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Build branch main with version main (ce40a4a)

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Build pipeline: viash-hub.rnaseq.main-b6jtr

Source commit: ce40a4a6d9

Source message: add unit tests
This commit is contained in:
CI
2024-11-27 09:19:16 +00:00
parent 20fef7a87e
commit 14e0d12189
295 changed files with 8300 additions and 8134 deletions
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4
target/executable/workflows/post_processing/.config.vsh.yaml
View File

@@ -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: "a4f2c7d5a1d0c27cc538c9b06ec4dec5c62f8d74"
git_remote: "https://x-access-token:ghs_hUComHHyuHIIVQYt2HdqulL85sCkXr3K9lOo@github.com/viash-hub/rnaseq"
git_commit: "ce40a4a6d9e94ca2d63978c9b4c2ea4004b9fcb3"
git_remote: "https://x-access-token:ghs_ot0XYuiYvcS5ZVYMUffn1TKOgZgnL00x8gE9@github.com/viash-hub/rnaseq"
dependencies:
- "target/nextflow/picard_markduplicates"
- "target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort"

284
target/executable/workflows/post_processing/post_processing
View File

@@ -1176,154 +1176,154 @@ workflow run_wf {
main:
output_ch = input_ch
| picard_markduplicates.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"bam": "genome_bam",
"fasta": "fasta",
"fai": "fai",
"extra_picard_args": "extra_picard_args"
],
toState: [
"processed_genome_bam": "output_bam",
"markduplicates_metrics": "metrics"
]
)
| samtools_sort.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
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": "processed_genome_bam",
"csi": "bam_csi_index"
],
toState: [ "genome_bam_index": "output" ],
key: "genome_sorted_MarkDuplicates",
)
| samtools_stats.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"input": "processed_genome_bam",
"bai": "genome_bam_index"
],
toState: [ "genome_bam_stats": "output" ],
key: "MarkDuplicates_stats"
)
| samtools_flagstat.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
| picard_markduplicates.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"bam": "genome_bam",
"fasta": "fasta",
"fai": "fai",
"extra_picard_args": "extra_picard_args"
],
toState: [
"processed_genome_bam": "output_bam",
"markduplicates_metrics": "metrics"
]
)
| samtools_sort.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
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": "processed_genome_bam",
"csi": "bam_csi_index"
],
toState: [ "genome_bam_index": "output" ],
key: "genome_sorted_MarkDuplicates",
)
| samtools_stats.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"input": "processed_genome_bam",
"bai": "genome_bam_index"
],
toState: [ "genome_bam_stats": "output" ],
key: "MarkDuplicates_stats"
)
| samtools_flagstat.run (
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"bam": "processed_genome_bam",
"bai": "genome_bam_index"
],
toState: [ "genome_bam_flagstat": "output" ],
key: "MarkDuplicates_flagstat"
)
| samtools_idxstats.run(
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"bam": "processed_genome_bam",
"bai": "genome_bam_index"
],
toState: [ "genome_bam_flagstat": "output" ],
key: "MarkDuplicates_flagstat"
)
| samtools_idxstats.run(
runIf: { id, state -> !state.skip_markduplicates && !state.with_umi },
fromState: [
"bam": "processed_genome_bam",
"bai": "genome_bam_index"
],
toState: [ "genome_bam_idxstats": "output" ],
key: "MarkDuplicates_idxstats"
)
],
toState: [ "genome_bam_idxstats": "output" ],
key: "MarkDuplicates_idxstats"
)
| stringtie.run (
runIf: { id, state -> !state.skip_stringtie },
fromState: [
"strandedness": "strandedness",
"bam": "processed_genome_bam",
"annotation_gtf": "gtf",
"extra_stringtie_args": "extra_stringtie_args"
],
toState: [
"stringtie_transcript_gtf": "transcript_gtf",
"stringtie_coverage_gtf": "coverage_gtf",
"stringtie_abundance": "abundance",
"stringtie_ballgown": "ballgown"
]
)
| stringtie.run (
runIf: { id, state -> !state.skip_stringtie },
fromState: [
"strandedness": "strandedness",
"bam": "processed_genome_bam",
"annotation_gtf": "gtf",
"extra_stringtie_args": "extra_stringtie_args"
],
toState: [
"stringtie_transcript_gtf": "transcript_gtf",
"stringtie_coverage_gtf": "coverage_gtf",
"stringtie_abundance": "abundance",
"stringtie_ballgown": "ballgown"
]
)
// Genome-wide coverage with BEDTools
// Genome-wide coverage with BEDTools
| bedtools_genomecov.run (
runIf: { id, state -> !state.skip_bigwig },
fromState: [
"strandedness": "strandedness",
"bam": "processed_genome_bam",
"extra_bedtools_args": "extra_bedtools_args"
],
toState: [
| bedtools_genomecov.run (
runIf: { id, state -> !state.skip_bigwig },
fromState: [
"strandedness": "strandedness",
"bam": "processed_genome_bam",
"extra_bedtools_args": "extra_bedtools_args"
],
toState: [
"bedgraph_forward": "bedgraph_forward",
"bedgraph_reverse": "bedgraph_reverse"
]
)
| bedclip.run (
runIf: { id, state -> !state.skip_bigwig },
fromState: [
"input_bedgraph": "bedgraph_forward",
"sizes": "chrom_sizes"
],
toState: [ "bedgraph_forward": "output_bedgraph" ],
key: "bedclip_forward"
)
| bedgraphtobigwig.run (
runIf: { id, state -> !state.skip_bigwig },
fromState: [
"bedgraph": "bedgraph_forward",
"sizes": "chrom_sizes"
],
toState: [ "bigwig_forward": "bigwig" ],
key: "bedgraphtobigwig_forward"
)
| bedclip.run (
runIf: { id, state -> !state.skip_bigwig },
fromState: [
"input_bedgraph": "bedgraph_reverse",
"sizes": "chrom_sizes",
],
toState: [ "bedgraph_reverse": "output_bedgraph" ],
key: "bedclip_reverse"
)
| bedgraphtobigwig.run (
runIf: { id, state -> !state.skip_bigwig },
fromState: [
"bedgraph": "bedgraph_reverse",
"sizes": "chrom_sizes"
],
toState: [ "bigwig_reverse": "bigwig" ],
key: "bedgraphtobigwig_reverse"
)
| map { id, state ->
def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() }
[ id, mod_state ]
}
| setState (
"processed_genome_bam": "processed_genome_bam",
"genome_bam_index": "genome_bam_index",
"genome_bam_stats": "genome_bam_stats",
"genome_bam_flagstat": "genome_bam_flagstat",
"genome_bam_idxstats": "genome_bam_idxstats",
"markduplicates_metrics": "markduplicates_metrics",
"stringtie_transcript_gtf": "stringtie_transcript_gtf",
"stringtie_coverage_gtf": "stringtie_coverage_gtf",
"stringtie_abundance": "stringtie_abundance",
"stringtie_ballgown": "stringtie_ballgown",
"bedgraph_forward": "bedgraph_forward",
"bedgraph_reverse": "bedgraph_reverse"
]
)
| bedclip.run (
runIf: { id, state -> !state.skip_bigwig },
fromState: [
"input_bedgraph": "bedgraph_forward",
"sizes": "chrom_sizes"
],
toState: [ "bedgraph_forward": "output_bedgraph" ],
key: "bedclip_forward"
)
| bedgraphtobigwig.run (
runIf: { id, state -> !state.skip_bigwig },
fromState: [
"bedgraph": "bedgraph_forward",
"sizes": "chrom_sizes"
],
toState: [ "bigwig_forward": "bigwig" ],
key: "bedgraphtobigwig_forward"
)
| bedclip.run (
runIf: { id, state -> !state.skip_bigwig },
fromState: [
"input_bedgraph": "bedgraph_reverse",
"sizes": "chrom_sizes",
],
toState: [ "bedgraph_reverse": "output_bedgraph" ],
key: "bedclip_reverse"
)
| bedgraphtobigwig.run (
runIf: { id, state -> !state.skip_bigwig },
fromState: [
"bedgraph": "bedgraph_reverse",
"sizes": "chrom_sizes"
],
toState: [ "bigwig_reverse": "bigwig" ],
key: "bedgraphtobigwig_reverse"
)
| map { id, state ->
def mod_state = state.findAll { key, value -> value instanceof java.nio.file.Path && value.exists() }
[ id, mod_state ]
}
| setState (
"processed_genome_bam": "processed_genome_bam",
"genome_bam_index": "genome_bam_index",
"genome_bam_stats": "genome_bam_stats",
"genome_bam_flagstat": "genome_bam_flagstat",
"genome_bam_idxstats": "genome_bam_idxstats",
"markduplicates_metrics": "markduplicates_metrics",
"stringtie_transcript_gtf": "stringtie_transcript_gtf",
"stringtie_coverage_gtf": "stringtie_coverage_gtf",
"stringtie_abundance": "stringtie_abundance",
"stringtie_ballgown": "stringtie_ballgown",
"bedgraph_forward": "bedgraph_forward",
"bedgraph_reverse": "bedgraph_reverse",
"bigwig_forward": "bigwig_forward",
"bigwig_reverse": "bigwig_reverse"
)
"bedgraph_reverse": "bedgraph_reverse",
"bigwig_forward": "bigwig_forward",
"bigwig_reverse": "bigwig_reverse"
)
emit:
output_ch