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Build branch main with version main (1d87dc7)

Browse Source 
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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16
target/executable/workflows/post_processing/.config.vsh.yaml
View File

@@ -199,7 +199,7 @@ argument_groups:
name: "--processed_genome_bam"
info: null
default:
- "$id.markdup.sorted.bam"
- "$id.genome.bam"
must_exist: true
create_parent: true
required: false
@@ -210,7 +210,7 @@ argument_groups:
name: "--genome_bam_index"
info: null
default:
- "$id.markdup.sorted.bam"
- "$id.genome.bam.bai"
must_exist: true
create_parent: true
required: false
@@ -221,7 +221,7 @@ argument_groups:
name: "--genome_bam_stats"
info: null
default:
- "$id.markdup.sorted.bam.stats"
- "$id.genome.stats"
must_exist: true
create_parent: true
required: false
@@ -232,7 +232,7 @@ argument_groups:
name: "--genome_bam_flagstat"
info: null
default:
- "$id.markdup.sorted.bam.flagstat"
- "$id.genome.flagstat"
must_exist: true
create_parent: true
required: false
@@ -243,7 +243,7 @@ argument_groups:
name: "--genome_bam_idxstats"
info: null
default:
- "$id.markdup.sorted.bam.idxstats"
- "$id.genome.idxstats"
must_exist: true
create_parent: true
required: false
@@ -254,7 +254,7 @@ argument_groups:
name: "--markduplicates_metrics"
info: null
default:
- "$id.markdup.sorted.MarkDuplicates.metrics.txt"
- "$id.MarkDuplicates.metrics.txt"
must_exist: true
create_parent: true
required: false
@@ -486,8 +486,8 @@ build_info:
output: "target/executable/workflows/post_processing"
executable: "target/executable/workflows/post_processing/post_processing"
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/picard_markduplicates"
- "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort"

44
target/executable/workflows/post_processing/post_processing
View File

@@ -269,27 +269,27 @@ function ViashHelp {
echo "Output:"
echo " --processed_genome_bam"
echo " type: file, output, file must exist"
echo " default: \$id.markdup.sorted.bam"
echo " default: \$id.genome.bam"
echo ""
echo " --genome_bam_index"
echo " type: file, output, file must exist"
echo " default: \$id.markdup.sorted.bam"
echo " default: \$id.genome.bam.bai"
echo ""
echo " --genome_bam_stats"
echo " type: file, output, file must exist"
echo " default: \$id.markdup.sorted.bam.stats"
echo " default: \$id.genome.stats"
echo ""
echo " --genome_bam_flagstat"
echo " type: file, output, file must exist"
echo " default: \$id.markdup.sorted.bam.flagstat"
echo " default: \$id.genome.flagstat"
echo ""
echo " --genome_bam_idxstats"
echo " type: file, output, file must exist"
echo " default: \$id.markdup.sorted.bam.idxstats"
echo " default: \$id.genome.idxstats"
echo ""
echo " --markduplicates_metrics"
echo " type: file, output, file must exist"
echo " default: \$id.markdup.sorted.MarkDuplicates.metrics.txt"
echo " default: \$id.MarkDuplicates.metrics.txt"
echo ""
echo " --stringtie_transcript_gtf"
echo " type: file, output, file must exist"
@@ -887,22 +887,22 @@ if [ -z ${VIASH_PAR_WITH_UMI+x} ]; then
VIASH_PAR_WITH_UMI="false"
fi
if [ -z ${VIASH_PAR_PROCESSED_GENOME_BAM+x} ]; then
VIASH_PAR_PROCESSED_GENOME_BAM="\$id.markdup.sorted.bam"
VIASH_PAR_PROCESSED_GENOME_BAM="\$id.genome.bam"
fi
if [ -z ${VIASH_PAR_GENOME_BAM_INDEX+x} ]; then
VIASH_PAR_GENOME_BAM_INDEX="\$id.markdup.sorted.bam"
VIASH_PAR_GENOME_BAM_INDEX="\$id.genome.bam.bai"
fi
if [ -z ${VIASH_PAR_GENOME_BAM_STATS+x} ]; then
VIASH_PAR_GENOME_BAM_STATS="\$id.markdup.sorted.bam.stats"
VIASH_PAR_GENOME_BAM_STATS="\$id.genome.stats"
fi
if [ -z ${VIASH_PAR_GENOME_BAM_FLAGSTAT+x} ]; then
VIASH_PAR_GENOME_BAM_FLAGSTAT="\$id.markdup.sorted.bam.flagstat"
VIASH_PAR_GENOME_BAM_FLAGSTAT="\$id.genome.flagstat"
fi
if [ -z ${VIASH_PAR_GENOME_BAM_IDXSTATS+x} ]; then
VIASH_PAR_GENOME_BAM_IDXSTATS="\$id.markdup.sorted.bam.idxstats"
VIASH_PAR_GENOME_BAM_IDXSTATS="\$id.genome.idxstats"
fi
if [ -z ${VIASH_PAR_MARKDUPLICATES_METRICS+x} ]; then
VIASH_PAR_MARKDUPLICATES_METRICS="\$id.markdup.sorted.MarkDuplicates.metrics.txt"
VIASH_PAR_MARKDUPLICATES_METRICS="\$id.MarkDuplicates.metrics.txt"
fi
if [ -z ${VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF+x} ]; then
VIASH_PAR_STRINGTIE_TRANSCRIPT_GTF="\$id.stringtie.transcripts.gtf"
@@ -1185,20 +1185,20 @@ workflow run_wf {
"extra_picard_args": "extra_picard_args"
],
toState: [
"genome_bam": "output_bam",
"processed_genome_bam": "output_bam",
"markduplicates_metrics": "metrics"
]
)
| samtools_sort.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [ "input": "genome_bam" ],
toState: [ "genome_bam": "output" ],
fromState: [ "input": "processed_genome_bam" ],
toState: [ "processed_genome_bam": "output" ],
key: "genome_sorted_MarkDuplicates"
)
| samtools_index.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"input": "genome_bam",
"input": "processed_genome_bam",
"csi": "bam_csi_index"
],
toState: [ "genome_bam_index": "output" ],
@@ -1207,7 +1207,7 @@ workflow run_wf {
| samtools_stats.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"input": "genome_bam",
"input": "processed_genome_bam",
"bai": "genome_bam_index"
],
toState: [ "genome_bam_stats": "output" ],
@@ -1216,7 +1216,7 @@ workflow run_wf {
| samtools_flagstat.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"bam": "genome_bam",
"bam": "processed_genome_bam",
"bai": "genome_bam_index"
],
toState: [ "genome_bam_flagstat": "output" ],
@@ -1225,7 +1225,7 @@ workflow run_wf {
| samtools_idxstats.run(
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"bam": "genome_bam",
"bam": "processed_genome_bam",
"bai": "genome_bam_index"
],
toState: [ "genome_bam_idxstats": "output" ],
@@ -1236,7 +1236,7 @@ workflow run_wf {
runIf: { id, state -> !state.skip_stringtie },
fromState: [
"strandedness": "strandedness",
"bam": "genome_bam",
"bam": "processed_genome_bam",
"annotation_gtf": "gtf",
"extra_stringtie_args": "extra_stringtie_args"
],
@@ -1254,7 +1254,7 @@ workflow run_wf {
runIf: { id, state -> !state.skip_bigwig },
fromState: [
"strandedness": "strandedness",
"bam": "genome_bam",
"bam": "processed_genome_bam",
"extra_bedtools_args": "extra_bedtools_args"
],
toState: [
@@ -1309,7 +1309,7 @@ workflow run_wf {
}
| setState (
"processed_genome_bam": "genome_bam",
"processed_genome_bam": "processed_genome_bam",
"genome_bam_index": "genome_bam_index",
"genome_bam_stats": "genome_bam_stats",
"genome_bam_flagstat": "genome_bam_flagstat",