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Alignment outputs in per sample folder [CW-7270]

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This commit is contained in:
Kiah McIntosh 2026-05-22 09:12:26 +00:00
parent 18e0c5e92f
commit f5e5f3a790
5 changed files with 13 additions and 13 deletions
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2
.gitlab-ci.yml
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@ -158,7 +158,7 @@ docker-run:
NF_BEFORE_SCRIPT: ":" NF_BEFORE_SCRIPT: ":"
NF_WORKFLOW_OPTS: "--fastq test_data/smoke/reads.fastq --sample sampleA --ref_genome test_data/smoke/reference.fa --ref_annotation test_data/smoke/annotation.gtf --direct_rna" NF_WORKFLOW_OPTS: "--fastq test_data/smoke/reads.fastq --sample sampleA --ref_genome test_data/smoke/reference.fa --ref_annotation test_data/smoke/annotation.gtf --direct_rna"
AFTER_NEXTFLOW_CMD: > AFTER_NEXTFLOW_CMD: >
test -f ${CI_PROJECT_NAME}/cohort/alignments/sampleA/reads.bam && test -f ${CI_PROJECT_NAME}/samples/sampleA/alignment/reads.bam &&
test -f ${CI_PROJECT_NAME}/samples/sampleA/sampleA_sqanti/classification_summary.tsv test -f ${CI_PROJECT_NAME}/samples/sampleA/sampleA_sqanti/classification_summary.tsv
# Smoke: end-to-end DE/DTU wiring and expected contrast output files. # Smoke: end-to-end DE/DTU wiring and expected contrast output files.

6
README.md
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@ -366,9 +366,9 @@ Output files may be aggregated including information for all samples or provided
| Per-read stats | ingress_results/{{ alias }}/fastcat_stats/per-read-stats.tsv.gz | Read statistics for individual reads in a sample, when this output is enabled. | per-sample | | Per-read stats | ingress_results/{{ alias }}/fastcat_stats/per-read-stats.tsv.gz | Read statistics for individual reads in a sample, when this output is enabled. | per-sample |
| Ingress reads | ingress_results/{{ alias }}/seqs.fastq.gz | Reads prepared from the input data for downstream analysis. | per-sample | | Ingress reads | ingress_results/{{ alias }}/seqs.fastq.gz | Reads prepared from the input data for downstream analysis. | per-sample |
| Ingress metadata | ingress_results/{{ alias }}/metamap.json | Per-sample metadata used by the workflow. | per-sample | | Ingress metadata | ingress_results/{{ alias }}/metamap.json | Per-sample metadata used by the workflow. | per-sample |
| Aligned BAM | cohort/alignments/{{ alias }}/reads.bam | Genome-aligned BAM used for bambu, optional SQANTI3 QC, and IGV. | per-sample | | Aligned BAM | samples/{{ alias }}/alignment/reads.bam | Genome-aligned BAM used for bambu, optional SQANTI3 QC, and IGV. | per-sample |
| Aligned BAM index | cohort/alignments/{{ alias }}/reads.bam.bai | Index for the aligned BAM. | per-sample | | Aligned BAM index | samples/{{ alias }}/alignment/reads.bam.bai | Index for the aligned BAM. | per-sample |
| Alignment summary | cohort/alignments/{{ alias }}/bamstats.flagstat.tsv | bamstats flagstat summary for the aligned BAM. | per-sample | | Alignment summary | samples/{{ alias }}/alignment/bamstats.flagstat.tsv | bamstats flagstat summary for the aligned BAM. | per-sample |
| Reference and annotation preparation summary | cohort/reference/annotation_reference_summary.json | Summary of reference and annotation preparation, including seqname overlap, build/provider hints, and excluded unstranded annotation counts. | aggregated | | Reference and annotation preparation summary | cohort/reference/annotation_reference_summary.json | Summary of reference and annotation preparation, including seqname overlap, build/provider hints, and excluded unstranded annotation counts. | aggregated |
| Excluded unstranded annotation records | cohort/reference/unstranded_annotation.gtf | Full set of annotation records excluded because their strand was not '+' or '-'. Present only when unstranded records are found. | aggregated | | Excluded unstranded annotation records | cohort/reference/unstranded_annotation.gtf | Full set of annotation records excluded because their strand was not '+' or '-'. Present only when unstranded records are found. | aggregated |
| Cohort transcriptome GTF | cohort/transcripts.gtf | Joint bambu transcript model used as the primary cohort transcriptome. | aggregated | | Cohort transcriptome GTF | cohort/transcripts.gtf | Joint bambu transcript model used as the primary cohort transcriptome. | aggregated |

6
docs/08_outputs.md
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@ -7,9 +7,9 @@ Output files may be aggregated including information for all samples or provided
| Per-read stats | ingress_results/{{ alias }}/fastcat_stats/per-read-stats.tsv.gz | Read statistics for individual reads in a sample, when this output is enabled. | per-sample | | Per-read stats | ingress_results/{{ alias }}/fastcat_stats/per-read-stats.tsv.gz | Read statistics for individual reads in a sample, when this output is enabled. | per-sample |
| Ingress reads | ingress_results/{{ alias }}/seqs.fastq.gz | Reads prepared from the input data for downstream analysis. | per-sample | | Ingress reads | ingress_results/{{ alias }}/seqs.fastq.gz | Reads prepared from the input data for downstream analysis. | per-sample |
| Ingress metadata | ingress_results/{{ alias }}/metamap.json | Per-sample metadata used by the workflow. | per-sample | | Ingress metadata | ingress_results/{{ alias }}/metamap.json | Per-sample metadata used by the workflow. | per-sample |
| Aligned BAM | cohort/alignments/{{ alias }}/reads.bam | Genome-aligned BAM used for bambu, optional SQANTI3 QC, and IGV. | per-sample | | Aligned BAM | samples/{{ alias }}/alignment/reads.bam | Genome-aligned BAM used for bambu, optional SQANTI3 QC, and IGV. | per-sample |
| Aligned BAM index | cohort/alignments/{{ alias }}/reads.bam.bai | Index for the aligned BAM. | per-sample | | Aligned BAM index | samples/{{ alias }}/alignment/reads.bam.bai | Index for the aligned BAM. | per-sample |
| Alignment summary | cohort/alignments/{{ alias }}/bamstats.flagstat.tsv | bamstats flagstat summary for the aligned BAM. | per-sample | | Alignment summary | samples/{{ alias }}/alignment/bamstats.flagstat.tsv | bamstats flagstat summary for the aligned BAM. | per-sample |
| Reference and annotation preparation summary | cohort/reference/annotation_reference_summary.json | Summary of reference and annotation preparation, including seqname overlap, build/provider hints, and excluded unstranded annotation counts. | aggregated | | Reference and annotation preparation summary | cohort/reference/annotation_reference_summary.json | Summary of reference and annotation preparation, including seqname overlap, build/provider hints, and excluded unstranded annotation counts. | aggregated |
| Excluded unstranded annotation records | cohort/reference/unstranded_annotation.gtf | Full set of annotation records excluded because their strand was not '+' or '-'. Present only when unstranded records are found. | aggregated | | Excluded unstranded annotation records | cohort/reference/unstranded_annotation.gtf | Full set of annotation records excluded because their strand was not '+' or '-'. Present only when unstranded records are found. | aggregated |
| Cohort transcriptome GTF | cohort/transcripts.gtf | Joint bambu transcript model used as the primary cohort transcriptome. | aggregated | | Cohort transcriptome GTF | cohort/transcripts.gtf | Joint bambu transcript model used as the primary cohort transcriptome. | aggregated |

6
main.nf
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@ -186,7 +186,7 @@ workflow pipeline {
generated_alignment_outputs = reads generated_alignment_outputs = reads
.filter { meta, bam, bai, stats -> meta.src_xam == null } .filter { meta, bam, bai, stats -> meta.src_xam == null }
.flatMap { meta, bam, bai, stats -> .flatMap { meta, bam, bai, stats ->
def outdir = "cohort/alignments/${meta.alias}" def outdir = "samples/${meta.alias}/alignment"
[ [
[bam, outdir], [bam, outdir],
[bai, outdir], [bai, outdir],
@ -344,8 +344,8 @@ workflow {
igv_alignment_paths = processed_samples igv_alignment_paths = processed_samples
.map { meta, bam, bai, stat -> [ .map { meta, bam, bai, stat -> [
meta.src_xam ?: "${meta.alias},cohort/alignments/${meta.alias}/reads.bam", meta.src_xam ?: "${meta.alias},samples/${meta.alias}/alignment/reads.bam",
meta.src_xai ?: "${meta.alias},cohort/alignments/${meta.alias}/reads.bam.bai" meta.src_xai ?: "${meta.alias},samples/${meta.alias}/alignment/reads.bam.bai"
] } ] }
.flatten() .flatten()

6
output_definition.json
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@ -41,7 +41,7 @@
"type": "per-sample" "type": "per-sample"
}, },
"sample-bam": { "sample-bam": {
"filepath": "cohort/alignments/{{ alias }}/reads.bam", "filepath": "samples/{{ alias }}/alignment/reads.bam",
"title": "Aligned BAM", "title": "Aligned BAM",
"description": "Genome-aligned BAM used for bambu, optional SQANTI3 QC, and IGV.", "description": "Genome-aligned BAM used for bambu, optional SQANTI3 QC, and IGV.",
"mime-type": "application/gzip", "mime-type": "application/gzip",
@ -49,7 +49,7 @@
"type": "per-sample" "type": "per-sample"
}, },
"sample-bai": { "sample-bai": {
"filepath": "cohort/alignments/{{ alias }}/reads.bam.bai", "filepath": "samples/{{ alias }}/alignment/reads.bam.bai",
"title": "Aligned BAM index", "title": "Aligned BAM index",
"description": "Index for the aligned BAM.", "description": "Index for the aligned BAM.",
"mime-type": "application/octet-stream", "mime-type": "application/octet-stream",
@ -57,7 +57,7 @@
"type": "per-sample" "type": "per-sample"
}, },
"sample-flagstat": { "sample-flagstat": {
"filepath": "cohort/alignments/{{ alias }}/bamstats.flagstat.tsv", "filepath": "samples/{{ alias }}/alignment/bamstats.flagstat.tsv",
"title": "Alignment summary", "title": "Alignment summary",
"description": "bamstats flagstat summary for the aligned BAM.", "description": "bamstats flagstat summary for the aligned BAM.",
"mime-type": "text/tab-separated-values", "mime-type": "text/tab-separated-values",