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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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25
target/nextflow/workflows/pre_processing/main.nf
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@@ -3482,7 +3482,7 @@ meta = [
"repository" : {
"type" : "vsh",
"repo" : "vsh/biobox",
"tag" : "v0.2.0"
"tag" : "main"
}
},
{
@@ -3508,7 +3508,7 @@ meta = [
"repository" : {
"type" : "vsh",
"repo" : "vsh/biobox",
"tag" : "v0.2.0"
"tag" : "main"
}
},
{
@@ -3522,7 +3522,7 @@ meta = [
"repository" : {
"type" : "vsh",
"repo" : "vsh/biobox",
"tag" : "v0.2.0"
"tag" : "main"
}
}
],
@@ -3531,7 +3531,7 @@ meta = [
"type" : "vsh",
"name" : "biobox",
"repo" : "vsh/biobox",
"tag" : "v0.2.0"
"tag" : "main"
},
{
"type" : "vsh",
@@ -3626,10 +3626,11 @@ meta = [
"engine" : "native",
"output" : "/workdir/root/repo/target/nextflow/workflows/pre_processing",
"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" : [
@@ -3644,7 +3645,7 @@ meta = [
"type" : "vsh",
"name" : "biobox",
"repo" : "vsh/biobox",
"tag" : "v0.2.0"
"tag" : "main"
},
{
"type" : "vsh",
@@ -3671,13 +3672,13 @@ meta = [
meta["root_dir"] = getRootDir()
include { fastqc } from "${meta.resources_dir}/../../../nextflow/fastqc/main.nf"
include { umitools_extract } from "${meta.resources_dir}/../../../nextflow/umitools/umitools_extract/main.nf"
include { umi_tools_extract } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/umi_tools/umi_tools_extract/main.nf"
include { umi_tools_extract } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/main.nf"
include { trimgalore } from "${meta.resources_dir}/../../../nextflow/trimgalore/main.nf"
include { bbmap_bbsplit } from "${meta.resources_dir}/../../../nextflow/bbmap_bbsplit/main.nf"
include { sortmerna } from "${meta.resources_dir}/../../../nextflow/sortmerna/main.nf"
include { fastp } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/fastp/main.nf"
include { fastp } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/main/nextflow/fastp/main.nf"
include { fq_subsample } from "${meta.resources_dir}/../../../nextflow/fq_subsample/main.nf"
include { salmon_quant } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/main.nf"
include { salmon_quant } from "${meta.root_dir}/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/main.nf"
// inner workflow
// user-provided Nextflow code
@@ -3822,9 +3823,11 @@ workflow run_wf {
runIf: { id, state -> state.remove_ribo_rna },
fromState: { id, state ->
def input = state.paired ? [ state.fastq_1, state.fastq_2 ] : [ state.fastq_1 ]
def filePaths = state.ribo_database_manifest.readLines()
def refs = filePaths.collect { it }
[ paired: state.paired,
input: input,
ribo_database_manifest: state.ribo_database_manifest ]
ribo_database_manifest: refs ]
},
toState: [
"fastq_1": "fastq_1",