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Build branch main with version main (1d87dc7)

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

Source commit: 1d87dc7c24

Source message: Multiple fixes (#23)

* multiple fixes

* update arguments and add test

* fix biobox module calls

* fix dependency

* add rsem merge counts

* exclude general stats in multiqc report

* output markduplicates metrics

* rename output reference files
This commit is contained in:
CI
2024-10-01 10:12:28 +00:00
parent 9b29e37466
commit c106022744
237 changed files with 9490 additions and 2187 deletions
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4
target/executable/workflows/prepare_genome/.config.vsh.yaml
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@@ -496,8 +496,8 @@ build_info:
output: "target/executable/workflows/prepare_genome"
executable: "target/executable/workflows/prepare_genome/prepare_genome"
viash_version: "0.9.0"
git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/gunzip"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread"

34
target/executable/workflows/prepare_genome/prepare_genome
View File

@@ -1172,9 +1172,15 @@ workflow run_wf {
// gff to gtf
| gffread.run (
runIf: {id, state -> !state.gtf && state.gff},
fromState: [ "input": "annotation" ],
fromState: [
"input": "gff",
"genome": "fasta"
],
toState: [ "gtf": "outfile" ],
args: [output: "gene_annotation.gtf"]
args: [
outfile: "gene_annotation.gtf",
gtf_output: true
]
)
| gtf_filter.run(
@@ -1253,13 +1259,19 @@ workflow run_wf {
| rsem_prepare_reference.run (
runIf: {id, state -> !state.transcript_fasta},
fromState: [
"fasta": "fasta",
"reference_fasta_files": "fasta",
"gtf": "gtf"
],
toState: [ "transcript_fasta": "transcript_fasta" ],
key: "make_transcript_fasta",
args: [transcript_fasta: "transcriptome.fasta"]
toState: [ "make_transcript_fasta_output": "output" ],
key: "make_transcript_fasta",\\
args: [reference_name: "genome"]
)
| map { id, state ->
def transcript_fasta = (!state.transcript_fasta) ?
state.make_transcript_fasta_output.listFiles().find{it.name == "genome.transcripts.fa"} :
state.transcript_fasta
[ id, state + [transcript_fasta: transcript_fasta] ]
}
// chromosome size and fai index
| getchromsizes.run (
@@ -1332,11 +1344,12 @@ workflow run_wf {
| rsem_prepare_reference.run (
runIf: {id, state -> !state.rsem_index && state.aligner == 'star_rsem'},
fromState: [
"fasta": "fasta",
"reference_fasta_files": "fasta",
"gtf": "gtf"
],
toState: [ "rsem_index": "rsem" ],
toState: [ "rsem_index": "output" ],
key: "generate_rsem_index",
args: [reference_name: "genome"]
)
// TODO: Uncompress HISAT2 index or generate from scratch if required
@@ -1366,10 +1379,7 @@ workflow run_wf {
// Uncompress Kallisto index or generate from scratch if required
| untar.run (
runIf: {id, state -> state.kallisto_index},
fromState: [
"input": "kallisto_index",
"pseudo_aligner_kmer_size": "pseudo_aligner_kmer_size"
],
fromState: [ "input": "kallisto_index" ],
toState: [ "kallisto_index": "output" ],
key: "untar_kallisto_index",
args: [output: "Kallisto_index"]