10-04T07:06:31Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
LABEL org.opencontainers.image.created="2024-10-25T08:58:45Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -655,70 +660,81 @@ while [[ $# -gt 0 ]]; do
VIASH_PAR_COUNTS=$(ViashRemoveFlags "$1")
shift 1
;;
--pca_header_multiqc)
[ -n "$VIASH_PAR_PCA_HEADER_MULTIQC" ] && ViashError Bad arguments for option \'--pca_header_multiqc\': \'$VIASH_PAR_PCA_HEADER_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_PCA_HEADER_MULTIQC="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --pca_header_multiqc. Use "--help" to get more information on the parameters. && exit 1
--vst)
[ -n "$VIASH_PAR_VST" ] && ViashError Bad arguments for option \'--vst\': \'$VIASH_PAR_VST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_VST="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --vst. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--pca_header_multiqc=*)
[ -n "$VIASH_PAR_PCA_HEADER_MULTIQC" ] && ViashError Bad arguments for option \'--pca_header_multiqc=*\': \'$VIASH_PAR_PCA_HEADER_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_PCA_HEADER_MULTIQC=$(ViashRemoveFlags "$1")
--vst=*)
[ -n "$VIASH_PAR_VST" ] && ViashError Bad arguments for option \'--vst=*\': \'$VIASH_PAR_VST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_VST=$(ViashRemoveFlags "$1")
shift 1
;;
--clustering_header_multiqc)
[ -n "$VIASH_PAR_CLUSTERING_HEADER_MULTIQC" ] && ViashError Bad arguments for option \'--clustering_header_multiqc\': \'$VIASH_PAR_CLUSTERING_HEADER_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_CLUSTERING_HEADER_MULTIQC="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --clustering_header_multiqc. Use "--help" to get more information on the parameters. && exit 1
--count_col)
[ -n "$VIASH_PAR_COUNT_COL" ] && ViashError Bad arguments for option \'--count_col\': \'$VIASH_PAR_COUNT_COL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_COUNT_COL="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --count_col. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--clustering_header_multiqc=*)
[ -n "$VIASH_PAR_CLUSTERING_HEADER_MULTIQC" ] && ViashError Bad arguments for option \'--clustering_header_multiqc=*\': \'$VIASH_PAR_CLUSTERING_HEADER_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_CLUSTERING_HEADER_MULTIQC=$(ViashRemoveFlags "$1")
--count_col=*)
[ -n "$VIASH_PAR_COUNT_COL" ] && ViashError Bad arguments for option \'--count_col=*\': \'$VIASH_PAR_COUNT_COL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_COUNT_COL=$(ViashRemoveFlags "$1")
shift 1
;;
--deseq2_vst)
[ -n "$VIASH_PAR_DESEQ2_VST" ] && ViashError Bad arguments for option \'--deseq2_vst\': \'$VIASH_PAR_DESEQ2_VST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_DESEQ2_VST="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --deseq2_vst. Use "--help" to get more information on the parameters. && exit 1
--id_col)
[ -n "$VIASH_PAR_ID_COL" ] && ViashError Bad arguments for option \'--id_col\': \'$VIASH_PAR_ID_COL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_ID_COL="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --id_col. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--deseq2_vst=*)
[ -n "$VIASH_PAR_DESEQ2_VST" ] && ViashError Bad arguments for option \'--deseq2_vst=*\': \'$VIASH_PAR_DESEQ2_VST\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_DESEQ2_VST=$(ViashRemoveFlags "$1")
--id_col=*)
[ -n "$VIASH_PAR_ID_COL" ] && ViashError Bad arguments for option \'--id_col=*\': \'$VIASH_PAR_ID_COL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_ID_COL=$(ViashRemoveFlags "$1")
shift 1
;;
--extra_args)
[ -n "$VIASH_PAR_EXTRA_ARGS" ] && ViashError Bad arguments for option \'--extra_args\': \'$VIASH_PAR_EXTRA_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_EXTRA_ARGS="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_args. Use "--help" to get more information on the parameters. && exit 1
--sample_suffix)
[ -n "$VIASH_PAR_SAMPLE_SUFFIX" ] && ViashError Bad arguments for option \'--sample_suffix\': \'$VIASH_PAR_SAMPLE_SUFFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SAMPLE_SUFFIX="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --sample_suffix. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--extra_args=*)
[ -n "$VIASH_PAR_EXTRA_ARGS" ] && ViashError Bad arguments for option \'--extra_args=*\': \'$VIASH_PAR_EXTRA_ARGS\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_EXTRA_ARGS=$(ViashRemoveFlags "$1")
--sample_suffix=*)
[ -n "$VIASH_PAR_SAMPLE_SUFFIX" ] && ViashError Bad arguments for option \'--sample_suffix=*\': \'$VIASH_PAR_SAMPLE_SUFFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SAMPLE_SUFFIX=$(ViashRemoveFlags "$1")
shift 1
;;
--extra_args2)
[ -n "$VIASH_PAR_EXTRA_ARGS2" ] && ViashError Bad arguments for option \'--extra_args2\': \'$VIASH_PAR_EXTRA_ARGS2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_EXTRA_ARGS2="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --extra_args2. Use "--help" to get more information on the parameters. && exit 1
--outprefix)
[ -n "$VIASH_PAR_OUTPREFIX" ] && ViashError Bad arguments for option \'--outprefix\': \'$VIASH_PAR_OUTPREFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_OUTPREFIX="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --outprefix. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--extra_args2=*)
[ -n "$VIASH_PAR_EXTRA_ARGS2" ] && ViashError Bad arguments for option \'--extra_args2=*\': \'$VIASH_PAR_EXTRA_ARGS2\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_EXTRA_ARGS2=$(ViashRemoveFlags "$1")
--outprefix=*)
[ -n "$VIASH_PAR_OUTPREFIX" ] && ViashError Bad arguments for option \'--outprefix=*\': \'$VIASH_PAR_OUTPREFIX\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_OUTPREFIX=$(ViashRemoveFlags "$1")
shift 1
;;
--deseq2_output)
[ -n "$VIASH_PAR_DESEQ2_OUTPUT" ] && ViashError Bad arguments for option \'--deseq2_output\': \'$VIASH_PAR_DESEQ2_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_DESEQ2_OUTPUT="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --deseq2_output. Use "--help" to get more information on the parameters. && exit 1
--label)
[ -n "$VIASH_PAR_LABEL" ] && ViashError Bad arguments for option \'--label\': \'$VIASH_PAR_LABEL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_LABEL="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --label. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--deseq2_output=*)
[ -n "$VIASH_PAR_DESEQ2_OUTPUT" ] && ViashError Bad arguments for option \'--deseq2_output=*\': \'$VIASH_PAR_DESEQ2_OUTPUT\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_DESEQ2_OUTPUT=$(ViashRemoveFlags "$1")
--label=*)
[ -n "$VIASH_PAR_LABEL" ] && ViashError Bad arguments for option \'--label=*\': \'$VIASH_PAR_LABEL\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_LABEL=$(ViashRemoveFlags "$1")
shift 1
;;
--outdir)
[ -n "$VIASH_PAR_OUTDIR" ] && ViashError Bad arguments for option \'--outdir\': \'$VIASH_PAR_OUTDIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_OUTDIR="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --outdir. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--outdir=*)
[ -n "$VIASH_PAR_OUTDIR" ] && ViashError Bad arguments for option \'--outdir=*\': \'$VIASH_PAR_OUTDIR\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_OUTDIR=$(ViashRemoveFlags "$1")
shift 1
;;
--pca_multiqc)
@@ -732,15 +748,15 @@ while [[ $# -gt 0 ]]; do
VIASH_PAR_PCA_MULTIQC=$(ViashRemoveFlags "$1")
shift 1
;;
--dists_multiqc)
[ -n "$VIASH_PAR_DISTS_MULTIQC" ] && ViashError Bad arguments for option \'--dists_multiqc\': \'$VIASH_PAR_DISTS_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_DISTS_MULTIQC="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --dists_multiqc. Use "--help" to get more information on the parameters. && exit 1
--sample_dists_multiqc)
[ -n "$VIASH_PAR_SAMPLE_DISTS_MULTIQC" ] && ViashError Bad arguments for option \'--sample_dists_multiqc\': \'$VIASH_PAR_SAMPLE_DISTS_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SAMPLE_DISTS_MULTIQC="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --sample_dists_multiqc. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--dists_multiqc=*)
[ -n "$VIASH_PAR_DISTS_MULTIQC" ] && ViashError Bad arguments for option \'--dists_multiqc=*\': \'$VIASH_PAR_DISTS_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_DISTS_MULTIQC=$(ViashRemoveFlags "$1")
--sample_dists_multiqc=*)
[ -n "$VIASH_PAR_SAMPLE_DISTS_MULTIQC" ] && ViashError Bad arguments for option \'--sample_dists_multiqc=*\': \'$VIASH_PAR_SAMPLE_DISTS_MULTIQC\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_SAMPLE_DISTS_MULTIQC=$(ViashRemoveFlags "$1")
shift 1
;;
---engine)
@@ -831,7 +847,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/deseq2_qc:main'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/deseq2_qc:main'
fi
# print dockerfile
@@ -915,6 +931,10 @@ fi
# check whether required parameters exist
if [ -z ${VIASH_PAR_COUNTS+x} ]; then
ViashError '--counts' is a required argument. Use "--help" to get more information on the parameters.
exit 1
fi
if [ -z ${VIASH_META_NAME+x} ]; then
ViashError 'name' is a required argument. Use "--help" to get more information on the parameters.
exit 1
@@ -941,29 +961,29 @@ if [ -z ${VIASH_META_TEMP_DIR+x} ]; then
fi
# filling in defaults
if [ -z ${VIASH_PAR_PCA_HEADER_MULTIQC+x} ]; then
VIASH_PAR_PCA_HEADER_MULTIQC="assets/multiqc/deseq2_pca_header.txt"
if [ -z ${VIASH_PAR_VST+x} ]; then
VIASH_PAR_VST="false"
fi
if [ -z ${VIASH_PAR_CLUSTERING_HEADER_MULTIQC+x} ]; then
VIASH_PAR_CLUSTERING_HEADER_MULTIQC="assets/multiqc/deseq2_clustering_header.txt"
if [ -z ${VIASH_PAR_COUNT_COL+x} ]; then
VIASH_PAR_COUNT_COL="3"
fi
if [ -z ${VIASH_PAR_DESEQ2_VST+x} ]; then
VIASH_PAR_DESEQ2_VST="true"
if [ -z ${VIASH_PAR_ID_COL+x} ]; then
VIASH_PAR_ID_COL="1"
fi
if [ -z ${VIASH_PAR_EXTRA_ARGS+x} ]; then
VIASH_PAR_EXTRA_ARGS="--id_col 1 --sample_suffix '' --outprefix deseq2 --count_col 3"
if [ -z ${VIASH_PAR_SAMPLE_SUFFIX+x} ]; then
VIASH_PAR_SAMPLE_SUFFIX=""
fi
if [ -z ${VIASH_PAR_EXTRA_ARGS2+x} ]; then
VIASH_PAR_EXTRA_ARGS2="star_salmon"
if [ -z ${VIASH_PAR_OUTPREFIX+x} ]; then
VIASH_PAR_OUTPREFIX="deseq2"
fi
if [ -z ${VIASH_PAR_DESEQ2_OUTPUT+x} ]; then
VIASH_PAR_DESEQ2_OUTPUT="deseq2"
if [ -z ${VIASH_PAR_OUTDIR+x} ]; then
VIASH_PAR_OUTDIR="deseq2"
fi
if [ -z ${VIASH_PAR_PCA_MULTIQC+x} ]; then
VIASH_PAR_PCA_MULTIQC="deseq2.pca.vals_mqc.tsv"
fi
if [ -z ${VIASH_PAR_DISTS_MULTIQC+x} ]; then
VIASH_PAR_DISTS_MULTIQC="deseq2.sample.dists_mqc.tsv"
if [ -z ${VIASH_PAR_SAMPLE_DISTS_MULTIQC+x} ]; then
VIASH_PAR_SAMPLE_DISTS_MULTIQC="deseq2.sample.dists_mqc.tsv"
fi
# check whether required files exist
@@ -971,19 +991,23 @@ if [ ! -z "$VIASH_PAR_COUNTS" ] && [ ! -e "$VIASH_PAR_COUNTS" ]; then
ViashError "Input file '$VIASH_PAR_COUNTS' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_PCA_HEADER_MULTIQC" ] && [ ! -e "$VIASH_PAR_PCA_HEADER_MULTIQC" ]; then
ViashError "Input file '$VIASH_PAR_PCA_HEADER_MULTIQC' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_CLUSTERING_HEADER_MULTIQC" ] && [ ! -e "$VIASH_PAR_CLUSTERING_HEADER_MULTIQC" ]; then
ViashError "Input file '$VIASH_PAR_CLUSTERING_HEADER_MULTIQC' does not exist."
exit 1
fi
# check whether parameters values are of the right type
if [[ -n "$VIASH_PAR_DESEQ2_VST" ]]; then
if ! [[ "$VIASH_PAR_DESEQ2_VST" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--deseq2_vst' has to be a boolean. Use "--help" to get more information on the parameters.
if [[ -n "$VIASH_PAR_VST" ]]; then
if ! [[ "$VIASH_PAR_VST" =~ ^(true|True|TRUE|false|False|FALSE|yes|Yes|YES|no|No|NO)$ ]]; then
ViashError '--vst' has to be a boolean. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_COUNT_COL" ]]; then
if ! [[ "$VIASH_PAR_COUNT_COL" =~ ^[-+]?[0-9]+$ ]]; then
ViashError '--count_col' has to be an integer. Use "--help" to get more information on the parameters.
exit 1
fi
fi
if [[ -n "$VIASH_PAR_ID_COL" ]]; then
if ! [[ "$VIASH_PAR_ID_COL" =~ ^[-+]?[0-9]+$ ]]; then
ViashError '--id_col' has to be an integer. Use "--help" to get more information on the parameters.
exit 1
fi
fi
@@ -1061,14 +1085,14 @@ if [[ -n "$VIASH_META_MEMORY_PIB" ]]; then
fi
# create parent directories of output files, if so desired
if [ ! -z "$VIASH_PAR_DESEQ2_OUTPUT" ] && [ ! -d "$(dirname "$VIASH_PAR_DESEQ2_OUTPUT")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_DESEQ2_OUTPUT")"
if [ ! -z "$VIASH_PAR_OUTDIR" ] && [ ! -d "$(dirname "$VIASH_PAR_OUTDIR")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_OUTDIR")"
fi
if [ ! -z "$VIASH_PAR_PCA_MULTIQC" ] && [ ! -d "$(dirname "$VIASH_PAR_PCA_MULTIQC")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_PCA_MULTIQC")"
fi
if [ ! -z "$VIASH_PAR_DISTS_MULTIQC" ] && [ ! -d "$(dirname "$VIASH_PAR_DISTS_MULTIQC")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_DISTS_MULTIQC")"
if [ ! -z "$VIASH_PAR_SAMPLE_DISTS_MULTIQC" ] && [ ! -d "$(dirname "$VIASH_PAR_SAMPLE_DISTS_MULTIQC")" ]; then
mkdir -p "$(dirname "$VIASH_PAR_SAMPLE_DISTS_MULTIQC")"
fi
if [ "$VIASH_ENGINE_ID" == "native" ] ; then
@@ -1087,28 +1111,20 @@ if [ ! -z "$VIASH_PAR_COUNTS" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_COUNTS")" )
VIASH_PAR_COUNTS=$(ViashDockerAutodetectMount "$VIASH_PAR_COUNTS")
fi
if [ ! -z "$VIASH_PAR_PCA_HEADER_MULTIQC" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_PCA_HEADER_MULTIQC")" )
VIASH_PAR_PCA_HEADER_MULTIQC=$(ViashDockerAutodetectMount "$VIASH_PAR_PCA_HEADER_MULTIQC")
fi
if [ ! -z "$VIASH_PAR_CLUSTERING_HEADER_MULTIQC" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_CLUSTERING_HEADER_MULTIQC")" )
VIASH_PAR_CLUSTERING_HEADER_MULTIQC=$(ViashDockerAutodetectMount "$VIASH_PAR_CLUSTERING_HEADER_MULTIQC")
fi
if [ ! -z "$VIASH_PAR_DESEQ2_OUTPUT" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_DESEQ2_OUTPUT")" )
VIASH_PAR_DESEQ2_OUTPUT=$(ViashDockerAutodetectMount "$VIASH_PAR_DESEQ2_OUTPUT")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_DESEQ2_OUTPUT" )
if [ ! -z "$VIASH_PAR_OUTDIR" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_OUTDIR")" )
VIASH_PAR_OUTDIR=$(ViashDockerAutodetectMount "$VIASH_PAR_OUTDIR")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_OUTDIR" )
fi
if [ ! -z "$VIASH_PAR_PCA_MULTIQC" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_PCA_MULTIQC")" )
VIASH_PAR_PCA_MULTIQC=$(ViashDockerAutodetectMount "$VIASH_PAR_PCA_MULTIQC")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_PCA_MULTIQC" )
fi
if [ ! -z "$VIASH_PAR_DISTS_MULTIQC" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_DISTS_MULTIQC")" )
VIASH_PAR_DISTS_MULTIQC=$(ViashDockerAutodetectMount "$VIASH_PAR_DISTS_MULTIQC")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_DISTS_MULTIQC" )
if [ ! -z "$VIASH_PAR_SAMPLE_DISTS_MULTIQC" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_SAMPLE_DISTS_MULTIQC")" )
VIASH_PAR_SAMPLE_DISTS_MULTIQC=$(ViashDockerAutodetectMount "$VIASH_PAR_SAMPLE_DISTS_MULTIQC")
VIASH_CHOWN_VARS+=( "$VIASH_PAR_SAMPLE_DISTS_MULTIQC" )
fi
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_META_RESOURCES_DIR")" )
@@ -1166,7 +1182,7 @@ fi
ViashDebug "Running command: $(echo $VIASH_CMD)"
cat << VIASHEOF | eval $VIASH_CMD
set -e
tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-deseq2_qc-XXXXXX").sh
tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-deseq2_qc-XXXXXX").R
function clean_up {
rm "\$tempscript"
}
@@ -1179,85 +1195,269 @@ trap interrupt INT SIGINT
cat > "\$tempscript" << 'VIASHMAIN'
## VIASH START
# The following code has been auto-generated by Viash.
$( if [ ! -z ${VIASH_PAR_COUNTS+x} ]; then echo "${VIASH_PAR_COUNTS}" | sed "s#'#'\"'\"'#g;s#.*#par_counts='&'#" ; else echo "# par_counts="; fi )
$( if [ ! -z ${VIASH_PAR_PCA_HEADER_MULTIQC+x} ]; then echo "${VIASH_PAR_PCA_HEADER_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_pca_header_multiqc='&'#" ; else echo "# par_pca_header_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_CLUSTERING_HEADER_MULTIQC+x} ]; then echo "${VIASH_PAR_CLUSTERING_HEADER_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_clustering_header_multiqc='&'#" ; else echo "# par_clustering_header_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_DESEQ2_VST+x} ]; then echo "${VIASH_PAR_DESEQ2_VST}" | sed "s#'#'\"'\"'#g;s#.*#par_deseq2_vst='&'#" ; else echo "# par_deseq2_vst="; fi )
$( if [ ! -z ${VIASH_PAR_EXTRA_ARGS+x} ]; then echo "${VIASH_PAR_EXTRA_ARGS}" | sed "s#'#'\"'\"'#g;s#.*#par_extra_args='&'#" ; else echo "# par_extra_args="; fi )
$( if [ ! -z ${VIASH_PAR_EXTRA_ARGS2+x} ]; then echo "${VIASH_PAR_EXTRA_ARGS2}" | sed "s#'#'\"'\"'#g;s#.*#par_extra_args2='&'#" ; else echo "# par_extra_args2="; fi )
$( if [ ! -z ${VIASH_PAR_DESEQ2_OUTPUT+x} ]; then echo "${VIASH_PAR_DESEQ2_OUTPUT}" | sed "s#'#'\"'\"'#g;s#.*#par_deseq2_output='&'#" ; else echo "# par_deseq2_output="; fi )
$( if [ ! -z ${VIASH_PAR_PCA_MULTIQC+x} ]; then echo "${VIASH_PAR_PCA_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_pca_multiqc='&'#" ; else echo "# par_pca_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_DISTS_MULTIQC+x} ]; then echo "${VIASH_PAR_DISTS_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_dists_multiqc='&'#" ; else echo "# par_dists_multiqc="; fi )
$( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
$( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi )
$( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi )
$( if [ ! -z ${VIASH_META_EXECUTABLE+x} ]; then echo "${VIASH_META_EXECUTABLE}" | sed "s#'#'\"'\"'#g;s#.*#meta_executable='&'#" ; else echo "# meta_executable="; fi )
$( if [ ! -z ${VIASH_META_CONFIG+x} ]; then echo "${VIASH_META_CONFIG}" | sed "s#'#'\"'\"'#g;s#.*#meta_config='&'#" ; else echo "# meta_config="; fi )
$( if [ ! -z ${VIASH_META_TEMP_DIR+x} ]; then echo "${VIASH_META_TEMP_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_temp_dir='&'#" ; else echo "# meta_temp_dir="; fi )
$( if [ ! -z ${VIASH_META_CPUS+x} ]; then echo "${VIASH_META_CPUS}" | sed "s#'#'\"'\"'#g;s#.*#meta_cpus='&'#" ; else echo "# meta_cpus="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_B+x} ]; then echo "${VIASH_META_MEMORY_B}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_b='&'#" ; else echo "# meta_memory_b="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_KB+x} ]; then echo "${VIASH_META_MEMORY_KB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_kb='&'#" ; else echo "# meta_memory_kb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_MB+x} ]; then echo "${VIASH_META_MEMORY_MB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_mb='&'#" ; else echo "# meta_memory_mb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_GB+x} ]; then echo "${VIASH_META_MEMORY_GB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_gb='&'#" ; else echo "# meta_memory_gb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_TB+x} ]; then echo "${VIASH_META_MEMORY_TB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_tb='&'#" ; else echo "# meta_memory_tb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_PB+x} ]; then echo "${VIASH_META_MEMORY_PB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pb='&'#" ; else echo "# meta_memory_pb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_KIB+x} ]; then echo "${VIASH_META_MEMORY_KIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_kib='&'#" ; else echo "# meta_memory_kib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_MIB+x} ]; then echo "${VIASH_META_MEMORY_MIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_mib='&'#" ; else echo "# meta_memory_mib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_GIB+x} ]; then echo "${VIASH_META_MEMORY_GIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_gib='&'#" ; else echo "# meta_memory_gib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "${VIASH_META_MEMORY_TIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_tib='&'#" ; else echo "# meta_memory_tib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pib='&'#" ; else echo "# meta_memory_pib="; fi )
# treat warnings as errors
.viash_orig_warn <- options(warn = 2)
par <- list(
"counts" = $( if [ ! -z ${VIASH_PAR_COUNTS+x} ]; then echo -n "'"; echo -n "$VIASH_PAR_COUNTS" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
"vst" = $( if [ ! -z ${VIASH_PAR_VST+x} ]; then echo -n "as.logical(toupper('"; echo -n "$VIASH_PAR_VST" | sed "s#['\\]#\\\\&#g"; echo "'))"; else echo NULL; fi ),
"count_col" = $( if [ ! -z ${VIASH_PAR_COUNT_COL+x} ]; then echo -n "as.integer('"; echo -n "$VIASH_PAR_COUNT_COL" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
"id_col" = $( if [ ! -z ${VIASH_PAR_ID_COL+x} ]; then echo -n "as.integer('"; echo -n "$VIASH_PAR_ID_COL" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
"sample_suffix" = $( if [ ! -z ${VIASH_PAR_SAMPLE_SUFFIX+x} ]; then echo -n "'"; echo -n "$VIASH_PAR_SAMPLE_SUFFIX" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
"outprefix" = $( if [ ! -z ${VIASH_PAR_OUTPREFIX+x} ]; then echo -n "'"; echo -n "$VIASH_PAR_OUTPREFIX" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
"label" = $( if [ ! -z ${VIASH_PAR_LABEL+x} ]; then echo -n "'"; echo -n "$VIASH_PAR_LABEL" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
"outdir" = $( if [ ! -z ${VIASH_PAR_OUTDIR+x} ]; then echo -n "'"; echo -n "$VIASH_PAR_OUTDIR" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
"pca_multiqc" = $( if [ ! -z ${VIASH_PAR_PCA_MULTIQC+x} ]; then echo -n "'"; echo -n "$VIASH_PAR_PCA_MULTIQC" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
"sample_dists_multiqc" = $( if [ ! -z ${VIASH_PAR_SAMPLE_DISTS_MULTIQC+x} ]; then echo -n "'"; echo -n "$VIASH_PAR_SAMPLE_DISTS_MULTIQC" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi )
)
meta <- list(
"name" = $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo -n "'"; echo -n "$VIASH_META_NAME" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
"functionality_name" = $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo -n "'"; echo -n "$VIASH_META_FUNCTIONALITY_NAME" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
"resources_dir" = $( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo -n "'"; echo -n "$VIASH_META_RESOURCES_DIR" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
"executable" = $( if [ ! -z ${VIASH_META_EXECUTABLE+x} ]; then echo -n "'"; echo -n "$VIASH_META_EXECUTABLE" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
"config" = $( if [ ! -z ${VIASH_META_CONFIG+x} ]; then echo -n "'"; echo -n "$VIASH_META_CONFIG" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
"temp_dir" = $( if [ ! -z ${VIASH_META_TEMP_DIR+x} ]; then echo -n "'"; echo -n "$VIASH_META_TEMP_DIR" | sed "s#['\\]#\\\\&#g"; echo "'"; else echo NULL; fi ),
"cpus" = $( if [ ! -z ${VIASH_META_CPUS+x} ]; then echo -n "as.integer('"; echo -n "$VIASH_META_CPUS" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
"memory_b" = $( if [ ! -z ${VIASH_META_MEMORY_B+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_B" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
"memory_kb" = $( if [ ! -z ${VIASH_META_MEMORY_KB+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_KB" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
"memory_mb" = $( if [ ! -z ${VIASH_META_MEMORY_MB+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_MB" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
"memory_gb" = $( if [ ! -z ${VIASH_META_MEMORY_GB+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_GB" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
"memory_tb" = $( if [ ! -z ${VIASH_META_MEMORY_TB+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_TB" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
"memory_pb" = $( if [ ! -z ${VIASH_META_MEMORY_PB+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_PB" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
"memory_kib" = $( if [ ! -z ${VIASH_META_MEMORY_KIB+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_KIB" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
"memory_mib" = $( if [ ! -z ${VIASH_META_MEMORY_MIB+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_MIB" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
"memory_gib" = $( if [ ! -z ${VIASH_META_MEMORY_GIB+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_GIB" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
"memory_tib" = $( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_TIB" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi ),
"memory_pib" = $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo -n "bit64::as.integer64('"; echo -n "$VIASH_META_MEMORY_PIB" | sed "s#['\\]#\\\\&#g"; echo "')"; else echo NULL; fi )
)
dep <- list(
)
# restore original warn setting
options(.viash_orig_warn)
rm(.viash_orig_warn)
## VIASH END
#!/bin/sh
set -eo pipefail
# REQUIREMENTS
if \$par_deseq2_vst; then
par_extra_args+=" --vst TRUE"
fi
## PCA, HEATMAP AND SCATTERPLOTS FOR SAMPLES IN COUNTS FILE
## - SAMPLE NAMES HAVE TO END IN e.g. "_R1" REPRESENTING REPLICATE ID. LAST 3 CHARACTERS OF SAMPLE NAME WILL BE TRIMMED TO OBTAIN GROUP ID FOR DESEQ2 COMPARISONS.
tolower() {
case \$1 in
*[[:upper:]]*)
printf "%s\\n" "\$1" | tr '[:upper:]' '[:lower:]'
;;
*)
printf "%s\\n" "\$1"
;;
esac
# LOAD LIBRARIES
library(DESeq2)
library(ggplot2)
library(RColorBrewer)
library(pheatmap)
library(stringr)
if (file.exists(par\$outdir) == FALSE) {
dir.create(par\$outdir, recursive = TRUE)
}
toupper() {
case \$1 in
*[[:lower:]]*)
printf "%s\\n" "\$1" | tr '[:lower:]' '[:upper:]'
;;
*)
printf "%s\\n" "\$1"
;;
esac
# READ IN COUNTS FILE
count_table <- read.delim(file = par\$counts, header = TRUE, row.names = NULL)
rownames(count_table) <- count_table[, par\$id_col]
count_table <- count_table[, par\$count_col:ncol(count_table), drop = FALSE]
colnames(count_table) <- gsub(par\$sample_suffix, "", colnames(count_table))
colnames(count_table) <- gsub(pattern = '\\\\.\$', replacement = '', colnames(count_table))
# RUN DESEQ2
samples_vec <- colnames(count_table)
name_components <- strsplit(samples_vec, "_")
n_components <- length(name_components[[1]])
decompose <- n_components != 1 && all(sapply(name_components, length) == n_components)
coldata <- data.frame(samples_vec, sample = samples_vec, row.names = 1)
if (decompose) {
groupings <- as.data.frame(lapply(1:n_components, function(i) sapply(name_components, "[[", i)))
n_distinct <- sapply(groupings, function(grp) length(unique(grp)))
groupings <- groupings[n_distinct != 1 & n_distinct != length(samples_vec)]
if (ncol(groupings) != 0) {
names(groupings) <- paste0("Group", 1:ncol(groupings))
coldata <- cbind(coldata, groupings)
} else {
decompose <- FALSE
}
}
label_lower=\$(tolower "\$par_extra_args2")
label_upper=\$(toupper "\$par_extra_args2")
DDSFile <- paste(par\$outdir, "/", par\$outprefix, ".dds.RData", sep = "")
Rscript "\$meta_resources_dir/deseq2_qc.r" \\
--count_file \$par_counts \\
--outdir \$par_deseq2_output \\
--cores \${meta_cpus:-1} \\
\$par_extra_args
counts <- count_table[, samples_vec, drop = FALSE]
dds <- DESeqDataSetFromMatrix(countData = round(counts), colData = coldata, design = ~1)
dds <- estimateSizeFactors(dds)
if [ -f "\$par_deseq2_output/R_sessionInfo.log" ]; then
sed "s/deseq2_pca/\${label_lower}_deseq2_pca/g" < \$par_pca_header_multiqc > tmp.txt
sed -i -e "s/DESeq2 PCA/\${label_upper} DESeq2 PCA/g" tmp.txt
cat tmp.txt \$par_deseq2_output/*.pca.vals.txt > \$par_pca_multiqc
# No point if only one sample, or one gene
if (min(dim(count_table)) <= 1) {
save(dds, file = DDSFile)
saveRDS(dds, file = sub("\\\\.dds\\\\.RData\$", ".rds", DDSFile))
warning("Not enough samples or genes in counts file for PCA.", call. = FALSE)
quit(save = "no", status = 0, runLast = FALSE)
}
sed "s/deseq2_clustering/\${label_lower}_deseq2_clustering/g" < \$par_clustering_header_multiqc > tmp.txt
sed -i -e "s/DESeq2 sample/\${label_upper} DESeq2 sample/g" tmp.txt
cat tmp.txt \$par_deseq2_output/*.sample.dists.txt > \$par_dists_multiqc
fi
if (!par\$vst) {
vst_name <- "rlog"
rld <- rlog(dds)
} else {
vst_name <- "vst"
rld <- varianceStabilizingTransformation(dds)
}
assay(dds, vst_name) <- assay(rld)
save(dds, file = DDSFile)
saveRDS(dds, file = sub("\\\\.dds\\\\.RData\$", ".rds", DDSFile))
# PLOT QC
##' PCA pre-processeor
##'
##' Generate all the necessary information to plot PCA from a DESeq2 object
##' in which an assay containing a variance-stabilised matrix of counts is
##' stored. Copied from DESeq2::plotPCA, but with additional ability to
##' say which assay to run the PCA on.
##'
##' @param object The DESeq2DataSet object.
##' @param ntop number of top genes to use for principla components, selected by highest row variance.
##' @param assay the name or index of the assay that stores the variance-stabilised data.
##' @return A data.frame containing the projected data alongside the grouping columns.
##' A 'percentVar' attribute is set which includes the percentage of variation each PC explains,
##' and additionally how much the variation within that PC is explained by the grouping variable.
##' @author Gavin Kelly
plotPCA_vst <- function(object, ntop = 500, assay = length(assays(object))) {
rv <- rowVars(assay(object, assay))
select <- order(rv, decreasing = TRUE)[seq_len(min(ntop, length(rv)))]
pca <- prcomp(t(assay(object, assay)[select, ]), center = TRUE, scale = FALSE)
percentVar <- pca\$sdev^2 / sum(pca\$sdev^2)
df <- cbind(as.data.frame(colData(object)), pca\$x)
# Order points so extreme samples are more likely to get label
ord <- order(abs(rank(df\$PC1) - median(df\$PC1)), abs(rank(df\$PC2) - median(df\$PC2)))
df <- df[ord, ]
attr(df, "percentVar") <- data.frame(PC = seq(along = percentVar), percentVar = 100 * percentVar)
return(df)
}
PlotFile <- paste(par\$outdir, "/", par\$outprefix, ".plots.pdf", sep = "")
pdf(file = PlotFile, onefile = TRUE, width = 7, height = 7)
## PCA
ntop <- c(500, Inf)
for (n_top_var in ntop) {
pca_data <- plotPCA_vst(dds, assay = vst_name, ntop = n_top_var)
percentVar <- round(attr(pca_data, "percentVar")\$percentVar)
plot_subtitle <- ifelse(n_top_var == Inf, "All genes", paste("Top", n_top_var, "genes"))
pl <- ggplot(pca_data, aes(PC1, PC2, label = paste0(" ", sample, " "))) +
geom_point() +
geom_text(check_overlap = TRUE, vjust = 0.5, hjust="inward") +
xlab(paste0("PC1: ", percentVar[1], "% variance")) +
ylab(paste0("PC2: ", percentVar[2], "% variance")) +
labs(title = paste0("First PCs on ", vst_name, "-transformed data"), subtitle = plot_subtitle) +
theme(legend.position = "top",
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_blank(),
panel.border = element_rect(colour = "black", fill = NA, size = 1))
print(pl)
if (decompose) {
pc_names <- paste0("PC", attr(pca_data, "percentVar")\$PC)
long_pc <- reshape(pca_data, varying=pc_names, direction="long", sep="", timevar="component", idvar="pcrow")
long_pc <- subset(long_pc, component <= 5)
long_pc_grp <- reshape(long_pc, varying = names(groupings), direction = "long", sep = "", timevar = "grouper")
long_pc_grp <- subset(long_pc_grp, grouper <= 5)
long_pc_grp\$component <- paste("PC", long_pc_grp\$component)
long_pc_grp\$grouper <- paste0(long_pc_grp\$grouper, c("st", "nd", "rd", "th", "th")[long_pc_grp\$grouper], " prefix")
pl <- ggplot(long_pc_grp, aes(x = Group, y = PC)) +
geom_point() +
stat_summary(fun = mean, geom = "line", aes(group = 1)) +
labs(x = NULL, y = NULL, subtitle = plot_subtitle, title = "PCs split by sample-name prefixes") +
facet_grid(component ~ grouper, scales = "free_x") +
scale_x_discrete(guide = guide_axis(n.dodge = 3))
print(pl)
}
} # at end of loop, we'll be using the user-defined ntop if any, else all genes
## WRITE PC1 vs PC2 VALUES TO FILE
pca_vals <- pca_data[, c("PC1", "PC2")]
colnames(pca_vals) <- paste0(colnames(pca_vals), ": ", percentVar[1:2], '% variance')
pca_vals <- cbind(sample = rownames(pca_vals), pca_vals)
pca_vals_file <- paste(par\$outdir, "/", par\$outprefix, ".pca_vals.txt", sep = "")
write.table(pca_vals, file = pca_vals_file,
row.names = FALSE, col.names = TRUE,
sep = "\\t", quote = TRUE)
## SAMPLE CORRELATION HEATMAP
sampleDists <- dist(t(assay(dds, vst_name)))
sampleDistMatrix <- as.matrix(sampleDists)
colors <- colorRampPalette(rev(brewer.pal(9, "Blues")))(255)
pheatmap(
sampleDistMatrix,
clustering_distance_rows = sampleDists,
clustering_distance_cols = sampleDists,
col = colors,
main = paste("Euclidean distance between", vst_name, "of samples")
)
## WRITE SAMPLE DISTANCES TO FILE
sample_dist_file <- paste(par\$outdir, "/", par\$outprefix, ".sample.dists.txt", sep = "")
write.table(cbind(sample = rownames(sampleDistMatrix), sampleDistMatrix),
file = sample_dist_file, row.names = FALSE,
col.names = TRUE, sep = "\\t", quote = FALSE)
dev.off()
# SAVE SIZE FACTORS
SizeFactorsDir <- paste0(par\$outdir, "/size_factors/")
if (file.exists(SizeFactorsDir) == FALSE) {
dir.create(SizeFactorsDir, recursive = TRUE)
}
NormFactorsFile <- paste(SizeFactorsDir, par\$outprefix, ".size_factors.RData", sep = "")
normFactors <- sizeFactors(dds)
save(normFactors, file = NormFactorsFile)
for (name in names(sizeFactors(dds))) {
sizeFactorFile <- paste(SizeFactorsDir, name, ".txt", sep = "")
write(as.numeric(sizeFactors(dds)[name]), file = sizeFactorFile)
}
# R SESSION INFO
RLogFile <- "R_sessionInfo.log"
sink(RLogFile)
a <- sessionInfo()
print(a)
sink()
# Prepare files for MultiQC
readLines(paste0(meta\$resources_dir, "/deseq2_pca_header.txt")) |>
stringr::str_replace(pattern = "#id: 'deseq2_pca'",
replace = paste0("#id: '", par\$label, "_deseq2_pca'")) |>
writeLines(con = "tmp.txt")
readLines(paste0("tmp.txt")) |>
stringr::str_replace(pattern = "#section_name: 'DESeq2 PCA plot'",
replace = paste0("#section_name: 'DESeq2 PCA plot - '", par\$label)) |>
writeLines(con = "tmp.txt")
system2("cat", args = paste0("tmp.txt ", pca_vals_file), stdout = par\$pca_multiqc)
readLines(paste0(meta\$resources_dir, "/deseq2_clustering_header.txt")) |>
stringr::str_replace(pattern = "#id: 'deseq2_clustering'",
replace = paste0("#id: '", par\$label, "_deseq2_clustering'")) |>
writeLines(con = "tmp.txt")
readLines(paste0("tmp.txt")) |>
stringr::str_replace(pattern = "#section_name: 'DESeq2 sample similarity'",
replace = paste0("#section_name: 'DESeq2 sample similarity - '", par\$label)) |>
writeLines(con = "tmp.txt")
system2("cat", args = paste0("tmp.txt ", sample_dist_file), stdout = par\$sample_dists_multiqc)
VIASHMAIN
bash "\$tempscript" &
Rscript "\$tempscript" &
wait "\$!"
VIASHEOF
@@ -1269,20 +1469,14 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
if [ ! -z "$VIASH_PAR_COUNTS" ]; then
VIASH_PAR_COUNTS=$(ViashDockerStripAutomount "$VIASH_PAR_COUNTS")
fi
if [ ! -z "$VIASH_PAR_PCA_HEADER_MULTIQC" ]; then
VIASH_PAR_PCA_HEADER_MULTIQC=$(ViashDockerStripAutomount "$VIASH_PAR_PCA_HEADER_MULTIQC")
fi
if [ ! -z "$VIASH_PAR_CLUSTERING_HEADER_MULTIQC" ]; then
VIASH_PAR_CLUSTERING_HEADER_MULTIQC=$(ViashDockerStripAutomount "$VIASH_PAR_CLUSTERING_HEADER_MULTIQC")
fi
if [ ! -z "$VIASH_PAR_DESEQ2_OUTPUT" ]; then
VIASH_PAR_DESEQ2_OUTPUT=$(ViashDockerStripAutomount "$VIASH_PAR_DESEQ2_OUTPUT")
if [ ! -z "$VIASH_PAR_OUTDIR" ]; then
VIASH_PAR_OUTDIR=$(ViashDockerStripAutomount "$VIASH_PAR_OUTDIR")
fi
if [ ! -z "$VIASH_PAR_PCA_MULTIQC" ]; then
VIASH_PAR_PCA_MULTIQC=$(ViashDockerStripAutomount "$VIASH_PAR_PCA_MULTIQC")
fi
if [ ! -z "$VIASH_PAR_DISTS_MULTIQC" ]; then
VIASH_PAR_DISTS_MULTIQC=$(ViashDockerStripAutomount "$VIASH_PAR_DISTS_MULTIQC")
if [ ! -z "$VIASH_PAR_SAMPLE_DISTS_MULTIQC" ]; then
VIASH_PAR_SAMPLE_DISTS_MULTIQC=$(ViashDockerStripAutomount "$VIASH_PAR_SAMPLE_DISTS_MULTIQC")
fi
if [ ! -z "$VIASH_META_RESOURCES_DIR" ]; then
VIASH_META_RESOURCES_DIR=$(ViashDockerStripAutomount "$VIASH_META_RESOURCES_DIR")
@@ -1300,16 +1494,16 @@ fi
# check whether required files exist
if [ ! -z "$VIASH_PAR_DESEQ2_OUTPUT" ] && [ ! -e "$VIASH_PAR_DESEQ2_OUTPUT" ]; then
ViashError "Output file '$VIASH_PAR_DESEQ2_OUTPUT' does not exist."
if [ ! -z "$VIASH_PAR_OUTDIR" ] && [ ! -e "$VIASH_PAR_OUTDIR" ]; then
ViashError "Output file '$VIASH_PAR_OUTDIR' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_PCA_MULTIQC" ] && [ ! -e "$VIASH_PAR_PCA_MULTIQC" ]; then
ViashError "Output file '$VIASH_PAR_PCA_MULTIQC' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_DISTS_MULTIQC" ] && [ ! -e "$VIASH_PAR_DISTS_MULTIQC" ]; then
ViashError "Output file '$VIASH_PAR_DISTS_MULTIQC' does not exist."
if [ ! -z "$VIASH_PAR_SAMPLE_DISTS_MULTIQC" ] && [ ! -e "$VIASH_PAR_SAMPLE_DISTS_MULTIQC" ]; then
ViashError "Output file '$VIASH_PAR_SAMPLE_DISTS_MULTIQC' does not exist."
exit 1
fi

246
target/executable/deseq2_qc/deseq2_qc.r
View File

@@ -1,246 +0,0 @@
#!/usr/bin/env Rscript
################################################
################################################
## REQUIREMENTS ##
################################################
################################################
## PCA, HEATMAP AND SCATTERPLOTS FOR SAMPLES IN COUNTS FILE
## - SAMPLE NAMES HAVE TO END IN e.g. "_R1" REPRESENTING REPLICATE ID. LAST 3 CHARACTERS OF SAMPLE NAME WILL BE TRIMMED TO OBTAIN GROUP ID FOR DESEQ2 COMPARISONS.
## - PACKAGES BELOW NEED TO BE AVAILABLE TO LOAD WHEN RUNNING R
################################################
################################################
## LOAD LIBRARIES ##
################################################
################################################
library(optparse)
library(DESeq2)
library(ggplot2)
library(RColorBrewer)
library(pheatmap)
################################################
################################################
## PARSE COMMAND-LINE PARAMETERS ##
################################################
################################################
option_list <- list(
make_option(c("-i", "--count_file"), type="character", default=NULL, metavar="path", help="Count file matrix where rows are genes and columns are samples."),
make_option(c("-f", "--count_col"), type="integer", default=3, metavar="integer", help="First column containing sample count data."),
make_option(c("-d", "--id_col"), type="integer", default=1, metavar="integer", help="Column containing identifiers to be used."),
make_option(c("-r", "--sample_suffix"), type="character", default='', metavar="string", help="Suffix to remove after sample name in columns e.g. '.rmDup.bam' if 'DRUG_R1.rmDup.bam'."),
make_option(c("-p", "--outprefix"), type="character", default='deseq2', metavar="string" , help="Output prefix."),
make_option(c("-v", "--vst"), type="logical", default=FALSE, metavar="boolean", help="Run vst transform instead of rlog."),
make_option(c("-c", "--cores"), type="integer", default=1, metavar="integer", help="Number of cores."),
make_option(c("-o", "--outdir"), type="character", default="./", metavar="path", help="Output directory.")
)
opt_parser <- OptionParser(option_list=option_list)
opt <- parse_args(opt_parser)
if (is.null(opt$count_file)){
print_help(opt_parser)
stop("Please provide a counts file.", call.=FALSE)
}
################################################
################################################
## READ IN COUNTS FILE ##
################################################
################################################
count.table <- read.delim(file=opt$count_file,header=TRUE, row.names=NULL)
rownames(count.table) <- count.table[,opt$id_col]
count.table <- count.table[,opt$count_col:ncol(count.table),drop=FALSE]
colnames(count.table) <- gsub(opt$sample_suffix,"",colnames(count.table))
colnames(count.table) <- gsub(pattern='\\.$', replacement='', colnames(count.table))
################################################
################################################
## RUN DESEQ2 ##
################################################
################################################
if (file.exists(opt$outdir) == FALSE) {
dir.create(opt$outdir, recursive=TRUE)
}
setwd(opt$outdir)
samples.vec <- colnames(count.table)
name_components <- strsplit(samples.vec, "_")
n_components <- length(name_components[[1]])
decompose <- n_components!=1 && all(sapply(name_components, length)==n_components)
coldata <- data.frame(samples.vec, sample=samples.vec, row.names=1)
if (decompose) {
groupings <- as.data.frame(lapply(1:n_components, function(i) sapply(name_components, "[[", i)))
n_distinct <- sapply(groupings, function(grp) length(unique(grp)))
groupings <- groupings[n_distinct!=1 & n_distinct!=length(samples.vec)]
if (ncol(groupings)!=0) {
names(groupings) <- paste0("Group", 1:ncol(groupings))
coldata <- cbind(coldata, groupings)
} else {
decompose <- FALSE
}
}
DDSFile <- paste(opt$outprefix,".dds.RData",sep="")
counts <- count.table[,samples.vec,drop=FALSE]
dds <- DESeqDataSetFromMatrix(countData=round(counts), colData=coldata, design=~ 1)
dds <- estimateSizeFactors(dds)
if (min(dim(count.table))<=1) { # No point if only one sample, or one gene
save(dds,file=DDSFile)
saveRDS(dds, file=sub("\\.dds\\.RData$", ".rds", DDSFile))
warning("Not enough samples or genes in counts file for PCA.", call.=FALSE)
quit(save = "no", status = 0, runLast = FALSE)
}
if (!opt$vst) {
vst_name <- "rlog"
rld <- rlog(dds)
} else {
vst_name <- "vst"
rld <- varianceStabilizingTransformation(dds)
}
assay(dds, vst_name) <- assay(rld)
save(dds,file=DDSFile)
saveRDS(dds, file=sub("\\.dds\\.RData$", ".rds", DDSFile))
################################################
################################################
## PLOT QC ##
################################################
################################################
##' PCA pre-processeor
##'
##' Generate all the necessary information to plot PCA from a DESeq2 object
##' in which an assay containing a variance-stabilised matrix of counts is
##' stored. Copied from DESeq2::plotPCA, but with additional ability to
##' say which assay to run the PCA on.
##'
##' @param object The DESeq2DataSet object.
##' @param ntop number of top genes to use for principla components, selected by highest row variance.
##' @param assay the name or index of the assay that stores the variance-stabilised data.
##' @return A data.frame containing the projected data alongside the grouping columns.
##' A 'percentVar' attribute is set which includes the percentage of variation each PC explains,
##' and additionally how much the variation within that PC is explained by the grouping variable.
##' @author Gavin Kelly
plotPCA_vst <- function (object, ntop = 500, assay=length(assays(object))) {
rv <- rowVars(assay(object, assay))
select <- order(rv, decreasing = TRUE)[seq_len(min(ntop, length(rv)))]
pca <- prcomp(t(assay(object, assay)[select, ]), center=TRUE, scale=FALSE)
percentVar <- pca$sdev^2/sum(pca$sdev^2)
df <- cbind( as.data.frame(colData(object)), pca$x)
#Order points so extreme samples are more likely to get label
ord <- order(abs(rank(df$PC1)-median(df$PC1)), abs(rank(df$PC2)-median(df$PC2)))
df <- df[ord,]
attr(df, "percentVar") <- data.frame(PC=seq(along=percentVar), percentVar=100*percentVar)
return(df)
}
PlotFile <- paste(opt$outprefix,".plots.pdf",sep="")
pdf(file=PlotFile, onefile=TRUE, width=7, height=7)
## PCA
ntop <- c(500, Inf)
for (n_top_var in ntop) {
pca.data <- plotPCA_vst(dds, assay=vst_name, ntop=n_top_var)
percentVar <- round(attr(pca.data, "percentVar")$percentVar)
plot_subtitle <- ifelse(n_top_var==Inf, "All genes", paste("Top", n_top_var, "genes"))
pl <- ggplot(pca.data, aes(PC1, PC2, label=paste0(" ", sample, " "))) +
geom_point() +
geom_text(check_overlap=TRUE, vjust=0.5, hjust="inward") +
xlab(paste0("PC1: ",percentVar[1],"% variance")) +
ylab(paste0("PC2: ",percentVar[2],"% variance")) +
labs(title = paste0("First PCs on ", vst_name, "-transformed data"), subtitle = plot_subtitle) +
theme(legend.position="top",
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
panel.background = element_blank(),
panel.border = element_rect(colour = "black", fill=NA, size=1))
print(pl)
if (decompose) {
pc_names <- paste0("PC", attr(pca.data, "percentVar")$PC)
long_pc <- reshape(pca.data, varying=pc_names, direction="long", sep="", timevar="component", idvar="pcrow")
long_pc <- subset(long_pc, component<=5)
long_pc_grp <- reshape(long_pc, varying=names(groupings), direction="long", sep="", timevar="grouper")
long_pc_grp <- subset(long_pc_grp, grouper<=5)
long_pc_grp$component <- paste("PC", long_pc_grp$component)
long_pc_grp$grouper <- paste0(long_pc_grp$grouper, c("st","nd","rd","th","th")[long_pc_grp$grouper], " prefix")
pl <- ggplot(long_pc_grp, aes(x=Group, y=PC)) +
geom_point() +
stat_summary(fun=mean, geom="line", aes(group = 1)) +
labs(x=NULL, y=NULL, subtitle = plot_subtitle, title="PCs split by sample-name prefixes") +
facet_grid(component~grouper, scales="free_x") +
scale_x_discrete(guide = guide_axis(n.dodge = 3))
print(pl)
}
} # at end of loop, we'll be using the user-defined ntop if any, else all genes
## WRITE PC1 vs PC2 VALUES TO FILE
pca.vals <- pca.data[,c("PC1","PC2")]
colnames(pca.vals) <- paste0(colnames(pca.vals), ": ", percentVar[1:2], '% variance')
pca.vals <- cbind(sample = rownames(pca.vals), pca.vals)
write.table(pca.vals, file = paste(opt$outprefix, ".pca.vals.txt", sep=""),
row.names = FALSE, col.names = TRUE, sep = "\t", quote = TRUE)
## SAMPLE CORRELATION HEATMAP
sampleDists <- dist(t(assay(dds, vst_name)))
sampleDistMatrix <- as.matrix(sampleDists)
colors <- colorRampPalette( rev(brewer.pal(9, "Blues")) )(255)
pheatmap(
sampleDistMatrix,
clustering_distance_rows=sampleDists,
clustering_distance_cols=sampleDists,
col=colors,
main=paste("Euclidean distance between", vst_name, "of samples")
)
## WRITE SAMPLE DISTANCES TO FILE
write.table(cbind(sample = rownames(sampleDistMatrix), sampleDistMatrix),file=paste(opt$outprefix, ".sample.dists.txt", sep=""),
row.names=FALSE, col.names=TRUE, sep="\t", quote=FALSE)
dev.off()
################################################
################################################
## SAVE SIZE FACTORS ##
################################################
################################################
SizeFactorsDir <- "size_factors/"
if (file.exists(SizeFactorsDir) == FALSE) {
dir.create(SizeFactorsDir, recursive=TRUE)
}
NormFactorsFile <- paste(SizeFactorsDir,opt$outprefix, ".size_factors.RData", sep="")
normFactors <- sizeFactors(dds)
save(normFactors, file=NormFactorsFile)
for (name in names(sizeFactors(dds))) {
sizeFactorFile <- paste(SizeFactorsDir,name, ".txt", sep="")
write(as.numeric(sizeFactors(dds)[name]), file=sizeFactorFile)
}
################################################
################################################
## R SESSION INFO ##
################################################
################################################
RLogFile <- "R_sessionInfo.log"
sink(RLogFile)
a <- sessionInfo()
print(a)
sink()
################################################
################################################
################################################
################################################

9
target/executable/dupradar/.config.vsh.yaml
View File

@@ -169,7 +169,7 @@ repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
@@ -266,9 +266,10 @@ build_info:
output: "target/executable/dupradar"
executable: "target/executable/dupradar/dupradar"
viash_version: "0.9.0"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"
info:
test_resources:
@@ -278,7 +279,7 @@ package_config:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"

8
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="2024-10-04T07:06:22Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
LABEL org.opencontainers.image.created="2024-10-25T08:58:45Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -882,7 +882,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/dupradar:main'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/dupradar:main'
fi
# print dockerfile

9
target/executable/fastqc/.config.vsh.yaml
View File

@@ -105,7 +105,7 @@ repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
@@ -198,9 +198,10 @@ build_info:
output: "target/executable/fastqc"
executable: "target/executable/fastqc/fastqc"
viash_version: "0.9.0"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"
info:
test_resources:
@@ -210,7 +211,7 @@ package_config:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"

8
target/executable/fastqc/fastqc
View File

@@ -490,9 +490,9 @@ RUN apt-get update && \
rm -rf /var/lib/apt/lists/*
LABEL org.opencontainers.image.description="Companion container for running component fastqc"
LABEL org.opencontainers.image.created="2024-10-04T07:06:13Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
LABEL org.opencontainers.image.created="2024-10-25T08:58:41Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -792,7 +792,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/fastqc:main'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/fastqc:main'
fi
# print dockerfile

9
target/executable/fq_subsample/.config.vsh.yaml
View File

@@ -78,7 +78,7 @@ repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
@@ -177,9 +177,10 @@ build_info:
output: "target/executable/fq_subsample"
executable: "target/executable/fq_subsample/fq_subsample"
viash_version: "0.9.0"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"
info:
test_resources:
@@ -189,7 +190,7 @@ package_config:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"

8
target/executable/fq_subsample/fq_subsample
View File

@@ -485,9 +485,9 @@ cargo install --locked --path . && \
mv /usr/local/fq/target/release/fq /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component fq_subsample"
LABEL org.opencontainers.image.created="2024-10-04T07:06:13Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
LABEL org.opencontainers.image.created="2024-10-25T08:58:42Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -765,7 +765,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/fq_subsample:main'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/fq_subsample:main'
fi
# print dockerfile

9
target/executable/getchromsizes/.config.vsh.yaml
View File

@@ -71,7 +71,7 @@ repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
@@ -167,9 +167,10 @@ build_info:
output: "target/executable/getchromsizes"
executable: "target/executable/getchromsizes/getchromsizes"
viash_version: "0.9.0"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"
info:
test_resources:
@@ -179,7 +180,7 @@ package_config:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"

8
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="2024-10-04T07:06:14Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
LABEL org.opencontainers.image.created="2024-10-25T08:58:40Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -754,7 +754,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/getchromsizes:main'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/getchromsizes:main'
fi
# print dockerfile

9
target/executable/gtf2bed/.config.vsh.yaml
View File

@@ -52,7 +52,7 @@ repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
@@ -145,9 +145,10 @@ build_info:
output: "target/executable/gtf2bed"
executable: "target/executable/gtf2bed/gtf2bed"
viash_version: "0.9.0"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"
info:
test_resources:
@@ -157,7 +158,7 @@ package_config:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"

8
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="2024-10-04T07:06:26Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
LABEL org.opencontainers.image.created="2024-10-25T08:58:39Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -718,7 +718,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/gtf2bed:main'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/gtf2bed:main'
fi
# print dockerfile

9
target/executable/gtf_filter/.config.vsh.yaml
View File

@@ -67,7 +67,7 @@ repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
@@ -155,9 +155,10 @@ build_info:
output: "target/executable/gtf_filter"
executable: "target/executable/gtf_filter/gtf_filter"
viash_version: "0.9.0"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"
info:
test_resources:
@@ -167,7 +168,7 @@ package_config:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"

8
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="2024-10-04T07:06:29Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
LABEL org.opencontainers.image.created="2024-10-25T08:58:45Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -738,7 +738,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/gtf_filter:main'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/gtf_filter:main'
fi
# print dockerfile

9
target/executable/gunzip/.config.vsh.yaml
View File

@@ -51,7 +51,7 @@ repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
@@ -144,9 +144,10 @@ build_info:
output: "target/executable/gunzip"
executable: "target/executable/gunzip/gunzip"
viash_version: "0.9.0"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"
info:
test_resources:
@@ -156,7 +157,7 @@ package_config:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"

8
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="2024-10-04T07:06:14Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
LABEL org.opencontainers.image.created="2024-10-25T08:58:43Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -718,7 +718,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/gunzip:main'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/gunzip:main'
fi
# print dockerfile

9
target/executable/kallisto/kallisto_index/.config.vsh.yaml
View File

@@ -60,7 +60,7 @@ repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
@@ -155,9 +155,10 @@ build_info:
output: "target/executable/kallisto/kallisto_index"
executable: "target/executable/kallisto/kallisto_index/kallisto_index"
viash_version: "0.9.0"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"
info:
test_resources:
@@ -167,7 +168,7 @@ package_config:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"

8
target/executable/kallisto/kallisto_index/kallisto_index
View File

@@ -471,9 +471,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \
mv kallisto/kallisto /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_index"
LABEL org.opencontainers.image.created="2024-10-04T07:06:28Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
LABEL org.opencontainers.image.created="2024-10-25T08:58:46Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -734,7 +734,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/kallisto/kallisto_index:main'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/kallisto/kallisto_index:main'
fi
# print dockerfile

9
target/executable/kallisto/kallisto_quant/.config.vsh.yaml
View File

@@ -158,7 +158,7 @@ repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
@@ -253,9 +253,10 @@ build_info:
output: "target/executable/kallisto/kallisto_quant"
executable: "target/executable/kallisto/kallisto_quant/kallisto_quant"
viash_version: "0.9.0"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"
info:
test_resources:
@@ -265,7 +266,7 @@ package_config:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"

8
target/executable/kallisto/kallisto_quant/kallisto_quant
View File

@@ -515,9 +515,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \
mv kallisto/kallisto /usr/local/bin/
LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_quant"
LABEL org.opencontainers.image.created="2024-10-04T07:06:27Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
LABEL org.opencontainers.image.created="2024-10-25T08:58:46Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -883,7 +883,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/kallisto/kallisto_quant:main'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/kallisto/kallisto_quant:main'
fi
# print dockerfile

37
target/executable/multiqc_custom_biotype/.config.vsh.yaml
View File

@@ -23,13 +23,12 @@ argument_groups:
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--biotypes_header"
- type: "string"
name: "--features"
description: "Features to count"
info: null
default:
- "assets/multiqc/biotypes_header.txt"
must_exist: true
create_parent: true
- "rRNA"
required: false
direction: "input"
multiple: false
@@ -59,14 +58,11 @@ argument_groups:
multiple: false
multiple_sep: ";"
resources:
- type: "bash_script"
path: "script.sh"
- type: "python_script"
path: "script.py"
is_executable: true
- type: "file"
path: "mqc_features_stat.py"
- type: "file"
path: "assets/multiqc/biotypes_header.txt"
dest: "assets/multiqc/biotypes_header.txt"
path: "biotypes_header.txt"
description: "Calculate features percentage for biotype counts"
info: null
status: "enabled"
@@ -77,7 +73,7 @@ repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
@@ -150,18 +146,10 @@ runners:
engines:
- type: "docker"
id: "docker"
image: "ubuntu:22.04"
image: "python:latest"
target_registry: "images.viash-hub.com"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "apt"
packages:
- "pip"
interactive: false
- type: "python"
user: false
upgrade: true
entrypoint: []
cmd: null
- type: "native"
@@ -173,9 +161,10 @@ build_info:
output: "target/executable/multiqc_custom_biotype"
executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype"
viash_version: "0.9.0"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"
info:
test_resources:
@@ -185,7 +174,7 @@ package_config:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"

0
target/executable/multiqc_custom_biotype/assets/multiqc/biotypes_header.txt → target/executable/multiqc_custom_biotype/biotypes_header.txt
View File

89
target/executable/multiqc_custom_biotype/mqc_features_stat.py
View File

@@ -1,89 +0,0 @@
#!/usr/bin/env python3
import argparse
import logging
import os
# Create a logger
logging.basicConfig(format="%(name)s - %(asctime)s %(levelname)s: %(message)s")
logger = logging.getLogger(__file__)
logger.setLevel(logging.INFO)
mqc_main = """#id: 'biotype-gs'
#plot_type: 'generalstats'
#pconfig:"""
mqc_pconf = """# percent_{ft}:
# title: '% {ft}'
# namespace: 'Biotype Counts'
# description: '% reads overlapping {ft} features'
# max: 100
# min: 0
# scale: 'RdYlGn-rev'
# format: '{{:.2f}}%'"""
def mqc_feature_stat(bfile, features, outfile, sname=None):
# If sample name not given use file name
if not sname:
sname = os.path.splitext(os.path.basename(bfile))[0]
# Try to parse and read biocount file
fcounts = {}
try:
with open(bfile, "r") as bfl:
for ln in bfl:
if ln.startswith("#"):
continue
ft, cn = ln.strip().split("\t")
fcounts[ft] = float(cn)
except:
logger.error("Trouble reading the biocount file {}".format(bfile))
return
total_count = sum(fcounts.values())
if total_count == 0:
logger.error("No biocounts found, exiting")
return
# Calculate percentage for each requested feature
fpercent = {f: (fcounts[f] / total_count) * 100 if f in fcounts else 0 for f in features}
if len(fpercent) == 0:
logger.error("Any of given features '{}' not found in the biocount file".format(", ".join(features), bfile))
return
# Prepare the output strings
out_head, out_value, out_mqc = ("Sample", "'{}'".format(sname), mqc_main)
for ft, pt in fpercent.items():
out_head = "{}\tpercent_{}".format(out_head, ft)
out_value = "{}\t{}".format(out_value, pt)
out_mqc = "{}\n{}".format(out_mqc, mqc_pconf.format(ft=ft))
# Write the output to a file
with open(outfile, "w") as ofl:
out_final = "\n".join([out_mqc, out_head, out_value]).strip()
ofl.write(out_final + "\n")
if __name__ == "__main__":
parser = argparse.ArgumentParser(description="""Calculate features percentage for biotype counts""")
parser.add_argument("biocount", type=str, help="File with all biocounts")
parser.add_argument(
"-f",
"--features",
dest="features",
required=True,
nargs="+",
help="Features to count",
)
parser.add_argument("-s", "--sample", dest="sample", type=str, help="Sample Name")
parser.add_argument(
"-o",
"--output",
dest="output",
default="biocount_percent.tsv",
type=str,
help="Sample Name",
)
args = parser.parse_args()
mqc_feature_stat(args.biocount, args.features, args.output, args.sample)

205
target/executable/multiqc_custom_biotype/multiqc_custom_biotype
View File

@@ -185,9 +185,10 @@ function ViashHelp {
echo " default: \$id"
echo " Sample name"
echo ""
echo " --biotypes_header"
echo " type: file, file must exist"
echo " default: assets/multiqc/biotypes_header.txt"
echo " --features"
echo " type: string"
echo " default: rRNA"
echo " Features to count"
echo ""
echo "Output:"
echo " --featurecounts_multiqc"
@@ -472,18 +473,12 @@ function ViashDockerfile {
if [[ "$engine_id" == "docker" ]]; then
cat << 'VIASHDOCKER'
FROM ubuntu:22.04
FROM python:latest
ENTRYPOINT []
RUN apt-get update && \
DEBIAN_FRONTEND=noninteractive apt-get install -y pip && \
rm -rf /var/lib/apt/lists/*
RUN pip install --upgrade pip
LABEL org.opencontainers.image.description="Companion container for running component multiqc_custom_biotype"
LABEL org.opencontainers.image.created="2024-10-04T07:06:22Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
LABEL org.opencontainers.image.created="2024-10-25T08:58:43Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -645,15 +640,15 @@ while [[ $# -gt 0 ]]; do
VIASH_PAR_ID=$(ViashRemoveFlags "$1")
shift 1
;;
--biotypes_header)
[ -n "$VIASH_PAR_BIOTYPES_HEADER" ] && ViashError Bad arguments for option \'--biotypes_header\': \'$VIASH_PAR_BIOTYPES_HEADER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BIOTYPES_HEADER="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --biotypes_header. Use "--help" to get more information on the parameters. && exit 1
--features)
[ -n "$VIASH_PAR_FEATURES" ] && ViashError Bad arguments for option \'--features\': \'$VIASH_PAR_FEATURES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_FEATURES="$2"
[ $# -lt 2 ] && ViashError Not enough arguments passed to --features. Use "--help" to get more information on the parameters. && exit 1
shift 2
;;
--biotypes_header=*)
[ -n "$VIASH_PAR_BIOTYPES_HEADER" ] && ViashError Bad arguments for option \'--biotypes_header=*\': \'$VIASH_PAR_BIOTYPES_HEADER\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_BIOTYPES_HEADER=$(ViashRemoveFlags "$1")
--features=*)
[ -n "$VIASH_PAR_FEATURES" ] && ViashError Bad arguments for option \'--features=*\': \'$VIASH_PAR_FEATURES\' \& \'$2\' - you should provide exactly one argument for this option. && exit 1
VIASH_PAR_FEATURES=$(ViashRemoveFlags "$1")
shift 1
;;
--featurecounts_multiqc)
@@ -766,7 +761,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/multiqc_custom_biotype:main'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/multiqc_custom_biotype:main'
fi
# print dockerfile
@@ -879,8 +874,8 @@ fi
if [ -z ${VIASH_PAR_ID+x} ]; then
VIASH_PAR_ID="\$id"
fi
if [ -z ${VIASH_PAR_BIOTYPES_HEADER+x} ]; then
VIASH_PAR_BIOTYPES_HEADER="assets/multiqc/biotypes_header.txt"
if [ -z ${VIASH_PAR_FEATURES+x} ]; then
VIASH_PAR_FEATURES="rRNA"
fi
if [ -z ${VIASH_PAR_FEATURECOUNTS_MULTIQC+x} ]; then
VIASH_PAR_FEATURECOUNTS_MULTIQC="\$id.biotype_counts_mqc.tsv"
@@ -894,10 +889,6 @@ if [ ! -z "$VIASH_PAR_BIOCOUNTS" ] && [ ! -e "$VIASH_PAR_BIOCOUNTS" ]; then
ViashError "Input file '$VIASH_PAR_BIOCOUNTS' does not exist."
exit 1
fi
if [ ! -z "$VIASH_PAR_BIOTYPES_HEADER" ] && [ ! -e "$VIASH_PAR_BIOTYPES_HEADER" ]; then
ViashError "Input file '$VIASH_PAR_BIOTYPES_HEADER' does not exist."
exit 1
fi
# check whether parameters values are of the right type
if [[ -n "$VIASH_META_CPUS" ]]; then
@@ -997,10 +988,6 @@ if [ ! -z "$VIASH_PAR_BIOCOUNTS" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_BIOCOUNTS")" )
VIASH_PAR_BIOCOUNTS=$(ViashDockerAutodetectMount "$VIASH_PAR_BIOCOUNTS")
fi
if [ ! -z "$VIASH_PAR_BIOTYPES_HEADER" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_BIOTYPES_HEADER")" )
VIASH_PAR_BIOTYPES_HEADER=$(ViashDockerAutodetectMount "$VIASH_PAR_BIOTYPES_HEADER")
fi
if [ ! -z "$VIASH_PAR_FEATURECOUNTS_MULTIQC" ]; then
VIASH_DIRECTORY_MOUNTS+=( "$(ViashDockerAutodetectMountArg "$VIASH_PAR_FEATURECOUNTS_MULTIQC")" )
VIASH_PAR_FEATURECOUNTS_MULTIQC=$(ViashDockerAutodetectMount "$VIASH_PAR_FEATURECOUNTS_MULTIQC")
@@ -1067,7 +1054,7 @@ fi
ViashDebug "Running command: $(echo $VIASH_CMD)"
cat << VIASHEOF | eval $VIASH_CMD
set -e
tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-multiqc_custom_biotype-XXXXXX").sh
tempscript=\$(mktemp "$VIASH_META_TEMP_DIR/viash-run-multiqc_custom_biotype-XXXXXX").py
function clean_up {
rm "\$tempscript"
}
@@ -1080,44 +1067,131 @@ trap interrupt INT SIGINT
cat > "\$tempscript" << 'VIASHMAIN'
## VIASH START
# The following code has been auto-generated by Viash.
$( if [ ! -z ${VIASH_PAR_BIOCOUNTS+x} ]; then echo "${VIASH_PAR_BIOCOUNTS}" | sed "s#'#'\"'\"'#g;s#.*#par_biocounts='&'#" ; else echo "# par_biocounts="; fi )
$( if [ ! -z ${VIASH_PAR_ID+x} ]; then echo "${VIASH_PAR_ID}" | sed "s#'#'\"'\"'#g;s#.*#par_id='&'#" ; else echo "# par_id="; fi )
$( if [ ! -z ${VIASH_PAR_BIOTYPES_HEADER+x} ]; then echo "${VIASH_PAR_BIOTYPES_HEADER}" | sed "s#'#'\"'\"'#g;s#.*#par_biotypes_header='&'#" ; else echo "# par_biotypes_header="; fi )
$( if [ ! -z ${VIASH_PAR_FEATURECOUNTS_MULTIQC+x} ]; then echo "${VIASH_PAR_FEATURECOUNTS_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_featurecounts_multiqc='&'#" ; else echo "# par_featurecounts_multiqc="; fi )
$( if [ ! -z ${VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC+x} ]; then echo "${VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC}" | sed "s#'#'\"'\"'#g;s#.*#par_featurecounts_rrna_multiqc='&'#" ; else echo "# par_featurecounts_rrna_multiqc="; fi )
$( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "${VIASH_META_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_name='&'#" ; else echo "# meta_name="; fi )
$( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "${VIASH_META_FUNCTIONALITY_NAME}" | sed "s#'#'\"'\"'#g;s#.*#meta_functionality_name='&'#" ; else echo "# meta_functionality_name="; fi )
$( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "${VIASH_META_RESOURCES_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_resources_dir='&'#" ; else echo "# meta_resources_dir="; fi )
$( if [ ! -z ${VIASH_META_EXECUTABLE+x} ]; then echo "${VIASH_META_EXECUTABLE}" | sed "s#'#'\"'\"'#g;s#.*#meta_executable='&'#" ; else echo "# meta_executable="; fi )
$( if [ ! -z ${VIASH_META_CONFIG+x} ]; then echo "${VIASH_META_CONFIG}" | sed "s#'#'\"'\"'#g;s#.*#meta_config='&'#" ; else echo "# meta_config="; fi )
$( if [ ! -z ${VIASH_META_TEMP_DIR+x} ]; then echo "${VIASH_META_TEMP_DIR}" | sed "s#'#'\"'\"'#g;s#.*#meta_temp_dir='&'#" ; else echo "# meta_temp_dir="; fi )
$( if [ ! -z ${VIASH_META_CPUS+x} ]; then echo "${VIASH_META_CPUS}" | sed "s#'#'\"'\"'#g;s#.*#meta_cpus='&'#" ; else echo "# meta_cpus="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_B+x} ]; then echo "${VIASH_META_MEMORY_B}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_b='&'#" ; else echo "# meta_memory_b="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_KB+x} ]; then echo "${VIASH_META_MEMORY_KB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_kb='&'#" ; else echo "# meta_memory_kb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_MB+x} ]; then echo "${VIASH_META_MEMORY_MB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_mb='&'#" ; else echo "# meta_memory_mb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_GB+x} ]; then echo "${VIASH_META_MEMORY_GB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_gb='&'#" ; else echo "# meta_memory_gb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_TB+x} ]; then echo "${VIASH_META_MEMORY_TB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_tb='&'#" ; else echo "# meta_memory_tb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_PB+x} ]; then echo "${VIASH_META_MEMORY_PB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pb='&'#" ; else echo "# meta_memory_pb="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_KIB+x} ]; then echo "${VIASH_META_MEMORY_KIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_kib='&'#" ; else echo "# meta_memory_kib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_MIB+x} ]; then echo "${VIASH_META_MEMORY_MIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_mib='&'#" ; else echo "# meta_memory_mib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_GIB+x} ]; then echo "${VIASH_META_MEMORY_GIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_gib='&'#" ; else echo "# meta_memory_gib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "${VIASH_META_MEMORY_TIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_tib='&'#" ; else echo "# meta_memory_tib="; fi )
$( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}" | sed "s#'#'\"'\"'#g;s#.*#meta_memory_pib='&'#" ; else echo "# meta_memory_pib="; fi )
par = {
'biocounts': $( if [ ! -z ${VIASH_PAR_BIOCOUNTS+x} ]; then echo "r'${VIASH_PAR_BIOCOUNTS//\'/\'\"\'\"r\'}'"; else echo None; fi ),
'id': $( if [ ! -z ${VIASH_PAR_ID+x} ]; then echo "r'${VIASH_PAR_ID//\'/\'\"\'\"r\'}'"; else echo None; fi ),
'features': $( if [ ! -z ${VIASH_PAR_FEATURES+x} ]; then echo "r'${VIASH_PAR_FEATURES//\'/\'\"\'\"r\'}'"; else echo None; fi ),
'featurecounts_multiqc': $( if [ ! -z ${VIASH_PAR_FEATURECOUNTS_MULTIQC+x} ]; then echo "r'${VIASH_PAR_FEATURECOUNTS_MULTIQC//\'/\'\"\'\"r\'}'"; else echo None; fi ),
'featurecounts_rrna_multiqc': $( if [ ! -z ${VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC+x} ]; then echo "r'${VIASH_PAR_FEATURECOUNTS_RRNA_MULTIQC//\'/\'\"\'\"r\'}'"; else echo None; fi )
}
meta = {
'name': $( if [ ! -z ${VIASH_META_NAME+x} ]; then echo "r'${VIASH_META_NAME//\'/\'\"\'\"r\'}'"; else echo None; fi ),
'functionality_name': $( if [ ! -z ${VIASH_META_FUNCTIONALITY_NAME+x} ]; then echo "r'${VIASH_META_FUNCTIONALITY_NAME//\'/\'\"\'\"r\'}'"; else echo None; fi ),
'resources_dir': $( if [ ! -z ${VIASH_META_RESOURCES_DIR+x} ]; then echo "r'${VIASH_META_RESOURCES_DIR//\'/\'\"\'\"r\'}'"; else echo None; fi ),
'executable': $( if [ ! -z ${VIASH_META_EXECUTABLE+x} ]; then echo "r'${VIASH_META_EXECUTABLE//\'/\'\"\'\"r\'}'"; else echo None; fi ),
'config': $( if [ ! -z ${VIASH_META_CONFIG+x} ]; then echo "r'${VIASH_META_CONFIG//\'/\'\"\'\"r\'}'"; else echo None; fi ),
'temp_dir': $( if [ ! -z ${VIASH_META_TEMP_DIR+x} ]; then echo "r'${VIASH_META_TEMP_DIR//\'/\'\"\'\"r\'}'"; else echo None; fi ),
'cpus': $( if [ ! -z ${VIASH_META_CPUS+x} ]; then echo "int(r'${VIASH_META_CPUS//\'/\'\"\'\"r\'}')"; else echo None; fi ),
'memory_b': $( if [ ! -z ${VIASH_META_MEMORY_B+x} ]; then echo "int(r'${VIASH_META_MEMORY_B//\'/\'\"\'\"r\'}')"; else echo None; fi ),
'memory_kb': $( if [ ! -z ${VIASH_META_MEMORY_KB+x} ]; then echo "int(r'${VIASH_META_MEMORY_KB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
'memory_mb': $( if [ ! -z ${VIASH_META_MEMORY_MB+x} ]; then echo "int(r'${VIASH_META_MEMORY_MB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
'memory_gb': $( if [ ! -z ${VIASH_META_MEMORY_GB+x} ]; then echo "int(r'${VIASH_META_MEMORY_GB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
'memory_tb': $( if [ ! -z ${VIASH_META_MEMORY_TB+x} ]; then echo "int(r'${VIASH_META_MEMORY_TB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
'memory_pb': $( if [ ! -z ${VIASH_META_MEMORY_PB+x} ]; then echo "int(r'${VIASH_META_MEMORY_PB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
'memory_kib': $( if [ ! -z ${VIASH_META_MEMORY_KIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_KIB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
'memory_mib': $( if [ ! -z ${VIASH_META_MEMORY_MIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_MIB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
'memory_gib': $( if [ ! -z ${VIASH_META_MEMORY_GIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_GIB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
'memory_tib': $( if [ ! -z ${VIASH_META_MEMORY_TIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_TIB//\'/\'\"\'\"r\'}')"; else echo None; fi ),
'memory_pib': $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "int(r'${VIASH_META_MEMORY_PIB//\'/\'\"\'\"r\'}')"; else echo None; fi )
}
dep = {
}
## VIASH END
#!/bin/bash
#!/usr/bin/env python3
set -eo pipefail
import argparse
import logging
import os
cut -f 1,7 \$par_biocounts | tail -n +3 | cat \$par_biotypes_header - >> \$par_featurecounts_multiqc
# Create a logger
logging.basicConfig(format="%(name)s - %(asctime)s %(levelname)s: %(message)s")
logger = logging.getLogger(__file__)
logger.setLevel(logging.INFO)
python3 "\$meta_resources_dir/mqc_features_stat.py" \\
\$par_featurecounts_multiqc \\
-s \$par_id \\
-f rRNA \\
-o \$par_featurecounts_rrna_multiqc
mqc_main = """#id: 'biotype-gs'
#plot_type: 'generalstats'
#pconfig:"""
mqc_pconf = """# percent_{ft}:
# title: '% {ft}'
# namespace: 'Biotype Counts'
# description: '% reads overlapping {ft} features'
# max: 100
# min: 0
# scale: 'RdYlGn-rev'
# format: '{{:.2f}}%'"""
def mqc_feature_stat(bfile, features, outfile, sname=None):
# If sample name not given use file name
if not sname:
sname = os.path.splitext(os.path.basename(bfile))[0]
# Try to parse and read biocount file
fcounts = {}
try:
with open(bfile, "r") as bfl:
for ln in bfl:
if ln.startswith("#"):
continue
ft, cn = ln.strip().split("\\t")
fcounts[ft] = float(cn)
except:
logger.error("Trouble reading the biocount file {}".format(bfile))
return
total_count = sum(fcounts.values())
if total_count == 0:
logger.error("No biocounts found, exiting")
return
# Calculate percentage for each requested feature
fpercent = {f: (fcounts[f] / total_count) * 100 if f in fcounts else 0 for f in features}
if len(fpercent) == 0:
logger.error("Any of given features '{}' not found in the biocount file".format(", ".join(features), bfile))
return
# Prepare the output strings
out_head, out_value, out_mqc = ("Sample", "'{}'".format(sname), mqc_main)
for ft, pt in fpercent.items():
out_head = "{}\\tpercent_{}".format(out_head, ft)
out_value = "{}\\t{}".format(out_value, pt)
out_mqc = "{}\\n{}".format(out_mqc, mqc_pconf.format(ft=ft))
# Write the output to a file
with open(outfile, "w") as ofl:
out_final = "\\n".join([out_mqc, out_head, out_value]).strip()
ofl.write(out_final + "\\n")
if __name__ == "__main__":
# Read the biotypes_header.txt file
biotypes_header_path = os.path.join(meta["resources_dir"], 'biotypes_header.txt')
with open(biotypes_header_path, 'r') as header_file:
biotypes_header = header_file.read()
# Extract specific columns (1 and 7) and skip the first two lines
filtered_lines = []
with open(par["biocounts"], 'r') as biocounts_file:
for i, line in enumerate(biocounts_file):
if i >= 2: # Skipping first two lines
columns = line.strip().split('\\t')
filtered_line = f"{columns[0]}\\t{columns[6]}" # Columns 1 and 7 (0-indexed)
filtered_lines.append(filtered_line)
# Concatenate the header and the processed lines
result = biotypes_header + '\\n' + '\\n'.join(filtered_lines) + '\\n'
# Write the result to par_featurecounts_multiqc
with open(par["featurecounts_multiqc"], 'w') as output_file:
output_file.write(result)
mqc_feature_stat(par["featurecounts_multiqc"], par["features"], par["featurecounts_rrna_multiqc"], par["id"])
VIASHMAIN
bash "\$tempscript" &
python -B "\$tempscript" &
wait "\$!"
VIASHEOF
@@ -1129,9 +1203,6 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
if [ ! -z "$VIASH_PAR_BIOCOUNTS" ]; then
VIASH_PAR_BIOCOUNTS=$(ViashDockerStripAutomount "$VIASH_PAR_BIOCOUNTS")
fi
if [ ! -z "$VIASH_PAR_BIOTYPES_HEADER" ]; then
VIASH_PAR_BIOTYPES_HEADER=$(ViashDockerStripAutomount "$VIASH_PAR_BIOTYPES_HEADER")
fi
if [ ! -z "$VIASH_PAR_FEATURECOUNTS_MULTIQC" ]; then
VIASH_PAR_FEATURECOUNTS_MULTIQC=$(ViashDockerStripAutomount "$VIASH_PAR_FEATURECOUNTS_MULTIQC")
fi

9
target/executable/picard_markduplicates/.config.vsh.yaml
View File

@@ -111,7 +111,7 @@ repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
@@ -207,9 +207,10 @@ build_info:
output: "target/executable/picard_markduplicates"
executable: "target/executable/picard_markduplicates/picard_markduplicates"
viash_version: "0.9.0"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"
info:
test_resources:
@@ -219,7 +220,7 @@ package_config:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"

8
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="2024-10-04T07:06:30Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
LABEL org.opencontainers.image.created="2024-10-25T08:58:41Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -801,7 +801,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/picard_markduplicates:main'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/picard_markduplicates:main'
fi
# print dockerfile

9
target/executable/prepare_multiqc_input/.config.vsh.yaml
View File

@@ -321,7 +321,7 @@ repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
@@ -409,9 +409,10 @@ build_info:
output: "target/executable/prepare_multiqc_input"
executable: "target/executable/prepare_multiqc_input/prepare_multiqc_input"
viash_version: "0.9.0"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"
info:
test_resources:
@@ -421,7 +422,7 @@ package_config:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"

8
target/executable/prepare_multiqc_input/prepare_multiqc_input
View File

@@ -557,9 +557,9 @@ function ViashDockerfile {
FROM ubuntu:22.04
ENTRYPOINT []
LABEL org.opencontainers.image.description="Companion container for running component prepare_multiqc_input"
LABEL org.opencontainers.image.created="2024-10-04T07:06:25Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
LABEL org.opencontainers.image.created="2024-10-25T08:58:39Z"
LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -1311,7 +1311,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
# determine docker image id
if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/prepare_multiqc_input:main'
VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/prepare_multiqc_input:main'
fi
# print dockerfile

9
target/executable/preprocess_transcripts_fasta/.config.vsh.yaml
View File

@@ -50,7 +50,7 @@ repositories:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"
@@ -138,9 +138,10 @@ build_info:
output: "target/executable/preprocess_transcripts_fasta"
executable: "target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta"
viash_version: "0.9.0"
git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
git_remote: "https://x-access-token:ghs_qP68SGVqiugFlLowIn73iXH8gzJeuD4MgS5A@github.com/viash-hub/rnaseq"
git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
package_config:
name: "rnaseq"
version: "main"
info:
test_resources:
@@ -150,7 +151,7 @@ package_config:
- type: "vsh"
name: "biobox"
repo: "vsh/biobox"
tag: "v0.2.0"
tag: "main"
- type: "vsh"
name: "craftbox"
repo: "craftbox"

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